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diff --git a/modules/tailfindr/meta.yml b/modules/nf-core/tailfindr/meta.yml
similarity index 100%
rename from modules/tailfindr/meta.yml
rename to modules/nf-core/tailfindr/meta.yml
diff --git a/modules/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf
similarity index 100%
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diff --git a/modules/tbprofiler/profile/meta.yml b/modules/nf-core/tbprofiler/profile/meta.yml
similarity index 100%
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diff --git a/modules/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf
similarity index 100%
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diff --git a/modules/tiddit/cov/meta.yml b/modules/nf-core/tiddit/cov/meta.yml
similarity index 100%
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diff --git a/modules/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf
similarity index 100%
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diff --git a/modules/tiddit/sv/meta.yml b/modules/nf-core/tiddit/sv/meta.yml
similarity index 100%
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diff --git a/modules/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf
similarity index 100%
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diff --git a/modules/transdecoder/longorf/meta.yml b/modules/nf-core/transdecoder/longorf/meta.yml
similarity index 100%
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diff --git a/modules/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf
similarity index 100%
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diff --git a/modules/transdecoder/predict/meta.yml b/modules/nf-core/transdecoder/predict/meta.yml
similarity index 100%
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diff --git a/modules/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf
similarity index 100%
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diff --git a/modules/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
similarity index 100%
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diff --git a/modules/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf
similarity index 100%
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diff --git a/modules/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf
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diff --git a/modules/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf
similarity index 100%
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diff --git a/modules/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf
similarity index 100%
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diff --git a/modules/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml
similarity index 100%
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diff --git a/modules/unicycler/main.nf b/modules/nf-core/unicycler/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/untar/main.nf b/modules/nf-core/untar/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/unzip/main.nf b/modules/nf-core/unzip/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/variantbam/main.nf b/modules/nf-core/variantbam/main.nf
similarity index 100%
rename from modules/variantbam/main.nf
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diff --git a/modules/variantbam/meta.yml b/modules/nf-core/variantbam/meta.yml
similarity index 100%
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diff --git a/modules/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf
similarity index 100%
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similarity index 100%
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diff --git a/modules/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf
similarity index 100%
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diff --git a/modules/vcflib/vcfbreakmulti/meta.yml b/modules/nf-core/vcflib/vcfbreakmulti/meta.yml
similarity index 100%
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diff --git a/modules/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf
similarity index 100%
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diff --git a/modules/vcflib/vcfuniq/meta.yml b/modules/nf-core/vcflib/vcfuniq/meta.yml
similarity index 100%
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diff --git a/modules/vcftools/main.nf b/modules/nf-core/vcftools/main.nf
similarity index 100%
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diff --git a/modules/vcftools/meta.yml b/modules/nf-core/vcftools/meta.yml
similarity index 100%
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diff --git a/modules/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf
similarity index 100%
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diff --git a/modules/vsearch/sintax/meta.yml b/modules/nf-core/vsearch/sintax/meta.yml
similarity index 100%
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diff --git a/modules/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf
similarity index 100%
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rename to modules/nf-core/vsearch/usearchglobal/main.nf
diff --git a/modules/vsearch/usearchglobal/meta.yml b/modules/nf-core/vsearch/usearchglobal/meta.yml
similarity index 100%
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diff --git a/modules/whamg/main.nf b/modules/nf-core/whamg/main.nf
similarity index 100%
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rename to modules/nf-core/whamg/main.nf
diff --git a/modules/whamg/meta.yml b/modules/nf-core/whamg/meta.yml
similarity index 100%
rename from modules/whamg/meta.yml
rename to modules/nf-core/whamg/meta.yml
diff --git a/modules/yara/index/main.nf b/modules/nf-core/yara/index/main.nf
similarity index 100%
rename from modules/yara/index/main.nf
rename to modules/nf-core/yara/index/main.nf
diff --git a/modules/yara/index/meta.yml b/modules/nf-core/yara/index/meta.yml
similarity index 100%
rename from modules/yara/index/meta.yml
rename to modules/nf-core/yara/index/meta.yml
diff --git a/modules/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf
similarity index 100%
rename from modules/yara/mapper/main.nf
rename to modules/nf-core/yara/mapper/main.nf
diff --git a/modules/yara/mapper/meta.yml b/modules/nf-core/yara/mapper/meta.yml
similarity index 100%
rename from modules/yara/mapper/meta.yml
rename to modules/nf-core/yara/mapper/meta.yml
diff --git a/subworkflows/nf-core/align_bowtie2/main.nf b/subworkflows/nf-core/align_bowtie2/main.nf
index ec453f8d317..d6d7cd60d4e 100644
--- a/subworkflows/nf-core/align_bowtie2/main.nf
+++ b/subworkflows/nf-core/align_bowtie2/main.nf
@@ -7,7 +7,7 @@ params.samtools_sort_options  = [:]
 params.samtools_index_options = [:]
 params.samtools_stats_options = [:]
 
-include { BOWTIE2_ALIGN     } from '../../../modules/bowtie2/align/main' addParams( options: params.align_options    )
+include { BOWTIE2_ALIGN     } from '../../../modules/nf-core/bowtie2/align/main' addParams( options: params.align_options    )
 include { BAM_SORT_SAMTOOLS } from '../bam_sort_samtools/main'           addParams( sort_options: params.samtools_sort_options, index_options: params.samtools_index_options, stats_options: params.samtools_stats_options )
 
 workflow ALIGN_BOWTIE2 {
diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index e38697c3eb9..57ffa46bf3c 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -2,9 +2,9 @@
 // Run QC steps on BAM/CRAM files using Picard
 //
 
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picard/collectmultiplemetrics/main'
-include { PICARD_COLLECTWGSMETRICS      } from '../../../modules/picard/collectwgsmetrics/main'
-include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picard/collecthsmetrics/main'
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main'
+include { PICARD_COLLECTWGSMETRICS      } from '../../../modules/nf-core/picard/collectwgsmetrics/main'
+include { PICARD_COLLECTHSMETRICS       } from '../../../modules/nf-core/picard/collecthsmetrics/main'
 
 workflow BAM_QC_PICARD {
     take:
diff --git a/subworkflows/nf-core/bam_sort_samtools/main.nf b/subworkflows/nf-core/bam_sort_samtools/main.nf
index c9be6a56e47..fc1a24df51a 100644
--- a/subworkflows/nf-core/bam_sort_samtools/main.nf
+++ b/subworkflows/nf-core/bam_sort_samtools/main.nf
@@ -6,8 +6,8 @@ params.sort_options  = [:]
 params.index_options = [:]
 params.stats_options = [:]
 
-include { SAMTOOLS_SORT      } from '../../../modules/samtools/sort/main'  addParams( options: params.sort_options  )
-include { SAMTOOLS_INDEX     } from '../../../modules/samtools/index/main' addParams( options: params.index_options )
+include { SAMTOOLS_SORT      } from '../../../modules/nf-core/samtools/sort/main'  addParams( options: params.sort_options  )
+include { SAMTOOLS_INDEX     } from '../../../modules/nf-core/samtools/index/main' addParams( options: params.index_options )
 include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main'           addParams( options: params.stats_options )
 
 workflow BAM_SORT_SAMTOOLS {
diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf
index 188894a2ab9..f4fab25bc8a 100644
--- a/subworkflows/nf-core/bam_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_stats_samtools/main.nf
@@ -2,9 +2,9 @@
 // Run SAMtools stats, flagstat and idxstats
 //
 
-include { SAMTOOLS_STATS    } from '../../../modules/samtools/stats/main'
-include { SAMTOOLS_IDXSTATS } from '../../../modules/samtools/idxstats/main'
-include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main'
+include { SAMTOOLS_STATS    } from '../../../modules/nf-core/samtools/stats/main'
+include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main'
+include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'
 
 workflow BAM_STATS_SAMTOOLS {
     take:
diff --git a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf
index 042d0bbd5e1..41aa787d953 100644
--- a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf
+++ b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf
@@ -5,15 +5,15 @@
 //
 
 
-include { BWAMEM2_INDEX                                         } from '../../../modules/bwamem2/index/main.nf'
-include { BWAMEM2_MEM                                           } from '../../../modules/bwamem2/mem/main'
-include { BWA_INDEX                         as BWAMEM1_INDEX    } from '../../../modules/bwa/index/main.nf'
-include { BWA_MEM                           as BWAMEM1_MEM      } from '../../../modules/bwa/mem/main'
-include { FGBIO_CALLMOLECULARCONSENSUSREADS as CALLUMICONSENSUS } from '../../../modules/fgbio/callmolecularconsensusreads/main.nf'
-include { FGBIO_FASTQTOBAM                  as FASTQTOBAM       } from '../../../modules/fgbio/fastqtobam/main'
-include { FGBIO_GROUPREADSBYUMI             as GROUPREADSBYUMI  } from '../../../modules/fgbio/groupreadsbyumi/main'
-include { SAMBLASTER                                            } from '../../../modules/samblaster/main'
-include { SAMTOOLS_BAM2FQ                   as BAM2FASTQ        } from '../../../modules/samtools/bam2fq/main.nf'
+include { BWAMEM2_INDEX                                         } from '../../../modules/nf-core/bwamem2/index/main.nf'
+include { BWAMEM2_MEM                                           } from '../../../modules/nf-core/bwamem2/mem/main'
+include { BWA_INDEX                         as BWAMEM1_INDEX    } from '../../../modules/nf-core/bwa/index/main.nf'
+include { BWA_MEM                           as BWAMEM1_MEM      } from '../../../modules/nf-core/bwa/mem/main'
+include { FGBIO_CALLMOLECULARCONSENSUSREADS as CALLUMICONSENSUS } from '../../../modules/nf-core/fgbio/callmolecularconsensusreads/main.nf'
+include { FGBIO_FASTQTOBAM                  as FASTQTOBAM       } from '../../../modules/nf-core/fgbio/fastqtobam/main'
+include { FGBIO_GROUPREADSBYUMI             as GROUPREADSBYUMI  } from '../../../modules/nf-core/fgbio/groupreadsbyumi/main'
+include { SAMBLASTER                                            } from '../../../modules/nf-core/samblaster/main'
+include { SAMTOOLS_BAM2FQ                   as BAM2FASTQ        } from '../../../modules/nf-core/samtools/bam2fq/main.nf'
 
 
 workflow CREATE_UMI_CONSENSUS {
diff --git a/subworkflows/nf-core/gatk_create_som_pon/main.nf b/subworkflows/nf-core/gatk_create_som_pon/main.nf
index 89a9566ee36..544289bcc8f 100644
--- a/subworkflows/nf-core/gatk_create_som_pon/main.nf
+++ b/subworkflows/nf-core/gatk_create_som_pon/main.nf
@@ -5,9 +5,9 @@ params.mutect2_options      = [args: '--max-mnp-distance 0']
 params.gendbimport_options  = [:]
 params.createsompon_options = [:]
 
-include { GATK4_MUTECT2                     } from '../../../modules/gatk4/mutect2/main'                     addParams( options: params.mutect2_options )
-include { GATK4_GENOMICSDBIMPORT            } from '../../../modules/gatk4/genomicsdbimport/main'            addParams( options: params.gendbimport_options )
-include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../modules/gatk4/createsomaticpanelofnormals/main' addParams( options: params.createsompon_options )
+include { GATK4_MUTECT2                     } from '../../../modules/nf-core/gatk4/mutect2/main'                     addParams( options: params.mutect2_options )
+include { GATK4_GENOMICSDBIMPORT            } from '../../../modules/nf-core/gatk4/genomicsdbimport/main'            addParams( options: params.gendbimport_options )
+include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../modules/nf-core/gatk4/createsomaticpanelofnormals/main' addParams( options: params.createsompon_options )
 
 workflow GATK_CREATE_SOM_PON {
     take:
diff --git a/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf
index 25c63687d78..81b543a9437 100644
--- a/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf
+++ b/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf
@@ -9,12 +9,12 @@ params.getpileup_normal_options = [suffix: '_normal']
 params.calccontam_options       = [:]
 params.filtercalls_options      = [suffix: '_filtered']
 
-include { GATK4_MUTECT2                   as MUTECT2 }                   from '../../../modules/gatk4/mutect2/main'                   addParams( options: params.mutect2_options )
-include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL } from '../../../modules/gatk4/learnreadorientationmodel/main' addParams( options: params.learnorientation_options )
-include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_TUMOR }  from '../../../modules/gatk4/getpileupsummaries/main'        addParams( options: params.getpileup_tumor_options )
-include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_NORMAL}  from '../../../modules/gatk4/getpileupsummaries/main'        addParams( options: params.getpileup_normal_options )
-include { GATK4_CALCULATECONTAMINATION    as CALCULATECONTAMINATION }    from '../../../modules/gatk4/calculatecontamination/main'    addParams( options: params.calccontam_options )
-include { GATK4_FILTERMUTECTCALLS         as FILTERMUTECTCALLS }         from '../../../modules/gatk4/filtermutectcalls/main'         addParams( options: params.filtercalls_options )
+include { GATK4_MUTECT2                   as MUTECT2 }                   from '../../../modules/nf-core/gatk4/mutect2/main'                   addParams( options: params.mutect2_options )
+include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL } from '../../../modules/nf-core/gatk4/learnreadorientationmodel/main' addParams( options: params.learnorientation_options )
+include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_TUMOR }  from '../../../modules/nf-core/gatk4/getpileupsummaries/main'        addParams( options: params.getpileup_tumor_options )
+include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_NORMAL}  from '../../../modules/nf-core/gatk4/getpileupsummaries/main'        addParams( options: params.getpileup_normal_options )
+include { GATK4_CALCULATECONTAMINATION    as CALCULATECONTAMINATION }    from '../../../modules/nf-core/gatk4/calculatecontamination/main'    addParams( options: params.calccontam_options )
+include { GATK4_FILTERMUTECTCALLS         as FILTERMUTECTCALLS }         from '../../../modules/nf-core/gatk4/filtermutectcalls/main'         addParams( options: params.filtercalls_options )
 
 workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING {
     take:
diff --git a/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/main.nf
index 20d8a176bab..ca3d78ff6d6 100644
--- a/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/main.nf
+++ b/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/main.nf
@@ -7,10 +7,10 @@ params.getpileup_options   = [:]
 params.calccontam_options  = [:]
 params.filtercalls_options = [suffix: '_filtered']
 
-include { GATK4_MUTECT2                as MUTECT2 }                  from '../../../modules/gatk4/mutect2/main'                addParams( options: params.mutect2_options )
-include { GATK4_GETPILEUPSUMMARIES     as GETPILEUPSUMMARIES }       from '../../../modules/gatk4/getpileupsummaries/main'     addParams( options: params.getpileup_options )
-include { GATK4_CALCULATECONTAMINATION as CALCULATECONTAMINATION }   from '../../../modules/gatk4/calculatecontamination/main' addParams( options: params.calccontam_options )
-include { GATK4_FILTERMUTECTCALLS      as FILTERMUTECTCALLS }        from '../../../modules/gatk4/filtermutectcalls/main'      addParams( options: params.filtercalls_options )
+include { GATK4_MUTECT2                as MUTECT2 }                  from '../../../modules/nf-core/gatk4/mutect2/main'                addParams( options: params.mutect2_options )
+include { GATK4_GETPILEUPSUMMARIES     as GETPILEUPSUMMARIES }       from '../../../modules/nf-core/gatk4/getpileupsummaries/main'     addParams( options: params.getpileup_options )
+include { GATK4_CALCULATECONTAMINATION as CALCULATECONTAMINATION }   from '../../../modules/nf-core/gatk4/calculatecontamination/main' addParams( options: params.calccontam_options )
+include { GATK4_FILTERMUTECTCALLS      as FILTERMUTECTCALLS }        from '../../../modules/nf-core/gatk4/filtermutectcalls/main'      addParams( options: params.filtercalls_options )
 
 workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING {
     take:
diff --git a/subworkflows/nf-core/srafastq/main.nf b/subworkflows/nf-core/srafastq/main.nf
index 26e8105eb6e..af52066243b 100644
--- a/subworkflows/nf-core/srafastq/main.nf
+++ b/subworkflows/nf-core/srafastq/main.nf
@@ -1,6 +1,6 @@
-include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/custom/sratoolsncbisettings/main'
-include { SRATOOLS_PREFETCH           } from '../../../modules/sratools/prefetch/main'
-include { SRATOOLS_FASTERQDUMP        } from '../../../modules/sratools/fasterqdump/main'
+include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/nf-core/custom/sratoolsncbisettings/main'
+include { SRATOOLS_PREFETCH           } from '../../../modules/nf-core/sratools/prefetch/main'
+include { SRATOOLS_FASTERQDUMP        } from '../../../modules/nf-core/sratools/fasterqdump/main'
 
 /**
  * Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 2b1f317f3ae..2c521019087 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1,2545 +1,2545 @@
 abacas:
-  - modules/abacas/**
-  - tests/modules/abacas/**
+  - modules/nf-core/abacas/**
+  - tests/modules/nf-core/abacas/**
 
 abricate/run:
-  - modules/abricate/run/**
-  - tests/modules/abricate/run/**
+  - modules/nf-core/abricate/run/**
+  - tests/modules/nf-core/abricate/run/**
 
 abricate/summary:
-  - modules/abricate/summary/**
-  - tests/modules/abricate/summary/**
+  - modules/nf-core/abricate/summary/**
+  - tests/modules/nf-core/abricate/summary/**
 
 adapterremoval:
-  - modules/adapterremoval/**
-  - tests/modules/adapterremoval/**
+  - modules/nf-core/adapterremoval/**
+  - tests/modules/nf-core/adapterremoval/**
 
 adapterremovalfixprefix:
-  - modules/adapterremovalfixprefix/**
-  - tests/modules/adapterremovalfixprefix/**
+  - modules/nf-core/adapterremovalfixprefix/**
+  - tests/modules/nf-core/adapterremovalfixprefix/**
 
 agrvate:
-  - modules/agrvate/**
-  - tests/modules/agrvate/**
+  - modules/nf-core/agrvate/**
+  - tests/modules/nf-core/agrvate/**
 
 allelecounter:
-  - modules/allelecounter/**
-  - tests/modules/allelecounter/**
+  - modules/nf-core/allelecounter/**
+  - tests/modules/nf-core/allelecounter/**
 
 ampir:
-  - modules/ampir/**
-  - tests/modules/ampir/**
+  - modules/nf-core/ampir/**
+  - tests/modules/nf-core/ampir/**
 
 amplify/predict:
-  - modules/amplify/predict/**
-  - tests/modules/amplify/predict/**
+  - modules/nf-core/amplify/predict/**
+  - tests/modules/nf-core/amplify/predict/**
 
 amps:
-  - modules/amps/**
-  - tests/modules/amps/**
+  - modules/nf-core/amps/**
+  - tests/modules/nf-core/amps/**
 
 amrfinderplus/run:
-  - modules/amrfinderplus/run/**
-  - tests/modules/amrfinderplus/run/**
+  - modules/nf-core/amrfinderplus/run/**
+  - tests/modules/nf-core/amrfinderplus/run/**
 
 amrfinderplus/update:
-  - modules/amrfinderplus/update/**
-  - tests/modules/amrfinderplus/update/**
+  - modules/nf-core/amrfinderplus/update/**
+  - tests/modules/nf-core/amrfinderplus/update/**
 
 angsd/docounts:
-  - modules/angsd/docounts/**
-  - tests/modules/angsd/docounts/**
+  - modules/nf-core/angsd/docounts/**
+  - tests/modules/nf-core/angsd/docounts/**
 
 antismash/antismashlite:
-  - modules/antismash/antismashlite/**
-  - tests/modules/antismash/antismashlite/**
+  - modules/nf-core/antismash/antismashlite/**
+  - tests/modules/nf-core/antismash/antismashlite/**
 
 antismash/antismashlitedownloaddatabases:
-  - modules/antismash/antismashlitedownloaddatabases/**
-  - tests/modules/antismash/antismashlitedownloaddatabases/**
+  - modules/nf-core/antismash/antismashlitedownloaddatabases/**
+  - tests/modules/nf-core/antismash/antismashlitedownloaddatabases/**
 
 ariba/getref:
-  - modules/ariba/getref/**
-  - tests/modules/ariba/getref/**
+  - modules/nf-core/ariba/getref/**
+  - tests/modules/nf-core/ariba/getref/**
 
 ariba/run:
-  - modules/ariba/run/**
-  - tests/modules/ariba/run/**
+  - modules/nf-core/ariba/run/**
+  - tests/modules/nf-core/ariba/run/**
 
 arriba:
-  - modules/arriba/**
-  - tests/modules/arriba/**
+  - modules/nf-core/arriba/**
+  - tests/modules/nf-core/arriba/**
 
 artic/guppyplex:
-  - modules/artic/guppyplex/**
-  - tests/modules/artic/guppyplex/**
+  - modules/nf-core/artic/guppyplex/**
+  - tests/modules/nf-core/artic/guppyplex/**
 
 artic/minion:
-  - modules/artic/minion/**
-  - tests/modules/artic/minion/**
+  - modules/nf-core/artic/minion/**
+  - tests/modules/nf-core/artic/minion/**
 
 ascat:
-  - modules/ascat/**
-  - tests/modules/ascat/**
+  - modules/nf-core/ascat/**
+  - tests/modules/nf-core/ascat/**
 
 assemblyscan:
-  - modules/assemblyscan/**
-  - tests/modules/assemblyscan/**
+  - modules/nf-core/assemblyscan/**
+  - tests/modules/nf-core/assemblyscan/**
 
 ataqv/ataqv:
-  - modules/ataqv/ataqv/**
-  - tests/modules/ataqv/ataqv/**
+  - modules/nf-core/ataqv/ataqv/**
+  - tests/modules/nf-core/ataqv/ataqv/**
 
 ataqv/mkarv:
-  - modules/ataqv/mkarv/**
-  - tests/modules/ataqv/mkarv/**
+  - modules/nf-core/ataqv/mkarv/**
+  - tests/modules/nf-core/ataqv/mkarv/**
 
 atlas/call:
-  - modules/atlas/call/**
-  - tests/modules/atlas/call/**
+  - modules/nf-core/atlas/call/**
+  - tests/modules/nf-core/atlas/call/**
 
 atlas/pmd:
-  - modules/atlas/pmd/**
-  - tests/modules/atlas/pmd/**
+  - modules/nf-core/atlas/pmd/**
+  - tests/modules/nf-core/atlas/pmd/**
 
 atlas/recal:
-  - modules/atlas/recal/**
-  - tests/modules/atlas/recal/**
+  - modules/nf-core/atlas/recal/**
+  - tests/modules/nf-core/atlas/recal/**
 
 atlas/splitmerge:
-  - modules/atlas/splitmerge/**
-  - tests/modules/atlas/splitmerge/**
+  - modules/nf-core/atlas/splitmerge/**
+  - tests/modules/nf-core/atlas/splitmerge/**
 
 bakta:
-  - modules/bakta/**
-  - tests/modules/bakta/**
+  - modules/nf-core/bakta/**
+  - tests/modules/nf-core/bakta/**
 
 bamaligncleaner:
-  - modules/bamaligncleaner/**
-  - tests/modules/bamaligncleaner/**
+  - modules/nf-core/bamaligncleaner/**
+  - tests/modules/nf-core/bamaligncleaner/**
 
 bamcmp:
-  - modules/bamcmp/**
-  - tests/modules/bamcmp/**
+  - modules/nf-core/bamcmp/**
+  - tests/modules/nf-core/bamcmp/**
 
 bamtools/convert:
-  - modules/bamtools/convert/**
-  - tests/modules/bamtools/convert/**
+  - modules/nf-core/bamtools/convert/**
+  - tests/modules/nf-core/bamtools/convert/**
 
 bamtools/split:
-  - modules/bamtools/split/**
-  - tests/modules/bamtools/split/**
+  - modules/nf-core/bamtools/split/**
+  - tests/modules/nf-core/bamtools/split/**
 
 bamtools/stats:
-  - modules/bamtools/stats/**
-  - tests/modules/bamtools/stats/**
+  - modules/nf-core/bamtools/stats/**
+  - tests/modules/nf-core/bamtools/stats/**
 
 bamutil/trimbam:
-  - modules/bamutil/trimbam/**
-  - tests/modules/bamutil/trimbam/**
+  - modules/nf-core/bamutil/trimbam/**
+  - tests/modules/nf-core/bamutil/trimbam/**
 
 bandage/image:
-  - modules/bandage/image/**
-  - tests/modules/bandage/image/**
+  - modules/nf-core/bandage/image/**
+  - tests/modules/nf-core/bandage/image/**
 
 bases2fastq:
-  - modules/bases2fastq/**
-  - tests/modules/bases2fastq/**
+  - modules/nf-core/bases2fastq/**
+  - tests/modules/nf-core/bases2fastq/**
 
 bbmap/align:
-  - modules/bbmap/align/**
-  - tests/modules/bbmap/align/**
+  - modules/nf-core/bbmap/align/**
+  - tests/modules/nf-core/bbmap/align/**
 
 bbmap/bbduk:
-  - modules/bbmap/bbduk/**
-  - tests/modules/bbmap/bbduk/**
+  - modules/nf-core/bbmap/bbduk/**
+  - tests/modules/nf-core/bbmap/bbduk/**
 
 bbmap/bbsplit:
-  - modules/bbmap/bbsplit/**
-  - tests/modules/bbmap/bbsplit/**
+  - modules/nf-core/bbmap/bbsplit/**
+  - tests/modules/nf-core/bbmap/bbsplit/**
 
 bbmap/clumpify:
-  - modules/bbmap/clumpify/**
-  - tests/modules/bbmap/clumpify/**
+  - modules/nf-core/bbmap/clumpify/**
+  - tests/modules/nf-core/bbmap/clumpify/**
 
 bbmap/index:
-  - modules/bbmap/index/**
-  - tests/modules/bbmap/index/**
+  - modules/nf-core/bbmap/index/**
+  - tests/modules/nf-core/bbmap/index/**
 
 bbmap/pileup:
-  - modules/bbmap/pileup/**
-  - tests/modules/bbmap/pileup/**
+  - modules/nf-core/bbmap/pileup/**
+  - tests/modules/nf-core/bbmap/pileup/**
 
 bcftools/annotate:
-  - modules/bcftools/annotate/**
-  - tests/modules/bcftools/annotate/**
+  - modules/nf-core/bcftools/annotate/**
+  - tests/modules/nf-core/bcftools/annotate/**
 
 bcftools/concat:
-  - modules/bcftools/concat/**
-  - tests/modules/bcftools/concat/**
+  - modules/nf-core/bcftools/concat/**
+  - tests/modules/nf-core/bcftools/concat/**
 
 bcftools/consensus:
-  - modules/bcftools/consensus/**
-  - tests/modules/bcftools/consensus/**
+  - modules/nf-core/bcftools/consensus/**
+  - tests/modules/nf-core/bcftools/consensus/**
 
 bcftools/convert:
-  - modules/bcftools/convert/**
-  - tests/modules/bcftools/convert/**
+  - modules/nf-core/bcftools/convert/**
+  - tests/modules/nf-core/bcftools/convert/**
 
 bcftools/filter:
-  - modules/bcftools/filter/**
-  - tests/modules/bcftools/filter/**
+  - modules/nf-core/bcftools/filter/**
+  - tests/modules/nf-core/bcftools/filter/**
 
 bcftools/index:
-  - modules/bcftools/index/**
-  - tests/modules/bcftools/index**
+  - modules/nf-core/bcftools/index/**
+  - tests/modules/nf-core/bcftools/index**
 
 bcftools/isec:
-  - modules/bcftools/isec/**
-  - tests/modules/bcftools/isec/**
+  - modules/nf-core/bcftools/isec/**
+  - tests/modules/nf-core/bcftools/isec/**
 
 bcftools/merge:
-  - modules/bcftools/merge/**
-  - tests/modules/bcftools/merge/**
+  - modules/nf-core/bcftools/merge/**
+  - tests/modules/nf-core/bcftools/merge/**
 
 bcftools/mpileup:
-  - modules/bcftools/mpileup/**
-  - tests/modules/bcftools/mpileup/**
+  - modules/nf-core/bcftools/mpileup/**
+  - tests/modules/nf-core/bcftools/mpileup/**
 
 bcftools/norm:
-  - modules/bcftools/norm/**
-  - tests/modules/bcftools/norm/**
+  - modules/nf-core/bcftools/norm/**
+  - tests/modules/nf-core/bcftools/norm/**
 
 bcftools/query:
-  - modules/bcftools/query/**
-  - tests/modules/bcftools/query/**
+  - modules/nf-core/bcftools/query/**
+  - tests/modules/nf-core/bcftools/query/**
 
 bcftools/reheader:
-  - modules/bcftools/reheader/**
-  - tests/modules/bcftools/reheader/**
+  - modules/nf-core/bcftools/reheader/**
+  - tests/modules/nf-core/bcftools/reheader/**
 
 bcftools/roh:
-  - modules/bcftools/roh/**
-  - tests/modules/bcftools/roh/**
+  - modules/nf-core/bcftools/roh/**
+  - tests/modules/nf-core/bcftools/roh/**
 
 bcftools/sort:
-  - modules/bcftools/sort/**
-  - tests/modules/bcftools/sort/**
+  - modules/nf-core/bcftools/sort/**
+  - tests/modules/nf-core/bcftools/sort/**
 
 bcftools/stats:
-  - modules/bcftools/stats/**
-  - tests/modules/bcftools/stats/**
+  - modules/nf-core/bcftools/stats/**
+  - tests/modules/nf-core/bcftools/stats/**
 
 bcftools/view:
-  - modules/bcftools/view/**
-  - tests/modules/bcftools/view/**
+  - modules/nf-core/bcftools/view/**
+  - tests/modules/nf-core/bcftools/view/**
 
 bcl2fastq:
-  - modules/bcl2fastq/**
-  - tests/modules/bcl2fastq/**
+  - modules/nf-core/bcl2fastq/**
+  - tests/modules/nf-core/bcl2fastq/**
 
 bclconvert:
-  - modules/bclconvert/**
-  - tests/modules/bclconvert/**
+  - modules/nf-core/bclconvert/**
+  - tests/modules/nf-core/bclconvert/**
 
 bedtools/bamtobed:
-  - modules/bedtools/bamtobed/**
-  - tests/modules/bedtools/bamtobed/**
+  - modules/nf-core/bedtools/bamtobed/**
+  - tests/modules/nf-core/bedtools/bamtobed/**
 
 bedtools/complement:
-  - modules/bedtools/complement/**
-  - tests/modules/bedtools/complement/**
+  - modules/nf-core/bedtools/complement/**
+  - tests/modules/nf-core/bedtools/complement/**
 
 bedtools/genomecov:
-  - modules/bedtools/genomecov/**
-  - tests/modules/bedtools/genomecov/**
+  - modules/nf-core/bedtools/genomecov/**
+  - tests/modules/nf-core/bedtools/genomecov/**
 
 bedtools/getfasta:
-  - modules/bedtools/getfasta/**
-  - tests/modules/bedtools/getfasta/**
+  - modules/nf-core/bedtools/getfasta/**
+  - tests/modules/nf-core/bedtools/getfasta/**
 
 bedtools/intersect:
-  - modules/bedtools/intersect/**
-  - tests/modules/bedtools/intersect/**
+  - modules/nf-core/bedtools/intersect/**
+  - tests/modules/nf-core/bedtools/intersect/**
 
 bedtools/makewindows:
-  - modules/bedtools/makewindows/**
-  - tests/modules/bedtools/makewindows/**
+  - modules/nf-core/bedtools/makewindows/**
+  - tests/modules/nf-core/bedtools/makewindows/**
 
 bedtools/maskfasta:
-  - modules/bedtools/maskfasta/**
-  - tests/modules/bedtools/maskfasta/**
+  - modules/nf-core/bedtools/maskfasta/**
+  - tests/modules/nf-core/bedtools/maskfasta/**
 
 bedtools/merge:
-  - modules/bedtools/merge/**
-  - tests/modules/bedtools/merge/**
+  - modules/nf-core/bedtools/merge/**
+  - tests/modules/nf-core/bedtools/merge/**
 
 bedtools/slop:
-  - modules/bedtools/slop/**
-  - tests/modules/bedtools/slop/**
+  - modules/nf-core/bedtools/slop/**
+  - tests/modules/nf-core/bedtools/slop/**
 
 bedtools/sort:
-  - modules/bedtools/sort/**
-  - tests/modules/bedtools/sort/**
+  - modules/nf-core/bedtools/sort/**
+  - tests/modules/nf-core/bedtools/sort/**
 
 bedtools/split:
-  - modules/bedtools/split/**
-  - tests/modules/bedtools/split/**
+  - modules/nf-core/bedtools/split/**
+  - tests/modules/nf-core/bedtools/split/**
 
 bedtools/subtract:
-  - modules/bedtools/subtract/**
-  - tests/modules/bedtools/subtract/**
+  - modules/nf-core/bedtools/subtract/**
+  - tests/modules/nf-core/bedtools/subtract/**
 
 biobambam/bammarkduplicates2:
-  - modules/biobambam/bammarkduplicates2/**
-  - tests/modules/biobambam/bammarkduplicates2/**
+  - modules/nf-core/biobambam/bammarkduplicates2/**
+  - tests/modules/nf-core/biobambam/bammarkduplicates2/**
 
 biobambam/bammerge:
-  - modules/biobambam/bammerge/**
-  - tests/modules/biobambam/bammerge/**
+  - modules/nf-core/biobambam/bammerge/**
+  - tests/modules/nf-core/biobambam/bammerge/**
 
 biobambam/bamsormadup:
-  - modules/biobambam/bamsormadup/**
-  - tests/modules/biobambam/bamsormadup/**
+  - modules/nf-core/biobambam/bamsormadup/**
+  - tests/modules/nf-core/biobambam/bamsormadup/**
 
 biscuit/align:
-  - modules/biscuit/index/**
-  - modules/biscuit/align/**
-  - tests/modules/biscuit/align/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/align/**
+  - tests/modules/nf-core/biscuit/align/**
 
 biscuit/biscuitblaster:
-  - modules/biscuit/index/**
-  - modules/biscuit/biscuitblaster/**
-  - tests/modules/biscuit/biscuitblaster/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/biscuitblaster/**
+  - tests/modules/nf-core/biscuit/biscuitblaster/**
 
 biscuit/bsconv:
-  - modules/biscuit/index/**
-  - modules/biscuit/bsconv/**
-  - tests/modules/biscuit/bsconv/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/bsconv/**
+  - tests/modules/nf-core/biscuit/bsconv/**
 
 biscuit/epiread:
-  - modules/biscuit/index/**
-  - modules/biscuit/epiread/**
-  - tests/modules/biscuit/epiread/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/epiread/**
+  - tests/modules/nf-core/biscuit/epiread/**
 
 biscuit/index:
-  - modules/biscuit/index/**
-  - tests/modules/biscuit/index/**
+  - modules/nf-core/biscuit/index/**
+  - tests/modules/nf-core/biscuit/index/**
 
 biscuit/mergecg:
-  - modules/biscuit/index/**
-  - modules/biscuit/mergecg/**
-  - tests/modules/biscuit/mergecg/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/mergecg/**
+  - tests/modules/nf-core/biscuit/mergecg/**
 
 biscuit/pileup:
-  - modules/biscuit/index/**
-  - modules/biscuit/pileup/**
-  - tests/modules/biscuit/pileup/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/pileup/**
+  - tests/modules/nf-core/biscuit/pileup/**
 
 biscuit/qc:
-  - modules/biscuit/index/**
-  - modules/biscuit/qc/**
-  - tests/modules/biscuit/qc/**
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/qc/**
+  - tests/modules/nf-core/biscuit/qc/**
 
 biscuit/vcf2bed:
-  - modules/biscuit/vcf2bed/**
-  - tests/modules/biscuit/vcf2bed/**
+  - modules/nf-core/biscuit/vcf2bed/**
+  - tests/modules/nf-core/biscuit/vcf2bed/**
 
 bismark/align:
-  - modules/bismark/align/**
-  - modules/bismark/genomepreparation/**
-  - tests/modules/bismark/align/**
+  - modules/nf-core/bismark/align/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - tests/modules/nf-core/bismark/align/**
 
 bismark/deduplicate:
-  - modules/bismark/deduplicate/**
-  - tests/modules/bismark/deduplicate/**
+  - modules/nf-core/bismark/deduplicate/**
+  - tests/modules/nf-core/bismark/deduplicate/**
 
 bismark/genomepreparation:
-  - modules/bismark/genomepreparation/**
-  - tests/modules/bismark/genomepreparation/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - tests/modules/nf-core/bismark/genomepreparation/**
 
 bismark/methylationextractor:
-  - modules/bismark/methylationextractor/**
-  - modules/bismark/genomepreparation/**
-  - tests/modules/bismark/methylationextractor/**
+  - modules/nf-core/bismark/methylationextractor/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - tests/modules/nf-core/bismark/methylationextractor/**
 
 bismark/report:
-  - modules/bismark/genomepreparation/**
-  - modules/bismark/align/**
-  - modules/bismark/deduplicate/**
-  - modules/bismark/methylationextractor/**
-  - modules/bismark/report/**
-  - tests/modules/bismark/report/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - modules/nf-core/bismark/align/**
+  - modules/nf-core/bismark/deduplicate/**
+  - modules/nf-core/bismark/methylationextractor/**
+  - modules/nf-core/bismark/report/**
+  - tests/modules/nf-core/bismark/report/**
 
 bismark/summary:
-  - modules/bismark/genomepreparation/**
-  - modules/bismark/align/**
-  - modules/bismark/deduplicate/**
-  - modules/bismark/methylationextractor/**
-  - modules/bismark/summary/**
-  - tests/modules/bismark/summary/**
+  - modules/nf-core/bismark/genomepreparation/**
+  - modules/nf-core/bismark/align/**
+  - modules/nf-core/bismark/deduplicate/**
+  - modules/nf-core/bismark/methylationextractor/**
+  - modules/nf-core/bismark/summary/**
+  - tests/modules/nf-core/bismark/summary/**
 
 blast/blastn:
-  - modules/blast/blastn/**
-  - tests/modules/blast/blastn/**
+  - modules/nf-core/blast/blastn/**
+  - tests/modules/nf-core/blast/blastn/**
 
 blast/makeblastdb:
-  - modules/blast/makeblastdb/**
-  - tests/modules/blast/makeblastdb/**
+  - modules/nf-core/blast/makeblastdb/**
+  - tests/modules/nf-core/blast/makeblastdb/**
 
 blast/tblastn:
-  - modules/blast/tblastn/**
-  - tests/modules/blast/tblastn/**
+  - modules/nf-core/blast/tblastn/**
+  - tests/modules/nf-core/blast/tblastn/**
 
 bowtie/align:
-  - modules/bowtie/align/**
-  - modules/bowtie/build/**
-  - tests/modules/bowtie/align/**
+  - modules/nf-core/bowtie/align/**
+  - modules/nf-core/bowtie/build/**
+  - tests/modules/nf-core/bowtie/align/**
 
 bowtie/build:
-  - modules/bowtie/build/**
-  - tests/modules/bowtie/build_test/**
+  - modules/nf-core/bowtie/build/**
+  - tests/modules/nf-core/bowtie/build_test/**
 
 bowtie2/align:
-  - modules/bowtie2/align/**
-  - modules/bowtie2/build/**
-  - tests/modules/bowtie2/align/**
+  - modules/nf-core/bowtie2/align/**
+  - modules/nf-core/bowtie2/build/**
+  - tests/modules/nf-core/bowtie2/align/**
 
 bowtie2/build:
-  - modules/bowtie2/build/**
-  - tests/modules/bowtie2/build_test/**
+  - modules/nf-core/bowtie2/build/**
+  - tests/modules/nf-core/bowtie2/build_test/**
 
 bracken/bracken:
-  - modules/bracken/bracken/**
-  - tests/modules/bracken/bracken/**
+  - modules/nf-core/bracken/bracken/**
+  - tests/modules/nf-core/bracken/bracken/**
 
 bracken/combinebrackenoutputs:
-  - modules/bracken/combinebrackenoutputs/**
-  - tests/modules/bracken/combinebrackenoutputs/**
+  - modules/nf-core/bracken/combinebrackenoutputs/**
+  - tests/modules/nf-core/bracken/combinebrackenoutputs/**
 
 busco:
-  - modules/busco/**
-  - tests/modules/busco/**
+  - modules/nf-core/busco/**
+  - tests/modules/nf-core/busco/**
 
 bwa/aln:
-  - modules/bwa/aln/**
-  - tests/modules/bwa/aln/**
+  - modules/nf-core/bwa/aln/**
+  - tests/modules/nf-core/bwa/aln/**
 
 bwa/index:
-  - modules/bwa/index/**
-  - tests/modules/bwa/index/**
+  - modules/nf-core/bwa/index/**
+  - tests/modules/nf-core/bwa/index/**
 
 bwa/mem:
-  - modules/bwa/mem/**
-  - tests/modules/bwa/mem/**
+  - modules/nf-core/bwa/mem/**
+  - tests/modules/nf-core/bwa/mem/**
 
 bwa/sampe:
-  - modules/bwa/sampe/**
-  - tests/modules/bwa/sampe/**
+  - modules/nf-core/bwa/sampe/**
+  - tests/modules/nf-core/bwa/sampe/**
 
 bwa/samse:
-  - modules/bwa/samse/**
-  - tests/modules/bwa/samse/**
+  - modules/nf-core/bwa/samse/**
+  - tests/modules/nf-core/bwa/samse/**
 
 bwamem2/index:
-  - modules/bwamem2/index/**
-  - tests/modules/bwamem2/index/**
+  - modules/nf-core/bwamem2/index/**
+  - tests/modules/nf-core/bwamem2/index/**
 
 bwamem2/mem:
-  - modules/bwamem2/mem/**
-  - tests/modules/bwamem2/mem/**
+  - modules/nf-core/bwamem2/mem/**
+  - tests/modules/nf-core/bwamem2/mem/**
 
 bwameth/align:
-  - modules/bwameth/align/**
-  - tests/modules/bwameth/align/**
+  - modules/nf-core/bwameth/align/**
+  - tests/modules/nf-core/bwameth/align/**
 
 bwameth/index:
-  - modules/bwameth/index/**
-  - tests/modules/bwameth/index/**
+  - modules/nf-core/bwameth/index/**
+  - tests/modules/nf-core/bwameth/index/**
 
 cat/cat:
-  - modules/cat/cat/**
-  - tests/modules/cat/cat/**
+  - modules/nf-core/cat/cat/**
+  - tests/modules/nf-core/cat/cat/**
 
 cat/fastq:
-  - modules/cat/fastq/**
-  - tests/modules/cat/fastq/**
+  - modules/nf-core/cat/fastq/**
+  - tests/modules/nf-core/cat/fastq/**
 
 cellranger/count:
-  - modules/cellranger/count/**
-  - tests/modules/cellranger/count/**
-  - modules/cellranger/mkref/**
-  - tests/modules/cellranger/mkref/**
-  - modules/cellranger/gtf/**
-  - tests/modules/cellranger/gtf/**
+  - modules/nf-core/cellranger/count/**
+  - tests/modules/nf-core/cellranger/count/**
+  - modules/nf-core/cellranger/mkref/**
+  - tests/modules/nf-core/cellranger/mkref/**
+  - modules/nf-core/cellranger/gtf/**
+  - tests/modules/nf-core/cellranger/gtf/**
 
 cellranger/gtf:
-  - modules/cellranger/gtf/**
-  - tests/modules/cellranger/gtf/**
+  - modules/nf-core/cellranger/gtf/**
+  - tests/modules/nf-core/cellranger/gtf/**
 
 cellranger/mkfastq:
-  - modules/cellranger/mkfastq/**
-  - tests/modules/cellranger/mkfastq/**
+  - modules/nf-core/cellranger/mkfastq/**
+  - tests/modules/nf-core/cellranger/mkfastq/**
 
 cellranger/mkgtf:
-  - modules/cellranger/mkgtf/**
-  - tests/modules/cellranger/mkgtf/**
+  - modules/nf-core/cellranger/mkgtf/**
+  - tests/modules/nf-core/cellranger/mkgtf/**
 
 cellranger/mkref:
-  - modules/cellranger/mkref/**
-  - tests/modules/cellranger/mkref/**
-  - modules/cellranger/gtf/**
-  - tests/modules/cellranger/gtf/**
+  - modules/nf-core/cellranger/mkref/**
+  - tests/modules/nf-core/cellranger/mkref/**
+  - modules/nf-core/cellranger/gtf/**
+  - tests/modules/nf-core/cellranger/gtf/**
 
 centrifuge/centrifuge:
-  - modules/centrifuge/centrifuge/**
-  - tests/modules/centrifuge/centrifuge/**
+  - modules/nf-core/centrifuge/centrifuge/**
+  - tests/modules/nf-core/centrifuge/centrifuge/**
 
 checkm/lineagewf:
-  - modules/checkm/lineagewf/**
-  - tests/modules/checkm/lineagewf/**
+  - modules/nf-core/checkm/lineagewf/**
+  - tests/modules/nf-core/checkm/lineagewf/**
 
 checkm/qa:
-  - modules/checkm/qa/**
-  - tests/modules/checkm/qa/**
+  - modules/nf-core/checkm/qa/**
+  - tests/modules/nf-core/checkm/qa/**
 
 chromap/chromap:
-  - modules/chromap/chromap/**
-  - tests/modules/chromap/chromap/**
+  - modules/nf-core/chromap/chromap/**
+  - tests/modules/nf-core/chromap/chromap/**
 
 chromap/index:
-  - modules/chromap/index/**
-  - tests/modules/chromap/index/**
+  - modules/nf-core/chromap/index/**
+  - tests/modules/nf-core/chromap/index/**
 
 clonalframeml:
-  - modules/clonalframeml/**
-  - tests/modules/clonalframeml/**
+  - modules/nf-core/clonalframeml/**
+  - tests/modules/nf-core/clonalframeml/**
 
 cmseq/polymut:
-  - modules/cmseq/polymut/**
-  - tests/modules/cmseq/polymut/**
+  - modules/nf-core/cmseq/polymut/**
+  - tests/modules/nf-core/cmseq/polymut/**
 
 cnvkit/antitarget:
-  - modules/cnvkit/antitarget/**
-  - tests/modules/cnvkit/antitarget/**
+  - modules/nf-core/cnvkit/antitarget/**
+  - tests/modules/nf-core/cnvkit/antitarget/**
 
 cnvkit/batch:
-  - modules/cnvkit/batch/**
-  - tests/modules/cnvkit/batch/**
+  - modules/nf-core/cnvkit/batch/**
+  - tests/modules/nf-core/cnvkit/batch/**
 
 cnvkit/reference:
-  - modules/cnvkit/reference/**
-  - tests/modules/cnvkit/reference/**
+  - modules/nf-core/cnvkit/reference/**
+  - tests/modules/nf-core/cnvkit/reference/**
 
 controlfreec/assesssignificance:
-  - modules/controlfreec/assesssignificance/**
-  - tests/modules/controlfreec/assesssignificance/**
+  - modules/nf-core/controlfreec/assesssignificance/**
+  - tests/modules/nf-core/controlfreec/assesssignificance/**
 
 controlfreec/freec:
-  - modules/controlfreec/freec/**
-  - tests/modules/controlfreec/freec/**
+  - modules/nf-core/controlfreec/freec/**
+  - tests/modules/nf-core/controlfreec/freec/**
 
 controlfreec/freec2bed:
-  - modules/controlfreec/freec2bed/**
-  - tests/modules/controlfreec/freec2bed/**
+  - modules/nf-core/controlfreec/freec2bed/**
+  - tests/modules/nf-core/controlfreec/freec2bed/**
 
 controlfreec/freec2circos:
-  - modules/controlfreec/freec2circos/**
-  - tests/modules/controlfreec/freec2circos/**
+  - modules/nf-core/controlfreec/freec2circos/**
+  - tests/modules/nf-core/controlfreec/freec2circos/**
 
 controlfreec/makegraph:
-  - modules/controlfreec/makegraph/**
-  - tests/modules/controlfreec/makegraph/**
+  - modules/nf-core/controlfreec/makegraph/**
+  - tests/modules/nf-core/controlfreec/makegraph/**
 
 cooler/cload:
-  - modules/cooler/cload/**
-  - tests/modules/cooler/cload/**
+  - modules/nf-core/cooler/cload/**
+  - tests/modules/nf-core/cooler/cload/**
 
 cooler/digest:
-  - modules/cooler/digest/**
-  - tests/modules/cooler/digest/**
+  - modules/nf-core/cooler/digest/**
+  - tests/modules/nf-core/cooler/digest/**
 
 cooler/dump:
-  - modules/cooler/dump/**
-  - tests/modules/cooler/dump/**
+  - modules/nf-core/cooler/dump/**
+  - tests/modules/nf-core/cooler/dump/**
 
 cooler/merge:
-  - modules/cooler/merge/**
-  - tests/modules/cooler/merge/**
+  - modules/nf-core/cooler/merge/**
+  - tests/modules/nf-core/cooler/merge/**
 
 cooler/zoomify:
-  - modules/cooler/zoomify/**
+  - modules/nf-core/cooler/zoomify/**
   - tests/software/cooler/zoomify/**
 
 csvtk/concat:
-  - modules/csvtk/concat/**
-  - tests/modules/csvtk/concat/**
+  - modules/nf-core/csvtk/concat/**
+  - tests/modules/nf-core/csvtk/concat/**
 
 csvtk/split:
-  - modules/csvtk/split/**
-  - tests/modules/csvtk/split/**
+  - modules/nf-core/csvtk/split/**
+  - tests/modules/nf-core/csvtk/split/**
 
 custom/dumpsoftwareversions:
-  - modules/custom/dumpsoftwareversions/**
-  - tests/modules/custom/dumpsoftwareversions/**
+  - modules/nf-core/custom/dumpsoftwareversions/**
+  - tests/modules/nf-core/custom/dumpsoftwareversions/**
 
 custom/getchromsizes:
-  - modules/custom/getchromsizes/**
-  - tests/modules/custom/getchromsizes/**
+  - modules/nf-core/custom/getchromsizes/**
+  - tests/modules/nf-core/custom/getchromsizes/**
 
 custom/sratoolsncbisettings:
-  - modules/custom/sratoolsncbisettings/**
-  - tests/modules/custom/sratoolsncbisettings/**
+  - modules/nf-core/custom/sratoolsncbisettings/**
+  - tests/modules/nf-core/custom/sratoolsncbisettings/**
 
 cutadapt:
-  - modules/cutadapt/**
-  - tests/modules/cutadapt/**
+  - modules/nf-core/cutadapt/**
+  - tests/modules/nf-core/cutadapt/**
 
 damageprofiler:
-  - modules/damageprofiler/**
-  - tests/modules/damageprofiler/**
+  - modules/nf-core/damageprofiler/**
+  - tests/modules/nf-core/damageprofiler/**
 
 dastool/dastool:
-  - modules/dastool/dastool/**
-  - tests/modules/dastool/dastool/**
+  - modules/nf-core/dastool/dastool/**
+  - tests/modules/nf-core/dastool/dastool/**
 
 dastool/fastatocontig2bin:
-  - modules/dastool/fastatocontig2bin/**
-  - tests/modules/dastool/fastatocontig2bin/**
+  - modules/nf-core/dastool/fastatocontig2bin/**
+  - tests/modules/nf-core/dastool/fastatocontig2bin/**
 
 dastool/scaffolds2bin:
-  - modules/dastool/scaffolds2bin/**
-  - tests/modules/dastool/scaffolds2bin/**
+  - modules/nf-core/dastool/scaffolds2bin/**
+  - tests/modules/nf-core/dastool/scaffolds2bin/**
 
 dedup:
-  - modules/dedup/**
-  - tests/modules/dedup/**
+  - modules/nf-core/dedup/**
+  - tests/modules/nf-core/dedup/**
 
 deeparg/downloaddata:
-  - modules/deeparg/downloaddata/**
-  - tests/modules/deeparg/downloaddata/**
+  - modules/nf-core/deeparg/downloaddata/**
+  - tests/modules/nf-core/deeparg/downloaddata/**
 
 deeparg/predict:
-  - modules/deeparg/predict/**
-  - tests/modules/deeparg/predict/**
+  - modules/nf-core/deeparg/predict/**
+  - tests/modules/nf-core/deeparg/predict/**
 
 deepbgc/download:
-  - modules/deepbgc/download/**
-  - tests/modules/deepbgc/download/**
+  - modules/nf-core/deepbgc/download/**
+  - tests/modules/nf-core/deepbgc/download/**
 
 deepbgc/pipeline:
-  - modules/deepbgc/pipeline/**
-  - tests/modules/deepbgc/pipeline/**
+  - modules/nf-core/deepbgc/pipeline/**
+  - tests/modules/nf-core/deepbgc/pipeline/**
 
 deeptools/bamcoverage:
-  - modules/deeptools/bamcoverage/**
-  - tests/modules/deeptools/bamcoverage/**
+  - modules/nf-core/deeptools/bamcoverage/**
+  - tests/modules/nf-core/deeptools/bamcoverage/**
 
 deeptools/computematrix:
-  - modules/deeptools/computematrix/**
-  - tests/modules/deeptools/computematrix/**
+  - modules/nf-core/deeptools/computematrix/**
+  - tests/modules/nf-core/deeptools/computematrix/**
 
 deeptools/plotfingerprint:
-  - modules/deeptools/plotfingerprint/**
-  - tests/modules/deeptools/plotfingerprint/**
+  - modules/nf-core/deeptools/plotfingerprint/**
+  - tests/modules/nf-core/deeptools/plotfingerprint/**
 
 deeptools/plotheatmap:
-  - modules/deeptools/plotheatmap/**
-  - tests/modules/deeptools/plotheatmap/**
+  - modules/nf-core/deeptools/plotheatmap/**
+  - tests/modules/nf-core/deeptools/plotheatmap/**
 
 deeptools/plotprofile:
-  - modules/deeptools/plotprofile/**
-  - tests/modules/deeptools/plotprofile/**
+  - modules/nf-core/deeptools/plotprofile/**
+  - tests/modules/nf-core/deeptools/plotprofile/**
 
 deepvariant:
-  - modules/deepvariant/**
-  - tests/modules/deepvariant/**
+  - modules/nf-core/deepvariant/**
+  - tests/modules/nf-core/deepvariant/**
 
 delly/call:
-  - modules/delly/call/**
-  - tests/modules/delly/call/**
+  - modules/nf-core/delly/call/**
+  - tests/modules/nf-core/delly/call/**
 
 diamond/blastp:
-  - modules/diamond/blastp/**
-  - tests/modules/diamond/blastp/**
+  - modules/nf-core/diamond/blastp/**
+  - tests/modules/nf-core/diamond/blastp/**
 
 diamond/blastx:
-  - modules/diamond/blastx/**
-  - tests/modules/diamond/blastx/**
+  - modules/nf-core/diamond/blastx/**
+  - tests/modules/nf-core/diamond/blastx/**
 
 diamond/makedb:
-  - modules/diamond/makedb/**
-  - tests/modules/diamond/makedb/**
+  - modules/nf-core/diamond/makedb/**
+  - tests/modules/nf-core/diamond/makedb/**
 
 dragmap/align:
-  - modules/dragmap/align/**
-  - tests/modules/dragmap/align/**
+  - modules/nf-core/dragmap/align/**
+  - tests/modules/nf-core/dragmap/align/**
 
 dragmap/hashtable:
-  - modules/dragmap/hashtable/**
-  - tests/modules/dragmap/hashtable/**
+  - modules/nf-core/dragmap/hashtable/**
+  - tests/modules/nf-core/dragmap/hashtable/**
 
 dragonflye:
-  - modules/dragonflye/**
-  - tests/modules/dragonflye/**
+  - modules/nf-core/dragonflye/**
+  - tests/modules/nf-core/dragonflye/**
 
 dshbio/exportsegments:
-  - modules/dshbio/exportsegments/**
-  - tests/modules/dshbio/exportsegments/**
+  - modules/nf-core/dshbio/exportsegments/**
+  - tests/modules/nf-core/dshbio/exportsegments/**
 
 dshbio/filterbed:
-  - modules/dshbio/filterbed/**
-  - tests/modules/dshbio/filterbed/**
+  - modules/nf-core/dshbio/filterbed/**
+  - tests/modules/nf-core/dshbio/filterbed/**
 
 dshbio/filtergff3:
-  - modules/dshbio/filtergff3/**
-  - tests/modules/dshbio/filtergff3/**
+  - modules/nf-core/dshbio/filtergff3/**
+  - tests/modules/nf-core/dshbio/filtergff3/**
 
 dshbio/splitbed:
-  - modules/dshbio/splitbed/**
-  - tests/modules/dshbio/splitbed/**
+  - modules/nf-core/dshbio/splitbed/**
+  - tests/modules/nf-core/dshbio/splitbed/**
 
 dshbio/splitgff3:
-  - modules/dshbio/splitgff3/**
-  - tests/modules/dshbio/splitgff3/**
+  - modules/nf-core/dshbio/splitgff3/**
+  - tests/modules/nf-core/dshbio/splitgff3/**
 
 ectyper:
-  - modules/ectyper/**
-  - tests/modules/ectyper/**
+  - modules/nf-core/ectyper/**
+  - tests/modules/nf-core/ectyper/**
 
 eido/convert:
-  - modules/eido/convert/**
-  - tests/modules/eido/convert/**
+  - modules/nf-core/eido/convert/**
+  - tests/modules/nf-core/eido/convert/**
 
 eido/validate:
-  - modules/eido/validate/**
-  - tests/modules/eido/validate/**
+  - modules/nf-core/eido/validate/**
+  - tests/modules/nf-core/eido/validate/**
 
 elprep/filter:
-  - modules/elprep/filter/**
-  - tests/modules/elprep/filter/**
+  - modules/nf-core/elprep/filter/**
+  - tests/modules/nf-core/elprep/filter/**
 
 elprep/merge:
-  - modules/elprep/merge/**
-  - tests/modules/elprep/merge/**
+  - modules/nf-core/elprep/merge/**
+  - tests/modules/nf-core/elprep/merge/**
 
 elprep/split:
-  - modules/elprep/split/**
-  - tests/modules/elprep/split/**
+  - modules/nf-core/elprep/split/**
+  - tests/modules/nf-core/elprep/split/**
 
 emboss/seqret:
-  - modules/emboss/seqret/**
-  - tests/modules/emboss/seqret/**
+  - modules/nf-core/emboss/seqret/**
+  - tests/modules/nf-core/emboss/seqret/**
 
 emmtyper:
-  - modules/emmtyper/**
-  - tests/modules/emmtyper/**
+  - modules/nf-core/emmtyper/**
+  - tests/modules/nf-core/emmtyper/**
 
 endorspy:
-  - modules/endorspy/**
-  - tests/modules/endorspy/**
+  - modules/nf-core/endorspy/**
+  - tests/modules/nf-core/endorspy/**
 
 ensemblvep:
-  - modules/ensemblvep/**
-  - tests/modules/ensemblvep/**
+  - modules/nf-core/ensemblvep/**
+  - tests/modules/nf-core/ensemblvep/**
 
 entrezdirect/esearch:
-  - modules/entrezdirect/esearch/**
-  - tests/modules/entrezdirect/esearch/**
+  - modules/nf-core/entrezdirect/esearch/**
+  - tests/modules/nf-core/entrezdirect/esearch/**
 
 entrezdirect/esummary:
-  - modules/entrezdirect/esummary/**
-  - tests/modules/entrezdirect/esummary/**
+  - modules/nf-core/entrezdirect/esummary/**
+  - tests/modules/nf-core/entrezdirect/esummary/**
 
 entrezdirect/xtract:
-  - modules/entrezdirect/xtract/**
-  - tests/modules/entrezdirect/xtract/**
+  - modules/nf-core/entrezdirect/xtract/**
+  - tests/modules/nf-core/entrezdirect/xtract/**
 
 epang:
-  - modules/epang/**
-  - tests/modules/epang/
+  - modules/nf-core/epang/**
+  - tests/modules/nf-core/epang/
 
 expansionhunter:
-  - modules/expansionhunter/**
-  - tests/modules/expansionhunter/**
+  - modules/nf-core/expansionhunter/**
+  - tests/modules/nf-core/expansionhunter/**
 
 faqcs:
-  - modules/faqcs/**
-  - tests/modules/faqcs/**
+  - modules/nf-core/faqcs/**
+  - tests/modules/nf-core/faqcs/**
 
 fargene:
-  - modules/fargene/**
-  - tests/modules/fargene/**
+  - modules/nf-core/fargene/**
+  - tests/modules/nf-core/fargene/**
 
 fastani:
-  - modules/fastani/**
-  - tests/modules/fastani/**
+  - modules/nf-core/fastani/**
+  - tests/modules/nf-core/fastani/**
 
 fastawindows:
-  - modules/fastawindows/**
-  - tests/modules/fastawindows/**
+  - modules/nf-core/fastawindows/**
+  - tests/modules/nf-core/fastawindows/**
 
 fastk/fastk:
-  - modules/fastk/fastk/**
-  - tests/modules/fastk/fastk/**
+  - modules/nf-core/fastk/fastk/**
+  - tests/modules/nf-core/fastk/fastk/**
 
 fastk/histex:
-  - modules/fastk/histex/**
-  - tests/modules/fastk/histex/**
+  - modules/nf-core/fastk/histex/**
+  - tests/modules/nf-core/fastk/histex/**
 
 fastk/merge:
-  - modules/fastk/merge/**
-  - tests/modules/fastk/merge/**
+  - modules/nf-core/fastk/merge/**
+  - tests/modules/nf-core/fastk/merge/**
 
 fastp:
-  - modules/fastp/**
-  - tests/modules/fastp/**
+  - modules/nf-core/fastp/**
+  - tests/modules/nf-core/fastp/**
 
 fastqc:
-  - modules/fastqc/**
-  - tests/modules/fastqc/**
+  - modules/nf-core/fastqc/**
+  - tests/modules/nf-core/fastqc/**
 
 fastqscan:
-  - modules/fastqscan/**
-  - tests/modules/fastqscan/**
+  - modules/nf-core/fastqscan/**
+  - tests/modules/nf-core/fastqscan/**
 
 fasttree:
-  - modules/fasttree/**
-  - tests/modules/fasttree/**
+  - modules/nf-core/fasttree/**
+  - tests/modules/nf-core/fasttree/**
 
 fcs/fcsadaptor:
-  - modules/fcs/fcsadaptor/**
-  - tests/modules/fcs/fcsadaptor/**
+  - modules/nf-core/fcs/fcsadaptor/**
+  - tests/modules/nf-core/fcs/fcsadaptor/**
 
 ffq:
-  - modules/ffq/**
-  - tests/modules/ffq/**
+  - modules/nf-core/ffq/**
+  - tests/modules/nf-core/ffq/**
 
 fgbio/callmolecularconsensusreads:
-  - modules/fgbio/callmolecularconsensusreads/**
-  - tests/modules/fgbio/callmolecularconsensusreads/**
+  - modules/nf-core/fgbio/callmolecularconsensusreads/**
+  - tests/modules/nf-core/fgbio/callmolecularconsensusreads/**
 
 fgbio/fastqtobam:
-  - modules/fgbio/fastqtobam/**
-  - tests/modules/fgbio/fastqtobam/**
+  - modules/nf-core/fgbio/fastqtobam/**
+  - tests/modules/nf-core/fgbio/fastqtobam/**
 
 fgbio/groupreadsbyumi:
-  - modules/fgbio/groupreadsbyumi/**
-  - tests/modules/fgbio/groupreadsbyumi/**
+  - modules/nf-core/fgbio/groupreadsbyumi/**
+  - tests/modules/nf-core/fgbio/groupreadsbyumi/**
 
 fgbio/sortbam:
-  - modules/fgbio/sortbam/**
-  - tests/modules/fgbio/sortbam/**
+  - modules/nf-core/fgbio/sortbam/**
+  - tests/modules/nf-core/fgbio/sortbam/**
 
 filtlong:
-  - modules/filtlong/**
-  - tests/modules/filtlong/**
+  - modules/nf-core/filtlong/**
+  - tests/modules/nf-core/filtlong/**
 
 flash:
-  - modules/flash/**
-  - tests/modules/flash/**
+  - modules/nf-core/flash/**
+  - tests/modules/nf-core/flash/**
 
 flye:
-  - modules/flye/**
-  - tests/modules/flye/**
+  - modules/nf-core/flye/**
+  - tests/modules/nf-core/flye/**
 
 fq/lint:
-  - modules/fq/lint/**
-  - tests/modules/fq/lint/**
+  - modules/nf-core/fq/lint/**
+  - tests/modules/nf-core/fq/lint/**
 
 freebayes:
-  - modules/freebayes/**
-  - tests/modules/freebayes/**
+  - modules/nf-core/freebayes/**
+  - tests/modules/nf-core/freebayes/**
 
 gamma/gamma:
-  - modules/gamma/gamma/**
-  - tests/modules/gamma/gamma/**
+  - modules/nf-core/gamma/gamma/**
+  - tests/modules/nf-core/gamma/gamma/**
 
 gappa/examineassign:
-  - modules/gappa/examineassign/**
-  - tests/modules/gappa/examineassign/**
+  - modules/nf-core/gappa/examineassign/**
+  - tests/modules/nf-core/gappa/examineassign/**
 
 gappa/examinegraft:
-  - modules/gappa/examinegraft/**
-  - tests/modules/gappa/examinegraft/**
+  - modules/nf-core/gappa/examinegraft/**
+  - tests/modules/nf-core/gappa/examinegraft/**
 
 gappa/examineheattree:
-  - modules/gappa/examineheattree/**
-  - tests/modules/gappa/examineheattree/**
+  - modules/nf-core/gappa/examineheattree/**
+  - tests/modules/nf-core/gappa/examineheattree/**
 
 gatk/indelrealigner:
-  - modules/gatk/indelrealigner/**
-  - tests/modules/gatk/indelrealigner/**
+  - modules/nf-core/gatk/indelrealigner/**
+  - tests/modules/nf-core/gatk/indelrealigner/**
 
 gatk/realignertargetcreator:
-  - modules/gatk/realignertargetcreator/**
-  - tests/modules/gatk/realignertargetcreator/**
+  - modules/nf-core/gatk/realignertargetcreator/**
+  - tests/modules/nf-core/gatk/realignertargetcreator/**
 
 gatk/unifiedgenotyper:
-  - modules/gatk/unifiedgenotyper/**
-  - tests/modules/gatk/unifiedgenotyper/**
+  - modules/nf-core/gatk/unifiedgenotyper/**
+  - tests/modules/nf-core/gatk/unifiedgenotyper/**
 
 gatk4/applybqsr:
-  - modules/gatk4/applybqsr/**
-  - tests/modules/gatk4/applybqsr/**
+  - modules/nf-core/gatk4/applybqsr/**
+  - tests/modules/nf-core/gatk4/applybqsr/**
 
 gatk4/applybqsrspark:
-  - modules/gatk4/applybqsrspark/**
-  - tests/modules/gatk4/applybqsrspark/**
+  - modules/nf-core/gatk4/applybqsrspark/**
+  - tests/modules/nf-core/gatk4/applybqsrspark/**
 
 gatk4/applyvqsr:
-  - modules/gatk4/applyvqsr/**
-  - tests/modules/gatk4/applyvqsr/**
+  - modules/nf-core/gatk4/applyvqsr/**
+  - tests/modules/nf-core/gatk4/applyvqsr/**
 
 gatk4/baserecalibrator:
-  - modules/gatk4/baserecalibrator/**
-  - tests/modules/gatk4/baserecalibrator/**
+  - modules/nf-core/gatk4/baserecalibrator/**
+  - tests/modules/nf-core/gatk4/baserecalibrator/**
 
 gatk4/baserecalibratorspark:
-  - modules/gatk4/baserecalibratorspark/**
-  - tests/modules/gatk4/baserecalibratorspark/**
+  - modules/nf-core/gatk4/baserecalibratorspark/**
+  - tests/modules/nf-core/gatk4/baserecalibratorspark/**
 
 gatk4/bedtointervallist:
-  - modules/gatk4/bedtointervallist/**
-  - tests/modules/gatk4/bedtointervallist/**
+  - modules/nf-core/gatk4/bedtointervallist/**
+  - tests/modules/nf-core/gatk4/bedtointervallist/**
 
 gatk4/calculatecontamination:
-  - modules/gatk4/calculatecontamination/**
-  - tests/modules/gatk4/calculatecontamination/**
+  - modules/nf-core/gatk4/calculatecontamination/**
+  - tests/modules/nf-core/gatk4/calculatecontamination/**
 
 gatk4/calibratedragstrmodel:
-  - modules/gatk4/calibratedragstrmodel/**
-  - tests/modules/gatk4/calibratedragstrmodel/**
+  - modules/nf-core/gatk4/calibratedragstrmodel/**
+  - tests/modules/nf-core/gatk4/calibratedragstrmodel/**
 
 gatk4/cnnscorevariants:
-  - modules/gatk4/cnnscorevariants/**
-  - tests/modules/gatk4/cnnscorevariants/**
+  - modules/nf-core/gatk4/cnnscorevariants/**
+  - tests/modules/nf-core/gatk4/cnnscorevariants/**
 
 gatk4/collectreadcounts:
-  - modules/gatk4/collectreadcounts/**
-  - tests/modules/gatk4/collectreadcounts/**
+  - modules/nf-core/gatk4/collectreadcounts/**
+  - tests/modules/nf-core/gatk4/collectreadcounts/**
 
 gatk4/collectsvevidence:
-  - modules/gatk4/collectsvevidence/**
-  - tests/modules/gatk4/collectsvevidence/**
+  - modules/nf-core/gatk4/collectsvevidence/**
+  - tests/modules/nf-core/gatk4/collectsvevidence/**
 
 gatk4/combinegvcfs:
-  - modules/gatk4/combinegvcfs/**
-  - tests/modules/gatk4/combinegvcfs/**
+  - modules/nf-core/gatk4/combinegvcfs/**
+  - tests/modules/nf-core/gatk4/combinegvcfs/**
 
 gatk4/composestrtablefile:
-  - modules/gatk4/composestrtablefile/**
-  - tests/modules/gatk4/composestrtablefile/**
+  - modules/nf-core/gatk4/composestrtablefile/**
+  - tests/modules/nf-core/gatk4/composestrtablefile/**
 
 gatk4/createsequencedictionary:
-  - modules/gatk4/createsequencedictionary/**
-  - tests/modules/gatk4/createsequencedictionary/**
+  - modules/nf-core/gatk4/createsequencedictionary/**
+  - tests/modules/nf-core/gatk4/createsequencedictionary/**
 
 gatk4/createsomaticpanelofnormals:
-  - modules/gatk4/createsomaticpanelofnormals/**
-  - tests/modules/gatk4/createsomaticpanelofnormals/**
+  - modules/nf-core/gatk4/createsomaticpanelofnormals/**
+  - tests/modules/nf-core/gatk4/createsomaticpanelofnormals/**
 
 gatk4/estimatelibrarycomplexity:
-  - modules/gatk4/estimatelibrarycomplexity/**
-  - tests/modules/gatk4/estimatelibrarycomplexity/**
+  - modules/nf-core/gatk4/estimatelibrarycomplexity/**
+  - tests/modules/nf-core/gatk4/estimatelibrarycomplexity/**
 
 gatk4/fastqtosam:
-  - modules/gatk4/fastqtosam/**
-  - tests/modules/gatk4/fastqtosam/**
+  - modules/nf-core/gatk4/fastqtosam/**
+  - tests/modules/nf-core/gatk4/fastqtosam/**
 
 gatk4/filtermutectcalls:
-  - modules/gatk4/filtermutectcalls/**
-  - tests/modules/gatk4/filtermutectcalls/**
+  - modules/nf-core/gatk4/filtermutectcalls/**
+  - tests/modules/nf-core/gatk4/filtermutectcalls/**
 
 gatk4/filtervarianttranches:
-  - modules/gatk4/filtervarianttranches/**
-  - tests/modules/gatk4/filtervarianttranches/**
+  - modules/nf-core/gatk4/filtervarianttranches/**
+  - tests/modules/nf-core/gatk4/filtervarianttranches/**
 
 gatk4/gatherbqsrreports:
-  - modules/gatk4/gatherbqsrreports/**
-  - tests/modules/gatk4/gatherbqsrreports/**
+  - modules/nf-core/gatk4/gatherbqsrreports/**
+  - tests/modules/nf-core/gatk4/gatherbqsrreports/**
 
 gatk4/gatherpileupsummaries:
-  - modules/gatk4/gatherpileupsummaries/**
-  - tests/modules/gatk4/gatherpileupsummaries/**
+  - modules/nf-core/gatk4/gatherpileupsummaries/**
+  - tests/modules/nf-core/gatk4/gatherpileupsummaries/**
 
 gatk4/genomicsdbimport:
-  - modules/gatk4/genomicsdbimport/**
-  - tests/modules/gatk4/genomicsdbimport/**
+  - modules/nf-core/gatk4/genomicsdbimport/**
+  - tests/modules/nf-core/gatk4/genomicsdbimport/**
 
 gatk4/genotypegvcfs:
-  - modules/gatk4/genotypegvcfs/**
-  - tests/modules/gatk4/genotypegvcfs/**
+  - modules/nf-core/gatk4/genotypegvcfs/**
+  - tests/modules/nf-core/gatk4/genotypegvcfs/**
 
 gatk4/getpileupsummaries:
-  - modules/gatk4/getpileupsummaries/**
-  - tests/modules/gatk4/getpileupsummaries/**
+  - modules/nf-core/gatk4/getpileupsummaries/**
+  - tests/modules/nf-core/gatk4/getpileupsummaries/**
 
 gatk4/haplotypecaller:
-  - modules/gatk4/haplotypecaller/**
-  - tests/modules/gatk4/haplotypecaller/**
+  - modules/nf-core/gatk4/haplotypecaller/**
+  - tests/modules/nf-core/gatk4/haplotypecaller/**
 
 gatk4/indexfeaturefile:
-  - modules/gatk4/indexfeaturefile/**
-  - tests/modules/gatk4/indexfeaturefile/**
+  - modules/nf-core/gatk4/indexfeaturefile/**
+  - tests/modules/nf-core/gatk4/indexfeaturefile/**
 
 gatk4/intervallisttobed:
-  - modules/gatk4/intervallisttobed/**
-  - tests/modules/gatk4/intervallisttobed/**
+  - modules/nf-core/gatk4/intervallisttobed/**
+  - tests/modules/nf-core/gatk4/intervallisttobed/**
 
 gatk4/intervallisttools:
-  - modules/gatk4/intervallisttools/**
-  - tests/modules/gatk4/intervallisttools/**
+  - modules/nf-core/gatk4/intervallisttools/**
+  - tests/modules/nf-core/gatk4/intervallisttools/**
 
 gatk4/learnreadorientationmodel:
-  - modules/gatk4/learnreadorientationmodel/**
-  - tests/modules/gatk4/learnreadorientationmodel/**
+  - modules/nf-core/gatk4/learnreadorientationmodel/**
+  - tests/modules/nf-core/gatk4/learnreadorientationmodel/**
 
 gatk4/leftalignandtrimvariants:
-  - modules/gatk4/leftalignandtrimvariants/**
-  - tests/modules/gatk4/leftalignandtrimvariants/**
+  - modules/nf-core/gatk4/leftalignandtrimvariants/**
+  - tests/modules/nf-core/gatk4/leftalignandtrimvariants/**
 
 gatk4/markduplicates:
-  - modules/gatk4/markduplicates/**
-  - tests/modules/gatk4/markduplicates/**
+  - modules/nf-core/gatk4/markduplicates/**
+  - tests/modules/nf-core/gatk4/markduplicates/**
 
 gatk4/markduplicatesspark:
-  - modules/gatk4/markduplicatesspark/**
-  - tests/modules/gatk4/markduplicatesspark/**
+  - modules/nf-core/gatk4/markduplicatesspark/**
+  - tests/modules/nf-core/gatk4/markduplicatesspark/**
 
 gatk4/mergebamalignment:
-  - modules/gatk4/mergebamalignment/**
-  - tests/modules/gatk4/mergebamalignment/**
+  - modules/nf-core/gatk4/mergebamalignment/**
+  - tests/modules/nf-core/gatk4/mergebamalignment/**
 
 gatk4/mergemutectstats:
-  - modules/gatk4/mergemutectstats/**
-  - tests/modules/gatk4/mergemutectstats/**
+  - modules/nf-core/gatk4/mergemutectstats/**
+  - tests/modules/nf-core/gatk4/mergemutectstats/**
 
 gatk4/mergevcfs:
-  - modules/gatk4/mergevcfs/**
-  - tests/modules/gatk4/mergevcfs/**
+  - modules/nf-core/gatk4/mergevcfs/**
+  - tests/modules/nf-core/gatk4/mergevcfs/**
 
 gatk4/mutect2:
-  - modules/gatk4/mutect2/**
-  - tests/modules/gatk4/mutect2/**
+  - modules/nf-core/gatk4/mutect2/**
+  - tests/modules/nf-core/gatk4/mutect2/**
 
 gatk4/printsvevidence:
-  - modules/gatk4/printsvevidence/**
-  - tests/modules/gatk4/printsvevidence/**
+  - modules/nf-core/gatk4/printsvevidence/**
+  - tests/modules/nf-core/gatk4/printsvevidence/**
 
 gatk4/reblockgvcf:
-  - modules/gatk4/reblockgvcf/**
-  - tests/modules/gatk4/reblockgvcf/**
+  - modules/nf-core/gatk4/reblockgvcf/**
+  - tests/modules/nf-core/gatk4/reblockgvcf/**
 
 gatk4/revertsam:
-  - modules/gatk4/revertsam/**
-  - tests/modules/gatk4/revertsam/**
+  - modules/nf-core/gatk4/revertsam/**
+  - tests/modules/nf-core/gatk4/revertsam/**
 
 gatk4/samtofastq:
-  - modules/gatk4/samtofastq/**
-  - tests/modules/gatk4/samtofastq/**
+  - modules/nf-core/gatk4/samtofastq/**
+  - tests/modules/nf-core/gatk4/samtofastq/**
 
 gatk4/selectvariants:
-  - modules/gatk4/selectvariants/**
-  - tests/modules/gatk4/selectvariants/**
+  - modules/nf-core/gatk4/selectvariants/**
+  - tests/modules/nf-core/gatk4/selectvariants/**
 
 gatk4/splitintervals:
-  - modules/gatk4/splitintervals/**
-  - tests/modules/gatk4/splitintervals/**
+  - modules/nf-core/gatk4/splitintervals/**
+  - tests/modules/nf-core/gatk4/splitintervals/**
 
 gatk4/splitncigarreads:
-  - modules/gatk4/splitncigarreads/**
-  - tests/modules/gatk4/splitncigarreads/**
+  - modules/nf-core/gatk4/splitncigarreads/**
+  - tests/modules/nf-core/gatk4/splitncigarreads/**
 
 gatk4/variantfiltration:
-  - modules/gatk4/variantfiltration/**
-  - tests/modules/gatk4/variantfiltration/**
+  - modules/nf-core/gatk4/variantfiltration/**
+  - tests/modules/nf-core/gatk4/variantfiltration/**
 
 gatk4/variantrecalibrator:
-  - modules/gatk4/variantrecalibrator/**
-  - tests/modules/gatk4/variantrecalibrator/**
+  - modules/nf-core/gatk4/variantrecalibrator/**
+  - tests/modules/nf-core/gatk4/variantrecalibrator/**
 
 gecco/run:
-  - modules/gecco/run/**
-  - tests/modules/gecco/run/**
+  - modules/nf-core/gecco/run/**
+  - tests/modules/nf-core/gecco/run/**
 
 genescopefk:
-  - modules/genescopefk/**
-  - tests/modules/genescopefk/**
+  - modules/nf-core/genescopefk/**
+  - tests/modules/nf-core/genescopefk/**
 
 genmap/index:
-  - modules/genmap/index/**
-  - tests/modules/genmap/index/**
+  - modules/nf-core/genmap/index/**
+  - tests/modules/nf-core/genmap/index/**
 
 genmap/mappability:
-  - modules/genmap/mappability/**
-  - tests/modules/genmap/mappability/**
+  - modules/nf-core/genmap/mappability/**
+  - tests/modules/nf-core/genmap/mappability/**
 
 genmod/annotate:
-  - modules/genmod/annotate/**
-  - tests/modules/genmod/annotate/**
+  - modules/nf-core/genmod/annotate/**
+  - tests/modules/nf-core/genmod/annotate/**
 
 genmod/compound:
-  - modules/genmod/compound/**
-  - tests/modules/genmod/compound/**
+  - modules/nf-core/genmod/compound/**
+  - tests/modules/nf-core/genmod/compound/**
 
 genmod/models:
-  - modules/genmod/models/**
-  - tests/modules/genmod/models/**
+  - modules/nf-core/genmod/models/**
+  - tests/modules/nf-core/genmod/models/**
 
 genmod/score:
-  - modules/genmod/score/**
-  - tests/modules/genmod/score/**
+  - modules/nf-core/genmod/score/**
+  - tests/modules/nf-core/genmod/score/**
 
 genomescope2:
-  - modules/genomescope2/**
-  - tests/modules/genomescope2/**
+  - modules/nf-core/genomescope2/**
+  - tests/modules/nf-core/genomescope2/**
 
 genotyphi/parse:
-  - modules/genotyphi/parse/**
-  - tests/modules/genotyphi/parse/**
+  - modules/nf-core/genotyphi/parse/**
+  - tests/modules/nf-core/genotyphi/parse/**
 
 genrich:
-  - modules/genrich/**
-  - tests/modules/genrich/**
+  - modules/nf-core/genrich/**
+  - tests/modules/nf-core/genrich/**
 
 gfaffix:
-  - modules/gfaffix/**
-  - tests/modules/gfaffix/**
+  - modules/nf-core/gfaffix/**
+  - tests/modules/nf-core/gfaffix/**
 
 gffread:
-  - modules/gffread/**
-  - tests/modules/gffread/**
+  - modules/nf-core/gffread/**
+  - tests/modules/nf-core/gffread/**
 
 glimpse/chunk:
-  - modules/glimpse/chunk/**
-  - tests/modules/glimpse/chunk/**
+  - modules/nf-core/glimpse/chunk/**
+  - tests/modules/nf-core/glimpse/chunk/**
 
 glnexus:
-  - modules/glnexus/**
-  - tests/modules/glnexus/**
+  - modules/nf-core/glnexus/**
+  - tests/modules/nf-core/glnexus/**
 
 goat/taxonsearch:
-  - modules/goat/taxonsearch/**
-  - tests/modules/goat/taxonsearch/**
+  - modules/nf-core/goat/taxonsearch/**
+  - tests/modules/nf-core/goat/taxonsearch/**
 
 graphmap2/align:
-  - modules/graphmap2/align/**
-  - tests/modules/graphmap2/align/**
+  - modules/nf-core/graphmap2/align/**
+  - tests/modules/nf-core/graphmap2/align/**
 
 graphmap2/index:
-  - modules/graphmap2/index/**
-  - tests/modules/graphmap2/index/**
+  - modules/nf-core/graphmap2/index/**
+  - tests/modules/nf-core/graphmap2/index/**
 
 gstama/collapse:
-  - modules/gstama/collapse/**
-  - tests/modules/gstama/collapse/**
+  - modules/nf-core/gstama/collapse/**
+  - tests/modules/nf-core/gstama/collapse/**
 
 gstama/merge:
-  - modules/gstama/merge/**
-  - tests/modules/gstama/merge/**
+  - modules/nf-core/gstama/merge/**
+  - tests/modules/nf-core/gstama/merge/**
 
 gstama/polyacleanup:
-  - modules/gstama/polyacleanup/**
-  - tests/modules/gstama/polyacleanup/**
+  - modules/nf-core/gstama/polyacleanup/**
+  - tests/modules/nf-core/gstama/polyacleanup/**
 
 gtdbtk/classifywf:
-  - modules/gtdbtk/classifywf/**
-  - tests/modules/gtdbtk/classifywf/**
+  - modules/nf-core/gtdbtk/classifywf/**
+  - tests/modules/nf-core/gtdbtk/classifywf/**
 
 gubbins:
-  - modules/gubbins/**
-  - tests/modules/gubbins/**
+  - modules/nf-core/gubbins/**
+  - tests/modules/nf-core/gubbins/**
 
 gunc/downloaddb:
-  - modules/gunc/downloaddb/**
-  - tests/modules/gunc/downloaddb/**
+  - modules/nf-core/gunc/downloaddb/**
+  - tests/modules/nf-core/gunc/downloaddb/**
 
 gunc/run:
-  - modules/gunc/run/**
-  - tests/modules/gunc/run/**
+  - modules/nf-core/gunc/run/**
+  - tests/modules/nf-core/gunc/run/**
 
 gunzip:
-  - modules/gunzip/**
-  - tests/modules/gunzip/**
+  - modules/nf-core/gunzip/**
+  - tests/modules/nf-core/gunzip/**
 
 gvcftools/extractvariants:
-  - modules/gvcftools/extractvariants/**
-  - tests/modules/gvcftools/extractvariants/**
+  - modules/nf-core/gvcftools/extractvariants/**
+  - tests/modules/nf-core/gvcftools/extractvariants/**
 
 hamronization/abricate:
-  - modules/hamronization/abricate/**
-  - tests/modules/hamronization/abricate/**
+  - modules/nf-core/hamronization/abricate/**
+  - tests/modules/nf-core/hamronization/abricate/**
 
 hamronization/amrfinderplus:
-  - modules/hamronization/amrfinderplus/**
-  - tests/modules/hamronization/amrfinderplus/**
+  - modules/nf-core/hamronization/amrfinderplus/**
+  - tests/modules/nf-core/hamronization/amrfinderplus/**
 
 hamronization/deeparg:
-  - modules/hamronization/deeparg/**
-  - tests/modules/hamronization/deeparg/**
+  - modules/nf-core/hamronization/deeparg/**
+  - tests/modules/nf-core/hamronization/deeparg/**
 
 hamronization/fargene:
-  - modules/hamronization/fargene/**
-  - tests/modules/hamronization/fargene/**
+  - modules/nf-core/hamronization/fargene/**
+  - tests/modules/nf-core/hamronization/fargene/**
 
 hamronization/rgi:
-  - modules/hamronization/rgi/**
-  - tests/modules/hamronization/rgi/**
+  - modules/nf-core/hamronization/rgi/**
+  - tests/modules/nf-core/hamronization/rgi/**
 
 hamronization/summarize:
-  - modules/hamronization/summarize/**
-  - tests/modules/hamronization/summarize/**
+  - modules/nf-core/hamronization/summarize/**
+  - tests/modules/nf-core/hamronization/summarize/**
 
 haplocheck:
-  - modules/haplocheck/**
-  - tests/modules/haplocheck/**
+  - modules/nf-core/haplocheck/**
+  - tests/modules/nf-core/haplocheck/**
 
 haplogrep2/classify:
-  - modules/haplogrep2/classify/**
-  - tests/modules/haplogrep2/classify/**
+  - modules/nf-core/haplogrep2/classify/**
+  - tests/modules/nf-core/haplogrep2/classify/**
 
 happy/happy:
-  - modules/happy/happy/**
-  - tests/modules/happy/happy/**
+  - modules/nf-core/happy/happy/**
+  - tests/modules/nf-core/happy/happy/**
 
 happy/prepy:
-  - modules/happy/prepy/**
-  - tests/modules/happy/prepy/**
+  - modules/nf-core/happy/prepy/**
+  - tests/modules/nf-core/happy/prepy/**
 
 hicap:
-  - modules/hicap/**
-  - tests/modules/hicap/**
+  - modules/nf-core/hicap/**
+  - tests/modules/nf-core/hicap/**
 
 hifiasm:
-  - modules/hifiasm/**
-  - tests/modules/hifiasm/**
+  - modules/nf-core/hifiasm/**
+  - tests/modules/nf-core/hifiasm/**
 
 hisat2/align:
-  - modules/hisat2/align/**
-  - modules/hisat2/build/**
-  - modules/hisat2/extractsplicesites/**
-  - tests/modules/hisat2/align/**
+  - modules/nf-core/hisat2/align/**
+  - modules/nf-core/hisat2/build/**
+  - modules/nf-core/hisat2/extractsplicesites/**
+  - tests/modules/nf-core/hisat2/align/**
 
 hisat2/build:
-  - modules/hisat2/build/**
-  - modules/hisat2/extractsplicesites/**
-  - tests/modules/hisat2/build_test/**
+  - modules/nf-core/hisat2/build/**
+  - modules/nf-core/hisat2/extractsplicesites/**
+  - tests/modules/nf-core/hisat2/build_test/**
 
 hisat2/extractsplicesites:
-  - modules/hisat2/extractsplicesites/**
-  - tests/modules/hisat2/extractsplicesites/**
+  - modules/nf-core/hisat2/extractsplicesites/**
+  - tests/modules/nf-core/hisat2/extractsplicesites/**
 
 hmmcopy/gccounter:
-  - modules/hmmcopy/gccounter/**
-  - tests/modules/hmmcopy/gccounter/**
+  - modules/nf-core/hmmcopy/gccounter/**
+  - tests/modules/nf-core/hmmcopy/gccounter/**
 
 hmmcopy/generatemap:
-  - modules/hmmcopy/generatemap/**
-  - tests/modules/hmmcopy/generatemap/**
+  - modules/nf-core/hmmcopy/generatemap/**
+  - tests/modules/nf-core/hmmcopy/generatemap/**
 
 hmmcopy/mapcounter:
-  - modules/hmmcopy/mapcounter/**
-  - tests/modules/hmmcopy/mapcounter/**
+  - modules/nf-core/hmmcopy/mapcounter/**
+  - tests/modules/nf-core/hmmcopy/mapcounter/**
 
 hmmcopy/readcounter:
-  - modules/hmmcopy/readcounter/**
-  - tests/modules/hmmcopy/readcounter/**
+  - modules/nf-core/hmmcopy/readcounter/**
+  - tests/modules/nf-core/hmmcopy/readcounter/**
 
 hmmer/eslalimask:
-  - modules/hmmer/eslalimask/**
-  - tests/modules/hmmer/eslalimask/**
+  - modules/nf-core/hmmer/eslalimask/**
+  - tests/modules/nf-core/hmmer/eslalimask/**
 
 hmmer/eslreformat:
-  - modules/hmmer/eslreformat/**
-  - tests/modules/hmmer/eslreformat/**
+  - modules/nf-core/hmmer/eslreformat/**
+  - tests/modules/nf-core/hmmer/eslreformat/**
 
 hmmer/hmmalign:
-  - modules/hmmer/hmmalign/**
-  - tests/modules/hmmer/hmmalign/**
+  - modules/nf-core/hmmer/hmmalign/**
+  - tests/modules/nf-core/hmmer/hmmalign/**
 
 hmmer/hmmbuild:
-  - modules/hmmer/hmmbuild/**
-  - tests/modules/hmmer/hmmbuild/**
+  - modules/nf-core/hmmer/hmmbuild/**
+  - tests/modules/nf-core/hmmer/hmmbuild/**
 
 hmmer/hmmsearch:
-  - modules/hmmer/hmmsearch/**
-  - tests/modules/hmmer/hmmsearch/**
+  - modules/nf-core/hmmer/hmmsearch/**
+  - tests/modules/nf-core/hmmer/hmmsearch/**
 
 hmtnote:
-  - modules/hmtnote/**
-  - tests/modules/hmtnote/**
+  - modules/nf-core/hmtnote/**
+  - tests/modules/nf-core/hmtnote/**
 
 homer/annotatepeaks:
-  - modules/homer/annotatepeaks/**
-  - tests/modules/homer/annotatepeaks/**
+  - modules/nf-core/homer/annotatepeaks/**
+  - tests/modules/nf-core/homer/annotatepeaks/**
 
 homer/findpeaks:
-  - modules/homer/findpeaks/**
-  - modules/homer/maketagdirectory/**
-  - tests/modules/homer/findpeaks/**
+  - modules/nf-core/homer/findpeaks/**
+  - modules/nf-core/homer/maketagdirectory/**
+  - tests/modules/nf-core/homer/findpeaks/**
 
 homer/maketagdirectory:
-  - modules/homer/maketagdirectory/**
-  - tests/modules/homer/maketagdirectory/**
+  - modules/nf-core/homer/maketagdirectory/**
+  - tests/modules/nf-core/homer/maketagdirectory/**
 
 homer/makeucscfile:
-  - modules/homer/makeucscfile/**
-  - tests/modules/homer/makeucscfile/**
+  - modules/nf-core/homer/makeucscfile/**
+  - tests/modules/nf-core/homer/makeucscfile/**
 
 homer/pos2bed:
-  - modules/homer/pos2bed/**
-  - modules/homer/maketagdirectory/**
-  - modules/homer/findpeaks/**
-  - tests/modules/homer/pos2bed/**
+  - modules/nf-core/homer/pos2bed/**
+  - modules/nf-core/homer/maketagdirectory/**
+  - modules/nf-core/homer/findpeaks/**
+  - tests/modules/nf-core/homer/pos2bed/**
 
 hpsuissero:
-  - modules/hpsuissero/**
-  - tests/modules/hpsuissero/**
+  - modules/nf-core/hpsuissero/**
+  - tests/modules/nf-core/hpsuissero/**
 
 ichorcna/createpon:
-  - modules/ichorcna/createpon/**
-  - tests/modules/ichorcna/createpon/**
+  - modules/nf-core/ichorcna/createpon/**
+  - tests/modules/nf-core/ichorcna/createpon/**
 
 ichorcna/run:
-  - modules/ichorcna/run/**
-  - tests/modules/ichorcna/run/**
+  - modules/nf-core/ichorcna/run/**
+  - tests/modules/nf-core/ichorcna/run/**
 
 idr:
-  - modules/idr/**
-  - tests/modules/idr/**
+  - modules/nf-core/idr/**
+  - tests/modules/nf-core/idr/**
 
 imputeme/vcftoprs:
-  - modules/imputeme/vcftoprs/**
-  - tests/modules/imputeme/vcftoprs/**
+  - modules/nf-core/imputeme/vcftoprs/**
+  - tests/modules/nf-core/imputeme/vcftoprs/**
 
 instrain/profile:
-  - modules/instrain/profile/**
-  - tests/modules/instrain/profile/**
+  - modules/nf-core/instrain/profile/**
+  - tests/modules/nf-core/instrain/profile/**
 
 iqtree:
-  - modules/iqtree/**
-  - tests/modules/iqtree/**
+  - modules/nf-core/iqtree/**
+  - tests/modules/nf-core/iqtree/**
 
 ismapper:
-  - modules/ismapper/**
-  - tests/modules/ismapper/**
+  - modules/nf-core/ismapper/**
+  - tests/modules/nf-core/ismapper/**
 
 isoseq3/cluster:
-  - modules/isoseq3/cluster/**
-  - tests/modules/isoseq3/cluster/**
+  - modules/nf-core/isoseq3/cluster/**
+  - tests/modules/nf-core/isoseq3/cluster/**
 
 isoseq3/refine:
-  - modules/isoseq3/refine/**
-  - tests/modules/isoseq3/refine/**
+  - modules/nf-core/isoseq3/refine/**
+  - tests/modules/nf-core/isoseq3/refine/**
 
 ivar/consensus:
-  - modules/ivar/consensus/**
-  - tests/modules/ivar/consensus/**
+  - modules/nf-core/ivar/consensus/**
+  - tests/modules/nf-core/ivar/consensus/**
 
 ivar/trim:
-  - modules/ivar/trim/**
-  - tests/modules/ivar/trim/**
+  - modules/nf-core/ivar/trim/**
+  - tests/modules/nf-core/ivar/trim/**
 
 ivar/variants:
-  - modules/ivar/variants/**
-  - tests/modules/ivar/variants/**
+  - modules/nf-core/ivar/variants/**
+  - tests/modules/nf-core/ivar/variants/**
 
 jupyternotebook:
-  - modules/jupyternotebook/**
-  - tests/modules/jupyternotebook/**
+  - modules/nf-core/jupyternotebook/**
+  - tests/modules/nf-core/jupyternotebook/**
 
 kaiju/kaiju:
-  - modules/kaiju/kaiju/**
-  - tests/modules/kaiju/kaiju/**
+  - modules/nf-core/kaiju/kaiju/**
+  - tests/modules/nf-core/kaiju/kaiju/**
 
 kaiju/kaiju2krona:
-  - modules/kaiju/kaiju2krona/**
-  - tests/modules/kaiju/kaiju2krona/**
+  - modules/nf-core/kaiju/kaiju2krona/**
+  - tests/modules/nf-core/kaiju/kaiju2krona/**
 
 kaiju/kaiju2table:
-  - modules/kaiju/kaiju2table/**
-  - tests/modules/kaiju/kaiju2table/**
+  - modules/nf-core/kaiju/kaiju2table/**
+  - tests/modules/nf-core/kaiju/kaiju2table/**
 
 kallisto/index:
-  - modules/kallisto/index/**
-  - tests/modules/kallisto/index/**
+  - modules/nf-core/kallisto/index/**
+  - tests/modules/nf-core/kallisto/index/**
 
 kallistobustools/count:
-  - modules/kallistobustools/count/**
-  - tests/modules/kallistobustools/count/**
+  - modules/nf-core/kallistobustools/count/**
+  - tests/modules/nf-core/kallistobustools/count/**
 
 kallistobustools/ref:
-  - modules/kallistobustools/ref/**
-  - tests/modules/kallistobustools/ref/**
+  - modules/nf-core/kallistobustools/ref/**
+  - tests/modules/nf-core/kallistobustools/ref/**
 
 kat/hist:
-  - modules/kat/hist/**
-  - tests/modules/kat/hist/**
+  - modules/nf-core/kat/hist/**
+  - tests/modules/nf-core/kat/hist/**
 
 khmer/normalizebymedian:
-  - modules/khmer/normalizebymedian/**
-  - tests/modules/khmer/normalizebymedian/**
+  - modules/nf-core/khmer/normalizebymedian/**
+  - tests/modules/nf-core/khmer/normalizebymedian/**
 
 khmer/uniquekmers:
-  - modules/khmer/uniquekmers/**
-  - tests/modules/khmer/uniquekmers/**
+  - modules/nf-core/khmer/uniquekmers/**
+  - tests/modules/nf-core/khmer/uniquekmers/**
 
 kleborate:
-  - modules/kleborate/**
-  - tests/modules/kleborate/**
+  - modules/nf-core/kleborate/**
+  - tests/modules/nf-core/kleborate/**
 
 kraken2/kraken2:
-  - modules/kraken2/kraken2/**
-  - modules/untar/**
-  - tests/modules/kraken2/kraken2/**
+  - modules/nf-core/kraken2/kraken2/**
+  - modules/nf-core/untar/**
+  - tests/modules/nf-core/kraken2/kraken2/**
 
 krakentools/combinekreports:
-  - modules/krakentools/combinekreports/**
-  - tests/modules/krakentools/combinekreports/**
+  - modules/nf-core/krakentools/combinekreports/**
+  - tests/modules/nf-core/krakentools/combinekreports/**
 
 krakentools/kreport2krona:
-  - modules/krakentools/kreport2krona/**
-  - tests/modules/krakentools/kreport2krona/**
+  - modules/nf-core/krakentools/kreport2krona/**
+  - tests/modules/nf-core/krakentools/kreport2krona/**
 
 krona/kronadb:
-  - modules/krona/kronadb/**
-  - tests/modules/krona/kronadb/**
+  - modules/nf-core/krona/kronadb/**
+  - tests/modules/nf-core/krona/kronadb/**
 
 krona/ktimporttaxonomy:
-  - modules/krona/ktimporttaxonomy/**
-  - tests/modules/krona/ktimporttaxonomy/**
+  - modules/nf-core/krona/ktimporttaxonomy/**
+  - tests/modules/nf-core/krona/ktimporttaxonomy/**
 
 krona/ktimporttext:
-  - modules/krona/ktimporttext/**
-  - tests/modules/krona/ktimporttext/**
+  - modules/nf-core/krona/ktimporttext/**
+  - tests/modules/nf-core/krona/ktimporttext/**
 
 krona/ktupdatetaxonomy:
-  - modules/krona/ktupdatetaxonomy/**
-  - tests/modules/krona/ktupdatetaxonomy/**
+  - modules/nf-core/krona/ktupdatetaxonomy/**
+  - tests/modules/nf-core/krona/ktupdatetaxonomy/**
 
 last/dotplot:
-  - modules/last/dotplot/**
-  - tests/modules/last/dotplot/**
+  - modules/nf-core/last/dotplot/**
+  - tests/modules/nf-core/last/dotplot/**
 
 last/lastal:
-  - modules/last/lastal/**
-  - tests/modules/last/lastal/**
+  - modules/nf-core/last/lastal/**
+  - tests/modules/nf-core/last/lastal/**
 
 last/lastdb:
-  - modules/last/lastdb/**
-  - tests/modules/last/lastdb/**
+  - modules/nf-core/last/lastdb/**
+  - tests/modules/nf-core/last/lastdb/**
 
 last/mafconvert:
-  - modules/last/mafconvert/**
-  - tests/modules/last/mafconvert/**
+  - modules/nf-core/last/mafconvert/**
+  - tests/modules/nf-core/last/mafconvert/**
 
 last/mafswap:
-  - modules/last/mafswap/**
-  - tests/modules/last/mafswap/**
+  - modules/nf-core/last/mafswap/**
+  - tests/modules/nf-core/last/mafswap/**
 
 last/postmask:
-  - modules/last/postmask/**
-  - tests/modules/last/postmask/**
+  - modules/nf-core/last/postmask/**
+  - tests/modules/nf-core/last/postmask/**
 
 last/split:
-  - modules/last/split/**
-  - tests/modules/last/split/**
+  - modules/nf-core/last/split/**
+  - tests/modules/nf-core/last/split/**
 
 last/train:
-  - modules/last/train/**
-  - tests/modules/last/train/**
+  - modules/nf-core/last/train/**
+  - tests/modules/nf-core/last/train/**
 
 leehom:
-  - modules/leehom/**
-  - tests/modules/leehom/**
+  - modules/nf-core/leehom/**
+  - tests/modules/nf-core/leehom/**
 
 legsta:
-  - modules/legsta/**
-  - tests/modules/legsta/**
+  - modules/nf-core/legsta/**
+  - tests/modules/nf-core/legsta/**
 
 lima:
-  - modules/lima/**
-  - tests/modules/lima/**
+  - modules/nf-core/lima/**
+  - tests/modules/nf-core/lima/**
 
 lissero:
-  - modules/lissero/**
-  - tests/modules/lissero/**
+  - modules/nf-core/lissero/**
+  - tests/modules/nf-core/lissero/**
 
 lofreq/call:
-  - modules/lofreq/call/**
-  - tests/modules/lofreq/call/**
+  - modules/nf-core/lofreq/call/**
+  - tests/modules/nf-core/lofreq/call/**
 
 lofreq/callparallel:
-  - modules/lofreq/callparallel/**
-  - tests/modules/lofreq/callparallel/**
+  - modules/nf-core/lofreq/callparallel/**
+  - tests/modules/nf-core/lofreq/callparallel/**
 
 lofreq/filter:
-  - modules/lofreq/filter/**
-  - tests/modules/lofreq/filter/**
+  - modules/nf-core/lofreq/filter/**
+  - tests/modules/nf-core/lofreq/filter/**
 
 lofreq/indelqual:
-  - modules/lofreq/indelqual/**
-  - tests/modules/lofreq/indelqual/**
+  - modules/nf-core/lofreq/indelqual/**
+  - tests/modules/nf-core/lofreq/indelqual/**
 
 macrel/contigs:
-  - modules/macrel/contigs/**
-  - tests/modules/macrel/contigs/**
+  - modules/nf-core/macrel/contigs/**
+  - tests/modules/nf-core/macrel/contigs/**
 
 macs2/callpeak:
-  - modules/macs2/callpeak/**
-  - tests/modules/macs2/callpeak/**
+  - modules/nf-core/macs2/callpeak/**
+  - tests/modules/nf-core/macs2/callpeak/**
 
 mafft:
-  - modules/mafft/**
-  - tests/modules/mafft/**
+  - modules/nf-core/mafft/**
+  - tests/modules/nf-core/mafft/**
 
 malt/build:
-  - modules/malt/build/**
-  - tests/modules/malt/build_test/**
+  - modules/nf-core/malt/build/**
+  - tests/modules/nf-core/malt/build_test/**
 
 malt/run:
-  - modules/malt/run/**
-  - tests/modules/malt/run/**
+  - modules/nf-core/malt/run/**
+  - tests/modules/nf-core/malt/run/**
 
 maltextract:
-  - modules/maltextract/**
-  - tests/modules/maltextract/**
+  - modules/nf-core/maltextract/**
+  - tests/modules/nf-core/maltextract/**
 
 manta/convertinversion:
-  - modules/manta/convertinversion/**
-  - tests/modules/manta/convertinversion/**
+  - modules/nf-core/manta/convertinversion/**
+  - tests/modules/nf-core/manta/convertinversion/**
 
 manta/germline:
-  - modules/manta/germline/**
-  - tests/modules/manta/germline/**
+  - modules/nf-core/manta/germline/**
+  - tests/modules/nf-core/manta/germline/**
 
 manta/somatic:
-  - modules/manta/somatic/**
-  - tests/modules/manta/somatic/**
+  - modules/nf-core/manta/somatic/**
+  - tests/modules/nf-core/manta/somatic/**
 
 manta/tumoronly:
-  - modules/manta/tumoronly/**
-  - tests/modules/manta/tumoronly/**
+  - modules/nf-core/manta/tumoronly/**
+  - tests/modules/nf-core/manta/tumoronly/**
 
 mapdamage2:
-  - modules/mapdamage2/**
-  - tests/modules/mapdamage2/**
+  - modules/nf-core/mapdamage2/**
+  - tests/modules/nf-core/mapdamage2/**
 
 mash/dist:
-  - modules/mash/dist/**
-  - tests/modules/mash/dist/**
+  - modules/nf-core/mash/dist/**
+  - tests/modules/nf-core/mash/dist/**
 
 mash/screen:
-  - modules/mash/screen/**
-  - tests/modules/mash/screen/**
+  - modules/nf-core/mash/screen/**
+  - tests/modules/nf-core/mash/screen/**
 
 mash/sketch:
-  - modules/mash/sketch/**
-  - tests/modules/mash/sketch/**
+  - modules/nf-core/mash/sketch/**
+  - tests/modules/nf-core/mash/sketch/**
 
 mashtree:
-  - modules/mashtree/**
-  - tests/modules/mashtree/**
+  - modules/nf-core/mashtree/**
+  - tests/modules/nf-core/mashtree/**
 
 maxbin2:
-  - modules/maxbin2/**
-  - tests/modules/maxbin2/**
+  - modules/nf-core/maxbin2/**
+  - tests/modules/nf-core/maxbin2/**
 
 maxquant/lfq:
-  - modules/maxquant/lfq/**
-  - tests/modules/maxquant/lfq/**
+  - modules/nf-core/maxquant/lfq/**
+  - tests/modules/nf-core/maxquant/lfq/**
 
 mcroni:
-  - modules/mcroni/**
-  - tests/modules/mcroni/**
+  - modules/nf-core/mcroni/**
+  - tests/modules/nf-core/mcroni/**
 
 md5sum:
-  - modules/md5sum/**
-  - tests/modules/md5sum/**
+  - modules/nf-core/md5sum/**
+  - tests/modules/nf-core/md5sum/**
 
 medaka:
-  - modules/medaka/**
-  - tests/modules/medaka/**
+  - modules/nf-core/medaka/**
+  - tests/modules/nf-core/medaka/**
 
 megahit:
-  - modules/megahit/**
-  - tests/modules/megahit/**
+  - modules/nf-core/megahit/**
+  - tests/modules/nf-core/megahit/**
 
 megan/daa2info:
-  - modules/megan/daa2info/**
-  - tests/modules/megan/daa2info/**
+  - modules/nf-core/megan/daa2info/**
+  - tests/modules/nf-core/megan/daa2info/**
 
 megan/rma2info:
-  - modules/megan/rma2info/**
-  - tests/modules/megan/rma2info/**
+  - modules/nf-core/megan/rma2info/**
+  - tests/modules/nf-core/megan/rma2info/**
 
 meningotype:
-  - modules/meningotype/**
-  - tests/modules/meningotype/**
+  - modules/nf-core/meningotype/**
+  - tests/modules/nf-core/meningotype/**
 
 merqury:
-  - modules/merqury/**
-  - tests/modules/merqury/**
+  - modules/nf-core/merqury/**
+  - tests/modules/nf-core/merqury/**
 
 merquryfk/katcomp:
-  - modules/merquryfk/katcomp/**
-  - tests/modules/merquryfk/katcomp/**
+  - modules/nf-core/merquryfk/katcomp/**
+  - tests/modules/nf-core/merquryfk/katcomp/**
 
 merquryfk/katgc:
-  - modules/merquryfk/katgc/**
-  - tests/modules/merquryfk/katgc/**
+  - modules/nf-core/merquryfk/katgc/**
+  - tests/modules/nf-core/merquryfk/katgc/**
 
 merquryfk/merquryfk:
-  - modules/merquryfk/merquryfk/**
-  - tests/modules/merquryfk/merquryfk/**
+  - modules/nf-core/merquryfk/merquryfk/**
+  - tests/modules/nf-core/merquryfk/merquryfk/**
 
 merquryfk/ploidyplot:
-  - modules/merquryfk/ploidyplot/**
-  - tests/modules/merquryfk/ploidyplot/**
+  - modules/nf-core/merquryfk/ploidyplot/**
+  - tests/modules/nf-core/merquryfk/ploidyplot/**
 
 meryl/count:
-  - modules/meryl/count/**
-  - tests/modules/meryl/count/**
+  - modules/nf-core/meryl/count/**
+  - tests/modules/nf-core/meryl/count/**
 
 meryl/histogram:
-  - modules/meryl/histogram/**
-  - tests/modules/meryl/histogram/**
+  - modules/nf-core/meryl/histogram/**
+  - tests/modules/nf-core/meryl/histogram/**
 
 meryl/unionsum:
-  - modules/meryl/unionsum/**
-  - tests/modules/meryl/unionsum/**
+  - modules/nf-core/meryl/unionsum/**
+  - tests/modules/nf-core/meryl/unionsum/**
 
 metabat2/jgisummarizebamcontigdepths:
-  - modules/metabat2/jgisummarizebamcontigdepths/**
-  - tests/modules/metabat2/jgisummarizebamcontigdepths/**
+  - modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
+  - tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
 
 metabat2/metabat2:
-  - modules/metabat2/metabat2/**
-  - tests/modules/metabat2/metabat2/**
+  - modules/nf-core/metabat2/metabat2/**
+  - tests/modules/nf-core/metabat2/metabat2/**
 
 metaphlan3/mergemetaphlantables:
-  - modules/metaphlan3/mergemetaphlantables/**
-  - tests/modules/metaphlan3/mergemetaphlantables/**
+  - modules/nf-core/metaphlan3/mergemetaphlantables/**
+  - tests/modules/nf-core/metaphlan3/mergemetaphlantables/**
 
 metaphlan3/metaphlan3:
-  - modules/metaphlan3/metaphlan3/**
-  - tests/modules/metaphlan3/metaphlan3/**
+  - modules/nf-core/metaphlan3/metaphlan3/**
+  - tests/modules/nf-core/metaphlan3/metaphlan3/**
 
 methyldackel/extract:
-  - modules/methyldackel/extract/**
-  - tests/modules/methyldackel/extract/**
+  - modules/nf-core/methyldackel/extract/**
+  - tests/modules/nf-core/methyldackel/extract/**
 
 methyldackel/mbias:
-  - modules/methyldackel/mbias/**
-  - tests/modules/methyldackel/mbias/**
+  - modules/nf-core/methyldackel/mbias/**
+  - tests/modules/nf-core/methyldackel/mbias/**
 
 minia:
-  - modules/minia/**
-  - tests/modules/minia/**
+  - modules/nf-core/minia/**
+  - tests/modules/nf-core/minia/**
 
 miniasm:
-  - modules/miniasm/**
-  - tests/modules/miniasm/**
+  - modules/nf-core/miniasm/**
+  - tests/modules/nf-core/miniasm/**
 
 minimap2/align:
-  - modules/minimap2/align/**
-  - tests/modules/minimap2/align/**
+  - modules/nf-core/minimap2/align/**
+  - tests/modules/nf-core/minimap2/align/**
 
 minimap2/index:
-  - modules/minimap2/index/**
-  - tests/modules/minimap2/index/**
+  - modules/nf-core/minimap2/index/**
+  - tests/modules/nf-core/minimap2/index/**
 
 mlst:
-  - modules/mlst/**
-  - tests/modules/mlst/**
+  - modules/nf-core/mlst/**
+  - tests/modules/nf-core/mlst/**
 
 mobsuite/recon:
-  - modules/mobsuite/recon/**
-  - tests/modules/mobsuite/recon/**
+  - modules/nf-core/mobsuite/recon/**
+  - tests/modules/nf-core/mobsuite/recon/**
 
 mosdepth:
-  - modules/mosdepth/**
-  - tests/modules/mosdepth/**
+  - modules/nf-core/mosdepth/**
+  - tests/modules/nf-core/mosdepth/**
 
 motus/downloaddb:
-  - modules/motus/downloaddb/**
-  - tests/modules/motus/downloaddb/**
+  - modules/nf-core/motus/downloaddb/**
+  - tests/modules/nf-core/motus/downloaddb/**
 
 motus/merge:
-  - modules/motus/merge/**
-  - tests/modules/motus/merge/**
+  - modules/nf-core/motus/merge/**
+  - tests/modules/nf-core/motus/merge/**
 
 motus/profile:
-  - modules/motus/profile/**
-  - tests/modules/motus/profile/**
+  - modules/nf-core/motus/profile/**
+  - tests/modules/nf-core/motus/profile/**
 
 msisensor/msi:
-  - modules/msisensor/msi/**
-  - tests/modules/msisensor/msi/**
+  - modules/nf-core/msisensor/msi/**
+  - tests/modules/nf-core/msisensor/msi/**
 
 msisensor/scan:
-  - modules/msisensor/scan/**
-  - tests/modules/msisensor/scan/**
+  - modules/nf-core/msisensor/scan/**
+  - tests/modules/nf-core/msisensor/scan/**
 
 msisensor2/msi:
-  - modules/msisensor2/msi/**
-  - tests/modules/msisensor2/msi/**
+  - modules/nf-core/msisensor2/msi/**
+  - tests/modules/nf-core/msisensor2/msi/**
 
 msisensor2/scan:
-  - modules/msisensor2/scan/**
-  - tests/modules/msisensor2/scan/**
+  - modules/nf-core/msisensor2/scan/**
+  - tests/modules/nf-core/msisensor2/scan/**
 
 msisensorpro/msi_somatic:
-  - modules/msisensorpro/msi_somatic/**
-  - tests/modules/msisensorpro/msi_somatic/**
+  - modules/nf-core/msisensorpro/msi_somatic/**
+  - tests/modules/nf-core/msisensorpro/msi_somatic/**
 
 msisensorpro/scan:
-  - modules/msisensorpro/scan/**
-  - tests/modules/msisensorpro/scan/**
+  - modules/nf-core/msisensorpro/scan/**
+  - tests/modules/nf-core/msisensorpro/scan/**
 
 mtnucratio:
-  - modules/mtnucratio/**
-  - tests/modules/mtnucratio/**
+  - modules/nf-core/mtnucratio/**
+  - tests/modules/nf-core/mtnucratio/**
 
 multiqc:
-  - modules/fastqc/**
-  - modules/multiqc/**
-  - tests/modules/multiqc/**
+  - modules/nf-core/fastqc/**
+  - modules/nf-core/multiqc/**
+  - tests/modules/nf-core/multiqc/**
 
 multivcfanalyzer:
-  - modules/multivcfanalyzer/**
-  - tests/modules/multivcfanalyzer/**
+  - modules/nf-core/multivcfanalyzer/**
+  - tests/modules/nf-core/multivcfanalyzer/**
 
 mummer:
-  - modules/mummer/**
-  - tests/modules/mummer/**
+  - modules/nf-core/mummer/**
+  - tests/modules/nf-core/mummer/**
 
 muscle:
-  - modules/muscle/**
-  - tests/modules/muscle/**
+  - modules/nf-core/muscle/**
+  - tests/modules/nf-core/muscle/**
 
 mykrobe/predict:
-  - modules/mykrobe/predict/**
-  - tests/modules/mykrobe/predict/**
+  - modules/nf-core/mykrobe/predict/**
+  - tests/modules/nf-core/mykrobe/predict/**
 
 nanolyse:
-  - modules/nanolyse/**
-  - tests/modules/nanolyse/**
+  - modules/nf-core/nanolyse/**
+  - tests/modules/nf-core/nanolyse/**
 
 nanoplot:
-  - modules/nanoplot/**
-  - tests/modules/nanoplot/**
+  - modules/nf-core/nanoplot/**
+  - tests/modules/nf-core/nanoplot/**
 
 ncbigenomedownload:
-  - modules/ncbigenomedownload/**
-  - tests/modules/ncbigenomedownload/**
+  - modules/nf-core/ncbigenomedownload/**
+  - tests/modules/nf-core/ncbigenomedownload/**
 
 nextclade/datasetget:
-  - modules/nextclade/datasetget/**
-  - tests/modules/nextclade/datasetget/**
+  - modules/nf-core/nextclade/datasetget/**
+  - tests/modules/nf-core/nextclade/datasetget/**
 
 nextclade/run:
-  - modules/nextclade/run/**
-  - tests/modules/nextclade/run/**
+  - modules/nf-core/nextclade/run/**
+  - tests/modules/nf-core/nextclade/run/**
 
 nextgenmap:
-  - modules/nextgenmap/**
-  - tests/modules/nextgenmap/**
+  - modules/nf-core/nextgenmap/**
+  - tests/modules/nf-core/nextgenmap/**
 
 ngmaster:
-  - modules/ngmaster/**
-  - tests/modules/ngmaster/**
+  - modules/nf-core/ngmaster/**
+  - tests/modules/nf-core/ngmaster/**
 
 ngscheckmate/ncm:
-  - modules/ngscheckmate/ncm/**
-  - tests/modules/ngscheckmate/ncm/**
+  - modules/nf-core/ngscheckmate/ncm/**
+  - tests/modules/nf-core/ngscheckmate/ncm/**
 
 nucmer:
-  - modules/nucmer/**
-  - tests/modules/nucmer/**
+  - modules/nf-core/nucmer/**
+  - tests/modules/nf-core/nucmer/**
 
 optitype:
-  - modules/optitype/**
-  - tests/modules/optitype/**
+  - modules/nf-core/optitype/**
+  - tests/modules/nf-core/optitype/**
 
 pairix:
-  - modules/pairix/**
-  - tests/modules/pairix/**
+  - modules/nf-core/pairix/**
+  - tests/modules/nf-core/pairix/**
 
 pairtools/dedup:
-  - modules/pairtools/dedup/**
-  - tests/modules/pairtools/dedup/**
+  - modules/nf-core/pairtools/dedup/**
+  - tests/modules/nf-core/pairtools/dedup/**
 
 pairtools/flip:
-  - modules/pairtools/flip/**
-  - tests/modules/pairtools/flip/**
+  - modules/nf-core/pairtools/flip/**
+  - tests/modules/nf-core/pairtools/flip/**
 
 pairtools/parse:
-  - modules/pairtools/parse/**
-  - tests/modules/pairtools/parse/**
+  - modules/nf-core/pairtools/parse/**
+  - tests/modules/nf-core/pairtools/parse/**
 
 pairtools/restrict:
-  - modules/pairtools/restrict/**
-  - tests/modules/pairtools/restrict/**
+  - modules/nf-core/pairtools/restrict/**
+  - tests/modules/nf-core/pairtools/restrict/**
 
 pairtools/select:
-  - modules/pairtools/select/**
-  - tests/modules/pairtools/select/**
+  - modules/nf-core/pairtools/select/**
+  - tests/modules/nf-core/pairtools/select/**
 
 pairtools/sort:
-  - modules/pairtools/sort/**
-  - tests/modules/pairtools/sort/**
+  - modules/nf-core/pairtools/sort/**
+  - tests/modules/nf-core/pairtools/sort/**
 
 panaroo/run:
-  - modules/panaroo/run/**
-  - tests/modules/panaroo/run/**
+  - modules/nf-core/panaroo/run/**
+  - tests/modules/nf-core/panaroo/run/**
 
 pangolin:
-  - modules/pangolin/**
-  - tests/modules/pangolin/**
+  - modules/nf-core/pangolin/**
+  - tests/modules/nf-core/pangolin/**
 
 paraclu:
-  - modules/paraclu/**
-  - tests/modules/paraclu/**
+  - modules/nf-core/paraclu/**
+  - tests/modules/nf-core/paraclu/**
 
 pasty:
-  - modules/pasty/**
-  - tests/modules/pasty/**
+  - modules/nf-core/pasty/**
+  - tests/modules/nf-core/pasty/**
 
 pbbam/pbmerge:
-  - modules/pbbam/pbmerge/**
-  - tests/modules/pbbam/pbmerge/**
+  - modules/nf-core/pbbam/pbmerge/**
+  - tests/modules/nf-core/pbbam/pbmerge/**
 
 pbccs:
-  - modules/pbccs/**
-  - tests/modules/pbccs/**
+  - modules/nf-core/pbccs/**
+  - tests/modules/nf-core/pbccs/**
 
 pbptyper:
-  - modules/pbptyper/**
-  - tests/modules/pbptyper/**
+  - modules/nf-core/pbptyper/**
+  - tests/modules/nf-core/pbptyper/**
 
 pear:
-  - modules/pear/**
-  - tests/modules/pear/**
+  - modules/nf-core/pear/**
+  - tests/modules/nf-core/pear/**
 
 peddy:
-  - modules/peddy/**
-  - tests/modules/peddy/**
+  - modules/nf-core/peddy/**
+  - tests/modules/nf-core/peddy/**
 
 phantompeakqualtools:
-  - modules/phantompeakqualtools/**
-  - tests/modules/phantompeakqualtools/**
+  - modules/nf-core/phantompeakqualtools/**
+  - tests/modules/nf-core/phantompeakqualtools/**
 
 phyloflash:
-  - modules/phyloflash/**
-  - tests/modules/phyloflash/**
+  - modules/nf-core/phyloflash/**
+  - tests/modules/nf-core/phyloflash/**
 
 picard/addorreplacereadgroups:
-  - modules/picard/addorreplacereadgroups/**
-  - tests/modules/picard/addorreplacereadgroups/**
+  - modules/nf-core/picard/addorreplacereadgroups/**
+  - tests/modules/nf-core/picard/addorreplacereadgroups/**
 
 picard/cleansam:
-  - modules/picard/cleansam/**
-  - tests/modules/picard/cleansam/**
+  - modules/nf-core/picard/cleansam/**
+  - tests/modules/nf-core/picard/cleansam/**
 
 picard/collecthsmetrics:
-  - modules/picard/collecthsmetrics/**
-  - tests/modules/picard/collecthsmetrics/**
+  - modules/nf-core/picard/collecthsmetrics/**
+  - tests/modules/nf-core/picard/collecthsmetrics/**
 
 picard/collectmultiplemetrics:
-  - modules/picard/collectmultiplemetrics/**
-  - tests/modules/picard/collectmultiplemetrics/**
+  - modules/nf-core/picard/collectmultiplemetrics/**
+  - tests/modules/nf-core/picard/collectmultiplemetrics/**
 
 picard/collectwgsmetrics:
-  - modules/picard/collectwgsmetrics/**
-  - tests/modules/picard/collectwgsmetrics/**
+  - modules/nf-core/picard/collectwgsmetrics/**
+  - tests/modules/nf-core/picard/collectwgsmetrics/**
 
 picard/createsequencedictionary:
-  - modules/picard/createsequencedictionary/**
-  - tests/modules/picard/createsequencedictionary/**
+  - modules/nf-core/picard/createsequencedictionary/**
+  - tests/modules/nf-core/picard/createsequencedictionary/**
 
 picard/crosscheckfingerprints:
-  - modules/picard/crosscheckfingerprints/**
-  - tests/modules/picard/crosscheckfingerprints/**
+  - modules/nf-core/picard/crosscheckfingerprints/**
+  - tests/modules/nf-core/picard/crosscheckfingerprints/**
 
 picard/fastqtosam:
-  - modules/picard/fastqtosam/**
-  - tests/modules/picard/fastqtosam/**
+  - modules/nf-core/picard/fastqtosam/**
+  - tests/modules/nf-core/picard/fastqtosam/**
 
 picard/filtersamreads:
-  - modules/picard/filtersamreads/**
-  - tests/modules/picard/filtersamreads/**
+  - modules/nf-core/picard/filtersamreads/**
+  - tests/modules/nf-core/picard/filtersamreads/**
 
 picard/fixmateinformation:
-  - modules/picard/fixmateinformation/**
-  - tests/modules/picard/fixmateinformation/**
+  - modules/nf-core/picard/fixmateinformation/**
+  - tests/modules/nf-core/picard/fixmateinformation/**
 
 picard/liftovervcf:
-  - modules/picard/liftovervcf/**
-  - tests/modules/picard/liftovervcf/**
+  - modules/nf-core/picard/liftovervcf/**
+  - tests/modules/nf-core/picard/liftovervcf/**
 
 picard/markduplicates:
-  - modules/picard/markduplicates/**
-  - tests/modules/picard/markduplicates/**
+  - modules/nf-core/picard/markduplicates/**
+  - tests/modules/nf-core/picard/markduplicates/**
 
 picard/mergesamfiles:
-  - modules/picard/mergesamfiles/**
-  - tests/modules/picard/mergesamfiles/**
+  - modules/nf-core/picard/mergesamfiles/**
+  - tests/modules/nf-core/picard/mergesamfiles/**
 
 picard/sortsam:
-  - modules/picard/sortsam/**
-  - tests/modules/picard/sortsam/**
+  - modules/nf-core/picard/sortsam/**
+  - tests/modules/nf-core/picard/sortsam/**
 
 picard/sortvcf:
-  - modules/picard/sortvcf/**
-  - tests/modules/picard/sortvcf/**
+  - modules/nf-core/picard/sortvcf/**
+  - tests/modules/nf-core/picard/sortvcf/**
 
 pints/caller:
-  - modules/pints/caller/**
-  - tests/modules/pints/caller/**
+  - modules/nf-core/pints/caller/**
+  - tests/modules/nf-core/pints/caller/**
 
 pirate:
-  - modules/pirate/**
-  - tests/modules/pirate/**
+  - modules/nf-core/pirate/**
+  - tests/modules/nf-core/pirate/**
 
 plasmidfinder:
-  - modules/plasmidfinder/**
-  - tests/modules/plasmidfinder/**
+  - modules/nf-core/plasmidfinder/**
+  - tests/modules/nf-core/plasmidfinder/**
 
 plasmidid:
-  - modules/plasmidid/**
-  - tests/modules/plasmidid/**
+  - modules/nf-core/plasmidid/**
+  - tests/modules/nf-core/plasmidid/**
 
 plink/extract:
-  - modules/plink/extract/**
-  - tests/modules/plink/extract/**
+  - modules/nf-core/plink/extract/**
+  - tests/modules/nf-core/plink/extract/**
 
 plink/vcf:
-  - modules/plink/vcf/**
-  - tests/modules/plink/vcf/**
+  - modules/nf-core/plink/vcf/**
+  - tests/modules/nf-core/plink/vcf/**
 
 plink2/extract:
-  - modules/plink2/extract/**
-  - tests/modules/plink2/extract/**
+  - modules/nf-core/plink2/extract/**
+  - tests/modules/nf-core/plink2/extract/**
 
 plink2/score:
-  - modules/plink2/score/**
-  - tests/modules/plink2/score/**
+  - modules/nf-core/plink2/score/**
+  - tests/modules/nf-core/plink2/score/**
 
 plink2/vcf:
-  - modules/plink2/vcf/**
-  - tests/modules/plink2/vcf/**
+  - modules/nf-core/plink2/vcf/**
+  - tests/modules/nf-core/plink2/vcf/**
 
 pmdtools/filter:
-  - modules/pmdtools/filter/**
-  - tests/modules/pmdtools/filter/**
+  - modules/nf-core/pmdtools/filter/**
+  - tests/modules/nf-core/pmdtools/filter/**
 
 porechop:
-  - modules/porechop/**
-  - tests/modules/porechop/**
+  - modules/nf-core/porechop/**
+  - tests/modules/nf-core/porechop/**
 
 preseq/ccurve:
-  - modules/preseq/ccurve/**
-  - tests/modules/preseq/ccurve/**
+  - modules/nf-core/preseq/ccurve/**
+  - tests/modules/nf-core/preseq/ccurve/**
 
 preseq/lcextrap:
-  - modules/preseq/lcextrap/**
-  - tests/modules/preseq/lcextrap/**
+  - modules/nf-core/preseq/lcextrap/**
+  - tests/modules/nf-core/preseq/lcextrap/**
 
 prinseqplusplus:
-  - modules/prinseqplusplus/**
-  - tests/modules/prinseqplusplus/**
+  - modules/nf-core/prinseqplusplus/**
+  - tests/modules/nf-core/prinseqplusplus/**
 
 prodigal:
-  - modules/prodigal/**
-  - tests/modules/prodigal/**
+  - modules/nf-core/prodigal/**
+  - tests/modules/nf-core/prodigal/**
 
 prokka:
-  - modules/prokka/**
-  - tests/modules/prokka/**
+  - modules/nf-core/prokka/**
+  - tests/modules/nf-core/prokka/**
 
 pycoqc:
-  - modules/pycoqc/**
-  - tests/modules/pycoqc/**
+  - modules/nf-core/pycoqc/**
+  - tests/modules/nf-core/pycoqc/**
 
 pydamage/analyze:
-  - modules/pydamage/analyze/**
-  - tests/modules/pydamage/analyze/**
+  - modules/nf-core/pydamage/analyze/**
+  - tests/modules/nf-core/pydamage/analyze/**
 
 pydamage/filter:
-  - modules/pydamage/filter/**
-  - tests/modules/pydamage/filter/**
+  - modules/nf-core/pydamage/filter/**
+  - tests/modules/nf-core/pydamage/filter/**
 
 qcat:
-  - modules/qcat/**
-  - tests/modules/qcat/**
+  - modules/nf-core/qcat/**
+  - tests/modules/nf-core/qcat/**
 
 qualimap/bamqc:
-  - modules/qualimap/bamqc/**
-  - tests/modules/qualimap/bamqc/**
+  - modules/nf-core/qualimap/bamqc/**
+  - tests/modules/nf-core/qualimap/bamqc/**
 
 qualimap/bamqccram:
-  - modules/qualimap/bamqccram/**
-  - tests/modules/qualimap/bamqccram/**
+  - modules/nf-core/qualimap/bamqccram/**
+  - tests/modules/nf-core/qualimap/bamqccram/**
 
 quast:
-  - modules/quast/**
-  - tests/modules/quast/**
+  - modules/nf-core/quast/**
+  - tests/modules/nf-core/quast/**
 
 racon:
-  - modules/racon/**
-  - tests/modules/racon/**
+  - modules/nf-core/racon/**
+  - tests/modules/nf-core/racon/**
 
 rapidnj:
-  - modules/rapidnj/**
-  - tests/modules/rapidnj/**
+  - modules/nf-core/rapidnj/**
+  - tests/modules/nf-core/rapidnj/**
 
 rasusa:
-  - modules/rasusa/**
-  - tests/modules/rasusa/**
+  - modules/nf-core/rasusa/**
+  - tests/modules/nf-core/rasusa/**
 
 raven:
-  - modules/raven/**
-  - tests/modules/raven/**
+  - modules/nf-core/raven/**
+  - tests/modules/nf-core/raven/**
 
 raxmlng:
-  - modules/raxmlng/**
-  - tests/modules/raxmlng/**
+  - modules/nf-core/raxmlng/**
+  - tests/modules/nf-core/raxmlng/**
 
 rgi/main:
-  - modules/rgi/main/**
-  - tests/modules/rgi/main/**
+  - modules/nf-core/rgi/main/**
+  - tests/modules/nf-core/rgi/main/**
 
 rhocall/annotate:
-  - modules/rhocall/annotate/**
-  - tests/modules/rhocall/annotate/**
+  - modules/nf-core/rhocall/annotate/**
+  - tests/modules/nf-core/rhocall/annotate/**
 
 rmarkdownnotebook:
-  - modules/rmarkdownnotebook/**
-  - tests/modules/rmarkdownnotebook/**
+  - modules/nf-core/rmarkdownnotebook/**
+  - tests/modules/nf-core/rmarkdownnotebook/**
 
 roary:
-  - modules/roary/**
-  - tests/modules/roary/**
+  - modules/nf-core/roary/**
+  - tests/modules/nf-core/roary/**
 
 rsem/calculateexpression:
-  - modules/rsem/calculateexpression/**
-  - tests/modules/rsem/calculateexpression/**
+  - modules/nf-core/rsem/calculateexpression/**
+  - tests/modules/nf-core/rsem/calculateexpression/**
 
 rsem/preparereference:
-  - modules/rsem/preparereference/**
-  - tests/modules/rsem/preparereference/**
+  - modules/nf-core/rsem/preparereference/**
+  - tests/modules/nf-core/rsem/preparereference/**
 
 rseqc/bamstat:
-  - modules/rseqc/bamstat/**
-  - tests/modules/rseqc/bamstat/**
+  - modules/nf-core/rseqc/bamstat/**
+  - tests/modules/nf-core/rseqc/bamstat/**
 
 rseqc/inferexperiment:
-  - modules/rseqc/inferexperiment/**
-  - tests/modules/rseqc/inferexperiment/**
+  - modules/nf-core/rseqc/inferexperiment/**
+  - tests/modules/nf-core/rseqc/inferexperiment/**
 
 rseqc/innerdistance:
-  - modules/rseqc/innerdistance/**
-  - tests/modules/rseqc/innerdistance/**
+  - modules/nf-core/rseqc/innerdistance/**
+  - tests/modules/nf-core/rseqc/innerdistance/**
 
 rseqc/junctionannotation:
-  - modules/rseqc/junctionannotation/**
-  - tests/modules/rseqc/junctionannotation/**
+  - modules/nf-core/rseqc/junctionannotation/**
+  - tests/modules/nf-core/rseqc/junctionannotation/**
 
 rseqc/junctionsaturation:
-  - modules/rseqc/junctionsaturation/**
-  - tests/modules/rseqc/junctionsaturation/**
+  - modules/nf-core/rseqc/junctionsaturation/**
+  - tests/modules/nf-core/rseqc/junctionsaturation/**
 
 rseqc/readdistribution:
-  - modules/rseqc/readdistribution/**
-  - tests/modules/rseqc/readdistribution/**
+  - modules/nf-core/rseqc/readdistribution/**
+  - tests/modules/nf-core/rseqc/readdistribution/**
 
 rseqc/readduplication:
-  - modules/rseqc/readduplication/**
-  - tests/modules/rseqc/readduplication/**
+  - modules/nf-core/rseqc/readduplication/**
+  - tests/modules/nf-core/rseqc/readduplication/**
 
 rseqc/tin:
-  - modules/rseqc/tin/**
-  - tests/modules/rseqc/tin/**
+  - modules/nf-core/rseqc/tin/**
+  - tests/modules/nf-core/rseqc/tin/**
 
 rtgtools/pedfilter:
-  - modules/rtgtools/pedfilter/**
-  - tests/modules/rtgtools/pedfilter/**
+  - modules/nf-core/rtgtools/pedfilter/**
+  - tests/modules/nf-core/rtgtools/pedfilter/**
 
 rtgtools/vcfeval:
-  - modules/rtgtools/vcfeval/**
-  - tests/modules/rtgtools/vcfeval/**
+  - modules/nf-core/rtgtools/vcfeval/**
+  - tests/modules/nf-core/rtgtools/vcfeval/**
 
 salmon/index:
-  - modules/salmon/index/**
-  - tests/modules/salmon/index/**
+  - modules/nf-core/salmon/index/**
+  - tests/modules/nf-core/salmon/index/**
 
 salmon/quant:
-  - modules/salmon/quant/**
-  - tests/modules/salmon/quant/**
+  - modules/nf-core/salmon/quant/**
+  - tests/modules/nf-core/salmon/quant/**
 
 samblaster:
-  - modules/samblaster/**
-  - tests/modules/samblaster/**
+  - modules/nf-core/samblaster/**
+  - tests/modules/nf-core/samblaster/**
 
 samtools/ampliconclip:
-  - modules/samtools/ampliconclip/**
-  - tests/modules/samtools/ampliconclip/**
+  - modules/nf-core/samtools/ampliconclip/**
+  - tests/modules/nf-core/samtools/ampliconclip/**
 
 samtools/bam2fq:
-  - modules/samtools/bam2fq/**
-  - tests/modules/samtools/bam2fq/**
+  - modules/nf-core/samtools/bam2fq/**
+  - tests/modules/nf-core/samtools/bam2fq/**
 
 samtools/collate:
-  - modules/samtools/collate/**
-  - tests/modules/samtools/collate/**
+  - modules/nf-core/samtools/collate/**
+  - tests/modules/nf-core/samtools/collate/**
 
 samtools/collatefastq:
-  - modules/samtools/collatefastq/**
-  - tests/modules/samtools/collatefastq/**
+  - modules/nf-core/samtools/collatefastq/**
+  - tests/modules/nf-core/samtools/collatefastq/**
 
 samtools/convert:
-  - modules/samtools/convert/**
-  - tests/modules/samtools/convert/**
+  - modules/nf-core/samtools/convert/**
+  - tests/modules/nf-core/samtools/convert/**
 
 samtools/depth:
-  - modules/samtools/depth/**
-  - tests/modules/samtools/depth/**
+  - modules/nf-core/samtools/depth/**
+  - tests/modules/nf-core/samtools/depth/**
 
 samtools/dict:
-  - modules/samtools/dict/**
-  - tests/modules/samtools/dict/**
+  - modules/nf-core/samtools/dict/**
+  - tests/modules/nf-core/samtools/dict/**
 
 samtools/faidx:
-  - modules/samtools/faidx/**
-  - tests/modules/samtools/faidx/**
+  - modules/nf-core/samtools/faidx/**
+  - tests/modules/nf-core/samtools/faidx/**
 
 samtools/fasta:
-  - modules/samtools/fasta/**
-  - tests/modules/samtools/fasta/**
+  - modules/nf-core/samtools/fasta/**
+  - tests/modules/nf-core/samtools/fasta/**
 
 samtools/fastq:
-  - modules/samtools/fastq/**
-  - tests/modules/samtools/fastq/**
+  - modules/nf-core/samtools/fastq/**
+  - tests/modules/nf-core/samtools/fastq/**
 
 samtools/fixmate:
-  - modules/samtools/fixmate/**
-  - tests/modules/samtools/fixmate/**
+  - modules/nf-core/samtools/fixmate/**
+  - tests/modules/nf-core/samtools/fixmate/**
 
 samtools/flagstat:
-  - modules/samtools/flagstat/**
-  - tests/modules/samtools/flagstat/**
+  - modules/nf-core/samtools/flagstat/**
+  - tests/modules/nf-core/samtools/flagstat/**
 
 samtools/getrg:
-  - modules/samtools/getrg/**
-  - tests/modules/samtools/getrg/**
+  - modules/nf-core/samtools/getrg/**
+  - tests/modules/nf-core/samtools/getrg/**
 
 samtools/idxstats:
-  - modules/samtools/idxstats/**
-  - tests/modules/samtools/idxstats/**
+  - modules/nf-core/samtools/idxstats/**
+  - tests/modules/nf-core/samtools/idxstats/**
 
 samtools/index:
-  - modules/samtools/index/**
-  - tests/modules/samtools/index/**
+  - modules/nf-core/samtools/index/**
+  - tests/modules/nf-core/samtools/index/**
 
 samtools/markdup:
-  - modules/samtools/markdup/**
-  - tests/modules/samtools/markdup/**
+  - modules/nf-core/samtools/markdup/**
+  - tests/modules/nf-core/samtools/markdup/**
 
 samtools/merge:
-  - modules/samtools/merge/**
-  - tests/modules/samtools/merge/**
+  - modules/nf-core/samtools/merge/**
+  - tests/modules/nf-core/samtools/merge/**
 
 samtools/mpileup:
-  - modules/samtools/mpileup/**
-  - tests/modules/samtools/mpileup/**
+  - modules/nf-core/samtools/mpileup/**
+  - tests/modules/nf-core/samtools/mpileup/**
 
 samtools/sort:
-  - modules/samtools/sort/**
-  - tests/modules/samtools/sort/**
+  - modules/nf-core/samtools/sort/**
+  - tests/modules/nf-core/samtools/sort/**
 
 samtools/stats:
-  - modules/samtools/stats/**
-  - tests/modules/samtools/stats/**
+  - modules/nf-core/samtools/stats/**
+  - tests/modules/nf-core/samtools/stats/**
 
 samtools/view:
-  - modules/samtools/view/**
-  - tests/modules/samtools/view/**
+  - modules/nf-core/samtools/view/**
+  - tests/modules/nf-core/samtools/view/**
 
 scoary:
-  - modules/scoary/**
-  - tests/modules/scoary/**
+  - modules/nf-core/scoary/**
+  - tests/modules/nf-core/scoary/**
 
 scramble/clusteranalysis:
-  - modules/scramble/clusteranalysis/**
-  - tests/modules/scramble/clusteranalysis/**
+  - modules/nf-core/scramble/clusteranalysis/**
+  - tests/modules/nf-core/scramble/clusteranalysis/**
 
 scramble/clusteridentifier:
-  - modules/scramble/clusteridentifier/**
-  - tests/modules/scramble/clusteridentifier/**
+  - modules/nf-core/scramble/clusteridentifier/**
+  - tests/modules/nf-core/scramble/clusteridentifier/**
 
 seacr/callpeak:
-  - modules/seacr/callpeak/**
-  - tests/modules/seacr/callpeak/**
+  - modules/nf-core/seacr/callpeak/**
+  - tests/modules/nf-core/seacr/callpeak/**
 
 seqkit/pair:
-  - modules/seqkit/pair/**
-  - tests/modules/seqkit/pair/**
+  - modules/nf-core/seqkit/pair/**
+  - tests/modules/nf-core/seqkit/pair/**
 
 seqkit/replace:
-  - modules/seqkit/replace/**
-  - tests/modules/seqkit/replace/**
+  - modules/nf-core/seqkit/replace/**
+  - tests/modules/nf-core/seqkit/replace/**
 
 seqkit/split2:
-  - modules/seqkit/split2/**
-  - tests/modules/seqkit/split2/**
+  - modules/nf-core/seqkit/split2/**
+  - tests/modules/nf-core/seqkit/split2/**
 
 seqkit/stats:
-  - modules/seqkit/stats/**
-  - tests/modules/seqkit/stats/**
+  - modules/nf-core/seqkit/stats/**
+  - tests/modules/nf-core/seqkit/stats/**
 
 seqsero2:
-  - modules/seqsero2/**
-  - tests/modules/seqsero2/**
+  - modules/nf-core/seqsero2/**
+  - tests/modules/nf-core/seqsero2/**
 
 seqtk/mergepe:
-  - modules/seqtk/mergepe/**
-  - tests/modules/seqtk/mergepe/**
+  - modules/nf-core/seqtk/mergepe/**
+  - tests/modules/nf-core/seqtk/mergepe/**
 
 seqtk/rename:
-  - modules/seqtk/rename/**
-  - tests/modules/seqtk/rename/**
+  - modules/nf-core/seqtk/rename/**
+  - tests/modules/nf-core/seqtk/rename/**
 
 seqtk/sample:
-  - modules/seqtk/sample/**
-  - tests/modules/seqtk/sample/**
+  - modules/nf-core/seqtk/sample/**
+  - tests/modules/nf-core/seqtk/sample/**
 
 seqtk/seq:
-  - modules/seqtk/seq/**
-  - tests/modules/seqtk/seq/**
+  - modules/nf-core/seqtk/seq/**
+  - tests/modules/nf-core/seqtk/seq/**
 
 seqtk/subseq:
-  - modules/seqtk/subseq/**
-  - tests/modules/seqtk/subseq/**
+  - modules/nf-core/seqtk/subseq/**
+  - tests/modules/nf-core/seqtk/subseq/**
 
 sequenzautils/bam2seqz:
-  - modules/sequenzautils/bam2seqz/**
-  - tests/modules/sequenzautils/bam2seqz/**
+  - modules/nf-core/sequenzautils/bam2seqz/**
+  - tests/modules/nf-core/sequenzautils/bam2seqz/**
 
 sequenzautils/gcwiggle:
-  - modules/sequenzautils/gcwiggle/**
-  - tests/modules/sequenzautils/gcwiggle/**
+  - modules/nf-core/sequenzautils/gcwiggle/**
+  - tests/modules/nf-core/sequenzautils/gcwiggle/**
 
 seqwish/induce:
-  - modules/seqwish/induce/**
-  - tests/modules/seqwish/induce/**
+  - modules/nf-core/seqwish/induce/**
+  - tests/modules/nf-core/seqwish/induce/**
 
 seroba/run:
-  - modules/seroba/run/**
-  - tests/modules/seroba/run/**
+  - modules/nf-core/seroba/run/**
+  - tests/modules/nf-core/seroba/run/**
 
 sexdeterrmine:
-  - modules/sexdeterrmine/**
-  - tests/modules/sexdeterrmine/**
+  - modules/nf-core/sexdeterrmine/**
+  - tests/modules/nf-core/sexdeterrmine/**
 
 shasta:
-  - modules/shasta/**
-  - tests/modules/shasta/**
+  - modules/nf-core/shasta/**
+  - tests/modules/nf-core/shasta/**
 
 shasum:
-  - modules/shasum/**
-  - tests/modules/shasum/**
+  - modules/nf-core/shasum/**
+  - tests/modules/nf-core/shasum/**
 
 shigatyper:
-  - modules/shigatyper/**
-  - tests/modules/shigatyper/**
+  - modules/nf-core/shigatyper/**
+  - tests/modules/nf-core/shigatyper/**
 
 shovill:
-  - modules/shovill/**
-  - tests/modules/shovill/**
+  - modules/nf-core/shovill/**
+  - tests/modules/nf-core/shovill/**
 
 sistr:
-  - modules/sistr/**
-  - tests/modules/sistr/**
+  - modules/nf-core/sistr/**
+  - tests/modules/nf-core/sistr/**
 
 slimfastq:
-  - modules/slimfastq/**
-  - tests/modules/slimfastq/**
+  - modules/nf-core/slimfastq/**
+  - tests/modules/nf-core/slimfastq/**
 
 snapaligner/align:
-  - modules/snapaligner/align/**
-  - tests/modules/snapaligner/align/**
+  - modules/nf-core/snapaligner/align/**
+  - tests/modules/nf-core/snapaligner/align/**
 
 snapaligner/index:
-  - modules/snapaligner/index/**
-  - tests/modules/snapaligner/index/**
+  - modules/nf-core/snapaligner/index/**
+  - tests/modules/nf-core/snapaligner/index/**
 
 snippy/core:
-  - modules/snippy/core/**
-  - tests/modules/snippy/core/**
+  - modules/nf-core/snippy/core/**
+  - tests/modules/nf-core/snippy/core/**
 
 snippy/run:
-  - modules/snippy/run/**
-  - tests/modules/snippy/run/**
+  - modules/nf-core/snippy/run/**
+  - tests/modules/nf-core/snippy/run/**
 
 snpdists:
-  - modules/snpdists/**
-  - tests/modules/snpdists/**
+  - modules/nf-core/snpdists/**
+  - tests/modules/nf-core/snpdists/**
 
 snpeff:
-  - modules/snpeff/**
-  - tests/modules/snpeff/**
+  - modules/nf-core/snpeff/**
+  - tests/modules/nf-core/snpeff/**
 
 snpsift/split:
-  - modules/snpsift/split/**
-  - tests/modules/snpsift/split/**
+  - modules/nf-core/snpsift/split/**
+  - tests/modules/nf-core/snpsift/split/**
 
 snpsites:
-  - modules/snpsites/**
-  - tests/modules/snpsites/**
+  - modules/nf-core/snpsites/**
+  - tests/modules/nf-core/snpsites/**
 
 somalier/extract:
-  - modules/somalier/extract/**
-  - tests/modules/somalier/extract/**
+  - modules/nf-core/somalier/extract/**
+  - tests/modules/nf-core/somalier/extract/**
 
 somalier/relate:
-  - modules/somalier/relate/**
-  - tests/modules/somalier/relate/**
+  - modules/nf-core/somalier/relate/**
+  - tests/modules/nf-core/somalier/relate/**
 
 sourmash/sketch:
-  - modules/sourmash/sketch/**
-  - tests/modules/sourmash/sketch/**
+  - modules/nf-core/sourmash/sketch/**
+  - tests/modules/nf-core/sourmash/sketch/**
 
 spades:
-  - modules/spades/**
-  - tests/modules/spades/**
+  - modules/nf-core/spades/**
+  - tests/modules/nf-core/spades/**
 
 spatyper:
-  - modules/spatyper/**
-  - tests/modules/spatyper/**
+  - modules/nf-core/spatyper/**
+  - tests/modules/nf-core/spatyper/**
 
 sratools/fasterqdump:
-  - modules/sratools/fasterqdump/**
-  - tests/modules/sratools/fasterqdump/**
+  - modules/nf-core/sratools/fasterqdump/**
+  - tests/modules/nf-core/sratools/fasterqdump/**
 
 sratools/prefetch:
-  - modules/sratools/prefetch/**
-  - tests/modules/sratools/prefetch/**
+  - modules/nf-core/sratools/prefetch/**
+  - tests/modules/nf-core/sratools/prefetch/**
 
 srst2/srst2:
-  - modules/srst2/srst2/**
-  - tests/modules/srst2/srst2/**
+  - modules/nf-core/srst2/srst2/**
+  - tests/modules/nf-core/srst2/srst2/**
 
 ssuissero:
-  - modules/ssuissero/**
-  - tests/modules/ssuissero/**
+  - modules/nf-core/ssuissero/**
+  - tests/modules/nf-core/ssuissero/**
 
 stadeniolib/scramble:
-  - modules/stadeniolib/scramble/**
-  - tests/modules/stadeniolib/scramble/**
+  - modules/nf-core/stadeniolib/scramble/**
+  - tests/modules/nf-core/stadeniolib/scramble/**
 
 staphopiasccmec:
-  - modules/staphopiasccmec/**
-  - tests/modules/staphopiasccmec/**
+  - modules/nf-core/staphopiasccmec/**
+  - tests/modules/nf-core/staphopiasccmec/**
 
 star/align:
-  - modules/star/align/**
-  - tests/modules/star/align/**
+  - modules/nf-core/star/align/**
+  - tests/modules/nf-core/star/align/**
 
 star/genomegenerate:
-  - modules/star/genomegenerate/**
-  - tests/modules/star/genomegenerate/**
+  - modules/nf-core/star/genomegenerate/**
+  - tests/modules/nf-core/star/genomegenerate/**
 
 stranger:
-  - modules/stranger/**
-  - tests/modules/stranger/**
+  - modules/nf-core/stranger/**
+  - tests/modules/nf-core/stranger/**
 
 strelka/germline:
-  - modules/strelka/germline/**
-  - tests/modules/strelka/germline/**
+  - modules/nf-core/strelka/germline/**
+  - tests/modules/nf-core/strelka/germline/**
 
 strelka/somatic:
-  - modules/strelka/somatic/**
-  - tests/modules/strelka/somatic/**
+  - modules/nf-core/strelka/somatic/**
+  - tests/modules/nf-core/strelka/somatic/**
 
 stringtie/merge:
-  - modules/stringtie/merge/**
-  - tests/modules/stringtie/merge/**
+  - modules/nf-core/stringtie/merge/**
+  - tests/modules/nf-core/stringtie/merge/**
 
 stringtie/stringtie:
-  - modules/stringtie/stringtie/**
-  - tests/modules/stringtie/stringtie/**
+  - modules/nf-core/stringtie/stringtie/**
+  - tests/modules/nf-core/stringtie/stringtie/**
 
 subread/featurecounts:
-  - modules/subread/featurecounts/**
-  - tests/modules/subread/featurecounts/**
+  - modules/nf-core/subread/featurecounts/**
+  - tests/modules/nf-core/subread/featurecounts/**
 
 subworkflows/bam_stats_samtools:
   - subworkflows/nf-core/bam_stats_samtools/**
   - tests/subworkflows/nf-core/bam_stats_samtools/**
 
 svdb/merge:
-  - modules/svdb/merge/**
-  - tests/modules/svdb/merge/**
+  - modules/nf-core/svdb/merge/**
+  - tests/modules/nf-core/svdb/merge/**
 
 svdb/query:
-  - modules/svdb/query/**
-  - tests/modules/svdb/query/**
+  - modules/nf-core/svdb/query/**
+  - tests/modules/nf-core/svdb/query/**
 
 svtk/standardize:
-  - modules/svtk/standardize/**
-  - tests/modules/svtk/standardize/**
+  - modules/nf-core/svtk/standardize/**
+  - tests/modules/nf-core/svtk/standardize/**
 
 tabix/bgzip:
-  - modules/tabix/bgzip/**
-  - tests/modules/tabix/bgzip/**
+  - modules/nf-core/tabix/bgzip/**
+  - tests/modules/nf-core/tabix/bgzip/**
 
 tabix/bgziptabix:
-  - modules/tabix/bgziptabix/**
-  - tests/modules/tabix/bgziptabix/**
+  - modules/nf-core/tabix/bgziptabix/**
+  - tests/modules/nf-core/tabix/bgziptabix/**
 
 tabix/tabix:
-  - modules/tabix/tabix/**
-  - tests/modules/tabix/tabix/**
+  - modules/nf-core/tabix/tabix/**
+  - tests/modules/nf-core/tabix/tabix/**
 
 tailfindr:
-  - modules/tailfindr/**
-  - tests/modules/tailfindr/**
+  - modules/nf-core/tailfindr/**
+  - tests/modules/nf-core/tailfindr/**
 
 tbprofiler/profile:
-  - modules/tbprofiler/profile/**
-  - tests/modules/tbprofiler/profile/**
+  - modules/nf-core/tbprofiler/profile/**
+  - tests/modules/nf-core/tbprofiler/profile/**
 
 tiddit/cov:
-  - modules/tiddit/cov/**
-  - tests/modules/tiddit/cov/**
+  - modules/nf-core/tiddit/cov/**
+  - tests/modules/nf-core/tiddit/cov/**
 
 tiddit/sv:
-  - modules/tiddit/sv/**
-  - tests/modules/tiddit/sv/**
+  - modules/nf-core/tiddit/sv/**
+  - tests/modules/nf-core/tiddit/sv/**
 
 transdecoder/longorf:
-  - modules/transdecoder/longorf/**
-  - tests/modules/transdecoder/longorf/**
+  - modules/nf-core/transdecoder/longorf/**
+  - tests/modules/nf-core/transdecoder/longorf/**
 
 transdecoder/predict:
-  - modules/transdecoder/predict/**
-  - tests/modules/transdecoder/predict/**
+  - modules/nf-core/transdecoder/predict/**
+  - tests/modules/nf-core/transdecoder/predict/**
 
 trimgalore:
-  - modules/trimgalore/**
-  - tests/modules/trimgalore/**
+  - modules/nf-core/trimgalore/**
+  - tests/modules/nf-core/trimgalore/**
 
 trimmomatic:
-  - modules/trimmomatic/**
-  - tests/modules/trimmomatic/**
+  - modules/nf-core/trimmomatic/**
+  - tests/modules/nf-core/trimmomatic/**
 
 ucsc/bedclip:
-  - modules/ucsc/bedclip/**
-  - tests/modules/ucsc/bedclip/**
+  - modules/nf-core/ucsc/bedclip/**
+  - tests/modules/nf-core/ucsc/bedclip/**
 
 ucsc/bedgraphtobigwig:
-  - modules/ucsc/bedgraphtobigwig/**
-  - tests/modules/ucsc/bedgraphtobigwig/**
+  - modules/nf-core/ucsc/bedgraphtobigwig/**
+  - tests/modules/nf-core/ucsc/bedgraphtobigwig/**
 
 ucsc/bedtobigbed:
-  - modules/ucsc/bedtobigbed/**
-  - tests/modules/ucsc/bedtobigbed/**
+  - modules/nf-core/ucsc/bedtobigbed/**
+  - tests/modules/nf-core/ucsc/bedtobigbed/**
 
 ucsc/bigwigaverageoverbed:
-  - modules/ucsc/bigwigaverageoverbed/**
-  - tests/modules/ucsc/bigwigaverageoverbed/**
+  - modules/nf-core/ucsc/bigwigaverageoverbed/**
+  - tests/modules/nf-core/ucsc/bigwigaverageoverbed/**
 
 ucsc/liftover:
-  - modules/ucsc/liftover/**
-  - tests/modules/ucsc/liftover/**
+  - modules/nf-core/ucsc/liftover/**
+  - tests/modules/nf-core/ucsc/liftover/**
 
 ucsc/wigtobigwig:
-  - modules/ucsc/wigtobigwig/**
-  - tests/modules/ucsc/wigtobigwig/**
+  - modules/nf-core/ucsc/wigtobigwig/**
+  - tests/modules/nf-core/ucsc/wigtobigwig/**
 
 ultra/align:
-  - modules/ultra/align/**
-  - tests/modules/ultra/align/**
+  - modules/nf-core/ultra/align/**
+  - tests/modules/nf-core/ultra/align/**
 
 ultra/index:
-  - modules/ultra/index/**
-  - tests/modules/ultra/index/**
+  - modules/nf-core/ultra/index/**
+  - tests/modules/nf-core/ultra/index/**
 
 ultra/pipeline:
-  - modules/ultra/pipeline/**
-  - tests/modules/ultra/pipeline/**
+  - modules/nf-core/ultra/pipeline/**
+  - tests/modules/nf-core/ultra/pipeline/**
 
 umitools/dedup:
-  - modules/umitools/dedup/**
-  - modules/umitools/extract/**
-  - tests/modules/umitools/dedup/**
+  - modules/nf-core/umitools/dedup/**
+  - modules/nf-core/umitools/extract/**
+  - tests/modules/nf-core/umitools/dedup/**
 
 umitools/extract:
-  - modules/umitools/extract/**
-  - tests/modules/umitools/extract/**
+  - modules/nf-core/umitools/extract/**
+  - tests/modules/nf-core/umitools/extract/**
 
 unicycler:
-  - modules/unicycler/**
-  - tests/modules/unicycler/**
+  - modules/nf-core/unicycler/**
+  - tests/modules/nf-core/unicycler/**
 
 untar:
-  - modules/untar/**
-  - tests/modules/untar/**
+  - modules/nf-core/untar/**
+  - tests/modules/nf-core/untar/**
 
 unzip:
-  - modules/unzip/**
-  - tests/modules/unzip/**
+  - modules/nf-core/unzip/**
+  - tests/modules/nf-core/unzip/**
 
 vardictjava:
-  - modules/vardictjava/**
-  - tests/modules/vardictjava/**
+  - modules/nf-core/vardictjava/**
+  - tests/modules/nf-core/vardictjava/**
 
 variantbam:
-  - modules/variantbam/**
-  - tests/modules/variantbam/**
+  - modules/nf-core/variantbam/**
+  - tests/modules/nf-core/variantbam/**
 
 vcf2db:
-  - modules/vcf2db/**
-  - tests/modules/vcf2db/**
+  - modules/nf-core/vcf2db/**
+  - tests/modules/nf-core/vcf2db/**
 
 vcf2maf:
-  - modules/vcf2maf/**
-  - tests/modules/vcf2maf/**
+  - modules/nf-core/vcf2maf/**
+  - tests/modules/nf-core/vcf2maf/**
 
 vcfanno:
-  - modules/vcfanno/**
-  - tests/modules/vcfanno/**
+  - modules/nf-core/vcfanno/**
+  - tests/modules/nf-core/vcfanno/**
 
 vcflib/vcfbreakmulti:
-  - modules/vcflib/vcfbreakmulti/**
-  - tests/modules/vcflib/vcfbreakmulti/**
+  - modules/nf-core/vcflib/vcfbreakmulti/**
+  - tests/modules/nf-core/vcflib/vcfbreakmulti/**
 
 vcflib/vcfuniq:
-  - modules/vcflib/vcfuniq/**
-  - tests/modules/vcflib/vcfuniq/**
+  - modules/nf-core/vcflib/vcfuniq/**
+  - tests/modules/nf-core/vcflib/vcfuniq/**
 
 vcftools:
-  - modules/vcftools/**
-  - tests/modules/vcftools/**
+  - modules/nf-core/vcftools/**
+  - tests/modules/nf-core/vcftools/**
 
 vsearch/sintax:
-  - modules/vsearch/sintax/**
-  - tests/modules/vsearch/sintax/**
+  - modules/nf-core/vsearch/sintax/**
+  - tests/modules/nf-core/vsearch/sintax/**
 
 vsearch/usearchglobal:
-  - modules/vsearch/usearchglobal/**
-  - tests/modules/vsearch/usearchglobal/**
+  - modules/nf-core/vsearch/usearchglobal/**
+  - tests/modules/nf-core/vsearch/usearchglobal/**
 
 whamg:
-  - modules/whamg/**
-  - tests/modules/whamg/**
+  - modules/nf-core/whamg/**
+  - tests/modules/nf-core/whamg/**
 
 yara/index:
-  - modules/yara/index/**
-  - tests/modules/yara/index/**
+  - modules/nf-core/yara/index/**
+  - tests/modules/nf-core/yara/index/**
 
 yara/mapper:
-  - modules/yara/mapper/**
-  - tests/modules/yara/mapper/**
+  - modules/nf-core/yara/mapper/**
+  - tests/modules/nf-core/yara/mapper/**
diff --git a/tests/modules/abacas/main.nf b/tests/modules/abacas/main.nf
deleted file mode 100644
index 542a67af07d..00000000000
--- a/tests/modules/abacas/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ABACAS } from '../../../modules/abacas/main.nf'
-
-workflow test_abacas {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
-            ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    ABACAS ( input, fasta )
-}
diff --git a/tests/modules/abacas/test.yml b/tests/modules/abacas/test.yml
deleted file mode 100644
index c466a6ed958..00000000000
--- a/tests/modules/abacas/test.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-- name: abacas
-  command: nextflow run ./tests/modules/abacas -entry test_abacas -c ./tests/config/nextflow.config -c ./tests/modules/abacas/nextflow.config
-  tags:
-    - abacas
-  files:
-    - path: output/abacas/test.abacas.bin
-    - path: output/abacas/test.abacas.crunch
-      md5sum: 9a95358a9bd8ee97d1f2253d95623a17
-    - path: output/abacas/test.abacas.fasta
-      md5sum: 5e6c403d3850d52f6bde956fa2403b13
-    - path: output/abacas/test.abacas.gaps
-      md5sum: 5361af445b8d18a85c3af6527a97c89a
-    - path: output/abacas/test.abacas.gaps.tab
-      md5sum: 193024ec9e5a553573519b218eb06e29
-    - path: output/abacas/test.abacas.nucmer.delta
-    - path: output/abacas/test.abacas.nucmer.filtered.delta
-    - path: output/abacas/test.abacas.nucmer.tiling
-      md5sum: 0adaa0ce800d92c149a523d447148d95
-    - path: output/abacas/test.abacas.tab
-      md5sum: a5b9b452516f519a4201ff809655ef69
-    - path: output/abacas/test.abacas.unused.contigs.out
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/abacas/test.abacas.MULTIFASTA.fa
-      md5sum: 46c899ad70dcef8d14b5829fd8fbab82
diff --git a/tests/modules/abricate/run/main.nf b/tests/modules/abricate/run/main.nf
deleted file mode 100644
index 19d1f8a83e3..00000000000
--- a/tests/modules/abricate/run/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ABRICATE_RUN } from '../../../../modules/abricate/run/main.nf'
-
-workflow test_abricate_run {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
-    ]
-
-    ABRICATE_RUN ( input )
-}
diff --git a/tests/modules/abricate/run/test.yml b/tests/modules/abricate/run/test.yml
deleted file mode 100644
index 3377623ccc3..00000000000
--- a/tests/modules/abricate/run/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: abricate run
-  command: nextflow run tests/modules/abricate/run -entry test_abricate_run -c tests/config/nextflow.config
-  tags:
-    - abricate
-    - abricate/run
-  files:
-    - path: output/abricate/test.txt
-      md5sum: cd07e2953b127aed8d09bf1b2b903a1f
-    - path: output/abricate/versions.yml
-      md5sum: ae9cafaae96a644bb852e337aa7251f3
diff --git a/tests/modules/abricate/summary/main.nf b/tests/modules/abricate/summary/main.nf
deleted file mode 100644
index 9acbdba9bc6..00000000000
--- a/tests/modules/abricate/summary/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ABRICATE_RUN } from '../../../../modules/abricate/run/main.nf'
-include { ABRICATE_SUMMARY } from '../../../../modules/abricate/summary/main.nf'
-
-workflow test_abricate_summary {
-
-    inputs = [
-        tuple([ id:'test1', single_end:false ], // meta map
-              file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)),
-        tuple([ id:'test2', single_end:false ],
-              file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true))
-    ]
-
-    ABRICATE_RUN ( Channel.fromList(inputs) )
-    ABRICATE_SUMMARY ( 
-        ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
-    )
-}
diff --git a/tests/modules/abricate/summary/test.yml b/tests/modules/abricate/summary/test.yml
deleted file mode 100644
index abbd747be50..00000000000
--- a/tests/modules/abricate/summary/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: abricate summary
-  command: nextflow run tests/modules/abricate/summary -entry test_abricate_summary -c tests/config/nextflow.config
-  tags:
-    - abricate
-    - abricate/summary
-  files:
-    - path: output/abricate/test1.txt
-      md5sum: cd07e2953b127aed8d09bf1b2b903a1f
-    - path: output/abricate/test2.txt
-      md5sum: 69af3321b0bc808b7ef85f102395736f
-    - path: output/abricate/test_summary.txt
-      md5sum: a4ec7010e75404ce3a1033f0c4b4a7f9
-    - path: output/abricate/versions.yml
-      md5sum: a18f0471c49e5f25ec0b0c4ad5fab08e
diff --git a/tests/modules/adapterremoval/main.nf b/tests/modules/adapterremoval/main.nf
deleted file mode 100644
index a427bfbfc2c..00000000000
--- a/tests/modules/adapterremoval/main.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ADAPTERREMOVAL                            } from '../../../modules/adapterremoval/main.nf'
-include { ADAPTERREMOVAL as ADAPTERREMOVAL_COLLAPSE } from '../../../modules/adapterremoval/main.nf'
-
-
-workflow test_adapterremoval_single_end {
-    input = [ [ id:'test', single_end:true, collapse:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ]
-
-    ADAPTERREMOVAL ( input, [] )
-}
-
-workflow test_adapterremoval_paired_end {
-    input = [ [ id:'test', single_end:false, collapse:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    ADAPTERREMOVAL ( input, [] )
-}
-
-workflow test_adapterremoval_paired_end_collapse {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    ADAPTERREMOVAL_COLLAPSE ( input, [] )
-}
-
diff --git a/tests/modules/adapterremoval/test.yml b/tests/modules/adapterremoval/test.yml
deleted file mode 100644
index e660da767fe..00000000000
--- a/tests/modules/adapterremoval/test.yml
+++ /dev/null
@@ -1,45 +0,0 @@
-- name: adapterremoval test_adapterremoval_single_end
-  command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
-  tags:
-    - adapterremoval
-  files:
-    - path: output/adapterremoval/test.discarded.fastq.gz
-    - path: output/adapterremoval/test.settings
-      md5sum: 2fd3d5d703b63ba33a83021fccf25f77
-    - path: output/adapterremoval/test.truncated.fastq.gz
-      md5sum: 62139afee94defad5b83bdd0b8475a1f
-    - path: output/adapterremoval/versions.yml
-      md5sum: ac5b46719719b7ee62739530b80869fc
-
-- name: adapterremoval test_adapterremoval_paired_end
-  command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
-  tags:
-    - adapterremoval
-  files:
-    - path: output/adapterremoval/test.discarded.fastq.gz
-    - path: output/adapterremoval/test.settings
-      md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
-    - path: output/adapterremoval/test.pair1.truncated.fastq.gz
-      md5sum: 294a6277f0139bd597e57c6fa31f39c7
-    - path: output/adapterremoval/test.pair2.truncated.fastq.gz
-      md5sum: de7b38e2c881bced8671acb1ab452d78
-    - path: output/adapterremoval/versions.yml
-      md5sum: fa621c887897da5a379c719399c17db7
-
-- name: adapterremoval test_adapterremoval_paired_end_collapse
-  command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
-  tags:
-    - adapterremoval
-  files:
-    - path: output/adapterremoval/test.collapsed.fastq.gz
-      md5sum: ff956de3532599a56c3efe5369f0953f
-    - path: output/adapterremoval/test.collapsed.truncated.fastq.gz
-    - path: output/adapterremoval/test.discarded.fastq.gz
-    - path: output/adapterremoval/test.settings
-      md5sum: 7f0b2328152226e46101a535cce718b3
-    - path: output/adapterremoval/test.pair1.truncated.fastq.gz
-      md5sum: 683be19bc1c83008944b6b719bfa34e1
-    - path: output/adapterremoval/test.pair2.truncated.fastq.gz
-      md5sum: e6548fe061f3ef86368b26da930174d0
-    - path: output/adapterremoval/versions.yml
-      md5sum: 78f589bb313c8da0147ca8ce77d7f3bf
diff --git a/tests/modules/adapterremovalfixprefix/main.nf b/tests/modules/adapterremovalfixprefix/main.nf
deleted file mode 100644
index 863a7ca81db..00000000000
--- a/tests/modules/adapterremovalfixprefix/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ADAPTERREMOVAL          } from '../../../modules/adapterremoval/main.nf'
-include { ADAPTERREMOVALFIXPREFIX } from '../../../modules/adapterremovalfixprefix/main.nf'
-
-workflow test_adapterremovalfixprefix {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    ADAPTERREMOVAL ( input, [] )
-    ADAPTERREMOVALFIXPREFIX ( ADAPTERREMOVAL.out.collapsed )
-}
diff --git a/tests/modules/adapterremovalfixprefix/test.yml b/tests/modules/adapterremovalfixprefix/test.yml
deleted file mode 100644
index 4d4b72e7f8e..00000000000
--- a/tests/modules/adapterremovalfixprefix/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: adapterremovalfixprefix test_adapterremovalfixprefix
-  command: nextflow run tests/modules/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c tests/config/nextflow.config
-  tags:
-    - adapterremovalfixprefix
-  files:
-    - path: output/adapterremovalfixprefix/test.fq.gz
-      md5sum: ff956de3532599a56c3efe5369f0953f
diff --git a/tests/modules/agrvate/main.nf b/tests/modules/agrvate/main.nf
deleted file mode 100644
index ac682bef93f..00000000000
--- a/tests/modules/agrvate/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { AGRVATE } from '../../../modules/agrvate/main.nf'
-
-workflow test_agrvate {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    AGRVATE ( input )
-}
diff --git a/tests/modules/agrvate/test.yml b/tests/modules/agrvate/test.yml
deleted file mode 100644
index 36e8886c8d7..00000000000
--- a/tests/modules/agrvate/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: agrvate
-  command: nextflow run ./tests/modules/agrvate -entry test_agrvate -c ./tests/config/nextflow.config -c ./tests/modules/agrvate/nextflow.config
-  tags:
-    - agrvate
-  files:
-    - path: output/agrvate/genome-results/genome-summary.tab
-      md5sum: 781a9e5fc6ebc9f90ddfe8753d1633db
diff --git a/tests/modules/allelecounter/main.nf b/tests/modules/allelecounter/main.nf
deleted file mode 100644
index 3fe11be3f30..00000000000
--- a/tests/modules/allelecounter/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.enable.dsl = 2
-
-include { ALLELECOUNTER } from '../../../modules/allelecounter/main.nf'
-
-workflow test_allelecounter_bam {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-            ]
-    positions = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
-
-    ALLELECOUNTER ( input, positions, [] )
-}
-
-
-workflow test_allelecounter_cram {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
-            ]
-    positions = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
-    fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    ALLELECOUNTER ( input, positions, fasta )
-}
diff --git a/tests/modules/allelecounter/test.yml b/tests/modules/allelecounter/test.yml
deleted file mode 100644
index a0afbc1250a..00000000000
--- a/tests/modules/allelecounter/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: allelecounter test_allelecounter_bam
-  command: nextflow run ./tests/modules/allelecounter -entry test_allelecounter_bam -c ./tests/config/nextflow.config -c ./tests/modules/allelecounter/nextflow.config
-  tags:
-    - allelecounter
-  files:
-    - path: output/allelecounter/test.alleleCount
-      md5sum: 2bbe9d7331b78bdac30fe30dbc5fdaf3
-
-- name: allelecounter test_allelecounter_cram
-  command: nextflow run ./tests/modules/allelecounter -entry test_allelecounter_cram -c ./tests/config/nextflow.config -c ./tests/modules/allelecounter/nextflow.config
-  tags:
-    - allelecounter
-  files:
-    - path: output/allelecounter/test.alleleCount
-      md5sum: 2f83352a185168c7c98e9e42550b2856
diff --git a/tests/modules/ampir/main.nf b/tests/modules/ampir/main.nf
deleted file mode 100644
index bee2ff90631..00000000000
--- a/tests/modules/ampir/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { AMPIR } from '../../../modules/ampir/main.nf'
-
-workflow test_ampir {
-
-    fasta = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true),
-    ]
-
-    model = "precursor"
-
-    min_length = []
-
-    min_probability = "0.7"
-
-    AMPIR ( fasta, model, min_length, min_probability )
-}
diff --git a/tests/modules/ampir/test.yml b/tests/modules/ampir/test.yml
deleted file mode 100644
index 54921e9a32a..00000000000
--- a/tests/modules/ampir/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: ampir test_ampir
-  command: nextflow run ./tests/modules/ampir -entry test_ampir -c ./tests/config/nextflow.config  -c ./tests/modules/ampir/nextflow.config
-  tags:
-    - ampir
-  files:
-    - path: output/ampir/test.tsv
-      contains: ["seq_name\tseq_aa\tprob_AMP", "WP_014895017.1"]
-    - path: output/ampir/test.faa
-      md5sum: 0435609144022c55ac196db053f0df89
-    - path: output/ampir/versions.yml
-      md5sum: 4a11d25b8a904a7ffb34ae88f6826888
diff --git a/tests/modules/amplify/predict/main.nf b/tests/modules/amplify/predict/main.nf
deleted file mode 100644
index 05db4cdbfdf..00000000000
--- a/tests/modules/amplify/predict/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PRODIGAL } from '../../../modules/prodigal/main.nf' addParams( options: [:] )
-include { AMPLIFY_PREDICT } from '../../../../modules/amplify/predict/main.nf' addParams( options: [:] )
-
-workflow amplify_predict {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
-    ]
-    model_dir = []
-
-    PRODIGAL ( input, "gff" )
-    AMPLIFY_PREDICT ( PRODIGAL.out.amino_acid_fasta, model_dir)
-}
diff --git a/tests/modules/amplify/predict/test.yml b/tests/modules/amplify/predict/test.yml
deleted file mode 100644
index 3bc92889cea..00000000000
--- a/tests/modules/amplify/predict/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: amplify predict amplify_predict
-  command: nextflow run tests/modules/amplify/predict -entry amplify_predict -c tests/config/nextflow.config
-  tags:
-    - amplify/predict
-    - amplify
-  files:
-    - path: output/amplify/test.tsv
-      md5sum: 1951084ce1d410028be86754997e5852
-    - path: output/amplify/versions.yml
diff --git a/tests/modules/amps/main.nf b/tests/modules/amps/main.nf
deleted file mode 100644
index 7c4969e9bfe..00000000000
--- a/tests/modules/amps/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNZIP as UNZIP_MALT        } from '../../../modules/unzip/main.nf'
-include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/unzip/main.nf'
-include { MALT_BUILD  } from  '../../../modules/malt/build/main.nf'
-include { MALT_RUN    } from '../../../modules/malt/run/main.nf'
-include { MALTEXTRACT } from '../../../modules/maltextract/main.nf'
-include { AMPS        } from '../../../modules/amps/main.nf'
-
-
-workflow test_amps {
-
-    fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff = []
-    seq_type = "DNA"
-    map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    mode = "BlastN"
-    taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
-    ncbi_dir = [ [], file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true) ]
-
-    UNZIP_MALT ( map_db )
-    UNZIP_MALTEXTRACT ( ncbi_dir )
-    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive.map{ it[1] } )
-    MALT_RUN ( input, mode, MALT_BUILD.out.index )
-    ch_input_to_maltextract = MALT_RUN.out.rma6.map{ it[1] }
-    MALTEXTRACT ( ch_input_to_maltextract, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive.map{ it[1] })
-
-    AMPS ( MALTEXTRACT.out.results, taxon_list, filter )
-}
diff --git a/tests/modules/amps/test.yml b/tests/modules/amps/test.yml
deleted file mode 100644
index f38320e4bef..00000000000
--- a/tests/modules/amps/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: amps
-  command: nextflow run ./tests/modules/amps -entry test_amps -c ./tests/config/nextflow.config -c ./tests/modules/amps/nextflow.config
-  tags:
-    - amps
-  files:
-    - path: output/amps/results/heatmap_overview_Wevid.json
-      md5sum: 82f484d02a9e3d0cc3d5bcdcc2965e44
-    - path: output/amps/results/heatmap_overview_Wevid.pdf
-    - path: output/amps/results/heatmap_overview_Wevid.tsv
-      md5sum: 1a7d565a37ef4d6054f7ade63fbadc2f
-    - path: output/amps/results/pdf_candidate_profiles/Severe_acute_respiratory_syndrome_coronavirus_2/stp1_test_1.rma6_Severe_acute_respiratory_syndrome_coronavirus_2_summary.pdf
diff --git a/tests/modules/amrfinderplus/run/main.nf b/tests/modules/amrfinderplus/run/main.nf
deleted file mode 100644
index 917ac28d46c..00000000000
--- a/tests/modules/amrfinderplus/run/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { AMRFINDERPLUS_UPDATE } from '../../../../modules/amrfinderplus/update/main.nf'
-include { AMRFINDERPLUS_RUN } from '../../../../modules/amrfinderplus/run/main.nf'
-
-workflow test_amrfinderplus_run {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
-    ]
-
-    AMRFINDERPLUS_UPDATE ( )
-    AMRFINDERPLUS_RUN ( input, AMRFINDERPLUS_UPDATE.out.db )
-}
diff --git a/tests/modules/amrfinderplus/run/test.yml b/tests/modules/amrfinderplus/run/test.yml
deleted file mode 100644
index 0529fe13a3c..00000000000
--- a/tests/modules/amrfinderplus/run/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: amrfinderplus run test_amrfinderplus_run
-  command: nextflow run ./tests/modules/amrfinderplus/run -entry test_amrfinderplus_run -c ./tests/config/nextflow.config  -c ./tests/modules/amrfinderplus/run/nextflow.config
-  tags:
-    - amrfinderplus
-    - amrfinderplus/run
-  files:
-    - path: output/amrfinderplus/test.tsv
-      md5sum: b4d261ace9be7d013c19d1f5c0005bfe
diff --git a/tests/modules/amrfinderplus/update/main.nf b/tests/modules/amrfinderplus/update/main.nf
deleted file mode 100644
index f3a34ea0d72..00000000000
--- a/tests/modules/amrfinderplus/update/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { AMRFINDERPLUS_UPDATE } from '../../../../modules/amrfinderplus/update/main.nf'
-
-workflow test_amrfinderplus_update {
-
-    AMRFINDERPLUS_UPDATE ( )
-
-}
diff --git a/tests/modules/amrfinderplus/update/test.yml b/tests/modules/amrfinderplus/update/test.yml
deleted file mode 100644
index df26973b309..00000000000
--- a/tests/modules/amrfinderplus/update/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: amrfinderplus update test_amrfinderplus_update
-  command: nextflow run tests/modules/amrfinderplus/update -entry test_amrfinderplus_update -c tests/config/nextflow.config
-  tags:
-    - amrfinderplus
-    - amrfinderplus/update
-  files:
-    - path: output/amrfinderplus/amrfinderdb.tar.gz
diff --git a/tests/modules/angsd/docounts/main.nf b/tests/modules/angsd/docounts/main.nf
deleted file mode 100644
index 59e999f1a47..00000000000
--- a/tests/modules/angsd/docounts/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ANGSD_DOCOUNTS } from '../../../../modules/angsd/docounts/main.nf'
-
-workflow test_angsd_docounts {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true),
-        []
-    ]
-
-    ANGSD_DOCOUNTS ( input )
-}
diff --git a/tests/modules/angsd/docounts/test.yml b/tests/modules/angsd/docounts/test.yml
deleted file mode 100644
index 7b7a9e583b0..00000000000
--- a/tests/modules/angsd/docounts/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: angsd docounts test_angsd_docounts
-  command: nextflow run ./tests/modules/angsd/docounts -entry test_angsd_docounts -c ./tests/config/nextflow.config  -c ./tests/modules/angsd/docounts/nextflow.config
-  tags:
-    - angsd/docounts
-    - angsd
-  files:
-    - path: output/angsd/test.counts.gz
-      contains: ["ind0TotDepth"]
-    - path: output/angsd/test.icnts.gz
-    - path: output/angsd/test.pos.gz
-      contains: ["chr	pos	totDepth"]
diff --git a/tests/modules/antismash/antismashlite/main.nf b/tests/modules/antismash/antismashlite/main.nf
deleted file mode 100644
index 2b23c400ff2..00000000000
--- a/tests/modules/antismash/antismashlite/main.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ANTISMASH_ANTISMASHLITE                  } from '../../../../modules/antismash/antismashlite/main.nf'
-include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
-include { GUNZIP as GUNZIP1 } from '../../../../modules/gunzip/main.nf'
-include { GUNZIP as GUNZIP2 } from '../../../../modules/gunzip/main.nf'
-include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
-include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
-include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
-
-workflow test_antismashlite {
-    genome_fna = [
-        [ id:'test' ],
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
-    ]
-
-    genome_gff = [
-        [],
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_gff_gz'], checkIfExists: true)
-    ]
-
-    antismash_css = [
-        [],
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
-    ]
-
-    antismash_detection = [
-        [],
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
-    ]
-
-    antismash_modules = [
-        [],
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
-    ]
-
-    GUNZIP1 ( genome_fna )
-    GUNZIP2 ( genome_gff )
-    UNTAR1 ( antismash_css )
-    UNTAR2 ( antismash_detection )
-    UNTAR3 ( antismash_modules )
-    ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
-    ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, GUNZIP2.out.gunzip.map{ it[1] } )
-}
diff --git a/tests/modules/antismash/antismashlite/test.yml b/tests/modules/antismash/antismashlite/test.yml
deleted file mode 100644
index 4642319c362..00000000000
--- a/tests/modules/antismash/antismashlite/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: antismash antismashlite test_antismashlite
-  command: nextflow run tests/modules/antismash/antismashlite -entry test_antismashlite -c tests/config/nextflow.config
-  tags:
-    - antismash/antismashlite
-    - antismash
-  files:
-    - path: output/antismash/test/NZ_CP069563.1.region001.gbk
-      contains: ['/tool="antismash"']
-    - path: output/antismash/test/NZ_CP069563.1.region002.gbk
-      contains: ['/tool="antismash"']
-    - path: output/antismash/test/css/bacteria.css
-      md5sum: 8b3c2f8b143d5245a5f42f55803c532c
-    - path: output/antismash/test/genome.gbk
-      contains: ['/tool="antismash"']
-    - path: output/antismash/test/genome.json
-      contains: ['{"version": "6.0.1", "input_file": "genome.fna", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
-    - path: output/antismash/test/genome.zip
-    - path: output/antismash/test/index.html
-      md5sum: de787e865c3a1eec143a19d2facb4de4
-    - path: output/antismash/test/js/antismash.js
-      md5sum: 58e90c3d783ae014cc3d51849bcb50a2
-    - path: output/antismash/test/js/jquery.js
-      md5sum: 397754ba49e9e0cf4e7c190da78dda05
-    - path: output/antismash/test/js/jquery.tablesorter.min.js
-      md5sum: 5e9e08cef4d1be0eaa538e6eb28809a7
-    - path: output/antismash/test/regions.js
-      contains: ['"seq_id": "NZ_CP069563.1"']
-    - path: output/antismash/test/test.log
-      contains: ["antiSMASH version: 6.0.1"]
-    - path: output/antismash/versions.yml
-      md5sum: 759431a43da33e2ef8e2d0ebd79a439b
-    - path: output/gunzip1/genome.fna
-      md5sum: dafd38f5454b54fbea38245d773062a5
-    - path: output/gunzip2/genome.gff
-      md5sum: 9b9c848b1946d43fa68128f4d6316052
diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/main.nf b/tests/modules/antismash/antismashlitedownloaddatabases/main.nf
deleted file mode 100644
index d7289acc0c7..00000000000
--- a/tests/modules/antismash/antismashlitedownloaddatabases/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
-include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
-include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
-include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
-
-workflow test_antismash_antismashlitedownloaddatabases {
-    input1 = [
-        [],
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
-    ]
-    input2 = [
-        [],
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
-    ]
-    input3 = [
-        [],
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
-    ]
-
-    UNTAR1 ( input1 )
-    UNTAR2 ( input2 )
-    UNTAR3 ( input3 )
-
-    ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
-}
diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
deleted file mode 100644
index b4a964a0b9b..00000000000
--- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
-  command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
-  tags:
-    - antismash/antismashlitedownloaddatabases
-    - antismash
-  files:
-    - path: output/antismash/versions.yml
-      md5sum: 24859c67023abab99de295d3675a24b6
-    - path: output/antismash/antismash_db
-    - path: output/antismash/antismash_db/clusterblast
-    - path: output/antismash/antismash_db/clustercompare
-    - path: output/antismash/antismash_db/pfam
-    - path: output/antismash/antismash_db/resfam
-    - path: output/antismash/antismash_db/tigrfam
-    - path: output/antismash/antismash_dir
-    - path: output/antismash/antismash_dir/detection/hmm_detection/data/bgc_seeds.hmm
diff --git a/tests/modules/ariba/getref/main.nf b/tests/modules/ariba/getref/main.nf
deleted file mode 100644
index 8af67f74450..00000000000
--- a/tests/modules/ariba/getref/main.nf
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ARIBA_GETREF } from '../../../../modules/ariba/getref/main.nf'
-
-workflow test_ariba_getref {
-    ARIBA_GETREF ( "card" )
-}
diff --git a/tests/modules/ariba/getref/test.yml b/tests/modules/ariba/getref/test.yml
deleted file mode 100644
index 7fcef3f7668..00000000000
--- a/tests/modules/ariba/getref/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: ariba getref test_ariba_getref
-  command: nextflow run ./tests/modules/ariba/getref -entry test_ariba_getref -c ./tests/config/nextflow.config  -c ./tests/modules/ariba/getref/nextflow.config
-  tags:
-    - ariba
-    - ariba/getref
-  files:
-    - path: output/ariba/card.tar.gz
diff --git a/tests/modules/ariba/run/main.nf b/tests/modules/ariba/run/main.nf
deleted file mode 100644
index 02244d9d4ae..00000000000
--- a/tests/modules/ariba/run/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ARIBA_GETREF } from '../../../../modules/ariba/getref/main.nf'
-include { ARIBA_RUN } from '../../../../modules/ariba/run/main.nf'
-
-workflow test_ariba_run {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    ARIBA_GETREF ( "card" )
-    ARIBA_RUN ( input, ARIBA_GETREF.out.db)
-}
diff --git a/tests/modules/ariba/run/test.yml b/tests/modules/ariba/run/test.yml
deleted file mode 100644
index c43b878f15a..00000000000
--- a/tests/modules/ariba/run/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: ariba run test_ariba_run
-  command: nextflow run ./tests/modules/ariba/run -entry test_ariba_run -c ./tests/config/nextflow.config  -c ./tests/modules/ariba/run/nextflow.config
-  tags:
-    - ariba
-    - ariba/run
-  files:
-    - path: output/ariba/test/assembled_genes.fa.gz
-    - path: output/ariba/test/assembled_seqs.fa.gz
-    - path: output/ariba/test/assemblies.fa.gz
-    - path: output/ariba/test/debug.report.tsv
-      contains: ["ariba_ref_name", "reads", "free_text", "known_var_change"]
-    - path: output/ariba/test/report.tsv
-      contains: ["ariba_ref_name", "reads", "free_text", "known_var_change"]
-    - path: output/ariba/test/version_info.txt
-      contains: ["ARIBA", "Python", "OK", "True"]
diff --git a/tests/modules/arriba/main.nf b/tests/modules/arriba/main.nf
deleted file mode 100644
index 205adf0f3c0..00000000000
--- a/tests/modules/arriba/main.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STAR_GENOMEGENERATE   } from '../../../modules/star/genomegenerate/main.nf'
-include { STAR_ALIGN            } from '../../../modules/star/align/main.nf'
-include { ARRIBA                } from '../../../modules/arriba/main.nf'
-
-workflow test_arriba_single_end {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-                [   file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    star_ignore_sjdbgtf = false
-    seq_platform = 'illumina'
-    seq_center = false
-
-    STAR_GENOMEGENERATE ( fasta, gtf )
-    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf , [], [], [], [], [])
-}
-
-workflow test_arriba_paired_end {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                [   file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    star_ignore_sjdbgtf = false
-    seq_platform = 'illumina'
-    seq_center = false
-
-    STAR_GENOMEGENERATE ( fasta, gtf )
-    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf, [], [], [], [], [])
-}
diff --git a/tests/modules/arriba/test.yml b/tests/modules/arriba/test.yml
deleted file mode 100644
index bdeab128db8..00000000000
--- a/tests/modules/arriba/test.yml
+++ /dev/null
@@ -1,92 +0,0 @@
-- name: arriba test_arriba_single_end
-  command: nextflow run ./tests/modules/arriba -entry test_arriba_single_end -c ./tests/config/nextflow.config -c ./tests/modules/arriba/nextflow.config
-  tags:
-    - arriba
-  files:
-    - path: output/arriba/test.fusions.discarded.tsv
-      md5sum: 7602ab4ccbbb0c54fbca12a942877e6d
-    - path: output/arriba/test.fusions.tsv
-      md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
-    - path: output/star/star/Genome
-      md5sum: a654229fbca6071dcb6b01ce7df704da
-    - path: output/star/star/Log.out
-    - path: output/star/star/SA
-      md5sum: 8c3edc46697b72c9e92440d4cf43506c
-    - path: output/star/star/SAindex
-      md5sum: 9f085c626553b1c52f2827421972ac10
-    - path: output/star/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/star/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/star/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/star/star/chrStart.txt
-      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
-    - path: output/star/star/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/star/star/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/star/star/geneInfo.tab
-      md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/star/star/genomeParameters.txt
-      md5sum: 9e42067b1ec70b773257529230dd7b3a
-    - path: output/star/star/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/star/star/sjdbList.fromGTF.out.tab
-      md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/star/star/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/star/star/transcriptInfo.tab
-      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
-    - path: output/star/test.Aligned.out.bam
-      md5sum: e6f850505492f1c7d47bb1ad05fddbfd
-    - path: output/star/test.Log.final.out
-    - path: output/star/test.Log.out
-    - path: output/star/test.Log.progress.out
-    - path: output/star/test.SJ.out.tab
-
-- name: arriba test_arriba_paired_end
-  command: nextflow run ./tests/modules/arriba -entry test_arriba_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/arriba/nextflow.config
-  tags:
-    - arriba
-  files:
-    - path: output/arriba/test.fusions.discarded.tsv
-      md5sum: 445cb87a27f063e751f93498cf8d10b5
-    - path: output/arriba/test.fusions.tsv
-      md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
-    - path: output/star/star/Genome
-      md5sum: a654229fbca6071dcb6b01ce7df704da
-    - path: output/star/star/Log.out
-    - path: output/star/star/SA
-      md5sum: 8c3edc46697b72c9e92440d4cf43506c
-    - path: output/star/star/SAindex
-      md5sum: 9f085c626553b1c52f2827421972ac10
-    - path: output/star/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/star/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/star/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/star/star/chrStart.txt
-      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
-    - path: output/star/star/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/star/star/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/star/star/geneInfo.tab
-      md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/star/star/genomeParameters.txt
-      md5sum: 9e42067b1ec70b773257529230dd7b3a
-    - path: output/star/star/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/star/star/sjdbList.fromGTF.out.tab
-      md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/star/star/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/star/star/transcriptInfo.tab
-      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
-    - path: output/star/test.Aligned.out.bam
-    - path: output/star/test.Log.final.out
-    - path: output/star/test.Log.out
-    - path: output/star/test.Log.progress.out
-    - path: output/star/test.SJ.out.tab
diff --git a/tests/modules/artic/guppyplex/main.nf b/tests/modules/artic/guppyplex/main.nf
deleted file mode 100644
index 89f67c746ee..00000000000
--- a/tests/modules/artic/guppyplex/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ARTIC_GUPPYPLEX } from '../../../../modules/artic/guppyplex/main.nf'
-
-process STAGE_FASTQ_DIR {
-    input:
-    tuple val(meta), path(fastq_file)
-
-    output:
-    tuple val(meta), path('fastq'), emit: fastq_dir
-
-    script:
-    """
-    mkdir fastq
-    mv ${fastq_file} fastq
-    """
-}
-
-workflow test_artic_guppyplex {
-
-    input =  [ [ id:'test' ],
-               file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
-
-    STAGE_FASTQ_DIR ( input )
-
-    ARTIC_GUPPYPLEX ( STAGE_FASTQ_DIR.out.fastq_dir )
-}
diff --git a/tests/modules/artic/guppyplex/test.yml b/tests/modules/artic/guppyplex/test.yml
deleted file mode 100644
index 6fd10898533..00000000000
--- a/tests/modules/artic/guppyplex/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: artic guppyplex
-  command: nextflow run ./tests/modules/artic/guppyplex -entry test_artic_guppyplex -c ./tests/config/nextflow.config -c ./tests/modules/artic/guppyplex/nextflow.config
-  tags:
-    - artic
-    - artic/guppyplex
-  files:
-    - path: output/artic/test.fastq.gz
diff --git a/tests/modules/artic/minion/main.nf b/tests/modules/artic/minion/main.nf
deleted file mode 100644
index b70b549e3f0..00000000000
--- a/tests/modules/artic/minion/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR        } from '../../../../modules/untar/main.nf'
-include { ARTIC_MINION } from '../../../../modules/artic/minion/main.nf'
-
-workflow test_artic_minion {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
-    ]
-    fast5_tar          = [ [], file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true) ]
-    sequencing_summary = file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true)
-    fasta              = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true)
-    bed                = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true)
-
-    fast5_dir = UNTAR ( fast5_tar ).untar.map{ it[1] }
-
-    ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, [], '', 'nCoV-2019', '3')
-}
diff --git a/tests/modules/artic/minion/test.yml b/tests/modules/artic/minion/test.yml
deleted file mode 100644
index c8ad52d720f..00000000000
--- a/tests/modules/artic/minion/test.yml
+++ /dev/null
@@ -1,260 +0,0 @@
-- name: artic minion
-  command: nextflow run ./tests/modules/artic/minion -entry test_artic_minion -c ./tests/config/nextflow.config -c ./tests/modules/artic/minion/nextflow.config
-  tags:
-    - artic
-    - artic/minion
-  files:
-    - path: output/artic/test.1.vcf
-      md5sum: f0278719cbb853addcad74b73d810a24
-    - path: output/artic/test.2.vcf
-      md5sum: f0278719cbb853addcad74b73d810a24
-    - path: output/artic/test.alignreport.er
-      md5sum: ddfff35c7ebc9837530c78f7a213cea0
-    - path: output/artic/test.alignreport.txt
-      md5sum: 0fcadf1467ac253476b2d43bbfa36616
-    - path: output/artic/test.consensus.fasta
-      md5sum: 60ace9fea33aca4c13f3502e330bff85
-    - path: output/artic/test.coverage_mask.txt
-      md5sum: 7abd414756c444c86766123a60687ed1
-    - path: output/artic/test.coverage_mask.txt.1.depths
-      md5sum: d4170a48491e12f34b0a15a336bdf5e6
-    - path: output/artic/test.coverage_mask.txt.2.depths
-      md5sum: 130f85d80c22fccc3e0bbd9de12d310d
-    - path: output/artic/test.fail.vcf
-      md5sum: e6e184f1fa153868e3acea0eab42e484
-    - path: output/artic/test.fastq.gz.index
-      md5sum: eaa2b34db5a53fb2d410c5b3bf857fd9
-    - path: output/artic/test.fastq.gz.index.fai
-      md5sum: 81d718eeaaaae68cb33003f56194e956
-    - path: output/artic/test.fastq.gz.index.gzi
-      md5sum: 7dea362b3fac8e00956a4952a3d4f474
-    - path: output/artic/test.fastq.gz.index.readdb
-      md5sum: 3c6296842e91578db93688b4021c8947
-    - path: output/artic/test.merged.vcf
-      md5sum: e6e184f1fa153868e3acea0eab42e484
-    - path: output/artic/test.minion.log.txt
-      contains:
-        - "artic_vcf_merge"
-    - path: output/artic/test.muscle.in.fasta
-      md5sum: 40ae4c89de797d1548c642f0da7a86cc
-    - path: output/artic/test.muscle.out.fasta
-      md5sum: 40ae4c89de797d1548c642f0da7a86cc
-    - path: output/artic/test.pass.vcf.gz
-      md5sum: baeafcfc2f738cce771ba895d66e9e01
-    - path: output/artic/test.pass.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/artic/test.preconsensus.fasta
-      md5sum: 12b16397bae7c68d38150571a6ac6185
-    - path: output/artic/test.primers.vcf
-      md5sum: e6e184f1fa153868e3acea0eab42e484
-    - path: output/artic/test.primersitereport.txt
-    - path: output/artic/test.primertrimmed.rg.sorted.bam
-    - path: output/artic/test.primertrimmed.rg.sorted.bam.bai
-      md5sum: 0d76977b2e36046cc176112776c5fa4e
-    - path: output/artic/test.sorted.bam
-      md5sum: 292611ae9885df12575b80853cb5508b
-    - path: output/artic/test.sorted.bam.bai
-      md5sum: 0d76977b2e36046cc176112776c5fa4e
-    - path: output/artic/test.trimmed.rg.sorted.bam
-    - path: output/artic/test.trimmed.rg.sorted.bam.bai
-      md5sum: 0d76977b2e36046cc176112776c5fa4e
-    - path: output/untar/fast5/100read_fast5/00068f7a-51b3-4933-8fc6-7d6e29181ff9.fast5
-      md5sum: b7aeb3cc877d858f97144d45551264bc
-    - path: output/untar/fast5/100read_fast5/001ed67f-906f-4f37-9770-85d40f5ffee6.fast5
-      md5sum: add9b8658095173f7cef6fc23236d913
-    - path: output/untar/fast5/100read_fast5/0043238c-3a78-48f1-a8ec-d492280da6e4.fast5
-      md5sum: 11d83db48d3b284017b919d476e44294
-    - path: output/untar/fast5/100read_fast5/004a65aa-6700-4ad7-9550-dc59f8708908.fast5
-      md5sum: fb9f124a05af59ea3ede371cd48e404c
-    - path: output/untar/fast5/100read_fast5/00c6481f-9022-4173-9b74-f375c34b9a9b.fast5
-      md5sum: c186053a4fee2d509e1d108be8e131e1
-    - path: output/untar/fast5/100read_fast5/00da3999-12fd-449d-bd07-32a879667a3d.fast5
-      md5sum: ec051e5ce357d632ff740a88087a08fd
-    - path: output/untar/fast5/100read_fast5/018c4b52-48fa-4cc8-a7b4-500f41420279.fast5
-      md5sum: 9d5bae9c9df0105b3b329777977d6f34
-    - path: output/untar/fast5/100read_fast5/01faaaa1-eca2-4bcd-8666-b4d69497107e.fast5
-      md5sum: 5855c80a192a242f03a93b74f12dfa46
-    - path: output/untar/fast5/100read_fast5/02085a68-dc6e-4275-bd1e-f112fed3bd83.fast5
-      md5sum: 6b30e06080aab94b6fa8f476e537f3d2
-    - path: output/untar/fast5/100read_fast5/022647b9-0e16-4318-a794-c5749705b67d.fast5
-      md5sum: 6606f2661a5463772f4ee30a3dba520e
-    - path: output/untar/fast5/100read_fast5/022fc908-aa6e-4d29-a5ad-6a30a9da7e3b.fast5
-      md5sum: 53d611cf6465ef914392c11b88339ba0
-    - path: output/untar/fast5/100read_fast5/02445dc2-39ee-49f1-8a42-51ebfea52c33.fast5
-      md5sum: f7c5844165cbc0566ce1569184fc4213
-    - path: output/untar/fast5/100read_fast5/031ff99b-b11f-40dc-9258-273ec97683f8.fast5
-      md5sum: e78faae6230537a20497d3114cffcafd
-    - path: output/untar/fast5/100read_fast5/03e0e732-cb7a-4084-8fc9-303180c83786.fast5
-      md5sum: 27c8ce19a0955d045053a6925e249ae4
-    - path: output/untar/fast5/100read_fast5/0457184e-6e09-4883-baf3-824d11101c43.fast5
-      md5sum: 7a89c45ae6b360bc585c8b14196ab3f7
-    - path: output/untar/fast5/100read_fast5/045f1e6a-9b5d-4840-bad9-c4b738b61267.fast5
-      md5sum: ee0c3e5fa1f6820968482594f45e8948
-    - path: output/untar/fast5/100read_fast5/046258fa-b951-43a1-bbed-66cdbeac8e71.fast5
-      md5sum: 262d3ee396bab6014505b25ba88cea90
-    - path: output/untar/fast5/100read_fast5/048d5d3a-16ed-4f36-aeb9-3311dd9dc593.fast5
-      md5sum: deea9c03b10aa287f873779baea2a649
-    - path: output/untar/fast5/100read_fast5/04a0ee1e-0406-4394-87ba-a67344318a5d.fast5
-      md5sum: 7f43a0e0de0053a63a28e36374ec20b4
-    - path: output/untar/fast5/100read_fast5/04c07133-cd56-48b9-9f16-86e12cacaf92.fast5
-      md5sum: d607992919072ddb025d766d8ba1a465
-    - path: output/untar/fast5/100read_fast5/052036a3-6af0-4650-9f96-e97e34c52bbc.fast5
-      md5sum: 22ccc03bee288edfc589d5f4b11cb70d
-    - path: output/untar/fast5/100read_fast5/0562aebd-b55b-4752-83eb-12323938c242.fast5
-      md5sum: 1668668f2d0658a6e3417b08ea093c43
-    - path: output/untar/fast5/100read_fast5/0565fd27-4849-4d14-83ff-2864dc3e109e.fast5
-      md5sum: 649ff949e10052b877d9ddb7d6a19009
-    - path: output/untar/fast5/100read_fast5/05f48799-d4ca-4f54-90e2-de208c0c1711.fast5
-      md5sum: 5bddb9c020ddd233adc399c806186af6
-    - path: output/untar/fast5/100read_fast5/064b4a28-a036-46cb-b466-62b8486de288.fast5
-      md5sum: 4f0d1d5400caa14c376c5c2ba5cf4e90
-    - path: output/untar/fast5/100read_fast5/064ef037-67eb-49a4-9a72-e2b2e34cfe5c.fast5
-      md5sum: e8420b20501c06a31223204611aacd44
-    - path: output/untar/fast5/100read_fast5/066c72de-139a-4514-aef9-36cc3927a2c6.fast5
-      md5sum: f703f4942aaa470e2d00706687cea430
-    - path: output/untar/fast5/100read_fast5/069ce6e7-41b9-41b2-a6d8-8d39c16dbaa2.fast5
-      md5sum: 4ef4d47bf346c9cca805e991a6f5400b
-    - path: output/untar/fast5/100read_fast5/06f0339b-75b5-4926-b1a7-878818b5fe67.fast5
-      md5sum: 163a97396e5cf91c40fab7432f52d101
-    - path: output/untar/fast5/100read_fast5/074ebef4-edbd-4d2a-af6c-46512693a990.fast5
-      md5sum: da9798ae314dca12f69ef45c10c8a5a7
-    - path: output/untar/fast5/100read_fast5/08239d1b-1710-4187-b96e-da861a0e4624.fast5
-      md5sum: 8ff2a720e61c52a29e2863d68f84c917
-    - path: output/untar/fast5/100read_fast5/084af0ac-0334-4840-a3a5-3ff62464ae71.fast5
-      md5sum: 3c2f27f6c21eefa53eafaa70252f9f49
-    - path: output/untar/fast5/100read_fast5/08db75dc-49a9-459d-afc8-5ed1d8e47901.fast5
-      md5sum: 6f25bb694f859d53b9dfd4047610d97f
-    - path: output/untar/fast5/100read_fast5/091fba78-028e-4ed2-a799-35e9ba64541c.fast5
-      md5sum: 58da6a195dad9cb15fb5ebb76f9ecd19
-    - path: output/untar/fast5/100read_fast5/094a4c34-c97b-4b83-bd02-1f69e6ccadc0.fast5
-      md5sum: adfb65496a10bae743e3f0e144220b43
-    - path: output/untar/fast5/100read_fast5/09b7f97c-fb32-4a4a-84d9-c45dfc2b46d0.fast5
-      md5sum: fcce7b510edcf012eae95662370d663c
-    - path: output/untar/fast5/100read_fast5/0a30e10c-26b5-4c23-a7ee-493e7b3ebffb.fast5
-      md5sum: fd730b0b9e01a9ce3a0a4f7b39ee838e
-    - path: output/untar/fast5/100read_fast5/0a86654b-30ec-4271-9882-b490de473b5e.fast5
-      md5sum: 9114d618e2713681e7db42932d4b5e92
-    - path: output/untar/fast5/100read_fast5/0a92fbf4-99b4-40cd-98e7-93cfbddeb35e.fast5
-      md5sum: 516a3d935f9cef2abf4eb0a781ba8d19
-    - path: output/untar/fast5/100read_fast5/0af92aee-911c-4402-ba14-ecaabdb73548.fast5
-      md5sum: ccbcd71ecb9a46bd2b657f2e2c11354a
-    - path: output/untar/fast5/100read_fast5/0b168ee0-74c4-494d-a593-a4b4b538a9cb.fast5
-      md5sum: 9f8abf45b60ac800d4195e79bad26ea1
-    - path: output/untar/fast5/100read_fast5/0b8b3929-730d-42a6-84e0-5689b7439c71.fast5
-      md5sum: 1d03a26a58ec0668a1c54cc38fb65c3a
-    - path: output/untar/fast5/100read_fast5/0bb9f17c-3b8f-486d-ac03-6550199a0a49.fast5
-      md5sum: b713ea7f1cd45b5f5041a3a97e87106d
-    - path: output/untar/fast5/100read_fast5/0c5e39bf-e1c5-4208-b110-9a00b55132e4.fast5
-      md5sum: 31e32600bbf9b3523233260868468b00
-    - path: output/untar/fast5/100read_fast5/0cc2613c-9ade-4ec9-96c7-07ab2820bbd7.fast5
-      md5sum: f84eb9bf15a0af603b9f656fb469f305
-    - path: output/untar/fast5/100read_fast5/0cc85c6c-ed86-422e-a093-d2b81089cc6b.fast5
-      md5sum: 536ad1a1c1f8e5c17d8183c7950034a0
-    - path: output/untar/fast5/100read_fast5/0d448640-aa67-4e58-9ce8-004ca23b0412.fast5
-      md5sum: c97a3ae4fcb9123ea4ca89e8a6e391af
-    - path: output/untar/fast5/100read_fast5/0dad8e5f-77e3-4fd1-b569-b06f5b87d8c3.fast5
-      md5sum: 1225db8f9879447708aa85f8a096aafb
-    - path: output/untar/fast5/100read_fast5/0dd4696c-a7dd-4e3a-9ce5-37a258b45373.fast5
-      md5sum: 361426f4430ad8edadae17ab4ddfd7cf
-    - path: output/untar/fast5/100read_fast5/0e5018bc-45fc-40d4-8806-e22e07a915d0.fast5
-      md5sum: f21cba587246cf4c9e0db4f4914db634
-    - path: output/untar/fast5/100read_fast5/0e51c070-d577-4293-8389-bd34fdda9eac.fast5
-      md5sum: e426287a64d0fe356878673c7990e457
-    - path: output/untar/fast5/100read_fast5/0e5ff4de-814b-4ee2-bf8f-3291b8bbdaae.fast5
-      md5sum: a2429274097a3762eb8fd9290208e35d
-    - path: output/untar/fast5/100read_fast5/0f06cd06-1136-4b10-b248-cd4324f6de22.fast5
-      md5sum: 4ddea20115ae9875bff711cb0f2cbcd3
-    - path: output/untar/fast5/100read_fast5/0f3ca011-bb96-4fe2-92e2-31b0bac90d97.fast5
-      md5sum: df29e75d7a273d3b6a75e807a814993a
-    - path: output/untar/fast5/100read_fast5/0f7db51f-ff49-45ea-b58a-9fb58daf249d.fast5
-      md5sum: 671423af2189b08850eaab29b42566ca
-    - path: output/untar/fast5/100read_fast5/0fd3ec80-6fb4-4378-bdb6-df4f84951049.fast5
-      md5sum: 7376ee3f340c041afda6bbd2c3df353f
-    - path: output/untar/fast5/100read_fast5/10361e9b-159a-447d-8cf0-1976515f00f4.fast5
-      md5sum: f73c994cb9b6ec891ea936c54aa2f7a2
-    - path: output/untar/fast5/100read_fast5/10508138-2f5e-4405-99f4-46af4452893c.fast5
-      md5sum: c6a0b38fcd5a4be72793b43149ba04be
-    - path: output/untar/fast5/100read_fast5/10ac42d4-2818-48f6-9d67-1c3019fde890.fast5
-      md5sum: 5e5ae354e0aa8f985f5e5e8bd811eb73
-    - path: output/untar/fast5/100read_fast5/10f98781-e47e-43c3-9006-6d73963ee710.fast5
-      md5sum: 93f6e790fc41c1e266b1c4b18f2ab0ee
-    - path: output/untar/fast5/100read_fast5/1147d9c6-c190-47e6-8007-2e0f18d88f2b.fast5
-      md5sum: 15fbf533ac4a98124cb043abef23d0ba
-    - path: output/untar/fast5/100read_fast5/11e4024c-1997-4372-b1d7-4c884cf58047.fast5
-      md5sum: 788bb232b0b3b059a7f39a72c1f8d1e5
-    - path: output/untar/fast5/100read_fast5/11e944d1-a2c9-409c-ac72-9c1563443df7.fast5
-      md5sum: 31975cf5048b6af550f14b1e217a8f5d
-    - path: output/untar/fast5/100read_fast5/123114b2-247c-4abc-be0c-3a94f02043a2.fast5
-      md5sum: 633689761b59db120dcc5d560587416c
-    - path: output/untar/fast5/100read_fast5/1294c94b-1dac-4c4c-9c36-e8e8996e7f09.fast5
-      md5sum: 161fc1cb25ce05775f81e778f5bb8e93
-    - path: output/untar/fast5/100read_fast5/12ac7997-50bc-4183-95c4-e953ad4eaad1.fast5
-      md5sum: 4a3a4966ede5f0251a65c93c99a66eeb
-    - path: output/untar/fast5/100read_fast5/13265c3e-bbb3-4ebe-b4db-9fbb4bdaff01.fast5
-      md5sum: ad799b6a66cb2d8c08acbf232c23bf49
-    - path: output/untar/fast5/100read_fast5/1377f442-7e38-4c3f-aacb-e8049ad884fe.fast5
-      md5sum: f202ebf7b46bf289b9b1d9e82d8e96db
-    - path: output/untar/fast5/100read_fast5/137cae6b-0009-4ee2-8a0e-7a2e88179c16.fast5
-      md5sum: 6afbc7da1554e1d5328f6e47cc086772
-    - path: output/untar/fast5/100read_fast5/139c8fcc-8dcb-4cf7-aa52-632718587fe7.fast5
-      md5sum: 6aade40bab37e9a4fe008d21732c6790
-    - path: output/untar/fast5/100read_fast5/13bc3b77-a88e-44b9-b119-cd56aa972f61.fast5
-      md5sum: 1d668e59bc724ce47d17f2a4850a9b43
-    - path: output/untar/fast5/100read_fast5/13dbd26f-978f-49ad-9ae6-ca909083b6ce.fast5
-      md5sum: 2106344b03e8b834c20fef4406cf2aa6
-    - path: output/untar/fast5/100read_fast5/151bd13c-c12f-41a6-be02-e97e70a57814.fast5
-      md5sum: 8718a5b883496cde586dbbb256f13bb2
-    - path: output/untar/fast5/100read_fast5/16325928-3440-4a49-94c5-a93b4f6da961.fast5
-      md5sum: da871b8be0d502e05ba6b105f9bd4673
-    - path: output/untar/fast5/100read_fast5/16d9892d-bead-4a6f-b6c5-736c6f602fc1.fast5
-      md5sum: b7844e2a38c120fad74dec350dfd8adf
-    - path: output/untar/fast5/100read_fast5/1721053e-98f4-47a1-ab93-f75bc1c03c79.fast5
-      md5sum: 839e7a9335d54c6dd185a1a9486d9b9e
-    - path: output/untar/fast5/100read_fast5/1730fabf-f1ac-4a02-aa2e-21dcd14fed00.fast5
-      md5sum: ee53b732d0c4dd87dd8742cf4346b311
-    - path: output/untar/fast5/100read_fast5/1783d96c-3955-4405-b765-472c6286be46.fast5
-      md5sum: 6bcbda04b219c8bf971253cc2423a527
-    - path: output/untar/fast5/100read_fast5/180da5c9-4574-48ab-8e6a-8f8a73767e30.fast5
-      md5sum: 8ef4d3255d87a6fb0fa24b621b72e75a
-    - path: output/untar/fast5/100read_fast5/1870a88c-439f-4125-a06c-38b1bf4416e4.fast5
-      md5sum: 62db261bbc152a16b0d910680202ba8a
-    - path: output/untar/fast5/100read_fast5/188b5eae-fce2-439c-b490-aff6c4327499.fast5
-      md5sum: c3157f03f56d03820726ff8ff981b8c9
-    - path: output/untar/fast5/100read_fast5/18cef30b-9fe5-40b4-9094-0389bb5aeb8e.fast5
-      md5sum: 9fc63db9ca59ac6ff6fa15cfe55b3106
-    - path: output/untar/fast5/100read_fast5/18ee103f-1cf8-4694-b2e7-ac228fe70ccd.fast5
-      md5sum: 24dc02b54e6712c583f5977bce1d3cd3
-    - path: output/untar/fast5/100read_fast5/190a9ebe-4d5f-43c0-a495-82ff58944d07.fast5
-      md5sum: 489aa874a1c7c0603076f7ef359d6ace
-    - path: output/untar/fast5/100read_fast5/190c4417-c4cf-40fe-a0df-db4b495a3f77.fast5
-      md5sum: 997a74664ddab756907435890465d554
-    - path: output/untar/fast5/100read_fast5/1a0c9927-e355-49c3-877a-e6b95bc1a402.fast5
-      md5sum: fdc9f5f461d0e30ad29cf84e03b6c18d
-    - path: output/untar/fast5/100read_fast5/1a276f1c-5a5b-4ed2-b071-87f59f7c5233.fast5
-      md5sum: 6269d04009267b7e0df724d7ce355346
-    - path: output/untar/fast5/100read_fast5/1a5c9192-aded-4e94-8dcb-9c04a402978e.fast5
-      md5sum: 78ce5c5d770d7905bc1986203d69ed49
-    - path: output/untar/fast5/100read_fast5/1af84d7e-8fc6-4dba-8750-a0d701f36d1d.fast5
-      md5sum: ed5970f92ecdcce95f84dbb1bd275b8e
-    - path: output/untar/fast5/100read_fast5/1b753736-87b1-4753-ab1d-bfd7e2d94e9e.fast5
-      md5sum: 6b5a2fd8b445d4e43eef6d8597932d88
-    - path: output/untar/fast5/100read_fast5/1b760e8d-7b17-47e0-ba96-5755fc4ddd63.fast5
-      md5sum: 43eb9e8276e9d0870a4c74882d42e5a0
-    - path: output/untar/fast5/100read_fast5/1b86544f-8075-46a2-91f4-baac36216ac2.fast5
-      md5sum: d6266147405391c00aa4dc0ad6797532
-    - path: output/untar/fast5/100read_fast5/1bd0dad7-1600-44a2-90b8-d5cd7b7caa6d.fast5
-      md5sum: 863226172b856834a779eb2013c3a765
-    - path: output/untar/fast5/100read_fast5/1d568051-bdd6-4204-ac34-97b5a3f7375c.fast5
-      md5sum: 7d4cdf29110898e5f6a3288a0a2b9342
-    - path: output/untar/fast5/100read_fast5/1d650a9e-4e67-456a-9abe-bd34b238abe4.fast5
-      md5sum: 3fac1d13ed49703e33e92b8aaab3dac6
-    - path: output/untar/fast5/100read_fast5/1d86c2b3-c2c6-43a1-97ed-8c1f0cbf6476.fast5
-      md5sum: 2eed32c760d94aac2dce49c2364f6cd9
-    - path: output/untar/fast5/100read_fast5/20586d1a-2cd0-45aa-abc2-04ac66d8ea46.fast5
-      md5sum: d89ef1d32a52fc5d45a17d7682e4de22
-    - path: output/untar/fast5/100read_fast5/206626c5-ccf2-4927-9987-164f627bdede.fast5
-      md5sum: 045d9fdb48f0b58456c7012b735c8101
-    - path: output/untar/fast5/100read_fast5/2109d790-67ec-4fd1-8931-6c7e61908ff3.fast5
-      md5sum: 623d2e3213f0423e33b7993d803e4ae5
-    - path: output/untar/fast5/100read_fast5/2166cca5-c0ab-49eb-aec1-fec09bdfbd83.fast5
-      md5sum: 54ac4ec12232104381d2dcd619c9b4be
diff --git a/tests/modules/ascat/main.nf b/tests/modules/ascat/main.nf
deleted file mode 100644
index 83b5eeb84b6..00000000000
--- a/tests/modules/ascat/main.nf
+++ /dev/null
@@ -1,113 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ASCAT as ASCAT_SIMPLE }            from '../../../modules/ascat/main.nf'
-include { ASCAT as ASCAT_PLOIDY_AND_PURITY } from '../../../modules/ascat/main.nf'
-include { ASCAT as ASCAT_CRAM }              from '../../../modules/ascat/main.nf'
-include { UNZIP as UNZIP_ALLELES }           from '../../../modules/unzip/main.nf'
-include { UNZIP as UNZIP_LOCI }              from '../../../modules/unzip/main.nf'
-include { UNZIP as UNZIP_GC }                from '../../../modules/unzip/main.nf'
-include { UNZIP as UNZIP_RT }                from '../../../modules/unzip/main.nf'
-
-
-
-workflow test_ascat {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-
-    ASCAT_SIMPLE ( input , [], [], [], [], [], [])
-}
-
-// extended tests running with 1000 genomes data. Data is downloaded as follows:
-// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
-// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
-// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
-// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
-
-// workflow test_ascat_with_ploidy_and_purity {
-//     input = [ [ id:'test', single_end:false ], // meta map
-//             file("/mnt/volume/ascat/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true),
-//             file("/mnt/volume/ascat/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true),
-//             file("/mnt/volume/ascat/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true),
-//             file("/mnt/volume/ascat/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true)
-//     ]
-
-//     allele_path  = file("/mnt/volume/repos/modules/test_ascat2/G1000_alleles_hg19.zip", checkIfExists: true)
-//     allele_files = [[ id: allele_path.BaseName ], allele_path  ]
-
-//     loci_path    = file("/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip", checkIfExists: true)
-//     loci_files   = [[ id: loci_path.BaseName ], loci_path  ]
-
-//     gc_path      = file("/mnt/volume/repos/modules/test_ascat2/GC_G1000_hg19.zip", checkIfExists: true)
-//     gc_file      = [[ id: gc_path.BaseName ], gc_path  ]
-
-//     rt_path     = file("/mnt/volume/repos/modules/test_ascat2/RT_G1000_hg19.zip", checkIfExists: true)
-//     rt_file     = [[ id: rt_path.BaseName ], rt_path  ]
-
-//     UNZIP_ALLELES(allele_files)
-//     UNZIP_LOCI(loci_files)
-//     UNZIP_GC(gc_file)
-
-//     ASCAT_PLOIDY_AND_PURITY ( input ,
-//                                 UNZIP_ALLELES.out.unzipped_archive.map{ it[1] },
-//                                 UNZIP_LOCI.out.unzipped_archive.map{ it[1] },
-//                                 [],                                             // optional bed_file for WES
-//                                 [],                                             // optional fasta
-//                                 UNZIP_GC.out.unzipped_archive.map{ it[1] },     // optional GC_correction
-//                                 [])     // optional RT_correction
-
-//
-
-// }
-
-// extended tests running with 1000 genomes data. Data is downloaded as follows:
-// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
-// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
-// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
-// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
-// workflow test_ascat_with_crams {
-//     input = [
-//        [ id:'test', single_end:false ], // meta map
-//         file("/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true),
-//         file("/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true),
-//         file("/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true),
-//         file("/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true)
-//     ]
-
-//     allele_path  = file("/mnt/volume/repos/modules/test_ascat2/G1000_alleles_hg19.zip", checkIfExists: true)
-//     allele_files = [[ id: allele_path.BaseName ], allele_path  ]
-
-//     loci_path    = file("/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip", checkIfExists: true)
-//     loci_files   = [[ id: loci_path.BaseName ], loci_path  ]
-
-//     gc_path      = file("/mnt/volume/repos/modules/test_ascat2/GC_G1000_hg19.zip", checkIfExists: true)
-//     gc_file      = [[ id: gc_path.BaseName ], gc_path  ]
-
-//     rt_path     = file("/mnt/volume/repos/modules/test_ascat2/RT_G1000_hg19.zip", checkIfExists: true)
-//     rt_file     = [[ id: rt_path.BaseName ], rt_path  ]
-
-//     fasta   = file("/mnt/volume/ascat/human_g1k_v37.fasta", checkIfExists: true)
-
-//     UNZIP_ALLELES(allele_files)
-//     UNZIP_LOCI(loci_files)
-//     UNZIP_GC(gc_file)
-//     UNZIP_RT(rt_file)
-
-//     ASCAT_CRAM ( input ,
-//                 UNZIP_ALLELES.out.unzipped_archive.map{ it[1] },
-//                 UNZIP_LOCI.out.unzipped_archive.map{ it[1] },
-//                 [],
-//                 fasta,
-//                 UNZIP_GC.out.unzipped_archive.map{ it[1] },
-//                 UNZIP_RT.out.unzipped_archive.map{ it[1] })
-
-// }
-
-
-
diff --git a/tests/modules/ascat/test.yml b/tests/modules/ascat/test.yml
deleted file mode 100644
index 67479559472..00000000000
--- a/tests/modules/ascat/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: ascat test_ascat
-  command: nextflow run tests/modules/ascat -entry test_ascat -c tests/config/nextflow.config -stub-run
-  tags:
-    - ascat
-  files:
-    - path: output/ascat/test.after_correction.gc_rt.test.tumour.germline.png
-    - path: output/ascat/test.after_correction.gc_rt.test.tumour.tumour.png
-    - path: output/ascat/test.before_correction.test.tumour.germline.png
-    - path: output/ascat/test.before_correction.test.tumour.tumour.png
-    - path: output/ascat/test.cnvs.txt
-    - path: output/ascat/test.metrics.txt
-    - path: output/ascat/test.normal_alleleFrequencies_chr21.txt
-    - path: output/ascat/test.normal_alleleFrequencies_chr22.txt
-    - path: output/ascat/test.purityploidy.txt
-    - path: output/ascat/test.segments.txt
-    - path: output/ascat/test.tumour.ASPCF.png
-    - path: output/ascat/test.tumour.sunrise.png
-    - path: output/ascat/test.tumour_alleleFrequencies_chr21.txt
-    - path: output/ascat/test.tumour_alleleFrequencies_chr22.txt
-    - path: output/ascat/test.tumour_normalBAF.txt
-    - path: output/ascat/test.tumour_normalLogR.txt
-    - path: output/ascat/test.tumour_tumourBAF.txt
-    - path: output/ascat/test.tumour_tumourLogR.txt
diff --git a/tests/modules/assemblyscan/main.nf b/tests/modules/assemblyscan/main.nf
deleted file mode 100644
index 7cd5f3932a1..00000000000
--- a/tests/modules/assemblyscan/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ASSEMBLYSCAN } from '../../../modules/assemblyscan/main.nf'
-
-workflow test_assemblyscan {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    ASSEMBLYSCAN ( input )
-}
diff --git a/tests/modules/assemblyscan/test.yml b/tests/modules/assemblyscan/test.yml
deleted file mode 100644
index 4a3ba5ec52e..00000000000
--- a/tests/modules/assemblyscan/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: assemblyscan test_assemblyscan
-  command: nextflow run ./tests/modules/assemblyscan -entry test_assemblyscan -c ./tests/config/nextflow.config -c ./tests/modules/assemblyscan/nextflow.config
-  tags:
-    - assemblyscan
-  files:
-    - path: output/assemblyscan/test.json
-      md5sum: 9140e3d43f2d676f62e1325ace5dd8bd
diff --git a/tests/modules/ataqv/ataqv/main.nf b/tests/modules/ataqv/ataqv/main.nf
deleted file mode 100644
index b1103350e8a..00000000000
--- a/tests/modules/ataqv/ataqv/main.nf
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATAQV_ATAQV } from '../../../../modules/ataqv/ataqv/main.nf'
-include { ATAQV_ATAQV as ATAQV_ATAQV_PROBLEM_READS} from '../../../../modules/ataqv/ataqv/main.nf'
-
-workflow test_ataqv_ataqv {
-    
-    input = [ 
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-        [],
-        []
-    ]
-    
-    ATAQV_ATAQV ( input, 'human', [], [], [] )
-}
-
-workflow test_ataqv_ataqv_problem_reads {
-    
-    input = [ 
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-        [],
-        []
-    ]
-    
-    ATAQV_ATAQV_PROBLEM_READS ( input, 'human', [], [], [] )
-}
-
-workflow test_ataqv_ataqv_peak {
-    
-    input = [ 
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        [],
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    ]
-    
-    ATAQV_ATAQV ( input, 'human', [], [], [] )
-}
-
-workflow test_ataqv_ataqv_tss {
-    
-    input = [ 
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        []
-    ] 
-    tss_file = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-   
-    ATAQV_ATAQV ( input, 'human', tss_file, [], [] )
-}
-
-workflow test_ataqv_ataqv_excluded_regs {
-    
-    input = [ 
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        []
-    ] 
-    tss_file = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    excl_regs_file = file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
-   
-    ATAQV_ATAQV ( input, 'human', tss_file, excl_regs_file, [] )
-}
diff --git a/tests/modules/ataqv/ataqv/test.yml b/tests/modules/ataqv/ataqv/test.yml
deleted file mode 100644
index d46de34673e..00000000000
--- a/tests/modules/ataqv/ataqv/test.yml
+++ /dev/null
@@ -1,50 +0,0 @@
-- name: ataqv ataqv test_ataqv_ataqv
-  command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
-  tags:
-    - ataqv
-    - ataqv/ataqv
-  files:
-    - path: output/ataqv/test.ataqv.json
-      contains:
-        - '"forward_mate_reads": 101'
-
-- name: ataqv ataqv test_ataqv_ataqv_problem_reads
-  command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_problem_reads -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
-  tags:
-    - ataqv
-    - ataqv/ataqv
-  files:
-    - path: output/ataqv/1.problems
-    - path: output/ataqv/test.ataqv.json
-      contains:
-        - '"forward_mate_reads": 101'
-
-- name: ataqv ataqv test_ataqv_ataqv_peak
-  command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_peak -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
-  tags:
-    - ataqv
-    - ataqv/ataqv
-  files:
-    - path: output/ataqv/test.ataqv.json
-      contains:
-        - '"forward_mate_reads": 101'
-
-- name: ataqv ataqv test_ataqv_ataqv_tss
-  command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_tss -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
-  tags:
-    - ataqv
-    - ataqv/ataqv
-  files:
-    - path: output/ataqv/test.ataqv.json
-      contains:
-        - '"forward_mate_reads": 101'
-
-- name: ataqv ataqv test_ataqv_ataqv_excluded_regs
-  command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_excluded_regs -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
-  tags:
-    - ataqv
-    - ataqv/ataqv
-  files:
-    - path: output/ataqv/test.ataqv.json
-      contains:
-        - '"forward_mate_reads": 101'
diff --git a/tests/modules/ataqv/mkarv/main.nf b/tests/modules/ataqv/mkarv/main.nf
deleted file mode 100644
index d5bab5c5c69..00000000000
--- a/tests/modules/ataqv/mkarv/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATAQV_ATAQV } from '../../../../modules/ataqv/ataqv/main.nf'
-include { ATAQV_MKARV } from '../../../../modules/ataqv/mkarv/main.nf'
-
-workflow test_ataqv_mkarv {
-
-    input = [
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-        [],
-        []
-    ]
-
-    ATAQV_ATAQV ( input, 'human', [], [], [] )
-    ATAQV_MKARV ( ATAQV_ATAQV.out.json.collect{ it[1]} )
-}
diff --git a/tests/modules/ataqv/mkarv/test.yml b/tests/modules/ataqv/mkarv/test.yml
deleted file mode 100644
index fc6e38018e0..00000000000
--- a/tests/modules/ataqv/mkarv/test.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-- name: ataqv mkarv test_ataqv_mkarv
-  command: nextflow run ./tests/modules/ataqv/mkarv -entry test_ataqv_mkarv -c ./tests/config/nextflow.config  -c ./tests/modules/ataqv/mkarv/nextflow.config
-  tags:
-    - ataqv/mkarv
-    - ataqv
-
-  files:
-    - path: output/ataqv/html/css/ataqv.css
-      md5sum: 7bb9e18974018dd29bdc12a46a6d6d65
-    - path: output/ataqv/html/css/datatables.buttons.min.css
-      md5sum: 675306abc9d3239314f2c66c0e22ef7a
-    - path: output/ataqv/html/css/datatables.fontawesome.css
-      md5sum: 716d7a3edd2c75e712b1ffe26f12a861
-    - path: output/ataqv/html/css/datatables.min.css
-      md5sum: 00ef3e39d9302618395ab189ec8bcd9f
-    - path: output/ataqv/html/css/font-awesome.min.css
-      md5sum: 89916fa773ce96569604016ef25cab50
-    - path: output/ataqv/html/css/normalize.css
-      md5sum: 40d20cc85100840580df4346bb99d7ed
-    - path: output/ataqv/html/data/1.json.gz
-    - path: output/ataqv/html/fonts/FontAwesome.otf
-      md5sum: 9ccfa32dd4cd1b8e83f68899d85bd5e6
-    - path: output/ataqv/html/fonts/fontawesome-webfont.eot
-      md5sum: 404a525502f8e5ba7e93b9f02d9e83a9
-    - path: output/ataqv/html/fonts/fontawesome-webfont.svg
-      md5sum: bae4a87c1e5dff40baa3f49d52f5347a
-    - path: output/ataqv/html/fonts/fontawesome-webfont.ttf
-      md5sum: fb650aaf10736ffb9c4173079616bf01
-    - path: output/ataqv/html/fonts/fontawesome-webfont.woff
-      md5sum: 891e3f340c1126b4c7c142e5f6e86816
-    - path: output/ataqv/html/fonts/fontawesome-webfont.woff2
-      md5sum: 926c93d201fe51c8f351e858468980c3
-    - path: output/ataqv/html/fonts/sourcesanspro-regular.woff
-      md5sum: f7bd788f18b8c4bb93dd37d140348e1e
-    - path: output/ataqv/html/fonts/sourcesanspro-regularit.woff
-      md5sum: c3638b17f4fd76dae12fe2ae14571e57
-    - path: output/ataqv/html/fonts/sourcesanspro-semibold.woff
-      md5sum: e7fc8925d9364e9d177d9e1d08bb1855
-    - path: output/ataqv/html/fonts/sourcesanspro-semiboldit.woff
-      md5sum: f1d255aa459786dfc6aa2e488ac01245
-    - path: output/ataqv/html/index.html
-      md5sum: bf7747be761e56ad7c54c842ac88461a
-    - path: output/ataqv/html/js/ataqv.js
-      md5sum: feb291b7839e9e43ed304565e3a605d9
-    - path: output/ataqv/html/js/configuration.js
-      md5sum: 073bc07f1371e28a97098f8b10469ae4
-    - path: output/ataqv/html/js/d3.min.js
-      md5sum: db69fb2626a71a286ee772d673138aca
-    - path: output/ataqv/html/js/datatables.min.js
-      md5sum: e369b872620dadb05e4eb555b81f9112
-    - path: output/ataqv/html/js/jszip.min.js
-      md5sum: 09e492cb492ffa75484bbe10f1f721d1
-    - path: output/ataqv/test.ataqv.json
-      contains:
-        - '"properly_paired_and_mapped_reads": 192,'
diff --git a/tests/modules/atlas/call/main.nf b/tests/modules/atlas/call/main.nf
deleted file mode 100644
index 945812ef395..00000000000
--- a/tests/modules/atlas/call/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATLAS_CALL } from '../../../../modules/atlas/call/main.nf'
-
-workflow test_atlas_call {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-    fasta         = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai           = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    recal         = []
-    pmd           = []
-    known_alleles = []
-    method        = 'randomBase'
-
-    ATLAS_CALL ( input, fasta, fai, recal, pmd, known_alleles, method )
-}
diff --git a/tests/modules/atlas/call/test.yml b/tests/modules/atlas/call/test.yml
deleted file mode 100644
index b3e13951243..00000000000
--- a/tests/modules/atlas/call/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: atlas call test_atlas_call
-  command: nextflow run ./tests/modules/atlas/call -entry test_atlas_call -c ./tests/config/nextflow.config  -c ./tests/modules/atlas/call/nextflow.config
-  tags:
-    - atlas
-    - atlas/call
-  files:
-    - path: output/atlas/test.paired_end.sorted_randomBase.vcf.gz
-      contains:
-        - "##source=atlas"
diff --git a/tests/modules/atlas/pmd/main.nf b/tests/modules/atlas/pmd/main.nf
deleted file mode 100644
index db552f8d7dc..00000000000
--- a/tests/modules/atlas/pmd/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATLAS_PMD } from '../../../../modules/atlas/pmd/main.nf'
-
-workflow test_atlas_pmd {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        []
-    ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    ATLAS_PMD ( input, fasta, fai )
-}
diff --git a/tests/modules/atlas/pmd/test.yml b/tests/modules/atlas/pmd/test.yml
deleted file mode 100644
index 69e3def21a4..00000000000
--- a/tests/modules/atlas/pmd/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: atlas pmd test_atlas_pmd
-  command: nextflow run ./tests/modules/atlas/pmd -entry test_atlas_pmd -c ./tests/config/nextflow.config  -c ./tests/modules/atlas/pmd/nextflow.config
-  tags:
-    - atlas/pmd
-    - atlas
-  files:
-    - path: output/atlas/test.paired_end.sorted_PMD_Table.txt
-      md5sum: b28a9f4784f30a711046708eb7d94642
-    - path: output/atlas/test.paired_end.sorted_PMD_Table_counts.txt
-      md5sum: 1aabfb83cfff6e0413f52d016c943e3e
-    - path: output/atlas/test.paired_end.sorted_PMD_input_Empiric.txt
-      md5sum: 8ff876f50ce05dc9aac0646a31682df0
-    - path: output/atlas/test.paired_end.sorted_PMD_input_Exponential.txt
-      md5sum: 2421450ef643316f4eacf5cb811e4df7
diff --git a/tests/modules/atlas/recal/main.nf b/tests/modules/atlas/recal/main.nf
deleted file mode 100644
index d74fa55a907..00000000000
--- a/tests/modules/atlas/recal/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATLAS_RECAL } from '../../../../modules/atlas/recal/main.nf'
-
-workflow test_atlas_recal {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        [],
-        []
-    ]
-    alleles = []
-    invariant_sites = []
-
-    ATLAS_RECAL ( input, alleles, invariant_sites )
-}
-
-
diff --git a/tests/modules/atlas/recal/test.yml b/tests/modules/atlas/recal/test.yml
deleted file mode 100644
index 45bb87673bd..00000000000
--- a/tests/modules/atlas/recal/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: atlas recal test_atlas_recal
-  command: nextflow run ./tests/modules/atlas/recal -entry test_atlas_recal -c ./tests/config/nextflow.config  -c ./tests/modules/atlas/recal/nextflow.config
-  tags:
-    - atlas/recal
-    - atlas
-  files:
-    - path: output/atlas/test_recalibrationEM.txt
-      contains: ["readGroup"]
diff --git a/tests/modules/atlas/splitmerge/main.nf b/tests/modules/atlas/splitmerge/main.nf
deleted file mode 100644
index 9334c27f60b..00000000000
--- a/tests/modules/atlas/splitmerge/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATLAS_SPLITMERGE } from '../../../../modules/atlas/splitmerge/main.nf'
-
-//MAIN
-workflow test_atlas_splitmerge {
-    meta = [ id:'test', single_end:false ]
-    bam = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    bai = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    settings = file(params.test_data['homo_sapiens']['illumina']['read_group_settings_txt'], checkIfExists: true)
-
-    ATLAS_SPLITMERGE ( [meta, bam, bai, settings, []] )
-}
diff --git a/tests/modules/atlas/splitmerge/test.yml b/tests/modules/atlas/splitmerge/test.yml
deleted file mode 100644
index 145a2e8ac48..00000000000
--- a/tests/modules/atlas/splitmerge/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: atlas splitmerge test_atlas_splitmerge
-  command: nextflow run tests/modules/atlas/splitmerge -entry test_atlas_splitmerge -c tests/config/nextflow.config
-  tags:
-    - atlas
-    - atlas/splitmerge
-  files:
-    - path: output/atlas/test.paired_end.sorted_ignoredReads.txt.gz
-      md5sum: 9b64c47313d2de89c26790f713707ee6
-    - path: output/atlas/test.paired_end.sorted_mergedReads.bam
-    - path: output/atlas/versions.yml
-      md5sum: 11735bec9c2f4b395b987fd00d4e4294
diff --git a/tests/modules/bakta/main.nf b/tests/modules/bakta/main.nf
deleted file mode 100644
index 1bc0062237b..00000000000
--- a/tests/modules/bakta/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAKTA } from '../../../modules/bakta/main.nf'
-
-workflow test_bakta {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    BAKTA ( input, [], [], [] )
-}
diff --git a/tests/modules/bakta/test.yml b/tests/modules/bakta/test.yml
deleted file mode 100644
index 1eb3d8a5002..00000000000
--- a/tests/modules/bakta/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: bakta
-  command: nextflow run ./tests/modules/bakta -entry test_bakta -c tests/config/nextflow.config -stub-run
-  tags:
-    - bakta
-  files:
-    - path: output/bakta/test.embl
-    - path: output/bakta/test.faa
-    - path: output/bakta/test.ffn
-    - path: output/bakta/test.fna
-    - path: output/bakta/test.gbff
-    - path: output/bakta/test.gff3
-    - path: output/bakta/test.hypotheticals.tsv
-    - path: output/bakta/test.hypotheticals.faa
-    - path: output/bakta/test.tsv
diff --git a/tests/modules/bamaligncleaner/main.nf b/tests/modules/bamaligncleaner/main.nf
deleted file mode 100644
index c9d517ae0fe..00000000000
--- a/tests/modules/bamaligncleaner/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAMALIGNCLEANER } from '../../../modules/bamaligncleaner/main.nf'
-
-workflow test_bamaligncleaner {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) ]
-
-    BAMALIGNCLEANER ( input )
-}
diff --git a/tests/modules/bamaligncleaner/test.yml b/tests/modules/bamaligncleaner/test.yml
deleted file mode 100644
index 4207b8c2873..00000000000
--- a/tests/modules/bamaligncleaner/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: bamaligncleaner
-  command: nextflow run ./tests/modules/bamaligncleaner -entry test_bamaligncleaner -c ./tests/config/nextflow.config -c ./tests/modules/bamaligncleaner/nextflow.config
-  tags:
-    - bamaligncleaner
-  files:
-    - path: output/bamaligncleaner/test.bam
-      md5sum: 173cdb4c2713b77c528cac36ca2610fb
diff --git a/tests/modules/bamcmp/main.nf b/tests/modules/bamcmp/main.nf
deleted file mode 100644
index cf7964063f0..00000000000
--- a/tests/modules/bamcmp/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_INDEX } from '../../../modules/bwa/index/main.nf'
-include { BWA_MEM   } from '../../../modules/bwa/mem/main.nf'
-include { BWA_INDEX as BWA_INDEX_COV2 } from '../../../modules/bwa/index/main.nf'
-include { BWA_MEM as BWA_MEM_COV2   } from '../../../modules/bwa/mem/main.nf'
-
-include { SAMTOOLS_SORT } from '../../../modules/samtools/sort/main.nf'
-include { SAMTOOLS_SORT as SAMTOOLS_SORT_COV2   } from '../../../modules/samtools/sort/main.nf'
-
-include { BAMCMP } from '../../../modules/bamcmp/main.nf'
-
-workflow test_bamcmp {
-
-    input = [
-        [ id:'test'], // meta map
-        [ file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    fasta1 = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta2 = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta1 )
-    BWA_MEM ( input, BWA_INDEX.out.index, false )
-    SAMTOOLS_SORT (BWA_MEM.out.bam)
-
-
-    BWA_INDEX_COV2 ( fasta2 )
-    BWA_MEM_COV2 ( input, BWA_INDEX_COV2.out.index, false )
-    SAMTOOLS_SORT_COV2 (BWA_MEM_COV2.out.bam)
-
-    BAMCMP (SAMTOOLS_SORT.out.bam.join(SAMTOOLS_SORT_COV2.out.bam, by: [0]))
-
-}
diff --git a/tests/modules/bamcmp/test.yml b/tests/modules/bamcmp/test.yml
deleted file mode 100644
index 58fba458642..00000000000
--- a/tests/modules/bamcmp/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: bamcmp test_bamcmp
-  command: nextflow run tests/modules/bamcmp -entry test_bamcmp -c tests/config/nextflow.config
-  tags:
-    - bamcmp
-  files:
-    - path: output/bamcmp/test_contamination.bam
-      md5sum: 1fe730936d489c637479c1e51dd8ca55
-    - path: output/bamcmp/test_primary.bam
-      md5sum: 80b9abd8ef83e63548a9b8b82be2a034
-    - path: output/bamcmp/versions.yml
-      md5sum: 34d569665ff0459e84114e966dd3483b
diff --git a/tests/modules/bamtools/convert/main.nf b/tests/modules/bamtools/convert/main.nf
deleted file mode 100644
index bf57f2489db..00000000000
--- a/tests/modules/bamtools/convert/main.nf
+++ /dev/null
@@ -1,104 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR }   from '../../../../modules/bamtools/convert/main.nf'
-include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
-include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED }         from '../../../../modules/bamtools/convert/main.nf'
-include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA }       from '../../../../modules/bamtools/convert/main.nf'
-include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ }       from '../../../../modules/bamtools/convert/main.nf'
-include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON }        from '../../../../modules/bamtools/convert/main.nf'
-include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP }      from '../../../../modules/bamtools/convert/main.nf'
-include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM }         from '../../../../modules/bamtools/convert/main.nf'
-include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML }        from '../../../../modules/bamtools/convert/main.nf'
-
-workflow test_bamtools_convert_ext_error {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_CONVERT_EXT_ERROR ( input )
-}
-
-workflow test_bamtools_convert_noext_error {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_CONVERT_NOEXT_ERROR ( input )
-}
-
-workflow test_bamtools_convert_bed {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_CONVERT_BED ( input )
-}
-
-workflow test_bamtools_convert_fasta {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_CONVERT_FASTA ( input )
-}
-
-workflow test_bamtools_convert_fastq {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_CONVERT_FASTQ ( input )
-}
-
-workflow test_bamtools_convert_json {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_CONVERT_JSON ( input )
-}
-
-workflow test_bamtools_convert_pileup {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_CONVERT_PILEUP ( input )
-}
-
-workflow test_bamtools_convert_sam {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_CONVERT_SAM ( input )
-}
-
-workflow test_bamtools_convert_yaml {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_CONVERT_YAML ( input )
-}
-
diff --git a/tests/modules/bamtools/convert/test.yml b/tests/modules/bamtools/convert/test.yml
deleted file mode 100644
index 3922ece2357..00000000000
--- a/tests/modules/bamtools/convert/test.yml
+++ /dev/null
@@ -1,90 +0,0 @@
-- name: bamtools convert test_bamtools_convert_ext_error
-  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_ext_error -c tests/config/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/convert
-  exit_code: 1
-
-- name: bamtools convert test_bamtools_convert_noext_error
-  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_noext_error -c tests/config/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/convert
-  exit_code: 1
-
-- name: bamtools convert test_bamtools_convert_bed
-  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_bed -c tests/config/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/convert
-  files:
-    - path: output/bamtools/test.bed
-      md5sum: 4e34cc15bf31e700f5f3a9f8fffb6c81
-    - path: output/bamtools/versions.yml
-      md5sum: eb7a144b8a97965d3482f6f96b8a8243
-
-- name: bamtools convert test_bamtools_convert_fasta
-  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fasta -c tests/config/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/convert
-  files:
-    - path: output/bamtools/test.fasta
-      md5sum: 52aeacf78571862b7e97c7d44ac8f827
-    - path: output/bamtools/versions.yml
-      md5sum: 42d19a2b2b07f05edb82b34369dfd754
-
-- name: bamtools convert test_bamtools_convert_fastq
-  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fastq -c tests/config/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/convert
-  files:
-    - path: output/bamtools/test.fastq
-      md5sum: e591c48daad2c56638e5d6f21f1f71c5
-    - path: output/bamtools/versions.yml
-      md5sum: 13f0bf8a3e1f8f527f96dabaa5c8051e
-
-- name: bamtools convert test_bamtools_convert_json
-  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_json -c tests/config/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/convert
-  files:
-    - path: output/bamtools/test.json
-      md5sum: 04afed696f9f14da85a460353645d1f5
-    - path: output/bamtools/versions.yml
-      md5sum: 33d633dbd6209cb93c9b071f8c0ed3b3
-
-- name: bamtools convert test_bamtools_convert_pileup
-  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_pileup -c tests/config/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/convert
-  files:
-    - path: output/bamtools/test.pileup
-      md5sum: e5a3cb4a3e1bf980a575fafce6a2826f
-    - path: output/bamtools/versions.yml
-      md5sum: fd3ad0edd1e085b1a002e0593d1d5814
-
-- name: bamtools convert test_bamtools_convert_sam
-  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_sam -c tests/config/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/convert
-  files:
-    - path: output/bamtools/test.sam
-      md5sum: 61ab3d0de16a9da8b651f9c692e19d5e
-    - path: output/bamtools/versions.yml
-      md5sum: 4be470ce3cc0143ae5ae415b612a4965
-
-- name: bamtools convert test_bamtools_convert_yaml
-  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_yaml -c tests/config/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/convert
-  files:
-    - path: output/bamtools/test.yaml
-      md5sum: 68b56f198da036fef33e150eb773dc3b
-    - path: output/bamtools/versions.yml
-      md5sum: 1116abc088c5edf11bee393961c18b3e
diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
deleted file mode 100644
index e5c15c3202d..00000000000
--- a/tests/modules/bamtools/split/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE   } from '../../../../modules/bamtools/split/main.nf'
-include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../modules/bamtools/split/main.nf'
-
-workflow test_bamtools_split_single_input {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_SPLIT_SINGLE ( input )
-}
-
-workflow test_bamtools_split_multiple {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
-        ]
-    ]
-
-    BAMTOOLS_SPLIT_MULTIPLE ( input )
-}
-
diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
deleted file mode 100644
index af639b43987..00000000000
--- a/tests/modules/bamtools/split/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: bamtools split test_bamtools_split_single_input
-  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/split
-  files:
-    - path: output/bamtools/test.REF_chr22.bam
-      md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
-    - path: output/bamtools/test.REF_unmapped.bam
-      md5sum: e0754bf72c51543b2d745d96537035fb
-    - path: output/bamtools/versions.yml
-
-- name: bamtools split test_bamtools_split_multiple
-  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
-  tags:
-    - bamtools
-    - bamtools/split
-  files:
-    - path: output/bamtools/test.REF_chr22.bam
-      md5sum: 585675bea34c48ebe9db06a561d4b4fa
-    - path: output/bamtools/test.REF_unmapped.bam
-      md5sum: 16ad644c87b9471f3026bc87c98b4963
-    - path: output/bamtools/versions.yml
diff --git a/tests/modules/bamtools/stats/main.nf b/tests/modules/bamtools/stats/main.nf
deleted file mode 100644
index e5fd3953116..00000000000
--- a/tests/modules/bamtools/stats/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAMTOOLS_STATS } from '../../../../modules/bamtools/stats/main.nf'
-
-workflow test_bamtools_stats {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BAMTOOLS_STATS ( input )
-}
diff --git a/tests/modules/bamtools/stats/test.yml b/tests/modules/bamtools/stats/test.yml
deleted file mode 100644
index 07811b19793..00000000000
--- a/tests/modules/bamtools/stats/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bamtools stats test_bamtools_stats
-  command: nextflow run ./tests/modules/bamtools/stats -entry test_bamtools_stats -c ./tests/config/nextflow.config  -c ./tests/modules/bamtools/stats/nextflow.config
-  tags:
-    - bamtools/stats
-    - bamtools
-  files:
-    - path: output/bamtools/test.bam.stats
-      md5sum: b7c3f01682673a652d664a2889b15b66
diff --git a/tests/modules/bamutil/trimbam/main.nf b/tests/modules/bamutil/trimbam/main.nf
deleted file mode 100644
index 2967b038f67..00000000000
--- a/tests/modules/bamutil/trimbam/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAMUTIL_TRIMBAM } from '../../../../modules/bamutil/trimbam/main.nf'
-
-workflow test_bamutil_trimbam {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-              2,
-              2 ]
-
-    BAMUTIL_TRIMBAM ( input )
-}
diff --git a/tests/modules/bamutil/trimbam/test.yml b/tests/modules/bamutil/trimbam/test.yml
deleted file mode 100644
index 443a4dedc7e..00000000000
--- a/tests/modules/bamutil/trimbam/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bamutil trimbam test_bamutil_trimbam
-  command: nextflow run ./tests/modules/bamutil/trimbam -entry test_bamutil_trimbam -c ./tests/config/nextflow.config -c ./tests/modules/bamutil/trimbam/nextflow.config
-  tags:
-    - bamutil/trimbam
-    - bamutil
-  files:
-    - path: output/bamutil/test.bam
-      md5sum: 9ddd0ecca82f7f3433383f3d1308970e
diff --git a/tests/modules/bandage/image/main.nf b/tests/modules/bandage/image/main.nf
deleted file mode 100644
index 15f01ab16bb..00000000000
--- a/tests/modules/bandage/image/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BANDAGE_IMAGE } from '../../../../modules/bandage/image/main.nf'
-
-workflow test_bandage_image {
-    input = [
-        [ id:'B-3106' ], // meta map
-        file( params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)
-    ]
-
-    BANDAGE_IMAGE ( input )
-}
diff --git a/tests/modules/bandage/image/test.yml b/tests/modules/bandage/image/test.yml
deleted file mode 100644
index 2abdd175c77..00000000000
--- a/tests/modules/bandage/image/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bandage image
-  command: nextflow run ./tests/modules/bandage/image -entry test_bandage_image -c ./tests/config/nextflow.config -c ./tests/modules/bandage/image/nextflow.config
-  tags:
-    - bandage
-    - bandage/image
-  files:
-    - path: output/bandage/B-3106.png
-    - path: output/bandage/B-3106.svg
diff --git a/tests/modules/bases2fastq/main.nf b/tests/modules/bases2fastq/main.nf
deleted file mode 100644
index abd1f92b613..00000000000
--- a/tests/modules/bases2fastq/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BASES2FASTQ } from '../../../modules/bases2fastq/main.nf'
-include { UNTAR      } from '../../../modules/untar/main.nf'
-
-workflow test_bases2fastq {
-    
-    input = Channel.value([
-        [ id:'sim-data' ], // meta map
-        file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv", checkIfExists: true),
-    ])
-
-    ch_input = input.join(
-        UNTAR ( [
-            [ id:'sim-data' ],
-            file("https://github.com/nf-core/test-datasets/raw/demultiplex/testdata/sim-data/sim-data.tar.gz", checkIfExists: true)
-        ]).untar
-    )
-
-    BASES2FASTQ ( ch_input )
-}
diff --git a/tests/modules/bases2fastq/test.yml b/tests/modules/bases2fastq/test.yml
deleted file mode 100644
index bc1245cd487..00000000000
--- a/tests/modules/bases2fastq/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: "bases2fastq"
-  command: nextflow run ./tests/modules/bases2fastq -entry test_bases2fastq -c ./tests/config/nextflow.config -c ./tests/modules/bases2fastq/nextflow.config
-  tags:
-    - "bases2fastq"
-  files:
-    - path: output/bases2fastq/output/Bases2Fastq-Sim_QC.html
-    - path: output/bases2fastq/output/Metrics.csv
-      md5sum: 0ec6da2b82e191098283474356024abf
-    - path: output/bases2fastq/output/RunManifest.json
-      md5sum: a07dce8ee25c2a6f9355b677c26b53e2
-    - path: output/bases2fastq/output/RunStats.json
-    - path: output/bases2fastq/output/UnassignedSequences.csv
-      md5sum: 11c1693830ce941b8cfb8d2431a59097
-    - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R1.fastq.gz
-      md5sum: 218abc70f61e8e8199a68f83ae836184
-    - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R2.fastq.gz
-      md5sum: b95109bfb204daa150b61239d3368ee2
-    - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_stats.json
diff --git a/tests/modules/bbmap/align/main.nf b/tests/modules/bbmap/align/main.nf
deleted file mode 100644
index c7a02e2a502..00000000000
--- a/tests/modules/bbmap/align/main.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf'
-include { BBMAP_ALIGN } from '../../../../modules/bbmap/align/main.nf'
-include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/bbmap/align/main.nf'
-
-workflow test_bbmap_align_paired_end_fasta_ref {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                [
-                    file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                    file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-                ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BBMAP_ALIGN ( input, fasta )
-}
-
-workflow test_bbmap_align_paired_end_index_ref {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                [
-                    file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                    file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-                ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BBMAP_INDEX ( fasta )
-    BBMAP_ALIGN ( input, BBMAP_INDEX.out.index )
-}
-
-workflow test_bbmap_align_single_end_index_ref {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-                file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BBMAP_INDEX ( fasta )
-    BBMAP_ALIGN ( input, BBMAP_INDEX.out.index )
-}
-
-workflow test_bbmap_align_paired_end_index_ref_pigz {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                [
-                    file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                    file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-                ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BBMAP_INDEX ( fasta )
-    BBMAP_ALIGN_PIGZ ( input, BBMAP_INDEX.out.index )
-}
diff --git a/tests/modules/bbmap/align/test.yml b/tests/modules/bbmap/align/test.yml
deleted file mode 100644
index aa3a9c1c54e..00000000000
--- a/tests/modules/bbmap/align/test.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-- name: bbmap align paired end fasta ref
-  command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_fasta_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
-  tags:
-    - bbmap
-    - bbmap/align
-  files:
-    - path: output/bbmap/test.bam
-      md5sum: 8549040067d23949bddb6fe2ad211c92
-    - path: output/bbmap/test.bbmap.log
-
-- name: bbmap align paired end index ref
-  command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
-  tags:
-    - bbmap
-    - bbmap/align
-  files:
-    - path: output/bbmap/test.bam
-      md5sum: aeb842491ca6c7806aa7103b5223620f
-    - path: output/bbmap/test.bbmap.log
-
-- name: bbmap align single end index ref
-  command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_single_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
-  tags:
-    - bbmap
-    - bbmap/align
-  files:
-    - path: output/bbmap/test.bam
-      md5sum: b6a41cb344a343d46244d8f94eb66ec0
-    - path: output/bbmap/test.bbmap.log
-
-- name: bbmap align paired end index ref pigz
-  command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
-  tags:
-    - bbmap
-    - bbmap/align
-  files:
-    - path: output/bbmap/test.bam
-      md5sum: 74944e24acccb8c5abc316dcdd623c84
-    - path: output/bbmap/test.bbmap.log
diff --git a/tests/modules/bbmap/bbduk/main.nf b/tests/modules/bbmap/bbduk/main.nf
deleted file mode 100644
index e1f0c2dee67..00000000000
--- a/tests/modules/bbmap/bbduk/main.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_BBDUK } from '../../../../modules/bbmap/bbduk/main.nf'
-
-workflow test_bbmap_bbduk_single_end {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    BBMAP_BBDUK ( input, [] )
-}
-
-workflow test_bbmap_bbduk_paired_end {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    BBMAP_BBDUK ( input, [] )
-}
-
-workflow test_bbmap_bbduk_se_ref {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    contaminants = [file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] // transciptome file - remove contaminants (*trim.fastq files empty)
-
-    BBMAP_BBDUK ( input, contaminants )
-}
-
-workflow test_bbmap_bbduk_pe_ref {
-
-    input =  [  [ id:'test', single_end:false ], // meta map
-                [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-             ]
-    contaminants = [file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-
-    BBMAP_BBDUK ( input, contaminants )
-}
diff --git a/tests/modules/bbmap/bbduk/test.yml b/tests/modules/bbmap/bbduk/test.yml
deleted file mode 100644
index 7ab5b9639fc..00000000000
--- a/tests/modules/bbmap/bbduk/test.yml
+++ /dev/null
@@ -1,47 +0,0 @@
-- name: bbmap bbduk test_bbmap_bbduk_single_end
-  command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config
-  tags:
-    - bbmap/bbduk
-  files:
-    - path: output/bbmap/test.trim.bbduk.log
-      contains:
-        - "Input is being processed as unpaired"
-    - path: output/bbmap/test.trim.fastq.gz
-      md5sum: a87d0cbd5ced7df8bf1751e4cb407482
-
-- name: bbmap bbduk test_bbmap_bbduk_paired_end
-  command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config
-  tags:
-    - bbmap/bbduk
-  files:
-    - path: output/bbmap/test.trim.bbduk.log
-      contains:
-        - "Input is being processed as paired"
-    - path: output/bbmap/test.trim_1.fastq.gz
-      md5sum: a87d0cbd5ced7df8bf1751e4cb407482
-    - path: output/bbmap/test.trim_2.fastq.gz
-      md5sum: 406e068fbe198f02b48e7e210cc0c69f
-
-- name: bbmap bbduk test_bbmap_bbduk_se_ref
-  command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_se_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config
-  tags:
-    - bbmap/bbduk
-  files:
-    - path: output/bbmap/test.trim.bbduk.log
-      contains:
-        - "Input is being processed as unpaired"
-    - path: output/bbmap/test.trim.fastq.gz
-      md5sum: 3970e82605c7d109bb348fc94e9eecc0
-
-- name: bbmap bbduk test_bbmap_bbduk_pe_ref
-  command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_pe_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config
-  tags:
-    - bbmap/bbduk
-  files:
-    - path: output/bbmap/test.trim.bbduk.log
-      contains:
-        - "Input is being processed as paired"
-    - path: output/bbmap/test.trim_1.fastq.gz
-      md5sum: 3970e82605c7d109bb348fc94e9eecc0
-    - path: output/bbmap/test.trim_2.fastq.gz
-      md5sum: 3970e82605c7d109bb348fc94e9eecc0
diff --git a/tests/modules/bbmap/bbsplit/main.nf b/tests/modules/bbmap/bbsplit/main.nf
deleted file mode 100644
index d12360618a6..00000000000
--- a/tests/modules/bbmap/bbsplit/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../modules/bbmap/bbsplit/main.nf'
-include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../modules/bbmap/bbsplit/main.nf'
-
-workflow test_bbmap_bbsplit {
-
-    input = [ 
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    bbsplit_fasta_list = [ 
-        ['human'],
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/chr22_23800000-23980000.fa', checkIfExists: true) 
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-	
-    BBMAP_BBSPLIT_INDEX ( [ [:], [] ], [], fasta, bbsplit_fasta_list, true )
-    BBMAP_BBSPLIT_SPLIT ( input, BBMAP_BBSPLIT_INDEX.out.index, fasta, bbsplit_fasta_list, true )
-}
diff --git a/tests/modules/bbmap/bbsplit/test.yml b/tests/modules/bbmap/bbsplit/test.yml
deleted file mode 100644
index a1933211848..00000000000
--- a/tests/modules/bbmap/bbsplit/test.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-- name: bbmap bbsplit test_bbmap_bbsplit
-  command: nextflow run ./tests/modules/bbmap/bbsplit -entry test_bbmap_bbsplit -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbsplit/nextflow.config
-  tags:
-    - bbmap/bbsplit
-    - bbmap
-  files:
-    - path: output/bbmap/bbsplit/ref/genome/1/chr1.chrom.gz
-    - path: output/bbmap/bbsplit/ref/genome/1/info.txt
-      contains:
-        - "Chromosome"
-    - path: output/bbmap/bbsplit/ref/genome/1/merged_ref_9222711925172838098.fa.gz
-    - path: output/bbmap/bbsplit/ref/genome/1/namelist.txt
-      md5sum: 45e7a4cdc7a11a39ada56844ca3a1e30
-    - path: output/bbmap/bbsplit/ref/genome/1/reflist.txt
-      contains:
-        - "genome.fasta"
-    - path: output/bbmap/bbsplit/ref/genome/1/scaffolds.txt.gz
-    - path: output/bbmap/bbsplit/ref/genome/1/summary.txt
-      contains:
-        - "scaffolds"
-    - path: output/bbmap/bbsplit/ref/index/1/chr1_index_k13_c13_b1.block
-      md5sum: 385913c1e84b77dc7bf36288ee1c8706
-    - path: output/bbmap/bbsplit/ref/index/1/chr1_index_k13_c13_b1.block2.gz
-      md5sum: 9de572b603abe5b6540056db8dee05a5
diff --git a/tests/modules/bbmap/clumpify/main.nf b/tests/modules/bbmap/clumpify/main.nf
deleted file mode 100644
index 54cbaadad90..00000000000
--- a/tests/modules/bbmap/clumpify/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_CLUMPIFY } from '../../../../modules/bbmap/clumpify/main.nf'
-
-workflow test_bbmap_clumpify_single_end {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    BBMAP_CLUMPIFY ( input )
-}
-
-workflow test_bbmap_clumpify_paired_end {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    BBMAP_CLUMPIFY ( input )
-}
diff --git a/tests/modules/bbmap/clumpify/test.yml b/tests/modules/bbmap/clumpify/test.yml
deleted file mode 100644
index 44529ea8801..00000000000
--- a/tests/modules/bbmap/clumpify/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: bbmap clumpify test_bbmap_clumpify_single_end
-  command: nextflow run ./tests/modules/bbmap/clumpify -entry test_bbmap_clumpify_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/bbmap/clumpify/nextflow.config
-  tags:
-    - bbmap/clumpify
-    - bbmap
-  files:
-    - path: output/bbmap/test.clumped.fastq.gz
-    - path: output/bbmap/test.clumpify.log
-
-- name: bbmap clumpify test_bbmap_clumpify_paired_end
-  command: nextflow run ./tests/modules/bbmap/clumpify -entry test_bbmap_clumpify_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/bbmap/clumpify/nextflow.config
-  tags:
-    - bbmap/clumpify
-    - bbmap
-  files:
-    - path: output/bbmap/test.clumpify.log
-    - path: output/bbmap/test_1.clumped.fastq.gz
-    - path: output/bbmap/test_2.clumped.fastq.gz
diff --git a/tests/modules/bbmap/index/main.nf b/tests/modules/bbmap/index/main.nf
deleted file mode 100644
index a6f111f4308..00000000000
--- a/tests/modules/bbmap/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf'
-
-workflow test_bbmap_index {
-    
-    input = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    BBMAP_INDEX ( input )
-}
diff --git a/tests/modules/bbmap/index/test.yml b/tests/modules/bbmap/index/test.yml
deleted file mode 100644
index 4e8d7196b81..00000000000
--- a/tests/modules/bbmap/index/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: bbmap index
-  command: nextflow run ./tests/modules/bbmap/index -entry test_bbmap_index -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/index/nextflow.config
-  tags:
-    - bbmap
-    - bbmap/index
-  files:
-    - path: output/bbmap/ref/genome/1/chr1.chrom.gz
-    - path: output/bbmap/ref/index/1/chr1_index_k13_c15_b1.block
-      md5sum: 9f0d9a7413c1d2c16cc24555b2381163
diff --git a/tests/modules/bbmap/pileup/main.nf b/tests/modules/bbmap/pileup/main.nf
deleted file mode 100644
index 943df9b5ba5..00000000000
--- a/tests/modules/bbmap/pileup/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_PILEUP } from '../../../../modules/bbmap/pileup/main.nf'
-
-workflow test_bbmap_pileup {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    BBMAP_PILEUP ( input )
-}
diff --git a/tests/modules/bbmap/pileup/test.yml b/tests/modules/bbmap/pileup/test.yml
deleted file mode 100644
index 272cdcf79a2..00000000000
--- a/tests/modules/bbmap/pileup/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: "bbmap pileup"
-  command: nextflow run ./tests/modules/bbmap/pileup -entry test_bbmap_pileup -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/pileup/nextflow.config
-  tags:
-    - "bbmap"
-    - "bbmap/pileup"
-  files:
-    - path: "output/bbmap/test.coverage.stats.txt"
-      md5sum: c3fc9d0681589b69e3301ca3cb27b7a4
-    - path: "output/bbmap/test.coverage.hist.txt"
-      md5sum: 96915920ef42ddc9483457dd4585a088
-    - path: output/bbmap/versions.yml
-      md5sum: e2bc51873b24e7fea269b7c1501de060
diff --git a/tests/modules/bcftools/annotate/main.nf b/tests/modules/bcftools/annotate/main.nf
deleted file mode 100644
index 0d096ca996e..00000000000
--- a/tests/modules/bcftools/annotate/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_ANNOTATE } from '../../../../modules/bcftools/annotate/main.nf'
-
-workflow test_bcftools_annotate_out_vcf {
-
-    input = [ 
-    [ id:'test_compressed_vcf', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
-
-    BCFTOOLS_ANNOTATE ( input )
-}
-
-workflow test_bcftools_annotate_out_bcf {
-
-    input = [ 
-    [ id:'test_compressed_bcf', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_bcf'], checkIfExists: true) ]
-
-    BCFTOOLS_ANNOTATE ( input )
-}
diff --git a/tests/modules/bcftools/annotate/test.yml b/tests/modules/bcftools/annotate/test.yml
deleted file mode 100644
index c3a183b0b3e..00000000000
--- a/tests/modules/bcftools/annotate/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: bcftools annotate test_bcftools_annotate_out_vcf
-  command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c tests/config/nextflow.config
-  tags:
-    - bcftools/annotate
-    - bcftools
-  files:
-    - path: output/bcftools/test_compressed_vcf_annotated.vcf.gz
-    - path: output/bcftools/versions.yml
-      md5sum: ff237d88fce62300fdab66b284e9aa95
-
-- name: bcftools annotate test_bcftools_annotate_out_bcf
-  command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c tests/config/nextflow.config
-  tags:
-    - bcftools/annotate
-    - bcftools
-  files:
-    - path: output/bcftools/test_compressed_bcf_annotated.bcf
-    - path: output/bcftools/versions.yml
-      md5sum: bbcefb8ebfca05c538a92dbfb94d977e
diff --git a/tests/modules/bcftools/concat/main.nf b/tests/modules/bcftools/concat/main.nf
deleted file mode 100644
index 777dc5b8ce0..00000000000
--- a/tests/modules/bcftools/concat/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf'
-
-workflow test_bcftools_concat_tbi {
-    
-    input = [ [ id:'test3' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) ]
-            ]
-
-    BCFTOOLS_CONCAT ( input )
-}
-
-workflow test_bcftools_concat_no_tbi {
-    
-    input = [ [ id:'test3' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
-              []
-            ]
-
-    BCFTOOLS_CONCAT ( input )
-}
diff --git a/tests/modules/bcftools/concat/test.yml b/tests/modules/bcftools/concat/test.yml
deleted file mode 100644
index cffe3d66690..00000000000
--- a/tests/modules/bcftools/concat/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: bcftools concat test_bcftools_concat_tbi
-  command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/concat/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/concat
-  files:
-    - path: output/bcftools/test3.vcf.gz
-      md5sum: 1f6a3ffdffbc56e0bc1b184e70ee88df
-
-- name: bcftools concat test_bcftools_concat_no_tbi
-  command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/concat/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/concat
-  files:
-    - path: output/bcftools/test3.vcf.gz
-      md5sum: 1f6a3ffdffbc56e0bc1b184e70ee88df
diff --git a/tests/modules/bcftools/consensus/main.nf b/tests/modules/bcftools/consensus/main.nf
deleted file mode 100644
index b2ee899bbcb..00000000000
--- a/tests/modules/bcftools/consensus/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_CONSENSUS } from '../../../../modules/bcftools/consensus/main.nf'
-
-workflow test_bcftools_consensus {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    BCFTOOLS_CONSENSUS ( input )
-}
diff --git a/tests/modules/bcftools/consensus/test.yml b/tests/modules/bcftools/consensus/test.yml
deleted file mode 100644
index 7fa4ecae9e3..00000000000
--- a/tests/modules/bcftools/consensus/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bcftools consensus test_bcftools_consensus
-  command: nextflow run ./tests/modules/bcftools/consensus -entry test_bcftools_consensus -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/consensus/nextflow.config
-  tags:
-    - bcftools/consensus
-    - bcftools
-  files:
-    - path: output/bcftools/test.fa
-      md5sum: e57d3e4d113f989bc069c5fd61627091
diff --git a/tests/modules/bcftools/convert/main.nf b/tests/modules/bcftools/convert/main.nf
deleted file mode 100644
index 9277b2d1251..00000000000
--- a/tests/modules/bcftools/convert/main.nf
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_GVCF } from '../../../../modules/bcftools/convert/main.nf'
-include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_BCF  } from '../../../../modules/bcftools/convert/main.nf'
-
-workflow test_bcftools_convert_gvcf {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-        []
-    ]
-
-    bed = []
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    BCFTOOLS_CONVERT_GVCF ( input, bed, fasta )
-}
-
-workflow test_bcftools_convert_gvcf_bed {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    BCFTOOLS_CONVERT_GVCF ( input, bed, fasta )
-}
-
-workflow test_bcftools_convert_gvcf_to_bcf {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-        []
-    ]
-
-    bed = []
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    BCFTOOLS_CONVERT_BCF ( input, bed, fasta )
-}
diff --git a/tests/modules/bcftools/convert/test.yml b/tests/modules/bcftools/convert/test.yml
deleted file mode 100644
index 2a031a1b2a9..00000000000
--- a/tests/modules/bcftools/convert/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: bcftools convert test_bcftools_convert_gvcf
-  command: nextflow run ./tests/modules/bcftools/convert -entry test_bcftools_convert_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/convert/nextflow.config
-  tags:
-    - bcftools/convert
-    - bcftools
-  files:
-    - path: output/bcftools/test.vcf.gz
-
-- name: bcftools convert test_bcftools_convert_gvcf_bed
-  command: nextflow run ./tests/modules/bcftools/convert -entry test_bcftools_convert_gvcf_bed -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/convert/nextflow.config
-  tags:
-    - bcftools/convert
-    - bcftools
-  files:
-    - path: output/bcftools/test.vcf.gz
-
-- name: bcftools convert test_bcftools_convert_gvcf_to_bcf
-  command: nextflow run ./tests/modules/bcftools/convert -entry test_bcftools_convert_gvcf_to_bcf -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/convert/nextflow.config
-  tags:
-    - bcftools/convert
-    - bcftools
-  files:
-    - path: output/bcftools/test.bcf.gz
diff --git a/tests/modules/bcftools/filter/main.nf b/tests/modules/bcftools/filter/main.nf
deleted file mode 100644
index 85fbf950e3a..00000000000
--- a/tests/modules/bcftools/filter/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-//keep --no-verson argument, otherwise md5 will change on each execution
-include { BCFTOOLS_FILTER } from '../../../../modules/bcftools/filter/main.nf'
-
-workflow test_bcftools_filter {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
-            ]
-
-    BCFTOOLS_FILTER ( input )
-}
diff --git a/tests/modules/bcftools/filter/test.yml b/tests/modules/bcftools/filter/test.yml
deleted file mode 100644
index 096071bd50e..00000000000
--- a/tests/modules/bcftools/filter/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bcftools filter test_bcftools_filter
-  command: nextflow run ./tests/modules/bcftools/filter -entry test_bcftools_filter -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/filter/nextflow.config
-  tags:
-    - bcftools/filter
-    - bcftools
-  files:
-    - path: output/bcftools/test.vcf.gz
-      md5sum: c5f2a6a912964c45e8231140420561f9
diff --git a/tests/modules/bcftools/index/main.nf b/tests/modules/bcftools/index/main.nf
deleted file mode 100644
index 839cd988c85..00000000000
--- a/tests/modules/bcftools/index/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_CSI } from '../../../../modules/bcftools/index/main.nf'
-include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_TBI } from '../../../../modules/bcftools/index/main.nf'
-
-
-workflow test_bcftools_index_csi {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
-
-    BCFTOOLS_INDEX_CSI ( input )
-}
-
-workflow test_bcftools_index_tbi {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
-
-    BCFTOOLS_INDEX_TBI ( input )
-}
diff --git a/tests/modules/bcftools/index/test.yml b/tests/modules/bcftools/index/test.yml
deleted file mode 100644
index b8a7d7052ac..00000000000
--- a/tests/modules/bcftools/index/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: bcftools index
-  command: nextflow run ./tests/modules/bcftools/index -entry test_bcftools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/index/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/index
-  files:
-    - path: output/bcftools/test.vcf.gz.csi
-      md5sum: 9c49464e5983cc02ba89c862c2f33cf8
-
-- name: bcftools index tbi
-  command: nextflow run ./tests/modules/bcftools/index -entry test_bcftools_index_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/index/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/index
-  files:
-    - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: a5c54806112b6b2464d4985b96b176c0
diff --git a/tests/modules/bcftools/isec/main.nf b/tests/modules/bcftools/isec/main.nf
deleted file mode 100644
index 0b8ffc5cd0e..00000000000
--- a/tests/modules/bcftools/isec/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_ISEC } from '../../../../modules/bcftools/isec/main.nf'
-
-workflow test_bcftools_isec {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)],
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)]
-            ]
-
-    BCFTOOLS_ISEC ( input )
-}
diff --git a/tests/modules/bcftools/isec/test.yml b/tests/modules/bcftools/isec/test.yml
deleted file mode 100644
index 6329c34e7fc..00000000000
--- a/tests/modules/bcftools/isec/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: bcftools isec test_bcftools_isec
-  command: nextflow run ./tests/modules/bcftools/isec -entry test_bcftools_isec -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/isec/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/isec
-  files:
-    - path: output/bcftools/test/0000.vcf.gz
-      md5sum: c5f2a6a912964c45e8231140420561f9
-    - path: output/bcftools/test/0001.vcf.gz.tbi
-      md5sum: a596568a2bbab1acd817427bf3ceb20e
-    - path: output/bcftools/test/sites.txt
-      md5sum: 1cea3fbde7f6d3c97f3d39036f9690df
-    - path: output/bcftools/test/0000.vcf.gz.tbi
-      md5sum: a596568a2bbab1acd817427bf3ceb20e
-    - path: output/bcftools/test/0001.vcf.gz
-      md5sum: c5f2a6a912964c45e8231140420561f9
-    - path: output/bcftools/test/README.txt
-      md5sum: 10fc33b66522645600d44afbd41fb792
diff --git a/tests/modules/bcftools/merge/main.nf b/tests/modules/bcftools/merge/main.nf
deleted file mode 100644
index 0ec188d2d96..00000000000
--- a/tests/modules/bcftools/merge/main.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-//keep --no-verson argument, otherwise md5 will change on each execution
-include { BCFTOOLS_MERGE                        } from '../../../../modules/bcftools/merge/main.nf'
-include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_GVCF } from '../../../../modules/bcftools/merge/main.nf'
-include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_BCF  } from '../../../../modules/bcftools/merge/main.nf'
-
-workflow test_bcftools_merge {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
-            ]
-
-    bed = []
-    fasta = []
-    fasta_fai = []
-
-    BCFTOOLS_MERGE ( input, bed, fasta, fasta_fai )
-}
-
-workflow test_bcftools_merge_bed {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
-            ]
-
-    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    fasta = []
-    fasta_fai = []
-
-    BCFTOOLS_MERGE ( input, bed, fasta, fasta_fai )
-}
-
-workflow test_bcftools_merge_gvcf {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ],
-              [ file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz_tbi'], checkIfExists: true) ]
-            ]
-
-    bed = []
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    BCFTOOLS_MERGE_GVCF ( input, bed, fasta, fasta_fai )
-}
-
-workflow test_bcftools_merge_bcf {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
-            ]
-
-    bed = []
-    fasta = []
-    fasta_fai = []
-
-    BCFTOOLS_MERGE_BCF ( input, bed, fasta, fasta_fai )
-}
diff --git a/tests/modules/bcftools/merge/test.yml b/tests/modules/bcftools/merge/test.yml
deleted file mode 100644
index 5bf3be4eb63..00000000000
--- a/tests/modules/bcftools/merge/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: bcftools merge test_bcftools_merge
-  command: nextflow run ./tests/modules/bcftools/merge -entry test_bcftools_merge -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/merge/nextflow.config
-  tags:
-    - bcftools/merge
-    - bcftools
-  files:
-    - path: output/bcftools/test.vcf.gz
-      md5sum: 744b28bef1469aabdcfd354293ef725d
-
-- name: bcftools merge test_bcftools_merge_bed
-  command: nextflow run ./tests/modules/bcftools/merge -entry test_bcftools_merge_bed -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/merge/nextflow.config
-  tags:
-    - bcftools/merge
-    - bcftools
-  files:
-    - path: output/bcftools/test.vcf.gz
-      md5sum: 9597e71ae1706f76f00707687be43240
-
-- name: bcftools merge test_bcftools_merge_gvcf
-  command: nextflow run ./tests/modules/bcftools/merge -entry test_bcftools_merge_gvcf -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/merge/nextflow.config
-  tags:
-    - bcftools/merge
-    - bcftools
-  files:
-    - path: output/bcftools/test.vcf.gz
-      md5sum: 8aef4d860228cb651e0cb920376f5118
-
-- name: bcftools merge test_bcftools_merge_bcf
-  command: nextflow run ./tests/modules/bcftools/merge -entry test_bcftools_merge_bcf -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/merge/nextflow.config
-  tags:
-    - bcftools/merge
-    - bcftools
-  files:
-    - path: output/bcftools/test.bcf.gz
-      md5sum: 3ca1ab0d9a6ede049c6eeadf88177eb9
diff --git a/tests/modules/bcftools/mpileup/main.nf b/tests/modules/bcftools/mpileup/main.nf
deleted file mode 100644
index 1568f157428..00000000000
--- a/tests/modules/bcftools/mpileup/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf'
-
-workflow test_bcftools_mpileup {
-
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_mpileup = false
-
-    BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
-}
-
-workflow test_bcftools_save_mpileup {
-
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_mpileup = true
-
-    BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
-}
diff --git a/tests/modules/bcftools/mpileup/test.yml b/tests/modules/bcftools/mpileup/test.yml
deleted file mode 100644
index 85749cdb7c2..00000000000
--- a/tests/modules/bcftools/mpileup/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: bcftools mpileup test_bcftools_mpileup
-  command: nextflow run ./tests/modules/bcftools/mpileup -entry test_bcftools_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config
-  tags:
-    - bcftools/mpileup
-    - bcftools
-  files:
-    - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 4bb496a523ce6b35432d3bbb6b24a885
-    - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: f5e9c86c2269138663c9fb3effe840da
-    - path: output/bcftools/test.vcf.gz
-      md5sum: f37c4bdb0b7a4330477d6716ae2778c2
-
-- name: bcftools mpileup test_bcftools_save_mpileup
-  command: nextflow run ./tests/modules/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config
-  tags:
-    - bcftools/mpileup
-    - bcftools
-  files:
-    - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 4bb496a523ce6b35432d3bbb6b24a885
-    - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: f5e9c86c2269138663c9fb3effe840da
-    - path: output/bcftools/test.vcf.gz
-      md5sum: f37c4bdb0b7a4330477d6716ae2778c2
-    - path: output/bcftools/test.mpileup
-      md5sum: d7c55262aa6637487ba1c621983cfb49
diff --git a/tests/modules/bcftools/norm/main.nf b/tests/modules/bcftools/norm/main.nf
deleted file mode 100644
index a9ac75ba53c..00000000000
--- a/tests/modules/bcftools/norm/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_NORM } from '../../../../modules/bcftools/norm/main.nf'
-
-workflow test_bcftools_norm_no_tbi {
-    
-    input = [ [ id:'test2', single_end:false ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-            []
-            ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BCFTOOLS_NORM ( input, fasta )
-}
-
-workflow test_bcftools_norm_tbi {
-    
-    input = [ [ id:'test2', single_end:false ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)            
-            ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BCFTOOLS_NORM ( input, fasta )
-}
diff --git a/tests/modules/bcftools/norm/test.yml b/tests/modules/bcftools/norm/test.yml
deleted file mode 100644
index bdc3ce3fdc0..00000000000
--- a/tests/modules/bcftools/norm/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: bcftools norm test_bcftools_norm_no_tbi
-  command: nextflow run ./tests/modules/bcftools/norm -entry test_bcftools_norm_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/norm/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/norm
-  files:
-    - path: output/bcftools/test2.vcf.gz
-
-- name: bcftools norm test_bcftools_norm_tbi
-  command: nextflow run ./tests/modules/bcftools/norm -entry test_bcftools_norm_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/norm/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/norm
-  files:
-    - path: output/bcftools/test2.vcf.gz
diff --git a/tests/modules/bcftools/query/main.nf b/tests/modules/bcftools/query/main.nf
deleted file mode 100644
index f40cb0faa7c..00000000000
--- a/tests/modules/bcftools/query/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_QUERY } from '../../../../modules/bcftools/query/main.nf'
-
-workflow test_bcftools_query {
-
-    input = [ [ id:'out' ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-    regions = []
-    targets = []
-    samples = []
-
-    BCFTOOLS_QUERY ( input, regions, targets, samples )
-}
-
-workflow test_bcftools_query_with_optional_files {
-
-    input = [ [ id:'out' ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-    regions = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
-    targets = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
-    samples = []
-
-    BCFTOOLS_QUERY ( input, regions, targets, samples )
-}
diff --git a/tests/modules/bcftools/query/test.yml b/tests/modules/bcftools/query/test.yml
deleted file mode 100644
index 69199109863..00000000000
--- a/tests/modules/bcftools/query/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: bcftools query
-  command: nextflow run ./tests/modules/bcftools/query -entry test_bcftools_query -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/query/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/query
-  files:
-    - path: output/bcftools/out.txt
-      md5sum: c32a6d28f185822d8fe1eeb7e42ec155
-
-- name: bcftools query with optional files
-  command: nextflow run ./tests/modules/bcftools/query -entry test_bcftools_query_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/query/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/query
-  files:
-    - path: output/bcftools/out.txt
-      md5sum: 5a87e0865df2f0ab2884fc113ec2a70d
diff --git a/tests/modules/bcftools/reheader/main.nf b/tests/modules/bcftools/reheader/main.nf
deleted file mode 100644
index d1dcd8b8269..00000000000
--- a/tests/modules/bcftools/reheader/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_REHEADER } from '../../../../modules/bcftools/reheader/main.nf'
-
-workflow test_bcftools_reheader_update_sequences {
-
-    input = [
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-    ]
-    fai    = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    header = []
-    BCFTOOLS_REHEADER ( input, fai, header )
-}
-
-workflow test_bcftools_reheader_new_header {
-
-    input = [
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-    ]
-    fai    = []
-    header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-
-    BCFTOOLS_REHEADER ( input, fai, header )
-}
-
-workflow test_bcftools_reheader_new_header_update_sequences {
-
-    input = [
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-    ]
-    fai    = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-
-    BCFTOOLS_REHEADER ( input, fai, header )
-}
diff --git a/tests/modules/bcftools/reheader/test.yml b/tests/modules/bcftools/reheader/test.yml
deleted file mode 100644
index 2a3e48689fa..00000000000
--- a/tests/modules/bcftools/reheader/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: bcftools reheader test_bcftools_reheader_update_sequences
-  command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config
-  tags:
-    - bcftools/reheader
-    - bcftools
-  files:
-    - path: output/bcftools/test.updated.vcf.gz
-      md5sum: c8a732976911c0c0815d973d5974769a
-
-- name: bcftools reheader test_bcftools_reheader_new_header
-  command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config
-  tags:
-    - bcftools/reheader
-    - bcftools
-  files:
-    - path: output/bcftools/test.updated.vcf.gz
-      md5sum: aba91c9ec58e38d73657f02df8457b66
-
-- name: bcftools reheader test_bcftools_reheader_new_header_update_sequences
-  command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config
-  tags:
-    - bcftools/reheader
-    - bcftools
-  files:
-    - path: output/bcftools/test.updated.vcf.gz
-      md5sum: c8a732976911c0c0815d973d5974769a
diff --git a/tests/modules/bcftools/roh/main.nf b/tests/modules/bcftools/roh/main.nf
deleted file mode 100644
index 3a2ef6402a6..00000000000
--- a/tests/modules/bcftools/roh/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf'
-
-workflow test_bcftools_roh {
-
-    input = [ [ id:'test' ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-
-    af_file = [[],[]]
-    gen_map = []
-    regions = []
-    targets = []
-    samples = []
-
-    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
-}
-
-workflow test_bcftools_roh_stub {
-
-    input = [ [ id:'test' ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-
-    af_file = [[],[]]
-    gen_map = []
-    regions = []
-    targets = []
-    samples = []
-
-    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
-}
diff --git a/tests/modules/bcftools/roh/test.yml b/tests/modules/bcftools/roh/test.yml
deleted file mode 100644
index 9cc50a6654d..00000000000
--- a/tests/modules/bcftools/roh/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: "bcftools roh"
-  command: nextflow run ./tests/modules/bcftools/roh -entry test_bcftools_roh -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/roh/nextflow.config
-  tags:
-    - "bcftools"
-    - "bcftools/roh"
-  files:
-    - path: "output/bcftools/test.roh"
-    - path: "output/bcftools/versions.yml"
-
-- name: "bcftools roh stub"
-  command: nextflow run ./tests/modules/bcftools/roh -entry test_bcftools_roh_stub -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/roh/nextflow.config
-  tags:
-    - "bcftools"
-    - "bcftools/roh"
-  files:
-    - path: "output/bcftools/test.roh"
-    - path: "output/bcftools/versions.yml"
diff --git a/tests/modules/bcftools/sort/main.nf b/tests/modules/bcftools/sort/main.nf
deleted file mode 100644
index fadb8270f8a..00000000000
--- a/tests/modules/bcftools/sort/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_SORT } from '../../../../modules/bcftools/sort/main.nf'
-
-workflow test_bcftools_sort {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
-
-    BCFTOOLS_SORT ( input )
-}
diff --git a/tests/modules/bcftools/sort/test.yml b/tests/modules/bcftools/sort/test.yml
deleted file mode 100644
index fbb18300ba9..00000000000
--- a/tests/modules/bcftools/sort/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: bcftools sort test_bcftools_sort
-  command: nextflow run tests/modules/bcftools/sort -entry test_bcftools_sort -c tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/sort
-  files:
-    - path: output/bcftools/test.vcf.gz
-      md5sum: c5f2a6a912964c45e8231140420561f9
-    - path: output/bcftools/versions.yml
-      md5sum: 70cbb59e64c37a6ab6131b0e470892f4
diff --git a/tests/modules/bcftools/stats/main.nf b/tests/modules/bcftools/stats/main.nf
deleted file mode 100644
index dbc3268ab27..00000000000
--- a/tests/modules/bcftools/stats/main.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_STATS } from '../../../../modules/bcftools/stats/main.nf'
-
-workflow test_bcftools_stats {
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-            []]
-    regions = []
-    targets = []
-    samples = []
-
-    BCFTOOLS_STATS ( input, regions, targets, samples )
-}
-
-workflow test_bcftools_stats_regions {
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-    regions = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
-    targets = []
-    samples = []
-
-    BCFTOOLS_STATS ( input, regions, targets, samples )
-}
-
-workflow test_bcftools_stats_targets {
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-            []]
-    regions = []
-    targets = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
-    samples = []
-
-    BCFTOOLS_STATS ( input, regions, targets, samples )
-}
diff --git a/tests/modules/bcftools/stats/test.yml b/tests/modules/bcftools/stats/test.yml
deleted file mode 100644
index 282764463ac..00000000000
--- a/tests/modules/bcftools/stats/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: bcftools stats test_bcftools_stats
-  command: nextflow run ./tests/modules/bcftools/stats -entry test_bcftools_stats -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/stats/nextflow.config
-  tags:
-    - bcftools/stats
-    - bcftools
-  files:
-    - path: output/bcftools/test.bcftools_stats.txt
-      contains: ["TSTV	0	6	2	3.00	6	2	3.00", "DP	0	1	0	0.000000	5	55.555556"]
-
-- name: bcftools stats test_bcftools_stats_regions
-  command: nextflow run ./tests/modules/bcftools/stats -entry test_bcftools_stats_regions -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/stats/nextflow.config
-  tags:
-    - bcftools/stats
-    - bcftools
-  files:
-    - path: output/bcftools/test.bcftools_stats.txt
-      contains: ["TSTV	0	5	1	5.00	5	1	5.00", "DP	0	1	0	0.000000	3	42.857143"]
-
-- name: bcftools stats test_bcftools_stats_targets
-  command: nextflow run ./tests/modules/bcftools/stats -entry test_bcftools_stats_targets -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/stats/nextflow.config
-  tags:
-    - bcftools/stats
-    - bcftools
-  files:
-    - path: output/bcftools/test.bcftools_stats.txt
-      contains: ["TSTV	0	6	2	3.00	6	2	3.00", "DP	0	1	0	0.000000	5	55.555556"]
diff --git a/tests/modules/bcftools/view/main.nf b/tests/modules/bcftools/view/main.nf
deleted file mode 100644
index f45d0284ac8..00000000000
--- a/tests/modules/bcftools/view/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_VIEW } from '../../../../modules/bcftools/view/main.nf'
-
-workflow test_bcftools_view {
-
-    regions = []
-    targets = []
-    samples = []
-
-    input = [[ id:'out', single_end:false ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-
-    BCFTOOLS_VIEW ( input, regions, targets, samples )
-}
-
-workflow test_bcftools_view_with_optional_files {
-
-    regions = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
-    targets = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
-    samples = []
-
-    input = [[ id:'out', single_end:false ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)]
-
-    BCFTOOLS_VIEW ( input, regions, targets, samples )
-}
diff --git a/tests/modules/bcftools/view/test.yml b/tests/modules/bcftools/view/test.yml
deleted file mode 100644
index b66402a352c..00000000000
--- a/tests/modules/bcftools/view/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: bcftools view
-  command: nextflow run ./tests/modules/bcftools/view -entry test_bcftools_view -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/view/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/view
-  files:
-    - path: output/bcftools/out.vcf.gz
-      md5sum: c5f2a6a912964c45e8231140420561f9
-
-- name: bcftools view with optional files
-  command: nextflow run ./tests/modules/bcftools/view -entry test_bcftools_view_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/view/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/view
-  files:
-    - path: output/bcftools/out.vcf.gz
-      md5sum: 265a36d06f8ac3bf52086e4467e537f8
diff --git a/tests/modules/bcl2fastq/main.nf b/tests/modules/bcl2fastq/main.nf
deleted file mode 100644
index 3564dbecc38..00000000000
--- a/tests/modules/bcl2fastq/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCL2FASTQ } from '../../../modules/bcl2fastq/main.nf'
-include { UNTAR      } from '../../../modules/untar/main.nf'
-
-workflow test_bcl2fastq {
-    ch_flowcell = Channel.value([
-            [id:'test', lane:1 ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)])
-
-    ch_flowcell
-    .multiMap { meta, ss, run ->
-        samplesheet: [meta, ss]
-        tar: [meta, run]
-    }.set{ ch_fc_split }
-
-    ch_flowcell_untar = ch_fc_split.samplesheet.join( UNTAR ( ch_fc_split.tar ).untar )
-
-    BCL2FASTQ (ch_flowcell_untar)
-}
diff --git a/tests/modules/bcl2fastq/test.yml b/tests/modules/bcl2fastq/test.yml
deleted file mode 100644
index 80837fec58a..00000000000
--- a/tests/modules/bcl2fastq/test.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-- name: bcl2fastq test_bcl2fastq
-  command: nextflow run ./tests/modules/bcl2fastq -entry test_bcl2fastq -c ./tests/config/nextflow.config  -c ./tests/modules/bcl2fastq/nextflow.config
-  tags:
-    - bcl2fastq
-  files:
-    - path: output/bcl2fastq/Sample1_S1_L001_R1_001.fastq.gz
-      md5sum: e92fce7b86c6447b053d72c5cb4be89c
-    - path: output/bcl2fastq/Stats/AdapterTrimming.txt
-      md5sum: 48ed2b914b1246c0b5d8667525550946
-    - path: output/bcl2fastq/Stats/ConversionStats.xml
-      md5sum: 8fe0f57f3f5d256a0762dba75ac62d05
-    - path: output/bcl2fastq/Stats/DemultiplexingStats.xml
-      md5sum: 2047ff18f5b9107c084de06e9ff943ad
-    - path: output/bcl2fastq/Stats/DemuxSummaryF1L1.txt
-      md5sum: 03e5fd0c1e3079c5f8c7b4d0501b37ff
-    - path: output/bcl2fastq/Stats/FastqSummaryF1L1.txt
-      md5sum: 0c6f2d87ee183b84d1051cde9a5643d1
-    - path: output/bcl2fastq/Stats/Stats.json
-      md5sum: 8e5f038b8aa9e465599d3575f930e604
-    - path: output/bcl2fastq/flowcell/InterOp/ControlMetricsOut.bin
-      md5sum: 6d77b38d0793a6e1ce1e85706e488953
-    - path: output/bcl2fastq/flowcell/InterOp/CorrectedIntMetricsOut.bin
-      md5sum: 2bbf84d3be72734addaa2fe794711434
-    - path: output/bcl2fastq/flowcell/InterOp/ErrorMetricsOut.bin
-      md5sum: 38c88def138e9bb832539911affdb286
-    - path: output/bcl2fastq/flowcell/InterOp/ExtractionMetricsOut.bin
-      md5sum: 7497c3178837eea8f09350b5cd252e99
-    - path: output/bcl2fastq/flowcell/InterOp/IndexMetricsOut.bin
-      md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
-    - path: output/bcl2fastq/flowcell/InterOp/QMetricsOut.bin
-      md5sum: 7e9f198d53ebdfbb699a5f94cf1ed51c
-    - path: output/bcl2fastq/flowcell/InterOp/TileMetricsOut.bin
-      md5sum: 83891751ec1c91a425a524b476b6ca3c
diff --git a/tests/modules/bclconvert/main.nf b/tests/modules/bclconvert/main.nf
deleted file mode 100644
index b2ba3b8639b..00000000000
--- a/tests/modules/bclconvert/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCLCONVERT } from '../../../modules/bclconvert/main.nf'
-include { UNTAR      } from '../../../modules/untar/main.nf'
-
-workflow test_bclconvert {
-    ch_flowcell = Channel.value([
-            [id:'test', lane:1 ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)])
-
-    ch_flowcell
-    .multiMap { meta, ss, run ->
-        samplesheet: [meta, ss]
-        tar: [meta, run]
-    }.set{ ch_fc_split }
-
-    ch_flowcell_untar = ch_fc_split.samplesheet.join( UNTAR ( ch_fc_split.tar ).untar )
-
-    BCLCONVERT (ch_flowcell_untar)
-}
diff --git a/tests/modules/bclconvert/test.yml b/tests/modules/bclconvert/test.yml
deleted file mode 100644
index 1ee3fac5ece..00000000000
--- a/tests/modules/bclconvert/test.yml
+++ /dev/null
@@ -1,50 +0,0 @@
-- name: bclconvert test_bclconvert
-  command: nextflow run ./tests/modules/bclconvert -entry test_bclconvert -c ./tests/config/nextflow.config  -c ./tests/modules/bclconvert/nextflow.config
-  tags:
-    - bclconvert
-  files:
-    - path: output/bclconvert/Logs/Errors.log
-    - path: output/bclconvert/Logs/FastqComplete.txt
-    - path: output/bclconvert/Logs/Info.log
-    - path: output/bclconvert/Logs/Warnings.log
-    - path: output/bclconvert/Reports/Adapter_Cycle_Metrics.csv
-      md5sum: 5a0c88793b4a0885fe3dda16609b576e
-    - path: output/bclconvert/Reports/Adapter_Metrics.csv
-      md5sum: 989240b8840b2169ac1061f952c90f6c
-    - path: output/bclconvert/Reports/Demultiplex_Stats.csv
-      md5sum: 93949a8cd96f907d83e0808c1ec2a04b
-    - path: output/bclconvert/Reports/Demultiplex_Tile_Stats.csv
-      md5sum: 83120160b0f22a1303fa1db31c19f6e9
-    - path: output/bclconvert/Reports/IndexMetricsOut.bin
-      md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
-    - path: output/bclconvert/Reports/Index_Hopping_Counts.csv
-      md5sum: 1059369e375fd8f8423c0f6c934be978
-    - path: output/bclconvert/Reports/Quality_Metrics.csv
-      md5sum: 6614accb1bb414fe312b17b81f5521f7
-    - path: output/bclconvert/Reports/Quality_Tile_Metrics.csv
-      md5sum: cdc89fd2962bdd4a24f71e186112118a
-    - path: output/bclconvert/Reports/RunInfo.xml
-      md5sum: 03038959f4dd181c86bc97ae71fe270a
-    - path: output/bclconvert/Reports/SampleSheet.csv
-      md5sum: dc0dffd39541dd6cc5b4801d768a8d2b
-    - path: output/bclconvert/Reports/Top_Unknown_Barcodes.csv
-      md5sum: 2e2faba761137f228e56bd3428453ccc
-    - path: output/bclconvert/Reports/fastq_list.csv
-      md5sum: 05bc84f51840f5754cfb8381b36f2cb0
-    - path: output/bclconvert/Sample1_S1_L001_R1_001.fastq.gz
-      md5sum: 0a0341e2990b4fa1d9ad4b4c603144c1
-    - path: output/bclconvert/Undetermined_S0_L001_R1_001.fastq.gz
-      md5sum: febef808ae5397ea4ee7ee40e5fd39e0
-    - path: output/bclconvert/flowcell/InterOp/ControlMetricsOut.bin
-      md5sum: 6d77b38d0793a6e1ce1e85706e488953
-    - path: output/bclconvert/flowcell/InterOp/CorrectedIntMetricsOut.bin
-      md5sum: 2bbf84d3be72734addaa2fe794711434
-    - path: output/bclconvert/flowcell/InterOp/ErrorMetricsOut.bin
-      md5sum: 38c88def138e9bb832539911affdb286
-    - path: output/bclconvert/flowcell/InterOp/ExtractionMetricsOut.bin
-      md5sum: 7497c3178837eea8f09350b5cd252e99
-    - path: output/bclconvert/flowcell/InterOp/IndexMetricsOut.bin
-    - path: output/bclconvert/flowcell/InterOp/QMetricsOut.bin
-      md5sum: 7e9f198d53ebdfbb699a5f94cf1ed51c
-    - path: output/bclconvert/flowcell/InterOp/TileMetricsOut.bin
-      md5sum: 83891751ec1c91a425a524b476b6ca3c
diff --git a/tests/modules/bedtools/bamtobed/main.nf b/tests/modules/bedtools/bamtobed/main.nf
deleted file mode 100644
index e7635a3d8b0..00000000000
--- a/tests/modules/bedtools/bamtobed/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_BAMTOBED } from '../../../../modules/bedtools/bamtobed/main.nf'
-
-workflow test_bedtools_bamtobed {
-    input = [ [ id:'test'], //meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
-            ]
-
-    BEDTOOLS_BAMTOBED ( input )
-}
diff --git a/tests/modules/bedtools/bamtobed/test.yml b/tests/modules/bedtools/bamtobed/test.yml
deleted file mode 100644
index b038467c7e0..00000000000
--- a/tests/modules/bedtools/bamtobed/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools bamtobed
-  command: nextflow run ./tests/modules/bedtools/bamtobed -entry test_bedtools_bamtobed -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/bamtobed/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/bamtobed
-  files:
-    - path: ./output/bedtools/test.bed
-      md5sum: 3c6b88e414debd889c10eb972180b687
diff --git a/tests/modules/bedtools/complement/main.nf b/tests/modules/bedtools/complement/main.nf
deleted file mode 100644
index a1cca0330c6..00000000000
--- a/tests/modules/bedtools/complement/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_COMPLEMENT } from '../../../../modules/bedtools/complement/main.nf'
-
-workflow test_bedtools_complement {
-    input = [ [ id:'test'],
-              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-            ]
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-
-    BEDTOOLS_COMPLEMENT ( input, sizes )
-}
diff --git a/tests/modules/bedtools/complement/test.yml b/tests/modules/bedtools/complement/test.yml
deleted file mode 100644
index 9dbeb36f028..00000000000
--- a/tests/modules/bedtools/complement/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools complement
-  command: nextflow run ./tests/modules/bedtools/complement -entry test_bedtools_complement -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/complement/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/complement
-  files:
-    - path: ./output/bedtools/test_out.bed
-      md5sum: d71df7e47aec0661c27b71e483e727f9
diff --git a/tests/modules/bedtools/genomecov/main.nf b/tests/modules/bedtools/genomecov/main.nf
deleted file mode 100644
index b507a2cdc3d..00000000000
--- a/tests/modules/bedtools/genomecov/main.nf
+++ /dev/null
@@ -1,57 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_GENOMECOV } from '../../../../modules/bedtools/genomecov/main.nf'
-
-workflow test_bedtools_genomecov_noscale {
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-        1
-    ]
-
-    sizes = []
-    extension = 'txt'
-
-    BEDTOOLS_GENOMECOV ( input, sizes, extension )
-}
-
-workflow test_bedtools_genomecov_nonbam_noscale {
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
-        1
-    ]
-
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-    extension = 'txt'
-
-    BEDTOOLS_GENOMECOV ( input, sizes, extension )
-}
-
-workflow test_bedtools_genomecov_scale {
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-        0.5
-    ]
-
-    sizes = file('dummy_chromosome_sizes')
-    extension = 'txt'
-
-    BEDTOOLS_GENOMECOV ( input, sizes, extension )
-}
-
-workflow test_bedtools_genomecov_nonbam_scale {
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
-        0.5
-    ]
-
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-    extension = 'txt'
-
-    BEDTOOLS_GENOMECOV ( input, sizes, extension )
-}
diff --git a/tests/modules/bedtools/genomecov/test.yml b/tests/modules/bedtools/genomecov/test.yml
deleted file mode 100644
index 8f63bde9cfd..00000000000
--- a/tests/modules/bedtools/genomecov/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: bedtools genomecov test_bedtools_genomecov_noscale
-  command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_noscale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/genomecov
-  files:
-    - path: output/bedtools/test_out.txt
-      md5sum: 66083198daca6c001d328ba9616e9b53
-
-- name: bedtools genomecov test_bedtools_genomecov_nonbam_noscale
-  command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_noscale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/genomecov
-  files:
-    - path: output/bedtools/test_out.txt
-      md5sum: f47b58840087426e5b643d8dfd155c1f
-
-- name: bedtools genomecov test_bedtools_genomecov_scale
-  command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_scale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/genomecov
-  files:
-    - path: output/bedtools/test_out.txt
-      md5sum: 01291b6e1beab72e046653e709eb0e10
-
-- name: bedtools genomecov test_bedtools_genomecov_nonbam_scale
-  command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_scale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/genomecov
-  files:
-    - path: output/bedtools/test_out.txt
-      md5sum: de3c59c0ea123bcdbbad27bc0a0a601e
diff --git a/tests/modules/bedtools/getfasta/main.nf b/tests/modules/bedtools/getfasta/main.nf
deleted file mode 100644
index 425c49d5f04..00000000000
--- a/tests/modules/bedtools/getfasta/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_GETFASTA } from '../../../../modules/bedtools/getfasta/main.nf'
-
-workflow test_bedtools_getfasta {
-    bed   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    
-    BEDTOOLS_GETFASTA ( bed, fasta )
-}
diff --git a/tests/modules/bedtools/getfasta/test.yml b/tests/modules/bedtools/getfasta/test.yml
deleted file mode 100644
index a455f861099..00000000000
--- a/tests/modules/bedtools/getfasta/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools getfasta
-  command: nextflow run ./tests/modules/bedtools/getfasta -entry test_bedtools_getfasta -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/getfasta/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/getfasta
-  files:
-    - path: ./output/bedtools/test.fa
-      md5sum: 41c3a45a57a16c04f828d8f8bb52df70
diff --git a/tests/modules/bedtools/intersect/main.nf b/tests/modules/bedtools/intersect/main.nf
deleted file mode 100644
index c17d03e6161..00000000000
--- a/tests/modules/bedtools/intersect/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_INTERSECT } from '../../../../modules/bedtools/intersect/main.nf'
-
-workflow test_bedtools_intersect {
-    input = [
-        [ id:'test' ],
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
-    ]
-
-    extension = 'bed'
-
-    BEDTOOLS_INTERSECT ( input, extension )
-}
-
-workflow test_bedtools_intersect_bam {
-    input = [
-        [ id:'test' ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
-    ]
-
-    extension = 'bam'
-
-    BEDTOOLS_INTERSECT ( input, extension )
-}
diff --git a/tests/modules/bedtools/intersect/test.yml b/tests/modules/bedtools/intersect/test.yml
deleted file mode 100644
index 86fe70cde03..00000000000
--- a/tests/modules/bedtools/intersect/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: bedtools intersect test_bedtools_intersect
-  command: nextflow run ./tests/modules/bedtools/intersect -entry test_bedtools_intersect -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/intersect/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/intersect
-  files:
-    - path: output/bedtools/test_out.bed
-      md5sum: afcbf01c2f2013aad71dbe8e34f2c15c
-
-- name: bedtools intersect test_bedtools_intersect_bam
-  command: nextflow run ./tests/modules/bedtools/intersect -entry test_bedtools_intersect_bam -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/intersect/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/intersect
-  files:
-    - path: output/bedtools/test_out.bam
-      md5sum: 738324efe2b1e442ceb6539a630c3fe6
diff --git a/tests/modules/bedtools/makewindows/main.nf b/tests/modules/bedtools/makewindows/main.nf
deleted file mode 100644
index ce37de725a9..00000000000
--- a/tests/modules/bedtools/makewindows/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf'
-
-workflow test_bedtools_makewindows {
-
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    ]
-
-    BEDTOOLS_MAKEWINDOWS ( input, true )
-}
diff --git a/tests/modules/bedtools/makewindows/test.yml b/tests/modules/bedtools/makewindows/test.yml
deleted file mode 100644
index 8accaa3613c..00000000000
--- a/tests/modules/bedtools/makewindows/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools makewindows test_bedtools_makewindows
-  command: nextflow run ./tests/modules/bedtools/makewindows -entry test_bedtools_makewindows -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/makewindows/nextflow.config
-  tags:
-    - bedtools/makewindows
-    - bedtools
-  files:
-    - path: output/bedtools/test.tab
-      md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e
diff --git a/tests/modules/bedtools/maskfasta/main.nf b/tests/modules/bedtools/maskfasta/main.nf
deleted file mode 100644
index 0da02ad3358..00000000000
--- a/tests/modules/bedtools/maskfasta/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_MASKFASTA } from '../../../../modules/bedtools/maskfasta/main.nf'
-
-workflow test_bedtools_maskfasta {
-    bed   = [ [ id:'test'],
-              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    
-    BEDTOOLS_MASKFASTA ( bed, fasta )
-}
diff --git a/tests/modules/bedtools/maskfasta/test.yml b/tests/modules/bedtools/maskfasta/test.yml
deleted file mode 100644
index f1e8f35a9ea..00000000000
--- a/tests/modules/bedtools/maskfasta/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools maskfasta
-  command: nextflow run ./tests/modules/bedtools/maskfasta -entry test_bedtools_maskfasta -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/maskfasta/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/maskfasta
-  files:
-    - path: ./output/bedtools/test.fa
-      md5sum: f4f6749698f11074228d2c79338e3b9c
diff --git a/tests/modules/bedtools/merge/main.nf b/tests/modules/bedtools/merge/main.nf
deleted file mode 100644
index 5fca0526b40..00000000000
--- a/tests/modules/bedtools/merge/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_MERGE } from '../../../../modules/bedtools/merge/main.nf'
-
-workflow test_bedtools_merge {
-    input = [ [ id:'test'],
-              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-            ]
-
-    BEDTOOLS_MERGE ( input )
-}
-
diff --git a/tests/modules/bedtools/merge/test.yml b/tests/modules/bedtools/merge/test.yml
deleted file mode 100644
index 5fc8b0344a8..00000000000
--- a/tests/modules/bedtools/merge/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools merge
-  command: nextflow run ./tests/modules/bedtools/merge -entry test_bedtools_merge -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/merge/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/merge
-  files:
-    - path: ./output/bedtools/test_out.bed
-      md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e
diff --git a/tests/modules/bedtools/slop/main.nf b/tests/modules/bedtools/slop/main.nf
deleted file mode 100644
index e7136fdc7be..00000000000
--- a/tests/modules/bedtools/slop/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_SLOP } from '../../../../modules/bedtools/slop/main.nf'
-
-workflow test_bedtools_slop {
-    input = [ [ id:'test'],
-              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-            ]
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-    
-    BEDTOOLS_SLOP ( input, sizes )
-}
-
diff --git a/tests/modules/bedtools/slop/test.yml b/tests/modules/bedtools/slop/test.yml
deleted file mode 100644
index 0d49e66b775..00000000000
--- a/tests/modules/bedtools/slop/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools slop
-  command: nextflow run ./tests/modules/bedtools/slop -entry test_bedtools_slop -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/slop/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/slop
-  files:
-    - path: ./output/bedtools/test_out.bed
-      md5sum: 4f1d8924925fe5d205c9e1981fe290a4
diff --git a/tests/modules/bedtools/sort/main.nf b/tests/modules/bedtools/sort/main.nf
deleted file mode 100644
index 342b411673a..00000000000
--- a/tests/modules/bedtools/sort/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_SORT } from '../../../../modules/bedtools/sort/main.nf'
-
-workflow test_bedtools_sort {
-    input = [ [ id:'test'],
-              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-            ]
-
-    BEDTOOLS_SORT ( input, "testext" )
-}
diff --git a/tests/modules/bedtools/sort/test.yml b/tests/modules/bedtools/sort/test.yml
deleted file mode 100644
index 173f0587aa5..00000000000
--- a/tests/modules/bedtools/sort/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools sort
-  command: nextflow run ./tests/modules/bedtools/sort -entry test_bedtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/sort/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/sort
-  files:
-    - path: ./output/bedtools/test_out.testext
-      md5sum: fe4053cf4de3aebbdfc3be2efb125a74
diff --git a/tests/modules/bedtools/split/main.nf b/tests/modules/bedtools/split/main.nf
deleted file mode 100644
index 7a1dc685b58..00000000000
--- a/tests/modules/bedtools/split/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_SPLIT } from '../../../../modules/bedtools/split/main.nf'
-
-workflow test_bedtools_split {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)
-    ]
-
-    number_of_files = 2
-
-    BEDTOOLS_SPLIT ( input, number_of_files )
-}
diff --git a/tests/modules/bedtools/split/test.yml b/tests/modules/bedtools/split/test.yml
deleted file mode 100644
index 92ac17fa318..00000000000
--- a/tests/modules/bedtools/split/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: bedtools split test_bedtools_split
-  command: nextflow run ./tests/modules/bedtools/split -entry test_bedtools_split -c ./tests/config/nextflow.config  -c ./tests/modules/bedtools/split/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/split
-  files:
-    - path: output/bedtools/test.00001.bed
-      md5sum: d58e5e46c2fcc3b8be5db0f023e93cb5
-    - path: output/bedtools/test.00002.bed
-      md5sum: 03caf952e9297a54620d2bbba8dc2823
diff --git a/tests/modules/bedtools/subtract/main.nf b/tests/modules/bedtools/subtract/main.nf
deleted file mode 100644
index 2a0e6eab7ef..00000000000
--- a/tests/modules/bedtools/subtract/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_SUBTRACT } from '../../../../modules/bedtools/subtract/main.nf'
-
-workflow test_bedtools_subtract {
-    input = [
-        [ id:'test_subtract' ],
-        file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    ]
-
-    BEDTOOLS_SUBTRACT ( input )
-}
diff --git a/tests/modules/bedtools/subtract/test.yml b/tests/modules/bedtools/subtract/test.yml
deleted file mode 100644
index 52b57436571..00000000000
--- a/tests/modules/bedtools/subtract/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools subtract
-  command: nextflow run ./tests/modules/bedtools/subtract -entry test_bedtools_subtract -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/subtract/nextflow.config
-  tags:
-    - bedtools
-    - bedtools/subtract
-  files:
-    - path: output/bedtools/test_subtract.bed
-      md5sum: 63513c4dc69e8b481ce3b4b2a9f24259
diff --git a/tests/modules/biobambam/bammarkduplicates2/main.nf b/tests/modules/biobambam/bammarkduplicates2/main.nf
deleted file mode 100644
index aeab18b9a57..00000000000
--- a/tests/modules/biobambam/bammarkduplicates2/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BIOBAMBAM_BAMMARKDUPLICATES2 } from '../../../../modules/biobambam/bammarkduplicates2/main.nf'
-
-workflow test_biobambam_bammarkduplicates2 {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
-    ]
-
-    BIOBAMBAM_BAMMARKDUPLICATES2 ( input )
-}
diff --git a/tests/modules/biobambam/bammarkduplicates2/test.yml b/tests/modules/biobambam/bammarkduplicates2/test.yml
deleted file mode 100644
index 7c16fcf1911..00000000000
--- a/tests/modules/biobambam/bammarkduplicates2/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: biobambam bammarkduplicates2 test_biobambam_bammarkduplicates2
-  command: nextflow run tests/modules/biobambam/bammarkduplicates2 -entry test_biobambam_bammarkduplicates2 -c tests/config/nextflow.config
-  tags:
-    - biobambam/bammarkduplicates2
-    - biobambam
-  files:
-    - path: output/biobambam/test.bam
-      md5sum: 603edff09029096ddf2bb8a3f12d7aa7
-    - path: output/biobambam/test.metrics.txt
-      md5sum: 30d6e7d90bb5df46329d4bc0144ce927
-    - path: output/biobambam/versions.yml
-      md5sum: dfdf2b084655d124acac0bfb4eda86cc
diff --git a/tests/modules/biobambam/bammerge/main.nf b/tests/modules/biobambam/bammerge/main.nf
deleted file mode 100644
index 7b4ee9cb6c8..00000000000
--- a/tests/modules/biobambam/bammerge/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BIOBAMBAM_BAMMERGE } from '../../../../modules/biobambam/bammerge/main.nf'
-
-workflow test_biobambam_bammerge_paired {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
-        ]
-    ]
-
-    BIOBAMBAM_BAMMERGE ( input )
-}
-
-workflow test_biobambam_bammerge_single {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-        ]
-    ]
-
-    BIOBAMBAM_BAMMERGE ( input )
-}
diff --git a/tests/modules/biobambam/bammerge/test.yml b/tests/modules/biobambam/bammerge/test.yml
deleted file mode 100644
index d68b70834a1..00000000000
--- a/tests/modules/biobambam/bammerge/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: biobambam bammerge test_biobambam_bammerge_paired
-  command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_paired -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bammerge/nextflow.config
-  tags:
-    - biobambam/bammerge
-    - biobambam
-  files:
-    - path: output/biobambam/test.bam
-      md5sum: bc3d32ab6a54d1894ca7cc79387dec57
-    - path: output/biobambam/test.bam.bai
-      md5sum: b8ae542a37a73d79de1c15c765207c53
-    - path: output/biobambam/test.md5
-      md5sum: 31c59857990ceb392242136429e30243
-
-- name: biobambam bammerge test_biobambam_bammerge_single
-  command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_single -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bammerge/nextflow.config
-  tags:
-    - biobambam/bammerge
-    - biobambam
-  files:
-    - path: output/biobambam/test.bam
-      md5sum: 86185d3d6895a7722d3b3a09c6f91bfc
-    - path: output/biobambam/test.bam.bai
-      md5sum: 973680feb6bc73cd1051ea83c7219418
-    - path: output/biobambam/test.md5
-      md5sum: 244a9d1cbc6d74724285c80220e5e427
diff --git a/tests/modules/biobambam/bamsormadup/main.nf b/tests/modules/biobambam/bamsormadup/main.nf
deleted file mode 100644
index 9bcb1cf3671..00000000000
--- a/tests/modules/biobambam/bamsormadup/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BIOBAMBAM_BAMSORMADUP } from '../../../../modules/biobambam/bamsormadup/main.nf'
-
-workflow test_biobambam_bamsormadup_multi_input {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
-    ]
-
-    BIOBAMBAM_BAMSORMADUP ( input, [] )
-}
-
-workflow test_biobambam_bamsormadup_single_input {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)],
-    ]
-
-    BIOBAMBAM_BAMSORMADUP ( input, [] )
-}
diff --git a/tests/modules/biobambam/bamsormadup/test.yml b/tests/modules/biobambam/bamsormadup/test.yml
deleted file mode 100644
index d197038ee86..00000000000
--- a/tests/modules/biobambam/bamsormadup/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: biobambam bamsormadup test_biobambam_bamsormadup_multi_input
-  command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup_multi_input -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bamsormadup/nextflow.config
-  tags:
-    - biobambam
-    - biobambam/bamsormadup
-  files:
-    - path: output/biobambam/test.bam
-      md5sum: 1d549a00b065584c298594180ca9f3bc
-    - path: output/biobambam/test.metrics.txt
-      md5sum: 1721879bea1f3888ecd33b35e6ee0e72
-
-- name: biobambam bamsormadup test_biobambam_bamsormadup_single_input
-  command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup_single_input -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bamsormadup/nextflow.config
-  tags:
-    - biobambam
-    - biobambam/bamsormadup
-  files:
-    - path: output/biobambam/test.bam
-      md5sum: 48e01431daec7fb17471d930a6d1d587
-    - path: output/biobambam/test.metrics.txt
-      md5sum: b97458eff0d4b259055e4902849ee53b
diff --git a/tests/modules/biscuit/align/main.nf b/tests/modules/biscuit/align/main.nf
deleted file mode 100644
index f3e3cb649cc..00000000000
--- a/tests/modules/biscuit/align/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISCUIT_INDEX }                     from '../../../../modules/biscuit/index/main.nf'
-include { BISCUIT_ALIGN as BISCUIT_ALIGN_SE } from '../../../../modules/biscuit/align/main.nf'
-include { BISCUIT_ALIGN as BISCUIT_ALIGN_PE } from '../../../../modules/biscuit/align/main.nf'
-
-
-// Single-end test
-workflow test_biscuit_align_single {
-
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX ( fasta )
-    BISCUIT_ALIGN_SE (input, BISCUIT_INDEX.out.index )
-}
-
-// paired-end test
-workflow test_biscuit_align_paired {
-
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX ( fasta )
-    BISCUIT_ALIGN_SE (input, BISCUIT_INDEX.out.index )
-}
diff --git a/tests/modules/biscuit/align/test.yml b/tests/modules/biscuit/align/test.yml
deleted file mode 100644
index bf778ff55ae..00000000000
--- a/tests/modules/biscuit/align/test.yml
+++ /dev/null
@@ -1,53 +0,0 @@
-- name: biscuit align test_biscuit_align_single
-  command: nextflow run tests/modules/biscuit/align -entry test_biscuit_align_single -c tests/config/nextflow.config
-  tags:
-    - biscuit
-    - biscuit/align
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test.bam
-      md5sum: eb36532425cb9b259410d6464a9e523a
-    - path: output/biscuit/versions.yml
-      md5sum: a86c4170bbf90cc75b93eb59ea124acd
-
-- name: biscuit align test_biscuit_align_paired
-  command: nextflow run tests/modules/biscuit/align -entry test_biscuit_align_paired -c tests/config/nextflow.config
-  tags:
-    - biscuit
-    - biscuit/align
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test.bam
-      md5sum: be3f6aa86c499d6a6b2996e5936e4f50
-    - path: output/biscuit/versions.yml
-      md5sum: f0b7dffd28f5e6bb1466fce6661d133f
diff --git a/tests/modules/biscuit/biscuitblaster/main.nf b/tests/modules/biscuit/biscuitblaster/main.nf
deleted file mode 100644
index 5e4bc95a999..00000000000
--- a/tests/modules/biscuit/biscuitblaster/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISCUIT_INDEX                         } from '../../../../modules/biscuit/index/main.nf'
-include { BISCUIT_BLASTER as BISCUIT_BLASTER_SE } from '../../../../modules/biscuit/biscuitblaster/main.nf'
-include { BISCUIT_BLASTER as BISCUIT_BLASTER_PE } from '../../../../modules/biscuit/biscuitblaster/main.nf'
-
-// Single-end test
-workflow test_biscuit_blaster_single {
-
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX ( fasta )
-    BISCUIT_BLASTER_SE (input, BISCUIT_INDEX.out.index )
-}
-
-// paired-end test
-workflow test_biscuit_blaster_paired {
-
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX ( fasta )
-    BISCUIT_BLASTER_PE (input, BISCUIT_INDEX.out.index )
-}
diff --git a/tests/modules/biscuit/biscuitblaster/test.yml b/tests/modules/biscuit/biscuitblaster/test.yml
deleted file mode 100644
index 37bb654360b..00000000000
--- a/tests/modules/biscuit/biscuitblaster/test.yml
+++ /dev/null
@@ -1,57 +0,0 @@
-- name: biscuit biscuitblaster test_biscuit_blaster_single
-  command: nextflow run tests/modules/biscuit/biscuitblaster -entry test_biscuit_blaster_single -c tests/config/nextflow.config
-  tags:
-    - biscuit/biscuitblaster
-    - biscuit
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test.bam
-      md5sum: 9ece50b67349382d38b20c2702e65675
-    - path: output/biscuit/test.bam.bai
-      md5sum: 8f14bb42fd38cc7ce4a3c3a9d7133ea4
-    - path: output/biscuit/versions.yml
-      md5sum: bfb660b5b0d92dde6817a1c6a2a302bb
-
-- name: biscuit biscuitblaster test_biscuit_blaster_paired
-  command: nextflow run tests/modules/biscuit/biscuitblaster -entry test_biscuit_blaster_paired -c tests/config/nextflow.config
-  tags:
-    - biscuit/biscuitblaster
-    - biscuit
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test.bam
-      md5sum: 0c6de35f38003df6ea5dd036170df91b
-    - path: output/biscuit/test.bam.bai
-      md5sum: 0d76977b2e36046cc176112776c5fa4e
-    - path: output/biscuit/versions.yml
-      md5sum: 82160a7ad29ccc3a21e59b1869399c04
diff --git a/tests/modules/biscuit/bsconv/main.nf b/tests/modules/biscuit/bsconv/main.nf
deleted file mode 100644
index f73388691fa..00000000000
--- a/tests/modules/biscuit/bsconv/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISCUIT_INDEX  } from '../../../../modules/biscuit/index/main.nf'
-include { BISCUIT_BSCONV } from '../../../../modules/biscuit/bsconv/main.nf'
-
-workflow test_biscuit_bsconv {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX( fasta )
-    BISCUIT_BSCONV ( input, BISCUIT_INDEX.out.index )
-}
diff --git a/tests/modules/biscuit/bsconv/test.yml b/tests/modules/biscuit/bsconv/test.yml
deleted file mode 100644
index 528a4fe5edd..00000000000
--- a/tests/modules/biscuit/bsconv/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: biscuit bsconv test_biscuit_bsconv
-  command: nextflow run tests/modules/biscuit/bsconv -entry test_biscuit_bsconv -c tests/config/nextflow.config
-  tags:
-    - biscuit
-    - biscuit/bsconv
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test.bam
-      md5sum: e33e9498d00dd32222b90a6bd981226f
-    - path: output/biscuit/versions.yml
-      md5sum: 7deec1f096203542bbb72ac4fa05f9ba
diff --git a/tests/modules/biscuit/epiread/main.nf b/tests/modules/biscuit/epiread/main.nf
deleted file mode 100644
index 54a73ae3ad1..00000000000
--- a/tests/modules/biscuit/epiread/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISCUIT_INDEX   } from '../../../../modules/biscuit/index/main.nf'
-include { BISCUIT_EPIREAD } from '../../../../modules/biscuit/epiread/main.nf'
-
-workflow test_biscuit_epiread_nosnp {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
-        [] //SNP BED file
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX( fasta )
-    BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
-}
-
-workflow test_biscuit_epiread_snp {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed')
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX( fasta )
-    BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
-}
-
-workflow test_biscuit_epiread_snp_decompress {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed.gz')
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX( fasta )
-    BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
-}
diff --git a/tests/modules/biscuit/epiread/test.yml b/tests/modules/biscuit/epiread/test.yml
deleted file mode 100644
index 1db86982a85..00000000000
--- a/tests/modules/biscuit/epiread/test.yml
+++ /dev/null
@@ -1,80 +0,0 @@
-- name: biscuit epiread test_biscuit_epiread_nosnp
-  command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_nosnp -c tests/config/nextflow.config
-  tags:
-    - biscuit
-    - biscuit/epiread
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test.bed.gz
-      md5sum: dbb30b59f4ef6fdfdee38630225c0574
-    - path: output/biscuit/versions.yml
-      md5sum: 674a77ac5ca8f4b42d30e58e30c3a9af
-
-- name: biscuit epiread test_biscuit_epiread_snp
-  command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_snp -c tests/config/nextflow.config
-  tags:
-    - biscuit
-    - biscuit/epiread
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test.bed.gz
-      md5sum: a29fea6ad74453ec94f8220747dab906
-    - path: output/biscuit/versions.yml
-      md5sum: f2f7c4ff3c6a135b1c8a3aff24a44d81
-
-- name: biscuit epiread test_biscuit_epiread_snp_decompress
-  command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_snp_decompress -c tests/config/nextflow.config
-  tags:
-    - biscuit
-    - biscuit/epiread
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test.bed.gz
-      md5sum: a29fea6ad74453ec94f8220747dab906
-    - path: output/biscuit/versions.yml
-      md5sum: cb0258ebf4e1a731a4310ec17c3dc442
diff --git a/tests/modules/biscuit/index/main.nf b/tests/modules/biscuit/index/main.nf
deleted file mode 100644
index c13d441bf00..00000000000
--- a/tests/modules/biscuit/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf'
-
-workflow test_biscuit_index {
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX ( fasta )
-}
diff --git a/tests/modules/biscuit/index/test.yml b/tests/modules/biscuit/index/test.yml
deleted file mode 100644
index a2e4cb67f78..00000000000
--- a/tests/modules/biscuit/index/test.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-- name: biscuit index test_biscuit_index
-  command: nextflow run tests/modules/biscuit/index -entry test_biscuit_index -c tests/config/nextflow.config
-  tags:
-    - biscuit/index
-    - biscuit
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/versions.yml
-      md5sum: 5c5873e482a57966db246648ffddf62f
diff --git a/tests/modules/biscuit/mergecg/main.nf b/tests/modules/biscuit/mergecg/main.nf
deleted file mode 100644
index 7d51f3b89bf..00000000000
--- a/tests/modules/biscuit/mergecg/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISCUIT_INDEX   } from '../../../../modules/biscuit/index/main.nf'
-include { BISCUIT_MERGECG } from '../../../../modules/biscuit/mergecg/main.nf'
-
-workflow test_biscuit_mergecg {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-cg.bed.gz', checkIfExists: true)
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX( fasta )
-    BISCUIT_MERGECG ( input, BISCUIT_INDEX.out.index )
-}
diff --git a/tests/modules/biscuit/mergecg/test.yml b/tests/modules/biscuit/mergecg/test.yml
deleted file mode 100644
index 7b2408bb95d..00000000000
--- a/tests/modules/biscuit/mergecg/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: biscuit mergecg test_biscuit_mergecg
-  command: nextflow run tests/modules/biscuit/mergecg -entry test_biscuit_mergecg -c tests/config/nextflow.config
-  tags:
-    - biscuit
-    - biscuit/mergecg
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test.bed.gz
-      md5sum: d693b28ddc81265f388860d391fc7c5b
-    - path: output/biscuit/versions.yml
-      md5sum: f670d63671af06bf8654677bf373b3a1
diff --git a/tests/modules/biscuit/pileup/main.nf b/tests/modules/biscuit/pileup/main.nf
deleted file mode 100644
index cf1914ece5c..00000000000
--- a/tests/modules/biscuit/pileup/main.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISCUIT_INDEX  } from '../../../../modules/biscuit/index/main.nf'
-include { BISCUIT_PILEUP } from '../../../../modules/biscuit/pileup/main.nf'
-
-workflow test_biscuit_pileup {
-
-    input = [ [ id:'test' ], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)],
-        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)],    
-	[], //tumor bam 
-	[] //tumor bai
-        ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX ( fasta )
-    BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
-
-}
-
-workflow test_biscuit_pileup_somatic {
-
-    input = [ [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)    
-        ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX ( fasta )
-    BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
-
-}
diff --git a/tests/modules/biscuit/pileup/test.yml b/tests/modules/biscuit/pileup/test.yml
deleted file mode 100644
index ad840737b9e..00000000000
--- a/tests/modules/biscuit/pileup/test.yml
+++ /dev/null
@@ -1,53 +0,0 @@
-- name: biscuit pileup test_biscuit_pileup
-  command: nextflow run tests/modules/biscuit/pileup -entry test_biscuit_pileup -c tests/config/nextflow.config
-  tags:
-    - biscuit
-    - biscuit/pileup
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: f315020d899597c1b57e5fe9f60f4c3e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 1891c1de381b3a96d4e72f590fde20c1
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: 668799eea40aefb8013cbf8ed6c47cfe
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 10541b05bbea44d0344b0345a6522ba8
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 2c38edd64234420add133f5fe1ff975d
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 7deee1aac3395d93bef1df11ab38379e
-    - path: output/biscuit/test.vcf.gz
-      md5sum: ef9798c318ead0f8a79ee7fdeb1ffbf9
-    - path: output/biscuit/versions.yml
-      md5sum: ae38b891fdbf9f7ff5c486408f949dc5
-
-- name: biscuit pileup test_biscuit_pileup_somatic
-  command: nextflow run tests/modules/biscuit/pileup -entry test_biscuit_pileup_somatic -c tests/config/nextflow.config
-  tags:
-    - biscuit
-    - biscuit/pileup
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: f315020d899597c1b57e5fe9f60f4c3e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 1891c1de381b3a96d4e72f590fde20c1
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: 668799eea40aefb8013cbf8ed6c47cfe
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 10541b05bbea44d0344b0345a6522ba8
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 2c38edd64234420add133f5fe1ff975d
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 7deee1aac3395d93bef1df11ab38379e
-    - path: output/biscuit/test.vcf.gz
-      md5sum: 692b4a6191b08fabe5efa5abe00da420
-    - path: output/biscuit/versions.yml
-      md5sum: cc51fd498d67fdc7cc067686eb855b93
diff --git a/tests/modules/biscuit/qc/main.nf b/tests/modules/biscuit/qc/main.nf
deleted file mode 100644
index 7c6d61cd63b..00000000000
--- a/tests/modules/biscuit/qc/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISCUIT_INDEX  } from '../../../../modules/biscuit/index/main.nf'
-include { BISCUIT_QC } from '../../../../modules/biscuit/qc/main.nf'
-
-workflow test_biscuit_qc {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISCUIT_INDEX( fasta )
-    BISCUIT_QC ( input, BISCUIT_INDEX.out.index )
-}
diff --git a/tests/modules/biscuit/qc/test.yml b/tests/modules/biscuit/qc/test.yml
deleted file mode 100644
index ed33dd30255..00000000000
--- a/tests/modules/biscuit/qc/test.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-- name: biscuit qc test_biscuit_qc
-  command: nextflow run tests/modules/biscuit/qc -entry test_biscuit_qc -c tests/config/nextflow.config
-  tags:
-    - biscuit/qc
-    - biscuit
-  files:
-    - path: output/biscuit/BiscuitIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
-      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
-    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
-      md5sum: 9c9e07fa1c75ef32d764274579c89b08
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
-      md5sum: 62eb83cd557a47b59589713d98024fc2
-    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
-      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
-    - path: output/biscuit/test_CpGRetentionByReadPos.txt
-      md5sum: 498b6c0af196fb34c8835371b9e9b68a
-    - path: output/biscuit/test_CpHRetentionByReadPos.txt
-      md5sum: a266942c5719cecab7f60f63cbe7335d
-    - path: output/biscuit/test_dup_report.txt
-      md5sum: 65bddf4fbe9e40d7c6c976060df53e3b
-    - path: output/biscuit/test_isize_table.txt
-      md5sum: aadf6f2e271abc334b6146cf164bdda3
-    - path: output/biscuit/test_mapq_table.txt
-      md5sum: c8adaac84bb8db3b7f48e1ed4fccad00
-    - path: output/biscuit/test_strand_table.txt
-      md5sum: 27068382ba6b2dbf313169a85c9dbb3a
-    - path: output/biscuit/test_totalReadConversionRate.txt
-      md5sum: 8f0c1fceaebfa74f2757720e3bc85fed
-    - path: output/biscuit/versions.yml
-      md5sum: a730fa4888e6882cf1b8ba92645b04ee
diff --git a/tests/modules/biscuit/vcf2bed/main.nf b/tests/modules/biscuit/vcf2bed/main.nf
deleted file mode 100644
index 25597d49bdf..00000000000
--- a/tests/modules/biscuit/vcf2bed/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISCUIT_VCF2BED } from '../../../../modules/biscuit/vcf2bed/main.nf'
-
-workflow test_biscuit_vcf2bed {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test.vcf.gz', checkIfExists: true)
-    ]
-
-    BISCUIT_VCF2BED ( input )
-
-}
diff --git a/tests/modules/biscuit/vcf2bed/test.yml b/tests/modules/biscuit/vcf2bed/test.yml
deleted file mode 100644
index 7eaa29727c0..00000000000
--- a/tests/modules/biscuit/vcf2bed/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: biscuit vcf2bed test_biscuit_vcf2bed
-  command: nextflow run tests/modules/biscuit/vcf2bed -entry test_biscuit_vcf2bed -c tests/config/nextflow.config
-  tags:
-    - biscuit/vcf2bed
-    - biscuit
-  files:
-    - path: output/biscuit/test.bed.gz
-      md5sum: e2dd492289dc8463f364285e31b9553a
-    - path: output/biscuit/versions.yml
-      md5sum: cd784276e2fb6739d55e1b60d12202cd
diff --git a/tests/modules/bismark/align/main.nf b/tests/modules/bismark/align/main.nf
deleted file mode 100644
index fe6d616a4c1..00000000000
--- a/tests/modules/bismark/align/main.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISMARK_GENOMEPREPARATION         } from '../../../../modules/bismark/genomepreparation/main.nf'
-include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../modules/bismark/align/main.nf'
-include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../modules/bismark/align/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_bismark_align_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISMARK_GENOMEPREPARATION ( fasta )
-    BISMARK_ALIGN_SE ( input, BISMARK_GENOMEPREPARATION.out.index )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_bismark_align_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISMARK_GENOMEPREPARATION ( fasta )
-    BISMARK_ALIGN_PE ( input, BISMARK_GENOMEPREPARATION.out.index )
-}
diff --git a/tests/modules/bismark/align/test.yml b/tests/modules/bismark/align/test.yml
deleted file mode 100644
index ffae05afc22..00000000000
--- a/tests/modules/bismark/align/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: bismark align single-end test workflow
-  command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bismark/align/nextflow.config
-  tags:
-    - bismark
-    - bismark/align
-  files:
-    - path: output/bismark/test.methylated_1_bismark_bt2.bam
-      md5sum: dca4ba9ff705b70446f812e59bdb1a32
-    - path: output/bismark/test.methylated_1_bismark_bt2_SE_report.txt
-
-- name: bismark align paired-end test workflow
-  command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bismark/align/nextflow.config
-  tags:
-    - bismark
-    - bismark/align
-  files:
-    - path: output/bismark/test.methylated_1_bismark_bt2_pe.bam
-      md5sum: 43943b1f30d056fcbd9ed26061ea0583
-    - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.txt
diff --git a/tests/modules/bismark/deduplicate/main.nf b/tests/modules/bismark/deduplicate/main.nf
deleted file mode 100644
index ad97d66aad3..00000000000
--- a/tests/modules/bismark/deduplicate/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf'
-
-workflow test_bismark_deduplicate {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_bam'], checkIfExists: true) ]
-            ]
-
-    BISMARK_DEDUPLICATE ( input )
-}
diff --git a/tests/modules/bismark/deduplicate/test.yml b/tests/modules/bismark/deduplicate/test.yml
deleted file mode 100644
index 12099750195..00000000000
--- a/tests/modules/bismark/deduplicate/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: bismark deduplicate test workflow
-  command: nextflow run ./tests/modules/bismark/deduplicate -entry test_bismark_deduplicate -c ./tests/config/nextflow.config -c ./tests/modules/bismark/deduplicate/nextflow.config
-  tags:
-    - bismark
-    - bismark/deduplicate
-  files:
-    - path: output/bismark/test.paired_end.methylated.deduplicated.bam
-      md5sum: 82213a207048bcb5d8cc1cee92703a29
-    - path: output/bismark/test.paired_end.methylated.deduplication_report.txt
-      md5sum: 86aaf87bac9ccdc3cc83628f20b902dc
diff --git a/tests/modules/bismark/genomepreparation/main.nf b/tests/modules/bismark/genomepreparation/main.nf
deleted file mode 100644
index a9111af3b68..00000000000
--- a/tests/modules/bismark/genomepreparation/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf'
-
-workflow test_bismark_genomepreparation {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISMARK_GENOMEPREPARATION ( fasta )
-}
diff --git a/tests/modules/bismark/genomepreparation/test.yml b/tests/modules/bismark/genomepreparation/test.yml
deleted file mode 100644
index a0d3c0724ae..00000000000
--- a/tests/modules/bismark/genomepreparation/test.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-- name: bismark genomepreparation test workflow
-  command: nextflow run ./tests/modules/bismark/genomepreparation -entry test_bismark_genomepreparation -c ./tests/config/nextflow.config -c ./tests/modules/bismark/genomepreparation/nextflow.config
-  tags:
-    - bismark
-    - bismark/genomepreparation
-  files:
-    - path: ./output/bismark/BismarkIndex/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa
-      md5sum: 903b9f357eea4a5f36e21e78e0fe1dfa
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.4.bt2
-      md5sum: 6c4f549575e5882ff3a97ae10ae2e7be
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.1.bt2
-      md5sum: 10a8854e5eeb95629f46d24b0d8da70c
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.3.bt2
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.2.bt2
-      md5sum: bc5d407e6fce3e1cdb4b23ab2a20f707
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2
-      md5sum: 48bf400de85cd7324fbf6bf38fe2dc95
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2
-      md5sum: d37d586b41b6a36efb25839961d242cb
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2
-      md5sum: 17f51e65f44477962226a83b369b2bc4
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2
-      md5sum: d36044c5dfe37af0411f60d446585bc6
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa
-      md5sum: e529375ec2039112161465b5169fcd59
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.4.bt2
-      md5sum: b1e855685ed634daa7df8e180c9b2fc4
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.1.bt2
-      md5sum: a6fa4068ed10872568f32568c66cb600
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.2.bt2
-      md5sum: fc5b634e2f5137801e3801d62ad05f74
-    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.3.bt2
-      md5sum: 4ed93abba181d8dfab2e303e33114777
diff --git a/tests/modules/bismark/methylationextractor/main.nf b/tests/modules/bismark/methylationextractor/main.nf
deleted file mode 100644
index ed857fe8d84..00000000000
--- a/tests/modules/bismark/methylationextractor/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISMARK_GENOMEPREPARATION    } from '../../../../modules/bismark/genomepreparation/main.nf'
-include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf'
-
-workflow test_bismark_methylationextractor {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_bam'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISMARK_GENOMEPREPARATION ( fasta )
-    BISMARK_METHYLATIONEXTRACTOR ( input, BISMARK_GENOMEPREPARATION.out.index )
-}
diff --git a/tests/modules/bismark/methylationextractor/test.yml b/tests/modules/bismark/methylationextractor/test.yml
deleted file mode 100644
index f25b7646957..00000000000
--- a/tests/modules/bismark/methylationextractor/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: bismark methylation extractor test workflow
-  command: nextflow run ./tests/modules/bismark/methylationextractor -entry test_bismark_methylationextractor -c ./tests/config/nextflow.config -c ./tests/modules/bismark/methylationextractor/nextflow.config
-  tags:
-    - bismark
-    - bismark/methylationextractor
-  files:
-    - path: output/bismark/CHG_OB_test.paired_end.methylated.txt.gz
-    - path: output/bismark/CHG_OT_test.paired_end.methylated.txt.gz
-    - path: output/bismark/CHH_OB_test.paired_end.methylated.txt.gz
-    - path: output/bismark/CHH_OT_test.paired_end.methylated.txt.gz
-    - path: output/bismark/CpG_OB_test.paired_end.methylated.txt.gz
-    - path: output/bismark/CpG_OT_test.paired_end.methylated.txt.gz
-    - path: output/bismark/test.paired_end.methylated.M-bias.txt
-      md5sum: 0b100924d46b3c35115f1206f34c4a59
-    - path: output/bismark/test.paired_end.methylated_splitting_report.txt
-      md5sum: f28a9dd8de8c42b8900b190b8f79647a
diff --git a/tests/modules/bismark/report/main.nf b/tests/modules/bismark/report/main.nf
deleted file mode 100644
index f80fb2bc6c7..00000000000
--- a/tests/modules/bismark/report/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISMARK_GENOMEPREPARATION    } from '../../../../modules/bismark/genomepreparation/main.nf'
-include { BISMARK_ALIGN                } from '../../../../modules/bismark/align/main.nf'
-include { BISMARK_DEDUPLICATE          } from '../../../../modules/bismark/deduplicate/main.nf'
-include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf'
-include { BISMARK_REPORT               } from '../../../../modules/bismark/report/main.nf'
-
-workflow test_bismark_report {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISMARK_GENOMEPREPARATION ( fasta )
-    BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
-    BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
-    BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
-    BISMARK_REPORT (
-        BISMARK_ALIGN.out.report
-            .join(BISMARK_DEDUPLICATE.out.report)
-            .join(BISMARK_METHYLATIONEXTRACTOR.out.report)
-            .join(BISMARK_METHYLATIONEXTRACTOR.out.mbias)
-    )
-}
diff --git a/tests/modules/bismark/report/test.yml b/tests/modules/bismark/report/test.yml
deleted file mode 100644
index 9195994cbcc..00000000000
--- a/tests/modules/bismark/report/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bismark report test workflow
-  command: nextflow run ./tests/modules/bismark/report -entry test_bismark_report -c ./tests/config/nextflow.config -c ./tests/modules/bismark/report/nextflow.config
-  tags:
-    - bismark
-    - bismark/report
-  files:
-    - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.html
-    - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.txt
diff --git a/tests/modules/bismark/summary/main.nf b/tests/modules/bismark/summary/main.nf
deleted file mode 100644
index 8eabe51f7b6..00000000000
--- a/tests/modules/bismark/summary/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISMARK_GENOMEPREPARATION    } from '../../../../modules/bismark/genomepreparation/main.nf'
-include { BISMARK_ALIGN                } from '../../../../modules/bismark/align/main.nf'
-include { BISMARK_DEDUPLICATE          } from '../../../../modules/bismark/deduplicate/main.nf'
-include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf'
-include { BISMARK_SUMMARY              } from '../../../../modules/bismark/summary/main.nf'
-
-workflow test_bismark_summary {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BISMARK_GENOMEPREPARATION ( fasta )
-    BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
-    BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
-    BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
-    BISMARK_SUMMARY (
-        BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam },
-        BISMARK_ALIGN.out.report.collect{ meta, report -> report },
-        BISMARK_DEDUPLICATE.out.report.collect{ meta, bam -> bam },
-        BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report },
-        BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
-    )
-}
diff --git a/tests/modules/bismark/summary/test.yml b/tests/modules/bismark/summary/test.yml
deleted file mode 100644
index 3b5196b919b..00000000000
--- a/tests/modules/bismark/summary/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: bismark summary test workflow
-  command: nextflow run ./tests/modules/bismark/summary -entry test_bismark_summary -c ./tests/config/nextflow.config -c ./tests/modules/bismark/summary/nextflow.config
-  tags:
-    - bismark
-    - bismark/summary
-  files:
-    - path: output/bismark/bismark_summary_report.html
-    - path: output/bismark/bismark_summary_report.txt
-      md5sum: fdfadd5399c4e7b2108da100e72036eb
diff --git a/tests/modules/blast/blastn/main.nf b/tests/modules/blast/blastn/main.nf
deleted file mode 100644
index 3c8496dc609..00000000000
--- a/tests/modules/blast/blastn/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf'
-include { BLAST_BLASTN      } from '../../../../modules/blast/blastn/main.nf'
-
-workflow test_blast_blastn {
-    input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    BLAST_MAKEBLASTDB ( input )
-    BLAST_BLASTN ( [ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db )
-}
diff --git a/tests/modules/blast/blastn/test.yml b/tests/modules/blast/blastn/test.yml
deleted file mode 100644
index 17522c9b822..00000000000
--- a/tests/modules/blast/blastn/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: blast_blastn
-  command: nextflow run ./tests/modules/blast/blastn -entry test_blast_blastn -c ./tests/config/nextflow.config -c ./tests/modules/blast/blastn/nextflow.config
-  tags:
-    - blast
-    - blast/blastn
-  files:
-    - path: ./output/blast/test.blastn.txt
-    - path: ./output/blast/blast_db/genome.fasta.nsq
-      md5sum: 982cbc7d9e38743b9b1037588862b9da
-    - path: ./output/blast/blast_db/genome.fasta.nin
-    - path: ./output/blast/blast_db/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: ./output/blast/blast_db/genome.fasta.nhr
-      md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
-    - path: ./output/blast/blast_db/genome.fasta.ndb
-      md5sum: 0d553c830656469211de113c5022f06d
-    - path: ./output/blast/blast_db/genome.fasta.not
-      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
-    - path: ./output/blast/blast_db/genome.fasta.nto
-      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
-    - path: ./output/blast/blast_db/genome.fasta.ntf
-      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
diff --git a/tests/modules/blast/makeblastdb/main.nf b/tests/modules/blast/makeblastdb/main.nf
deleted file mode 100644
index 9d778457e9f..00000000000
--- a/tests/modules/blast/makeblastdb/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf'
-
-workflow test_blast_makeblastdb {
-    input =  [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    BLAST_MAKEBLASTDB ( input )
-}
diff --git a/tests/modules/blast/makeblastdb/test.yml b/tests/modules/blast/makeblastdb/test.yml
deleted file mode 100644
index 3b59f3f67db..00000000000
--- a/tests/modules/blast/makeblastdb/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: blast_makeblastdb
-  command: nextflow run ./tests/modules/blast/makeblastdb -entry test_blast_makeblastdb -c ./tests/config/nextflow.config -c ./tests/modules/blast/makeblastdb/nextflow.config
-  tags:
-    - blast
-    - blast/makeblastdb
-  files:
-    - path: ./output/blast/blast_db/genome.fasta.nsq
-      md5sum: 982cbc7d9e38743b9b1037588862b9da
-    - path: ./output/blast/blast_db/genome.fasta.nin
-    - path: ./output/blast/blast_db/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: ./output/blast/blast_db/genome.fasta.nhr
-      md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
-    - path: ./output/blast/blast_db/genome.fasta.ndb
-      md5sum: 0d553c830656469211de113c5022f06d
-    - path: ./output/blast/blast_db/genome.fasta.not
-      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
-    - path: ./output/blast/blast_db/genome.fasta.nto
-      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
-    - path: ./output/blast/blast_db/genome.fasta.ntf
-      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
diff --git a/tests/modules/blast/tblastn/main.nf b/tests/modules/blast/tblastn/main.nf
deleted file mode 100644
index 6d343660193..00000000000
--- a/tests/modules/blast/tblastn/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BLAST_TBLASTN } from '../../../../modules/blast/tblastn/main.nf'
-include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf'
-
-workflow test_blast_tblastn {
-
-    input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-    input_pep = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-
-    BLAST_MAKEBLASTDB ( input )
-    BLAST_TBLASTN ( [ [id:'test'], input_pep ], BLAST_MAKEBLASTDB.out.db )
-}
diff --git a/tests/modules/blast/tblastn/test.yml b/tests/modules/blast/tblastn/test.yml
deleted file mode 100644
index b545edbe2c7..00000000000
--- a/tests/modules/blast/tblastn/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: blast tblastn
-  command: nextflow run ./tests/modules/blast/tblastn -entry test_blast_tblastn -c ./tests/config/nextflow.config -c ./tests/modules/blast/tblastn/nextflow.config
-  tags:
-    - blast
-    - blast/tblastn
-  files:
-    - path: ./output/blast/test.tblastn.txt
-      md5sum: c26ccfa5ceae82fc6affdc77f5505b62
-    - path: ./output/blast/versions.yml
-      md5sum: 6d23563b8d75e2fe1e03d3fbe10098a9
-    - path: ./output/blast/blast_db/genome.fasta.nsq
-      md5sum: 982cbc7d9e38743b9b1037588862b9da
-    - path: ./output/blast/blast_db/genome.fasta.nin
-    - path: ./output/blast/blast_db/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: ./output/blast/blast_db/genome.fasta.nhr
-      md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
-    - path: ./output/blast/blast_db/genome.fasta.ndb
-      md5sum: 0d553c830656469211de113c5022f06d
-    - path: ./output/blast/blast_db/genome.fasta.not
-      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
-    - path: ./output/blast/blast_db/genome.fasta.nto
-      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
-    - path: ./output/blast/blast_db/genome.fasta.ntf
-      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
diff --git a/tests/modules/bowtie/align/main.nf b/tests/modules/bowtie/align/main.nf
deleted file mode 100644
index e773cd38cef..00000000000
--- a/tests/modules/bowtie/align/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf'
-include { BOWTIE_ALIGN } from '../../../../modules/bowtie/align/main.nf'
-
-workflow test_bowtie_align_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BOWTIE_BUILD ( fasta )
-    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
-}
-
-workflow test_bowtie_align_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BOWTIE_BUILD ( fasta )
-    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
-}
diff --git a/tests/modules/bowtie/align/test.yml b/tests/modules/bowtie/align/test.yml
deleted file mode 100644
index 1f8d1294b3d..00000000000
--- a/tests/modules/bowtie/align/test.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-- name: bowtie align single-end
-  command: nextflow run ./tests/modules/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie/align/nextflow.config
-  tags:
-    - bowtie
-    - bowtie/align
-  files:
-    - path: ./output/bowtie/test.bam
-    - path: ./output/bowtie/test.out
-      md5sum: 4b9140ceadb8a18ae9330885370f8a0b
-    - path: ./output/bowtie/bowtie/genome.3.ebwt
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie/bowtie/genome.2.ebwt
-      md5sum: 02b44af9f94c62ecd3c583048e25d4cf
-    - path: ./output/bowtie/bowtie/genome.rev.2.ebwt
-      md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
-    - path: ./output/bowtie/bowtie/genome.4.ebwt
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie/bowtie/genome.rev.1.ebwt
-      md5sum: b37aaf11853e65a3b13561f27a912b06
-    - path: ./output/bowtie/bowtie/genome.1.ebwt
-      md5sum: d9b76ecf9fd0413240173273b38d8199
-
-- name: bowtie align paired-end
-  command: nextflow run ./tests/modules/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie/align/nextflow.config
-  tags:
-    - bowtie
-    - bowtie/align
-  files:
-    - path: ./output/bowtie/test.bam
-    - path: ./output/bowtie/test.out
-    - path: ./output/bowtie/bowtie/genome.3.ebwt
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie/bowtie/genome.2.ebwt
-      md5sum: 02b44af9f94c62ecd3c583048e25d4cf
-    - path: ./output/bowtie/bowtie/genome.rev.2.ebwt
-      md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
-    - path: ./output/bowtie/bowtie/genome.4.ebwt
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie/bowtie/genome.rev.1.ebwt
-      md5sum: b37aaf11853e65a3b13561f27a912b06
-    - path: ./output/bowtie/bowtie/genome.1.ebwt
-      md5sum: d9b76ecf9fd0413240173273b38d8199
diff --git a/tests/modules/bowtie/build_test/main.nf b/tests/modules/bowtie/build_test/main.nf
deleted file mode 100644
index 7a36fb5582f..00000000000
--- a/tests/modules/bowtie/build_test/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf'
-
-workflow test_bowtie_build {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BOWTIE_BUILD ( fasta )
-}
diff --git a/tests/modules/bowtie/build_test/test.yml b/tests/modules/bowtie/build_test/test.yml
deleted file mode 100644
index c51d1e8a362..00000000000
--- a/tests/modules/bowtie/build_test/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: bowtie build
-  command: nextflow run ./tests/modules/bowtie/build_test -entry test_bowtie_build -c ./tests/config/nextflow.config -c ./tests/modules/bowtie/build/nextflow.config
-  tags:
-    - bowtie
-    - bowtie/build
-  files:
-    - path: ./output/bowtie/bowtie/genome.3.ebwt
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie/bowtie/genome.2.ebwt
-      md5sum: 02b44af9f94c62ecd3c583048e25d4cf
-    - path: ./output/bowtie/bowtie/genome.rev.2.ebwt
-      md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
-    - path: ./output/bowtie/bowtie/genome.4.ebwt
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie/bowtie/genome.rev.1.ebwt
-      md5sum: b37aaf11853e65a3b13561f27a912b06
-    - path: ./output/bowtie/bowtie/genome.1.ebwt
-      md5sum: d9b76ecf9fd0413240173273b38d8199
diff --git a/tests/modules/bowtie2/align/main.nf b/tests/modules/bowtie2/align/main.nf
deleted file mode 100644
index 4f08b53304f..00000000000
--- a/tests/modules/bowtie2/align/main.nf
+++ /dev/null
@@ -1,99 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf'
-include { BOWTIE2_ALIGN } from '../../../../modules/bowtie2/align/main.nf'
-
-workflow test_bowtie2_align_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_unaligned = false
-    sort = false
-
-    BOWTIE2_BUILD ( fasta )
-    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
-}
-
-workflow test_bowtie2_align_single_end_sorted {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_unaligned = false
-    sort = true
-
-    BOWTIE2_BUILD ( fasta )
-    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
-}
-
-workflow test_bowtie2_align_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_unaligned = false
-    sort = false
-
-    BOWTIE2_BUILD ( fasta )
-    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
-}
-
-workflow test_bowtie2_align_paired_end_sorted {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_unaligned = false
-    sort = true
-
-    BOWTIE2_BUILD ( fasta )
-    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
-}
-
-workflow test_bowtie2_align_single_end_large_index {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_unaligned = false
-    sort = false
-
-    BOWTIE2_BUILD ( fasta )
-    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
-}
-
-workflow test_bowtie2_align_paired_end_large_index {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_unaligned = false
-    sort = false
-
-    BOWTIE2_BUILD ( fasta )
-    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
-}
diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml
deleted file mode 100644
index 9c9ff7a1a6f..00000000000
--- a/tests/modules/bowtie2/align/test.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-- name: bowtie2 align test_bowtie2_align_single_end
-  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
-  tags:
-    - bowtie2
-    - bowtie2/align
-  files:
-    - path: ./output/bowtie2/test.bam
-    - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/versions.yml
-
-- name: bowtie2 align test_bowtie2_align_single_end_sorted
-  command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_sorted -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
-  tags:
-    - bowtie2
-    - bowtie2/align
-  files:
-    - path: ./output/bowtie2/test.bam
-    - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/versions.yml
-
-- name: bowtie2 align test_bowtie2_align_paired_end
-  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config
-  tags:
-    - bowtie2
-    - bowtie2/align
-  files:
-    - path: ./output/bowtie2/test.bam
-    - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/versions.yml
-
-- name: bowtie2 align test_bowtie2_align_single_end_large_index
-  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index
-  tags:
-    - bowtie2
-    - bowtie2/align
-  files:
-    - path: ./output/bowtie2/test.bam
-    - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/versions.yml
-
-- name: bowtie2 align test_bowtie2_align_paired_end_large_index
-  command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index
-  tags:
-    - bowtie2
-    - bowtie2/align
-  files:
-    - path: ./output/bowtie2/test.bam
-    - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/versions.yml
diff --git a/tests/modules/bowtie2/build_test/main.nf b/tests/modules/bowtie2/build_test/main.nf
deleted file mode 100644
index f1d35083c80..00000000000
--- a/tests/modules/bowtie2/build_test/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf'
-
-workflow test_bowtie2_build {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BOWTIE2_BUILD ( fasta )
-}
diff --git a/tests/modules/bowtie2/build_test/test.yml b/tests/modules/bowtie2/build_test/test.yml
deleted file mode 100644
index 88e6c3ada1d..00000000000
--- a/tests/modules/bowtie2/build_test/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: bowtie2 build
-  command: nextflow run ./tests/modules/bowtie2/build_test -entry test_bowtie2_build -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/build/nextflow.config
-  tags:
-    - bowtie2
-    - bowtie2/build
-  files:
-    - path: ./output/bowtie2/bowtie2/genome.3.bt2
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie2/bowtie2/genome.2.bt2
-      md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: ./output/bowtie2/bowtie2/genome.1.bt2
-      md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
-    - path: ./output/bowtie2/bowtie2/genome.4.bt2
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
-      md5sum: 52be6950579598a990570fbcf5372184
-    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
-      md5sum: e3b4ef343dea4dd571642010a7d09597
diff --git a/tests/modules/bracken/bracken/main.nf b/tests/modules/bracken/bracken/main.nf
deleted file mode 100644
index 190aeb7051e..00000000000
--- a/tests/modules/bracken/bracken/main.nf
+++ /dev/null
@@ -1,57 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR           } from '../../../../modules/untar/main.nf'
-include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
-include { BRACKEN_BRACKEN } from '../../../../modules/bracken/bracken/main.nf'
-
-workflow test_bracken_bracken_single_end_default_args {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
-
-    ch_db = UNTAR ( [[:], db] ).untar
-        .map { it[1] }
-    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
-    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
-}
-
-workflow test_bracken_bracken_single_end_custom_args {
-    input = [ [ id:'test', single_end:true, threshold:0, taxonomic_level:'G', read_length:100 ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
-
-    ch_db = UNTAR ( [[:], db] ).untar
-        .map { it[1] }
-    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
-    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
-}
-
-workflow test_bracken_bracken_paired_end_default_args {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
-
-    ch_db = UNTAR ( [[:], db] ).untar
-        .map { it[1] }
-    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
-    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
-}
-
-workflow test_bracken_bracken_paired_end_custom_args {
-    input = [ [ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
-
-    ch_db = UNTAR ( [[:], db] ).untar
-        .map { it[1] }
-    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
-    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
-}
diff --git a/tests/modules/bracken/bracken/test.yml b/tests/modules/bracken/bracken/test.yml
deleted file mode 100644
index 373314f7ea9..00000000000
--- a/tests/modules/bracken/bracken/test.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-- name: bracken bracken test_bracken_bracken_single_end_default_args
-  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_single_end_default_args -c tests/config/nextflow.config
-  tags:
-    - bracken/bracken
-    - bracken
-  files:
-    - path: output/bracken/test_S.tsv
-      md5sum: 4a21ae14ff8a0311d55f139af5247838
-    - path: output/bracken/versions.yml
-      md5sum: e0abdac999c0d58becd8c868dd12028b
-
-- name: bracken bracken test_bracken_bracken_single_end_custom_args
-  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_single_end_custom_args -c tests/config/nextflow.config
-  tags:
-    - bracken/bracken
-    - bracken
-  files:
-    - path: output/bracken/test_G.tsv
-      md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
-    - path: output/bracken/versions.yml
-      md5sum: 7d0a1629ece197a8062271d39ed8ef74
-
-- name: bracken bracken test_bracken_bracken_paired_end_default_args
-  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_default_args -c tests/config/nextflow.config
-  tags:
-    - bracken/bracken
-    - bracken
-  files:
-    - path: output/bracken/test_S.tsv
-      md5sum: 4a21ae14ff8a0311d55f139af5247838
-    - path: output/bracken/versions.yml
-      md5sum: 7b58898d0b9cce1ca170ac5a82d8ecf1
-
-- name: bracken bracken test_bracken_bracken_paired_end_custom_args
-  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_custom_args -c tests/config/nextflow.config
-  tags:
-    - bracken/bracken
-    - bracken
-  files:
-    - path: output/bracken/test_G.tsv
-      md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
-    - path: output/bracken/versions.yml
-      md5sum: 3c9160394af663ae7808c0f77fcedae8
diff --git a/tests/modules/bracken/combinebrackenoutputs/main.nf b/tests/modules/bracken/combinebrackenoutputs/main.nf
deleted file mode 100644
index d382d907179..00000000000
--- a/tests/modules/bracken/combinebrackenoutputs/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR           } from '../../../../modules/untar/main.nf'
-include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
-include { BRACKEN_BRACKEN } from '../../../../modules/bracken/bracken/main.nf'
-include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../../../modules/bracken/combinebrackenoutputs/main.nf'
-
-workflow test_bracken_combinebrackenoutputs {
-
-    input = Channel.of(
-        [[ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
-        [[ id:'test2', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
-    )
-    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
-
-    ch_db = UNTAR ( [[:], db] ).untar
-        .map { it[1] }
-    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
-    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
-
-    BRACKEN_COMBINEBRACKENOUTPUTS ( BRACKEN_BRACKEN.out.reports.map{it[1]}.collect() )
-}
-
diff --git a/tests/modules/bracken/combinebrackenoutputs/test.yml b/tests/modules/bracken/combinebrackenoutputs/test.yml
deleted file mode 100644
index 057a215f32a..00000000000
--- a/tests/modules/bracken/combinebrackenoutputs/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: bracken combinebrackenoutputs test_bracken_combinebrackenoutputs
-  command: nextflow run ./tests/modules/bracken/combinebrackenoutputs -entry test_bracken_combinebrackenoutputs -c ./tests/config/nextflow.config  -c ./tests/modules/bracken/combinebrackenoutputs/nextflow.config
-  tags:
-    - bracken/combinebrackenoutputs
-    - bracken
-  files:
-    - path: output/bracken/bracken_combined.txt
-      contains:
-        - "name	taxonomy_id	taxonomy_lvl"
diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf
deleted file mode 100644
index 2313bd06a82..00000000000
--- a/tests/modules/busco/main.nf
+++ /dev/null
@@ -1,104 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BUSCO } from '../../../modules/busco/main.nf'
-
-workflow test_busco_genome_single_fasta {
-
-    input = [
-        [ id:'test' ], // meta map
-        file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
-    ]
-
-    BUSCO (
-        input,
-        'bacteria_odb10', // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
-        [], // Download busco lineage
-        [] // No config
-    )
-
-}
-
-workflow test_busco_genome_multi_fasta {
-
-    input = [
-        [ id:'test' ], // meta map
-        [
-            file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
-            file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
-        ]
-    ]
-
-    BUSCO (
-        input,
-        'bacteria_odb10',
-        [], // Download busco lineage
-        [] // No config
-    )
-
-}
-
-workflow test_busco_eukaryote_metaeuk {
-
-    input = [
-        [ id:'test' ], // meta map
-        file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    BUSCO (
-        input,
-        'eukaryota_odb10',
-        [], // Download busco lineage
-        [] // No config
-    )
-
-}
-
-workflow test_busco_eukaryote_augustus {
-
-    input = [
-        [ id:'test' ], // meta map
-        file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    BUSCO (
-        input,
-        'eukaryota_odb10',
-        [], // Download busco lineage
-        [] // No config
-    )
-
-}
-
-workflow test_busco_protein {
-
-    input = [
-        [ id:'test' ], // meta map
-        file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true)
-    ]
-
-    BUSCO (
-        input,
-        'bacteria_odb10',
-        [], // Download busco lineage
-        [] // No config
-    )
-
-}
-
-workflow test_busco_transcriptome {
-
-    input = [
-        [ id:'test' ], // meta map
-        file( params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
-    ]
-
-    BUSCO (
-        input,
-        'bacteria_odb10',
-        [], // Download busco lineage
-        [] // No config
-    )
-
-}
diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml
deleted file mode 100644
index 562f427fa8d..00000000000
--- a/tests/modules/busco/test.yml
+++ /dev/null
@@ -1,610 +0,0 @@
-- name: busco test_busco_genome_single_fasta
-  command: nextflow run ./tests/modules/busco -entry test_busco_genome_single_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
-  tags:
-    - busco
-  files:
-    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
-      contains:
-        - "BUSCO version"
-        - "The lineage dataset is"
-        - "BUSCO was run in mode"
-        - "Complete BUSCOs"
-        - "Missing BUSCOs"
-        - "Dependencies and versions"
-    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
-      md5sum: bc2440f8a68d7fbf931ff911c1c3fdfa
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
-      contains:
-        - "IUPAC"
-        - "genome scaffold"
-        - "Coverage"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
-      contains:
-        - "# hmmsearch :: search profile(s) against a sequence database"
-        - "# target sequence database:"
-        - "Internal pipeline statistics summary:"
-        - "[ok]"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
-      md5sum: 538510cfc7483498210f01e53fe035ad
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
-      md5sum: 61050b0706addc9498b2088a2d6efa9a
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
-      contains:
-        - "Tool: prodigal"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
-      md5sum: 836e9a80d33d8b89168f07ddc13ee991
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
-      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
-      md5sum: 836e9a80d33d8b89168f07ddc13ee991
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
-      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
-      md5sum: 538510cfc7483498210f01e53fe035ad
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
-      md5sum: 61050b0706addc9498b2088a2d6efa9a
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
-      contains:
-        - "Tool: bbtools"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
-      md5sum: 275a7ece09ef61aa59ee7a811289e3d8
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
-      md5sum: ab574cde031a3fbff471976ea61e215d
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "lineage_dataset"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
-      contains:
-        - "# BUSCO version is:"
-        - "Results:"
-        - "busco:"
-    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
-      contains:
-        - "DEBUG:busco.run_BUSCO"
-        - "Results from dataset"
-        - "how to cite BUSCO"
-
-- name: busco test_busco_genome_multi_fasta
-  command: nextflow run ./tests/modules/busco -entry test_busco_genome_multi_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
-  tags:
-    - busco
-  files:
-    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.txt
-      contains:
-        - "BUSCO version"
-        - "The lineage dataset is"
-        - "BUSCO was run in mode"
-        - "Complete BUSCOs"
-        - "Missing BUSCOs"
-        - "Dependencies and versions"
-    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
-      contains:
-        - "BUSCO version"
-        - "The lineage dataset is"
-        - "BUSCO was run in mode"
-        - "Complete BUSCOs"
-        - "Missing BUSCOs"
-        - "Dependencies and versions"
-    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
-      contains:
-        - "Input_file"
-        - "genome.fna"
-        - "genome.fasta"
-        - "bacteria_odb10"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_err.log
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_out.log
-      contains:
-        - "IUPAC"
-        - "genome scaffold"
-        - "Coverage"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_err.log
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_out.log
-      contains:
-        - "# hmmsearch :: search profile(s) against a sequence database"
-        - "# target sequence database:"
-        - "Internal pipeline statistics summary:"
-        - "[ok]"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_err.log
-      md5sum: c1fdc6977332f53dfe7f632733bb4585
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_out.log
-      md5sum: 50752acb1c5a20be886bfdfc06635bcb
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/.checkpoint
-      contains:
-        - "Tool: prodigal"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.faa
-      md5sum: 8166471fc5f08c82fd5643ab42327f9d
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.fna
-      md5sum: ddc508a18f60e7f3314534df50cdf8ca
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
-      md5sum: 8166471fc5f08c82fd5643ab42327f9d
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
-      md5sum: ddc508a18f60e7f3314534df50cdf8ca
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
-      md5sum: c1fdc6977332f53dfe7f632733bb4585
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
-      md5sum: 50752acb1c5a20be886bfdfc06635bcb
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.faa
-      md5sum: e56fd59c38248dc21ac94355dca98121
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.fna
-      md5sum: b365f84bf99c68357952e0b98ed7ce42
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_err.log
-      md5sum: e5f14d7925ba14a0f9850542f3739894
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_out.log
-      md5sum: d41971bfc1b621d4ffd2633bc47017ea
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/.bbtools_output/.checkpoint
-      contains:
-        - "Tool: bbtools"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/full_table.tsv
-      md5sum: f473ded1f1db2463533d51be6ed6fd2d
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/missing_busco_list.tsv
-      md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.txt
-      contains:
-        - "# BUSCO version is:"
-        - "Results:"
-        - "busco:"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
-      contains:
-        - "IUPAC"
-        - "genome scaffold"
-        - "Coverage"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
-      contains:
-        - "# hmmsearch :: search profile(s) against a sequence database"
-        - "# target sequence database:"
-        - "Internal pipeline statistics summary:"
-        - "[ok]"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
-      md5sum: 538510cfc7483498210f01e53fe035ad
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
-      md5sum: 61050b0706addc9498b2088a2d6efa9a
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
-      contains:
-        - "Tool: prodigal"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
-      md5sum: 836e9a80d33d8b89168f07ddc13ee991
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
-      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
-      md5sum: 836e9a80d33d8b89168f07ddc13ee991
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
-      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
-      md5sum: 538510cfc7483498210f01e53fe035ad
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
-      md5sum: 61050b0706addc9498b2088a2d6efa9a
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
-      contains:
-        - "Tool: bbtools"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
-      md5sum: 275a7ece09ef61aa59ee7a811289e3d8
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
-      md5sum: ab574cde031a3fbff471976ea61e215d
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
-      contains:
-        - "# BUSCO version is:"
-        - "Results:"
-        - "busco:"
-    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
-      contains:
-        - "DEBUG:busco.run_BUSCO"
-        - "Results from dataset"
-        - "how to cite BUSCO"
-
-- name: busco test_busco_eukaryote_metaeuk
-  command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_metaeuk -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
-  tags:
-    - busco
-  files:
-    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.txt
-      contains:
-        - "BUSCO version"
-        - "The lineage dataset is"
-        - "BUSCO was run in mode"
-        - "Complete BUSCOs"
-        - "Missing BUSCOs"
-        - "Dependencies and versions"
-    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
-      md5sum: ff6d8277e452a83ce9456bbee666feb6
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
-      contains:
-        - "IUPAC"
-        - "genome scaffold"
-        - "Coverage"
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_err.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_out.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_err.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_out.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_err.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_out.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
-      contains:
-        - "Tool: bbtools"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/full_table.tsv
-      md5sum: ff1b64c2adadcf9f0a954a19893e421b
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/hmmer_output.tar.gz
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/.checkpoint
-      contains:
-        - "Tool: metaeuk"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/combined_pred_proteins.fas
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.codon.fas
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.fas
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.gff
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.headersMap.tsv
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/refseq_db_rerun.faa
-      md5sum: d80b8fa4cb5ed0d47d63d6aa93635bc2
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.codon.fas
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.fas
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.gff
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.headersMap.tsv
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/missing_busco_list.tsv
-      md5sum: 6c17c7e06991db898b318b932d686406
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.txt
-      contains:
-        - "# BUSCO version is:"
-        - "Results:"
-        - "busco:"
-    - path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
-      contains:
-        - "DEBUG:busco.run_BUSCO"
-        - "Results from dataset"
-        - "how to cite BUSCO"
-
-- name: busco test_busco_eukaryote_augustus
-  command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_augustus -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
-  tags:
-    - busco
-  files:
-    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
-      md5sum: cdd3ffd590a778cdd2f0f367ee86eba7
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/.checkpoint
-      contains:
-        - "Tool: makeblastdb"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ndb
-      md5sum: 0d553c830656469211de113c5022f06d
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nhr
-      md5sum: 82396da5130a85faf6d454e2889a1d45
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nin
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.njs
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.not
-      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nsq
-      md5sum: 4bc119903ac72152363f47612645046a
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ntf
-      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nto
-      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
-      contains:
-        - "IUPAC"
-        - "genome scaffold"
-        - "Coverage"
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_err.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_out.log
-      contains:
-        - "Building a new DB"
-        - "Adding sequences from FASTA"
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_err.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_out.log
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
-      contains:
-        - "Tool: bbtools"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/.checkpoint
-      contains:
-        - "Tool: tblastn"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/coordinates.tsv
-    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/tblastn.tsv
-      contains:
-        - "TBLASTN"
-        - "BLAST processed"
-        - "queries"
-    - path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
-      contains:
-        - "DEBUG:busco.run_BUSCO"
-        - "Running Augustus gene predictor"
-
-- name: busco test_busco_protein
-  command: nextflow run ./tests/modules/busco -entry test_busco_protein -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
-  tags:
-    - busco
-  files:
-    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.txt
-      contains:
-        - "BUSCO version"
-        - "The lineage dataset is"
-        - "BUSCO was run in mode"
-        - "Complete BUSCOs"
-        - "Missing BUSCOs"
-        - "Dependencies and versions"
-    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
-      md5sum: 7a65e6cbb6c56a2ea4e739ae0aa3297d
-    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
-      contains:
-        - "DEBUG:busco.run_BUSCO"
-        - "Results from dataset"
-        - "how to cite BUSCO"
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_err.log
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_out.log
-      contains:
-        - "# hmmsearch :: search profile(s) against a sequence database"
-        - "# target sequence database:"
-        - "Internal pipeline statistics summary:"
-        - "[ok]"
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/full_table.tsv
-      md5sum: 81e0e9a5897bb72fffbb1866779f6834
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/missing_busco_list.tsv
-      md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.txt
-      contains:
-        - "# BUSCO version is:"
-        - "Results:"
-        - "busco:"
-
-- name: busco test_busco_transcriptome
-  command: nextflow run ./tests/modules/busco -entry test_busco_transcriptome -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
-  tags:
-    - busco
-  files:
-    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
-      contains:
-        - "BUSCO version"
-        - "The lineage dataset is"
-        - "BUSCO was run in mode"
-        - "Complete BUSCOs"
-        - "Missing BUSCOs"
-        - "Dependencies and versions"
-    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
-      md5sum: 46118ecf60d1b87d22b96d80f4f03632
-    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
-      contains:
-        - "DEBUG:busco.run_BUSCO"
-        - "Results from dataset"
-        - "how to cite BUSCO"
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/.checkpoint
-      contains:
-        - "Tool: makeblastdb"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ndb
-      md5sum: 3788c017fe5e6f0f58224e9cdd21822b
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nhr
-      md5sum: 8ecd2ce392bb5e25ddbe1d85f879582e
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nin
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.njs
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.not
-      md5sum: 0c340e376c7e85d19f82ec1a833e6a6e
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nsq
-      md5sum: 532d5c0a7ea00fe95ca3c97cb3be6198
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ntf
-      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nto
-      md5sum: ff74bd41f9cc9b011c63a32c4f7693bf
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_err.log
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_out.log
-      contains:
-        - "# hmmsearch :: search profile(s) against a sequence database"
-        - "# target sequence database:"
-        - "Internal pipeline statistics summary:"
-        - "[ok]"
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_err.log
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_out.log
-      contains:
-        - "Building a new DB"
-        - "Adding sequences from FASTA"
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_err.log
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_out.log
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/.checkpoint
-      contains:
-        - "Tool: tblastn"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/coordinates.tsv
-      md5sum: cc30eed321944af293452bdbcfc24292
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_101.temp
-      md5sum: 73e9c65fc83fedc58f57f09b08f08238
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_119.temp
-      md5sum: 7fa4cc7955ec0cc36330a221c579b975
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_129.temp
-      md5sum: 6f1601c875d019e3f6f1f98ed8e988d4
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_138.temp
-      md5sum: 3f8e034686cd240c2330650d791bcae2
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_143.temp
-      md5sum: df3dfa8e9ba30ed70cf75b5e7abf2179
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_172.temp
-      md5sum: 7d463e0e6cf7169bc9077d8dc776dda1
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_178.temp
-      md5sum: 2288edf7fa4f88f51b4cf4d94086f77e
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_188.temp
-      md5sum: 029906abbad6d87fc57830dd548cac24
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_195.temp
-      md5sum: 4937f3b348774a31b1160a00297c29cc
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_210.temp
-      md5sum: afcb20ba4c466479d6b91c8c62251e1f
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_232.temp
-      md5sum: 2e1e823ce017345bd998191a39fa9924
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_268.temp
-      md5sum: 08c2d82c34ecffbe1c638b410349412e
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_29.temp
-      md5sum: cd9b63cf93524284781535c888313764
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_44.temp
-      md5sum: d1929b742b24ebe379bf4801ca882dca
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_58.temp
-      md5sum: 69215765b010c05336538cb322c900b3
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_72.temp
-      md5sum: 6feaa1cc3b0899a147ea9d466878f3e3
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_80.temp
-      md5sum: 13625eae14e860a96ce17cd4e37e9d01
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_81.temp
-      md5sum: e14b2484649b0dbc8926815c207b806d
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_93.temp
-      md5sum: 6902c93691df00e690faea914c71839e
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_97.temp
-      md5sum: 0a0d9d38a83acbd5ad43c29cdf429988
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/tblastn.tsv
-      contains:
-        - "TBLASTN"
-        - "BLAST processed"
-        - "queries"
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/full_table.tsv
-      md5sum: 14bb2d7788bd0aa547e4a99df6659f1e
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/hmmer_output.tar.gz
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/missing_busco_list.tsv
-      md5sum: 485902b7b62403985ee9f781e17b20ab
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/short_summary.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/short_summary.txt
-      contains:
-        - "# BUSCO version is:"
-        - "Results:"
-        - "busco:"
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/single_copy_proteins.faa
-      md5sum: e04b9465733577ae6e4bccb7aa01e720
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1024388at2.faa
-      md5sum: 7333c39a20258f20c7019ea0cd83157c
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1054741at2.faa
-      md5sum: ebb481e77a824685fbe04d8a2f3a0d7d
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1093223at2.faa
-      md5sum: 34621c7d499034e8f8e6b92fd4020a93
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1151822at2.faa
-      md5sum: aa89ca381c1c70c9c4e1380351ca7c2a
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/143460at2.faa
-      md5sum: f2e91d78b8dd3722840378789f29e8c8
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1491686at2.faa
-      md5sum: 73c25aef5c9cba7f4151804941b146ea
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1504821at2.faa
-      md5sum: cda556018d1f84ebe517e89f6fc107d0
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1574817at2.faa
-      md5sum: a9096c9fb8b25c78a72871ab0463acdc
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1592033at2.faa
-      md5sum: e463d25ce186c0cebfd749474f3a4c64
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1623045at2.faa
-      md5sum: f2cfd241590c6d8377286d6135480937
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1661836at2.faa
-      md5sum: 586569546fb9861502468e3d9ba2775c
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1674344at2.faa
-      md5sum: 24c658bee14ad84b062d81ad96642eb8
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1698718at2.faa
-      md5sum: 0b8e26ddf5149bbd8805be7af125208d
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1990650at2.faa
-      md5sum: 159320712ee01fb2ccb31a25df44eead
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/223233at2.faa
-      md5sum: 812629c0b06ac3d18661c2ca78de0c08
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/402899at2.faa
-      md5sum: f7ff4e1591342d30b77392a2e84b57d9
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/505485at2.faa
-      md5sum: 7b34a24fc49c540d46fcf96ff5129564
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/665824at2.faa
-      md5sum: 4cff2df64f6bcaff8bc19c234c8bcccd
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/776861at2.faa
-      md5sum: 613af7a3fea30ea2bece66f603b9284a
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/874197at2.faa
-      md5sum: a7cd1b13c9ef91c7ef4e31614166f197
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/932854at2.faa
-      md5sum: fe313ffd5efdb0fed887a04fba352552
-    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/95696at2.faa
-      md5sum: 4e1f30a2fea4dfbf9bb7fae2700622a0
diff --git a/tests/modules/bwa/aln/main.nf b/tests/modules/bwa/aln/main.nf
deleted file mode 100644
index 909e7a2d849..00000000000
--- a/tests/modules/bwa/aln/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
-include { BWA_ALN   } from '../../../../modules/bwa/aln/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_bwa_aln_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta )
-    BWA_ALN ( input, BWA_INDEX.out.index )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_bwa_aln_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta )
-    BWA_ALN ( input, BWA_INDEX.out.index )
-}
diff --git a/tests/modules/bwa/aln/test.yml b/tests/modules/bwa/aln/test.yml
deleted file mode 100644
index c89c47be844..00000000000
--- a/tests/modules/bwa/aln/test.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-- name: bwa aln single-end
-  command: nextflow run ./tests/modules/bwa/aln -entry test_bwa_aln_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/aln/nextflow.config
-  tags:
-    - bwa
-    - bwa/aln
-  files:
-    - path: ./output/bwa/test.sai
-      md5sum: aaaf39b6814c96ca1a5eacc662adf926
-    - path: ./output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: ./output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-
-- name: bwa aln paired-end
-  command: nextflow run ./tests/modules/bwa/aln -entry test_bwa_aln_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/aln/nextflow.config
-  tags:
-    - bwa
-    - bwa/aln
-  files:
-    - path: ./output/bwa/test.1.sai
-      md5sum: aaaf39b6814c96ca1a5eacc662adf926
-    - path: ./output/bwa/test.2.sai
-      md5sum: b4f185d9b4cb256dd5c377070a536124
-    - path: ./output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: ./output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
diff --git a/tests/modules/bwa/index/main.nf b/tests/modules/bwa/index/main.nf
deleted file mode 100644
index fe040cb22ed..00000000000
--- a/tests/modules/bwa/index/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
-
-workflow test_bwa_index {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta )
-}
diff --git a/tests/modules/bwa/index/test.yml b/tests/modules/bwa/index/test.yml
deleted file mode 100644
index a9dab91d632..00000000000
--- a/tests/modules/bwa/index/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: bwa index test_bwa_index
-  command: nextflow run ./tests/modules/bwa/index -entry test_bwa_index -c ./tests/config/nextflow.config -c ./tests/modules/bwa/index/nextflow.config
-  tags:
-    - bwa
-    - bwa/index
-  files:
-    - path: output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
diff --git a/tests/modules/bwa/mem/main.nf b/tests/modules/bwa/mem/main.nf
deleted file mode 100644
index c9c57197048..00000000000
--- a/tests/modules/bwa/mem/main.nf
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
-include { BWA_MEM   } from '../../../../modules/bwa/mem/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_bwa_mem_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta )
-    BWA_MEM ( input, BWA_INDEX.out.index, false )
-}
-
-//
-// Test with single-end data and sort
-//
-workflow test_bwa_mem_single_end_sort {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta )
-    BWA_MEM ( input, BWA_INDEX.out.index, true )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_bwa_mem_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta )
-    BWA_MEM ( input, BWA_INDEX.out.index, false )
-}
-
-//
-// Test with paired-end data and sort
-//
-workflow test_bwa_mem_paired_end_sort {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta )
-    BWA_MEM ( input, BWA_INDEX.out.index, true )
-}
diff --git a/tests/modules/bwa/mem/test.yml b/tests/modules/bwa/mem/test.yml
deleted file mode 100644
index 8fe2ee6b015..00000000000
--- a/tests/modules/bwa/mem/test.yml
+++ /dev/null
@@ -1,71 +0,0 @@
-- name: bwa mem single-end
-  command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config
-  tags:
-    - bwa
-    - bwa/mem
-  files:
-    - path: ./output/bwa/test.bam
-    - path: ./output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: ./output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-
-- name: bwa mem single-end sort
-  command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config
-  tags:
-    - bwa
-    - bwa/mem
-  files:
-    - path: ./output/bwa/test.bam
-    - path: ./output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: ./output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-
-- name: bwa mem paired-end
-  command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config
-  tags:
-    - bwa
-    - bwa/mem
-  files:
-    - path: ./output/bwa/test.bam
-    - path: ./output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: ./output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-
-- name: bwa mem paired-end sort
-  command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config
-  tags:
-    - bwa
-    - bwa/mem
-  files:
-    - path: ./output/bwa/test.bam
-    - path: ./output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: ./output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
diff --git a/tests/modules/bwa/sampe/main.nf b/tests/modules/bwa/sampe/main.nf
deleted file mode 100644
index abd25566a42..00000000000
--- a/tests/modules/bwa/sampe/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
-include { BWA_ALN   } from '../../../../modules/bwa/aln/main.nf'
-include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf'
-
-workflow test_bwa_sampe {
-
-    Channel
-        .fromList(
-            [
-                [ id:'test', single_end:false ],
-                [ [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
-            ]
-        ).collect()
-        .set { input }
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta )
-    BWA_ALN ( input, BWA_INDEX.out.index )
-    BWA_SAMPE ( input.join(BWA_ALN.out.sai), BWA_INDEX.out.index )
-}
diff --git a/tests/modules/bwa/sampe/test.yml b/tests/modules/bwa/sampe/test.yml
deleted file mode 100644
index c3eb42f8789..00000000000
--- a/tests/modules/bwa/sampe/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bwa sampe
-  command: nextflow run ./tests/modules/bwa/sampe -entry test_bwa_sampe -c ./tests/config/nextflow.config -c ./tests/modules/bwa/sampe/nextflow.config
-  tags:
-    - bwa
-    - bwa/sampe
-  files:
-    - path: output/bwa/test.bam
-      md5sum: 67528d633a1a78e3d0e8d1486c1a960a
diff --git a/tests/modules/bwa/samse/main.nf b/tests/modules/bwa/samse/main.nf
deleted file mode 100644
index 17912c36b0d..00000000000
--- a/tests/modules/bwa/samse/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
-include { BWA_ALN   } from '../../../../modules/bwa/aln/main.nf'
-include { BWA_SAMSE } from '../../../../modules/bwa/samse/main.nf'
-
-workflow test_bwa_samse {
-
-    Channel
-        .fromList(
-            [ [ id:'test', single_end:true ],
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-        ).collect()
-        .set { input }
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX ( fasta )
-    BWA_ALN ( input, BWA_INDEX.out.index )
-    BWA_SAMSE ( input.join(BWA_ALN.out.sai, by:[0]), BWA_INDEX.out.index )
-}
diff --git a/tests/modules/bwa/samse/test.yml b/tests/modules/bwa/samse/test.yml
deleted file mode 100644
index 3af39258e0d..00000000000
--- a/tests/modules/bwa/samse/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bwa samse
-  command: nextflow run ./tests/modules/bwa/samse -entry test_bwa_samse -c ./tests/config/nextflow.config -c ./tests/modules/bwa/samse/nextflow.config
-  tags:
-    - bwa
-    - bwa/samse
-  files:
-    - path: output/bwa/test.bam
-      md5sum: 9a0ca9678a03e6fa4bda459c04c99bd6
diff --git a/tests/modules/bwamem2/index/main.nf b/tests/modules/bwamem2/index/main.nf
deleted file mode 100644
index eca045e257c..00000000000
--- a/tests/modules/bwamem2/index/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf'
-
-workflow test_bwamem2_index {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWAMEM2_INDEX ( [ [id:'test'], fasta] )
-}
diff --git a/tests/modules/bwamem2/index/test.yml b/tests/modules/bwamem2/index/test.yml
deleted file mode 100644
index efada6ec54f..00000000000
--- a/tests/modules/bwamem2/index/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: bwamem2 index
-  command: nextflow run ./tests/modules/bwamem2/index -entry test_bwamem2_index -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/index/nextflow.config
-  tags:
-    - bwamem2
-    - bwamem2/index
-  files:
-    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
-      md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
-      md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
diff --git a/tests/modules/bwamem2/mem/main.nf b/tests/modules/bwamem2/mem/main.nf
deleted file mode 100644
index 386bf5319eb..00000000000
--- a/tests/modules/bwamem2/mem/main.nf
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf'
-include { BWAMEM2_MEM   } from '../../../../modules/bwamem2/mem/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_bwamem2_mem_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWAMEM2_INDEX ( [ [:], fasta ] )
-    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
-}
-
-//
-// Test with single-end data and sort
-//
-workflow test_bwamem2_mem_single_end_sort {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWAMEM2_INDEX ( [ [:], fasta ] )
-    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
-}
-
-
-//
-// Test with paired-end data
-//
-workflow test_bwamem2_mem_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWAMEM2_INDEX ( [ [:], fasta ] )
-    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
-}
-
-//
-// Test with paired-end data and sort
-//
-workflow test_bwamem2_mem_paired_end_sort {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWAMEM2_INDEX ( [ [:], fasta ] )
-    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
-}
diff --git a/tests/modules/bwamem2/mem/test.yml b/tests/modules/bwamem2/mem/test.yml
deleted file mode 100644
index bf445ebeeeb..00000000000
--- a/tests/modules/bwamem2/mem/test.yml
+++ /dev/null
@@ -1,71 +0,0 @@
-- name: bwamem2 mem single-end
-  command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
-  tags:
-    - bwamem2
-    - bwamem2/mem
-  files:
-    - path: ./output/bwamem2/test.bam
-    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
-      md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
-      md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-
-- name: bwamem2 mem single-end sort
-  command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
-  tags:
-    - bwamem2
-    - bwamem2/mem
-  files:
-    - path: ./output/bwamem2/test.bam
-    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
-      md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
-      md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-
-- name: bwamem2 mem paired-end
-  command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
-  tags:
-    - bwamem2
-    - bwamem2/mem
-  files:
-    - path: ./output/bwamem2/test.bam
-    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
-      md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
-      md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-
-- name: bwamem2 mem paired-end sort
-  command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
-  tags:
-    - bwamem2
-    - bwamem2/mem
-  files:
-    - path: ./output/bwamem2/test.bam
-    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
-      md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
-      md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
diff --git a/tests/modules/bwameth/align/main.nf b/tests/modules/bwameth/align/main.nf
deleted file mode 100644
index 8066941c359..00000000000
--- a/tests/modules/bwameth/align/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf'
-include { BWAMETH_ALIGN } from '../../../../modules/bwameth/align/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_bwameth_align_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWAMETH_INDEX ( fasta )
-    BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_bwameth_align_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWAMETH_INDEX ( fasta )
-    BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
-}
diff --git a/tests/modules/bwameth/align/test.yml b/tests/modules/bwameth/align/test.yml
deleted file mode 100644
index 161c627f7c1..00000000000
--- a/tests/modules/bwameth/align/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: bwameth align single-end test workflow
-  command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwameth/align/nextflow.config
-  tags:
-    - bwameth
-    - bwameth/align
-  files:
-    - path: output/bwameth/test.bam
-
-- name: bwameth align paired-end test workflow
-  command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwameth/align/nextflow.config
-  tags:
-    - bwameth
-    - bwameth/align
-  files:
-    - path: output/bwameth/test.bam
diff --git a/tests/modules/bwameth/index/main.nf b/tests/modules/bwameth/index/main.nf
deleted file mode 100644
index b70fd1f7967..00000000000
--- a/tests/modules/bwameth/index/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf'
-
-workflow test_bwameth_index {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWAMETH_INDEX ( fasta )
-}
diff --git a/tests/modules/bwameth/index/test.yml b/tests/modules/bwameth/index/test.yml
deleted file mode 100644
index 9783c511e60..00000000000
--- a/tests/modules/bwameth/index/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: bwameth index test workflow
-  command: nextflow run ./tests/modules/bwameth/index -entry test_bwameth_index -c ./tests/config/nextflow.config -c ./tests/modules/bwameth/index/nextflow.config
-  tags:
-    - bwameth
-    - bwameth/index
-  files:
-    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t
-      md5sum: 98039984526a41d04d6bd92fcc040c62
-    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.pac
-      md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653
-    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.amb
-      md5sum: 249a4195069071ce47cd0bae68abe376
-    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.ann
-      md5sum: 46524d4359dcdfb203a235ab3b930dbb
-    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.bwt
-      md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b
-    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.sa
-      md5sum: d25f6486f5134f57ed5b258f6fbb8673
diff --git a/tests/modules/cat/cat/main.nf b/tests/modules/cat/cat/main.nf
deleted file mode 100644
index 24e1d00df55..00000000000
--- a/tests/modules/cat/cat/main.nf
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CAT_CAT                        } from '../../../../modules/cat/cat/main.nf'
-include { CAT_CAT as CAT_UNZIPPED_ZIPPED } from '../../../../modules/cat/cat/main.nf'
-include { CAT_CAT as CAT_ZIPPED_UNZIPPED } from '../../../../modules/cat/cat/main.nf'
-
-workflow test_cat_unzipped_unzipped {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) ]
-    ]
-
-    CAT_CAT ( input )
-}
-
-workflow test_cat_zipped_zipped {
-
-    input = [
-         [ id:'test', single_end:true ], // meta map
-        [file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
-    ]
-
-    CAT_CAT ( input )
-}
-
-workflow test_cat_zipped_unzipped {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
-    ]
-
-    CAT_ZIPPED_UNZIPPED ( input )
-}
-
-workflow test_cat_unzipped_zipped {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)]
-    ]
-
-    CAT_UNZIPPED_ZIPPED ( input )
-}
-
-workflow test_cat_one_file_unzipped_zipped {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    CAT_UNZIPPED_ZIPPED ( input )
-}
diff --git a/tests/modules/cat/cat/test.yml b/tests/modules/cat/cat/test.yml
deleted file mode 100644
index 9710b6659ae..00000000000
--- a/tests/modules/cat/cat/test.yml
+++ /dev/null
@@ -1,81 +0,0 @@
-- name: cat unzipped unzipped
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/test.fasta
-      md5sum: f44b33a0e441ad58b2d3700270e2dbe2
-
-- name: cat unzipped unzipped stub
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/test.fasta
-
-- name: cat zipped zipped
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/test.gz
-
-- name: cat zipped zipped stub
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/test.gz
-
-- name: cat zipped unzipped
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/cat.txt
-      md5sum: c439d3b60e7bc03e8802a451a0d9a5d9
-
-- name: cat zipped unzipped stub
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/cat.txt
-
-- name: cat unzipped zipped
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/cat.txt.gz
-
-- name: cat unzipped zipped stub
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/cat.txt.gz
-
-- name: cat one file unzipped zipped
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/cat.txt.gz
-
-- name: cat one file unzipped zipped stub
-  command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
-  tags:
-    - cat
-    - cat/cat
-  files:
-    - path: output/cat/cat.txt.gz
diff --git a/tests/modules/cat/fastq/main.nf b/tests/modules/cat/fastq/main.nf
deleted file mode 100644
index 671d01e2da1..00000000000
--- a/tests/modules/cat/fastq/main.nf
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CAT_FASTQ } from '../../../../modules/cat/fastq/main.nf'
-
-workflow test_cat_fastq_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    CAT_FASTQ ( input )
-}
-
-workflow test_cat_fastq_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    CAT_FASTQ ( input )
-}
-
-workflow test_cat_fastq_single_end_same_name {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    CAT_FASTQ ( input )
-}
-
-workflow test_cat_fastq_paired_end_same_name {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    CAT_FASTQ ( input )
-}
-
-workflow test_cat_fastq_single_end_single_file {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-    ]
-
-    CAT_FASTQ ( input )
-}
diff --git a/tests/modules/cat/fastq/test.yml b/tests/modules/cat/fastq/test.yml
deleted file mode 100644
index 416f1a8b449..00000000000
--- a/tests/modules/cat/fastq/test.yml
+++ /dev/null
@@ -1,82 +0,0 @@
-- name: cat fastq single-end
-  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
-  tags:
-    - cat
-    - cat/fastq
-  files:
-    - path: ./output/cat/test.merged.fastq.gz
-      md5sum: f9cf5e375f7de81a406144a2c70cc64d
-
-- name: cat fastq fastqc_paired_end
-  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
-  tags:
-    - cat
-    - cat/fastq
-  files:
-    - path: ./output/cat/test_2.merged.fastq.gz
-      md5sum: 77c8e966e130d8c6b6ec9be52fcb2bda
-    - path: ./output/cat/test_1.merged.fastq.gz
-      md5sum: f9cf5e375f7de81a406144a2c70cc64d
-
-- name: cat fastq single-end-same-name
-  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
-  tags:
-    - cat
-    - cat/fastq
-  files:
-    - path: ./output/cat/test.merged.fastq.gz
-      md5sum: 63f817db7a29a03eb538104495556f66
-
-- name: cat fastq fastqc_paired_end_same_name
-  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
-  tags:
-    - cat
-    - cat/fastq
-  files:
-    - path: ./output/cat/test_1.merged.fastq.gz
-      md5sum: 63f817db7a29a03eb538104495556f66
-    - path: ./output/cat/test_2.merged.fastq.gz
-      md5sum: fe9f266f43a6fc3dcab690a18419a56e
-
-- name: cat fastq single-end-single-file
-  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_single_file -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
-  tags:
-    - cat
-    - cat/fastq
-  files:
-    - path: ./output/cat/test.merged.fastq.gz
-      md5sum: e325ef7deb4023447a1f074e285761af
-
-- name: cat fastq single-end stub
-  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
-  tags:
-    - cat
-    - cat/fastq
-  files:
-    - path: ./output/cat/test.merged.fastq.gz
-
-- name: cat fastq fastqc_paired_end stub
-  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
-  tags:
-    - cat
-    - cat/fastq
-  files:
-    - path: ./output/cat/test_2.merged.fastq.gz
-    - path: ./output/cat/test_1.merged.fastq.gz
-
-- name: cat fastq single-end-same-name stub
-  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
-  tags:
-    - cat
-    - cat/fastq
-  files:
-    - path: ./output/cat/test.merged.fastq.gz
-
-- name: cat fastq fastqc_paired_end_same_name stub
-  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
-  tags:
-    - cat
-    - cat/fastq
-  files:
-    - path: ./output/cat/test_1.merged.fastq.gz
-    - path: ./output/cat/test_2.merged.fastq.gz
diff --git a/tests/modules/cellranger/count/main.nf b/tests/modules/cellranger/count/main.nf
deleted file mode 100644
index bb9e11d1b9f..00000000000
--- a/tests/modules/cellranger/count/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CELLRANGER_MKGTF } from '../../../../modules/cellranger/mkgtf/main.nf'
-include { CELLRANGER_MKREF } from '../../../../modules/cellranger/mkref/main.nf'
-include { CELLRANGER_COUNT } from '../../../../modules/cellranger/count/main.nf'
-
-workflow test_cellranger_count {
-
-    input = [ [ id:'test', single_end:true, strandedness:'forward', gem: '123', samples: ["test_10x"] ], // meta map
-             [ file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    reference_name = "homo_sapiens_chr22_reference"
-
-    CELLRANGER_MKGTF ( gtf )
-
-    CELLRANGER_MKREF (
-        fasta,
-        CELLRANGER_MKGTF.out.gtf,
-        reference_name
-    )
-
-    CELLRANGER_COUNT(
-        input,
-        CELLRANGER_MKREF.out.reference
-    )
-}
diff --git a/tests/modules/cellranger/count/test.yml b/tests/modules/cellranger/count/test.yml
deleted file mode 100644
index 93e52c4a5fe..00000000000
--- a/tests/modules/cellranger/count/test.yml
+++ /dev/null
@@ -1,65 +0,0 @@
-- name: cellranger count test_cellranger_count
-  command: nextflow run ./tests/modules/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config  -c ./tests/modules/cellranger/count/nextflow.config
-  tags:
-    - cellranger/count
-    - cellranger
-  files:
-    - path: output/cellranger/genome.filtered.gtf
-      md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
-    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
-      md5sum: f315020d899597c1b57e5fe9f60f4c3e
-    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
-      md5sum: 3520cd30e1b100e55f578db9c855f685
-    - path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
-      md5sum: d1e05cd46684fa26d852b6bc9f05e31f
-    - path: output/cellranger/homo_sapiens_chr22_reference/reference.json
-      md5sum: 8405fd7f527a944eafb9c2909045840b
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
-      md5sum: 897cec2d191945335f8b320438bd9135
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/SA
-      md5sum: 7961129ac5d0e1706105be1d31c6b30c
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
-      md5sum: dcceb480b30cda93fb8c63ddc339093b
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
-      md5sum: bc73df776dd3d5bb9cfcbcba60880519
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
-      md5sum: 9129691eeb4ed0d02b17be879fa3edb0
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
-      md5sum: 209b82f0683efd03e17d2c729676554f
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
-      md5sum: 02a8f4575bdfcd4a42b4d8d07f2e9369
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
-      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
-      md5sum: cedcb5f4e7d97bc548cd5daa022e092c
-    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
-      md5sum: f8b6b7cc8248151a98c46d4ebec450c6
-    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
-    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/features.tsv.gz
-    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
-    - path: output/cellranger/sample-123/outs/metrics_summary.csv
-      md5sum: 707df0f101d479d93f412ca74f9c4131
-    - path: output/cellranger/sample-123/outs/molecule_info.h5
-      md5sum: a13bd7425f441c8d0eac8ffc50082996
-    - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
-      md5sum: 15441da9cfceea0bb48c8b66b1b860df
-    - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
-      md5sum: 7c3d49c77016a09535aff61a027f750c
-    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
-      md5sum: a5290f3e300a4070f3d68a0c2e215f54
-    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/barcodes.tsv.gz
-      md5sum: 5cc39ef0c7ac85f2b758b164aabf9157
-    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/features.tsv.gz
-      md5sum: 07d497c7ce3e22f374af7b2cf9b97d72
-    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/matrix.mtx.gz
-      md5sum: bdce94a51f16e22d40301724080b76ee
-    - path: output/cellranger/sample-123/outs/web_summary.html
diff --git a/tests/modules/cellranger/mkfastq/main.nf b/tests/modules/cellranger/mkfastq/main.nf
deleted file mode 100644
index 7bad0feca80..00000000000
--- a/tests/modules/cellranger/mkfastq/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR          } from '../../../../modules/untar/main.nf'
-include { CELLRANGER_MKFASTQ } from '../../../../modules/cellranger/mkfastq/main.nf'
-
-workflow test_cellranger_mkfastq_simple {
-
-    simple_csv = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true)
-    tiny_bcl = [ [], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true) ]
-
-    UNTAR ( tiny_bcl )
-
-    CELLRANGER_MKFASTQ ( UNTAR.out.untar.map{ it[1] }, simple_csv)
-}
-
-workflow test_cellranger_mkfastq_illumina {
-
-    samplesheet_csv = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv", checkIfExists: true)
-    tiny_bcl = [ [], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true) ]
-
-    UNTAR ( tiny_bcl )
-
-    CELLRANGER_MKFASTQ ( UNTAR.out.untar.map{ it[1] }, samplesheet_csv)
-}
diff --git a/tests/modules/cellranger/mkfastq/test.yml b/tests/modules/cellranger/mkfastq/test.yml
deleted file mode 100644
index 273d8fca029..00000000000
--- a/tests/modules/cellranger/mkfastq/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: cellranger mkfastq test_cellranger_mkfastq_simple
-  command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
-  tags:
-    - cellranger
-    - cellranger/mkfastq
-  files:
-    - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
-- name: cellranger mkfastq test_cellranger_mkfastq_illumina
-  command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
-  tags:
-    - cellranger
-    - cellranger/mkfastq
-  files:
-    - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
diff --git a/tests/modules/cellranger/mkgtf/main.nf b/tests/modules/cellranger/mkgtf/main.nf
deleted file mode 100644
index 19e2cba0d30..00000000000
--- a/tests/modules/cellranger/mkgtf/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CELLRANGER_MKGTF } from '../../../../modules/cellranger/mkgtf/main.nf'
-
-workflow test_cellranger_mkgtf {
-    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-
-    CELLRANGER_MKGTF ( gtf )
-}
diff --git a/tests/modules/cellranger/mkgtf/test.yml b/tests/modules/cellranger/mkgtf/test.yml
deleted file mode 100644
index 59eb9072654..00000000000
--- a/tests/modules/cellranger/mkgtf/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: cellranger mkgtf test_cellranger_mkgtf
-  command: nextflow run ./tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config  -c ./tests/modules/cellranger/mkgtf/nextflow.config
-  tags:
-    - cellranger/mkgtf
-    - cellranger
-  files:
-    - path: output/cellranger/genome.filtered.gtf
-      md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
diff --git a/tests/modules/cellranger/mkref/main.nf b/tests/modules/cellranger/mkref/main.nf
deleted file mode 100644
index ad98ed1a73c..00000000000
--- a/tests/modules/cellranger/mkref/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CELLRANGER_MKREF } from '../../../../modules/cellranger/mkref/main.nf'
-
-workflow test_cellranger_mkref {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    reference_name = "homo_sapiens_chr22_reference"
-
-    CELLRANGER_MKREF ( fasta,
-                        gtf,
-                        reference_name )
-}
diff --git a/tests/modules/cellranger/mkref/test.yml b/tests/modules/cellranger/mkref/test.yml
deleted file mode 100644
index 83ec5f9502e..00000000000
--- a/tests/modules/cellranger/mkref/test.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-- name: cellranger mkref test_cellranger_mkref
-  command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config  -c ./tests/modules/cellranger/mkref/nextflow.config
-  tags:
-    - cellranger/mkref
-    - cellranger
-  files:
-    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
-      md5sum: f315020d899597c1b57e5fe9f60f4c3e
-    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
-      md5sum: 3520cd30e1b100e55f578db9c855f685
-    - path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
-      md5sum: 6d9b5f409bfea95022bc25b9590e194e
-    - path: output/cellranger/homo_sapiens_chr22_reference/reference.json
-      md5sum: 6cc817f0923062e780e6573806840cea
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
-      md5sum: 22102926fadf5890e905ca71b2da3f35
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/SA
-      md5sum: bcf3e1a855783105150b46c905465333
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
-      md5sum: b93fb07d342e6c32a00ebc4311c0ad38
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
-      md5sum: bc73df776dd3d5bb9cfcbcba60880519
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
-      md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
-      md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
-      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
diff --git a/tests/modules/centrifuge/centrifuge/main.nf b/tests/modules/centrifuge/centrifuge/main.nf
deleted file mode 100644
index 35deeb583f6..00000000000
--- a/tests/modules/centrifuge/centrifuge/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR                 } from '../../../../modules/untar/main.nf'
-include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/centrifuge/centrifuge/main.nf'
-
-workflow test_centrifuge_centrifuge_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
-    save_unaligned = true
-    save_aligned = false
-    sam_format = false
-
-    UNTAR ( db )
-    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
-
-}
-
-workflow test_centrifuge_centrifuge_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-     db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
-     save_unaligned = true
-     save_aligned = false
-     sam_format = false
-
-    UNTAR ( db )
-    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
-
-
-}
diff --git a/tests/modules/centrifuge/centrifuge/test.yml b/tests/modules/centrifuge/centrifuge/test.yml
deleted file mode 100644
index 641ca7ef5e0..00000000000
--- a/tests/modules/centrifuge/centrifuge/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: centrifuge centrifuge test_centrifuge_centrifuge_single_end
-  command: nextflow run tests/modules/centrifuge/centrifuge -entry test_centrifuge_centrifuge_single_end -c tests/config/nextflow.config
-  tags:
-    - centrifuge
-    - centrifuge/centrifuge
-  files:
-    - path: output/centrifuge/test.report.txt
-    - path: output/centrifuge/test.results.txt
-    - path: output/centrifuge/test.unmapped.fastq.gz
-    - path: output/centrifuge/versions.yml
-
-- name: centrifuge centrifuge test_centrifuge_centrifuge_paired_end
-  command: nextflow run tests/modules/centrifuge/centrifuge -entry test_centrifuge_centrifuge_paired_end -c tests/config/nextflow.config
-  tags:
-    - centrifuge
-    - centrifuge/centrifuge
-  files:
-    - path: output/centrifuge/test.report.txt
-    - path: output/centrifuge/test.results.txt
-    - path: output/centrifuge/test.unmapped.fastq.1.gz
-    - path: output/centrifuge/test.unmapped.fastq.2.gz
-    - path: output/centrifuge/versions.yml
diff --git a/tests/modules/centrifuge/kreport/main.nf b/tests/modules/centrifuge/kreport/main.nf
deleted file mode 100644
index 397d33aa18a..00000000000
--- a/tests/modules/centrifuge/kreport/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR                } from '../../../../modules/untar/main.nf'
-include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/centrifuge/centrifuge/main.nf'
-include { CENTRIFUGE_KREPORT    } from '../../../../modules/centrifuge/kreport/main.nf'
-
-workflow test_centrifuge_kreport_single_end {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
-
-    ch_db = UNTAR ( db )
-    CENTRIFUGE_CENTRIFUGE ( input, ch_db.untar.map{ it[1] }, false, false, false )
-    CENTRIFUGE_KREPORT ( CENTRIFUGE_CENTRIFUGE.out.results, ch_db.untar.map{ it[1] } )
-}
-
-workflow test_centrifuge_kreport_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-     db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
-
-    ch_db = UNTAR ( db )
-    CENTRIFUGE_CENTRIFUGE ( input, ch_db.untar.map{ it[1] }, false, false, false )
-    CENTRIFUGE_KREPORT ( CENTRIFUGE_CENTRIFUGE.out.results, ch_db.untar.map{ it[1] } )
-}
-
diff --git a/tests/modules/centrifuge/kreport/test.yml b/tests/modules/centrifuge/kreport/test.yml
deleted file mode 100644
index ab614c53982..00000000000
--- a/tests/modules/centrifuge/kreport/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: centrifuge kreport test_centrifuge_kreport_single_end
-  command: nextflow run ./tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/centrifuge/kreport/nextflow.config
-  tags:
-    - centrifuge/kreport
-    - centrifuge
-  files:
-    - path: output/centrifuge/test.report.txt
-    - path: output/centrifuge/test.results.txt
-    - path: output/centrifuge/test.txt
-
-- name: centrifuge kreport test_centrifuge_kreport_paired_end
-  command: nextflow run ./tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/centrifuge/kreport/nextflow.config
-  tags:
-    - centrifuge/kreport
-    - centrifuge
-  files:
-    - path: output/centrifuge/test.report.txt
-    - path: output/centrifuge/test.results.txt
-    - path: output/centrifuge/test.txt
diff --git a/tests/modules/checkm/lineagewf/main.nf b/tests/modules/checkm/lineagewf/main.nf
deleted file mode 100644
index cb7c7baec5b..00000000000
--- a/tests/modules/checkm/lineagewf/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CHECKM_LINEAGEWF } from '../../../../modules/checkm/lineagewf/main.nf'
-
-workflow test_checkm_lineagewf {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
-    fasta_ext = 'fasta'
-
-    CHECKM_LINEAGEWF ( input, fasta_ext, [] )
-}
-
-workflow test_checkm_lineagewf_multi {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
-                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ]
-    fasta_ext = 'fasta'
-
-    CHECKM_LINEAGEWF ( input, fasta_ext, [] )
-}
diff --git a/tests/modules/checkm/lineagewf/test.yml b/tests/modules/checkm/lineagewf/test.yml
deleted file mode 100644
index f81e8c9c0ee..00000000000
--- a/tests/modules/checkm/lineagewf/test.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-- name: checkm lineagewf
-  command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf -c ./tests/config/nextflow.config -c ./tests/modules/checkm/lineagewf/nextflow.config
-  tags:
-    - checkm
-    - checkm/lineagewf
-  files:
-    - path: output/checkm/test.tsv
-      md5sum: d5559764f563c4b55223e4e4a3dc1ec9
-    - path: output/checkm/test/checkm.log
-      contains:
-        - "INFO: Parsing HMM hits to marker genes:"
-    - path: output/checkm/test/lineage.ms
-      contains:
-        - "# [Lineage Marker File]"
-        - "contigs"
-        - "UID1"
-
-- name: checkm lineagewf_multi
-  command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf_multi -c ./tests/config/nextflow.config -c ./tests/modules/checkm/lineagewf/nextflow.config
-  tags:
-    - checkm
-    - checkm/lineagewf
-  files:
-    - path: output/checkm/test.tsv
-      md5sum: 7e0fa177dcf151b84b7751813fbde3d1
-    - path: output/checkm/test/checkm.log
-      contains:
-        - "INFO: Parsing HMM hits to marker genes:"
-    - path: output/checkm/test/lineage.ms
-      contains:
-        - "# [Lineage Marker File]"
-        - "contigs"
-        - "UID1"
-        - "genome"
diff --git a/tests/modules/checkm/qa/main.nf b/tests/modules/checkm/qa/main.nf
deleted file mode 100644
index 2be2dd67898..00000000000
--- a/tests/modules/checkm/qa/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CHECKM_LINEAGEWF              } from '../../../../modules/checkm/lineagewf/main.nf'
-include { CHECKM_LINEAGEWF as CHECKM_LINEAGEWF_FASTA        } from '../../../../modules/checkm/lineagewf/main.nf'
-include { CHECKM_QA                     } from '../../../../modules/checkm/qa/main.nf'
-include { CHECKM_QA as CHECKM_QA_FASTA  } from '../../../../modules/checkm/qa/main.nf'
-
-workflow test_checkm_qa {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
-    fasta_ext = 'fasta'
-
-    CHECKM_LINEAGEWF ( input, fasta_ext, [] )
-
-    ch_checkmqa_input = CHECKM_LINEAGEWF.out.checkm_output
-        .join(CHECKM_LINEAGEWF.out.marker_file)
-        .map{
-            meta, dir, marker ->
-            [ meta, dir, marker, []]
-        }
-
-    CHECKM_QA ( ch_checkmqa_input, [] )
-}
-
-workflow test_checkm_qa_fasta {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
-    fasta_ext = 'fasta'
-
-    CHECKM_LINEAGEWF_FASTA ( input, fasta_ext, [] )
-
-    ch_checkmqa_input =  CHECKM_LINEAGEWF_FASTA.out.checkm_output
-        .join(CHECKM_LINEAGEWF_FASTA.out.marker_file)
-        .map{
-            meta, dir, marker ->
-            [ meta, dir, marker, []]
-        }
-
-    CHECKM_QA_FASTA ( ch_checkmqa_input, [] )
-}
diff --git a/tests/modules/checkm/qa/test.yml b/tests/modules/checkm/qa/test.yml
deleted file mode 100644
index 0c3fa4c803b..00000000000
--- a/tests/modules/checkm/qa/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: checkm qa test_checkm_qa
-  command: nextflow run ./tests/modules/checkm/qa -entry test_checkm_qa -c ./tests/config/nextflow.config  -c ./tests/modules/checkm/qa/nextflow.config
-  tags:
-    - checkm/qa
-    - checkm
-  files:
-    - path: output/checkm/test.qa.txt
-      md5sum: 645f4282569afb4b171396732b2d2582
-
-- name: checkm qa test_checkm_qa_fasta
-  command: nextflow run ./tests/modules/checkm/qa -entry test_checkm_qa_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/checkm/qa/nextflow.config
-  tags:
-    - checkm/qa
-    - checkm
-  files:
-    - path: output/checkm/test.qa.fasta
diff --git a/tests/modules/chromap/chromap/main.nf b/tests/modules/chromap/chromap/main.nf
deleted file mode 100644
index 5522f2b5f39..00000000000
--- a/tests/modules/chromap/chromap/main.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CHROMAP_INDEX                           } from '../../../../modules/chromap/index/main.nf'
-include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_BASE } from '../../../../modules/chromap/chromap/main.nf'
-include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_SAM  } from '../../../../modules/chromap/chromap/main.nf'
-
-workflow test_chromap_chromap_single_end {
-
-    // Test single-end and gz compressed output
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    CHROMAP_INDEX ( fasta )
-    CHROMAP_CHROMAP_BASE (
-        input,                      // meta + read data
-        fasta,                      // reference genome
-        CHROMAP_INDEX.out.index,    // reference index
-        [],                         // barcode file
-        [],                         // barcode whitelist
-        [],                         // chromosome order file
-        []                          // pairs chromosome order file
-    )
-}
-
-workflow test_chromap_chromap_paired_end {
-
-    // Test paired-end and gz compressed output
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    CHROMAP_INDEX ( fasta )
-    CHROMAP_CHROMAP_BASE (
-        input,                      // meta + read data
-        fasta,                      // reference genome
-        CHROMAP_INDEX.out.index,    // reference index
-        [],                         // barcode file
-        [],                         // barcode whitelist
-        [],                         // chromosome order file
-        []                          // pairs chromosome order file
-    )
-}
-
-workflow test_chromap_chromap_paired_bam {
-
-    // Test paired-end and bam output
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    CHROMAP_INDEX ( fasta )
-    CHROMAP_CHROMAP_SAM (
-        input,                      // meta + read data
-        fasta,                      // reference genome
-        CHROMAP_INDEX.out.index,    // reference index
-        [],                         // barcode file
-        [],                         // barcode whitelist
-        [],                         // chromosome order file
-        []                          // pairs chromosome order file
-    )
-}
diff --git a/tests/modules/chromap/chromap/test.yml b/tests/modules/chromap/chromap/test.yml
deleted file mode 100644
index d089922ab79..00000000000
--- a/tests/modules/chromap/chromap/test.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-- name: chromap chromap test_chromap_chromap_single_end
-  command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_single_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
-  tags:
-    - chromap/chromap
-    - chromap
-  files:
-    - path: output/chromap/genome.index
-    - path: output/chromap/test.bed.gz
-      md5sum: 25e40bde24c7b447292cd68573728694
-    - path: output/chromap/versions.yml
-
-- name: chromap chromap test_chromap_chromap_paired_end
-  command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
-  tags:
-    - chromap/chromap
-    - chromap
-  files:
-    - path: output/chromap/genome.index
-    - path: output/chromap/test.bed.gz
-      md5sum: 7cdc8448882b75811e0c784f5f20aef2
-    - path: output/chromap/versions.yml
-
-- name: chromap chromap test_chromap_chromap_paired_bam
-  command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
-  tags:
-    - chromap/chromap
-    - chromap
-  files:
-    - path: output/chromap/genome.index
-    - path: output/chromap/test.bam
-      md5sum: 0cb45628d1abe4b4359650040c501aef
-    - path: output/chromap/versions.yml
diff --git a/tests/modules/chromap/index/main.nf b/tests/modules/chromap/index/main.nf
deleted file mode 100644
index 18b4200627b..00000000000
--- a/tests/modules/chromap/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CHROMAP_INDEX } from '../../../../modules/chromap/index/main.nf'
-
-workflow test_chromap_index {
-
-    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    CHROMAP_INDEX ( input )
-}
diff --git a/tests/modules/chromap/index/test.yml b/tests/modules/chromap/index/test.yml
deleted file mode 100644
index 3e1d6fa60fe..00000000000
--- a/tests/modules/chromap/index/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: chromap index test_chromap_index
-  command: nextflow run ./tests/modules/chromap/index -entry test_chromap_index -c ./tests/config/nextflow.config -c ./tests/modules/chromap/index/nextflow.config
-  tags:
-    - chromap/index
-    - chromap
-  files:
-    - path: output/chromap/genome.index
-    - path: output/chromap/versions.yml
-      md5sum: fc5c80190d0622ea3e979e6862f8e32b
diff --git a/tests/modules/clonalframeml/main.nf b/tests/modules/clonalframeml/main.nf
deleted file mode 100644
index 73773113479..00000000000
--- a/tests/modules/clonalframeml/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CLONALFRAMEML } from '../../../modules/clonalframeml/main.nf'
-
-workflow test_clonalframeml {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['haemophilus_influenzae']['genome']['genome_aln_nwk'], checkIfExists: true),
-        file(params.test_data['haemophilus_influenzae']['genome']['genome_aln_gz'], checkIfExists: true)
-    ]
-
-    CLONALFRAMEML ( input )
-}
diff --git a/tests/modules/clonalframeml/test.yml b/tests/modules/clonalframeml/test.yml
deleted file mode 100644
index 8ea11d164b9..00000000000
--- a/tests/modules/clonalframeml/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: clonalframeml test_clonalframeml
-  command: nextflow run ./tests/modules/clonalframeml -entry test_clonalframeml -c ./tests/config/nextflow.config -c ./tests/modules/clonalframeml/nextflow.config
-  tags:
-    - clonalframeml
-  files:
-    - path: output/clonalframeml/test.ML_sequence.fasta
-      md5sum: 1b75cdaea78f5920ebb92125422a2589
-    - path: output/clonalframeml/test.em.txt
-      md5sum: 5439d59897a9a90390bb175207bf2b9b
-    - path: output/clonalframeml/test.importation_status.txt
-      md5sum: 6ce9dbc7746b1c884af042fa02311fba
-    - path: output/clonalframeml/test.labelled_tree.newick
-      md5sum: aa47754eea8a3b6bab56bd7c83ba78db
-    - path: output/clonalframeml/test.position_cross_reference.txt
-      md5sum: 8ff60768b348fc6f7a1e787aca72f596
diff --git a/tests/modules/cmseq/polymut/main.nf b/tests/modules/cmseq/polymut/main.nf
deleted file mode 100644
index df6a0ac13ef..00000000000
--- a/tests/modules/cmseq/polymut/main.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CMSEQ_POLYMUT } from '../../../../modules/cmseq/polymut/main.nf'
-
-workflow test_cmseq_polymut_1 {
-
-    input_1 = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              [],
-              file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
-              [] ]
-
-    CMSEQ_POLYMUT( input_1 )
-    
-}
-
-workflow test_cmseq_polymut_2 {
-    input_2 = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
-              [] ]
-
-    CMSEQ_POLYMUT( input_2 )
-}
-
-workflow test_cmseq_polymut_3 {
-    input_3 = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), ]
-
-    CMSEQ_POLYMUT( input_3 )
-}
-    
diff --git a/tests/modules/cmseq/polymut/test.yml b/tests/modules/cmseq/polymut/test.yml
deleted file mode 100644
index 05887fa81a4..00000000000
--- a/tests/modules/cmseq/polymut/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: cmseq polymut test_cmseq_polymut_1
-  command: nextflow run ./tests/modules/cmseq/polymut -entry test_cmseq_polymut_1 -c ./tests/config/nextflow.config -c ./tests/modules/cmseq/polymut/nextflow.config
-  tags:
-    - cmseq/polymut
-    - cmseq
-  files:
-    - path: output/cmseq/test.txt
-      md5sum: fd325c1724ee23d132a9115c64494efc
-
-- name: cmseq polymut test_cmseq_polymut_2
-  command: nextflow run ./tests/modules/cmseq/polymut -entry test_cmseq_polymut_2 -c ./tests/config/nextflow.config -c ./tests/modules/cmseq/polymut/nextflow.config
-  tags:
-    - cmseq/polymut
-    - cmseq
-  files:
-    - path: output/cmseq/test.txt
-      md5sum: fd325c1724ee23d132a9115c64494efc
-
-- name: cmseq polymut test_cmseq_polymut_3
-  command: nextflow run ./tests/modules/cmseq/polymut -entry test_cmseq_polymut_3 -c ./tests/config/nextflow.config -c ./tests/modules/cmseq/polymut/nextflow.config
-  tags:
-    - cmseq/polymut
-    - cmseq
-  files:
-    - path: output/cmseq/test.txt
-      md5sum: fd325c1724ee23d132a9115c64494efc
diff --git a/tests/modules/cnvkit/antitarget/main.nf b/tests/modules/cnvkit/antitarget/main.nf
deleted file mode 100644
index 44e49eb2123..00000000000
--- a/tests/modules/cnvkit/antitarget/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CNVKIT_ANTITARGET } from '../../../../modules/cnvkit/antitarget/main.nf'
-
-workflow test_cnvkit_antitarget {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-    ]
-
-    CNVKIT_ANTITARGET ( input )
-}
-
diff --git a/tests/modules/cnvkit/antitarget/test.yml b/tests/modules/cnvkit/antitarget/test.yml
deleted file mode 100644
index e1c3d0c8fce..00000000000
--- a/tests/modules/cnvkit/antitarget/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: cnvkit antitarget test_cnvkit_antitarget
-  command: nextflow run ./tests/modules/cnvkit/antitarget -entry test_cnvkit_antitarget -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/antitarget/nextflow.config
-  tags:
-    - cnvkit
-    - cnvkit/antitarget
-  files:
-    - path: output/cnvkit/test.antitarget.bed
-      md5sum: 3d4d20f9f23b39970865d29ef239d20b
diff --git a/tests/modules/cnvkit/batch/main.nf b/tests/modules/cnvkit/batch/main.nf
deleted file mode 100755
index daf87a37cb1..00000000000
--- a/tests/modules/cnvkit/batch/main.nf
+++ /dev/null
@@ -1,99 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CNVKIT_BATCH as CNVKIT_HYBRID    } from '../../../../modules/cnvkit/batch/main.nf'
-include { CNVKIT_BATCH as CNVKIT_WGS       } from '../../../../modules/cnvkit/batch/main.nf'
-include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
-include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf'
-
-workflow test_cnvkit_hybrid_somatic {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
-    ]
-    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
-
-    CNVKIT_HYBRID ( input, fasta, [], targets, [] )
-}
-
-workflow test_cnvkit_wgs_somatic {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    CNVKIT_WGS ( input, fasta, [], [], [] )
-}
-
-workflow test_cnvkit_cram_wgs_somatic {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
-    ]
-    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    CNVKIT_WGS ( input, fasta, fasta_fai, [], [] )
-}
-
-
-workflow test_cnvkit_tumoronly_hybrid_bam {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        []
-    ]
-    reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
-
-    CNVKIT_TUMORONLY ( input, [], [],  [], reference )
-}
-
-workflow test_cnvkit_tumoronly_hybrid_cram {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        []
-    ]
-    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
-
-    CNVKIT_TUMORONLY ( input, fasta, [], [], reference )
-}
-
-workflow test_cnvkit_germline_hybrid_cram {
-
-    input = [
-        [ id:'test'], // meta map
-        [],
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
-    ]
-    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    CNVKIT_GERMLINE ( input, fasta, fasta_fai, targets,  [])
-}
-
-workflow test_cnvkit_germline_hybrid_bam {
-
-    input = [
-        [ id:'test'], // meta map
-        [],
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
-    ]
-    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    CNVKIT_GERMLINE ( input, fasta, [], targets,  [])
-}
diff --git a/tests/modules/cnvkit/batch/test.yml b/tests/modules/cnvkit/batch/test.yml
deleted file mode 100755
index 006e142f292..00000000000
--- a/tests/modules/cnvkit/batch/test.yml
+++ /dev/null
@@ -1,183 +0,0 @@
-- name: cnvkit batch test_cnvkit_hybrid_somatic
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
-  tags:
-    - cnvkit
-    - cnvkit/batch
-  files:
-    - path: output/cnvkit/baits.antitarget.bed
-    - path: output/cnvkit/baits.target.bed
-      md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
-    - path: output/cnvkit/reference.cnn
-      md5sum: 035d031f54c5f1b43b903da96559b475
-    - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
-      md5sum: 203caf8cef6935bb50b4138097955cb8
-    - path: output/cnvkit/test.paired_end.sorted.bintest.cns
-      md5sum: 6544d979475def8a9f69ba42a985668d
-    - path: output/cnvkit/test.paired_end.sorted.call.cns
-      md5sum: f2ca59b4d50b0c317adc526c1b99b622
-    - path: output/cnvkit/test.paired_end.sorted.cnr
-      md5sum: 7e37d73ab604dbc3fe4ebb56aca9bdc3
-    - path: output/cnvkit/test.paired_end.sorted.cns
-      md5sum: 060af1aa637ed51812af19bcce24fcfe
-    - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
-      md5sum: 3fe80b6013ffc3e9968345e810158215
-    - path: output/cnvkit/test.single_end.sorted.antitargetcoverage.cnn
-      md5sum: 203caf8cef6935bb50b4138097955cb8
-    - path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
-      md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
-
-- name: cnvkit batch test_cnvkit_wgs_somatic
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
-  tags:
-    - cnvkit
-    - cnvkit/batch
-  files:
-    - path: output/cnvkit/genome.antitarget.bed
-    - path: output/cnvkit/genome.bed
-      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
-    - path: output/cnvkit/genome.target.bed
-      md5sum: a13353ae9c8405e701390c069255bbd2
-    - path: output/cnvkit/reference.cnn
-      md5sum: 1606a85410bfaa79464be6e98699aa83
-    - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
-      md5sum: 203caf8cef6935bb50b4138097955cb8
-    - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
-      md5sum: ff526714696aa49bdc1dc8d00d965266
-    - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
-      md5sum: 203caf8cef6935bb50b4138097955cb8
-    - path: output/cnvkit/test2.paired_end.sorted.bintest.cns
-      md5sum: 6544d979475def8a9f69ba42a985668d
-    - path: output/cnvkit/test2.paired_end.sorted.call.cns
-      md5sum: f6de754c34f780e6befee5b3ff0893f8
-    - path: output/cnvkit/test2.paired_end.sorted.cnr
-      md5sum: 80318d06c6b095945a0fb0e85e887cbc
-    - path: output/cnvkit/test2.paired_end.sorted.cns
-      md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
-    - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
-      md5sum: 6ae6b3fce7299eedca6133d911c38fe1
-
-- name: cnvkit batch test_cnvkit_cram_wgs_somatic
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
-  tags:
-    - cnvkit
-    - cnvkit/batch
-  files:
-    - path: output/cnvkit/genome.antitarget.bed
-    - path: output/cnvkit/genome.bed
-      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
-    - path: output/cnvkit/genome.target.bed
-      md5sum: a13353ae9c8405e701390c069255bbd2
-    - path: output/cnvkit/reference.cnn
-      md5sum: 1606a85410bfaa79464be6e98699aa83
-    - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
-      md5sum: 203caf8cef6935bb50b4138097955cb8
-    - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
-      md5sum: ff526714696aa49bdc1dc8d00d965266
-    - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
-      md5sum: 203caf8cef6935bb50b4138097955cb8
-    - path: output/cnvkit/test2.paired_end.sorted.bintest.cns
-      md5sum: 6544d979475def8a9f69ba42a985668d
-    - path: output/cnvkit/test2.paired_end.sorted.call.cns
-      md5sum: f6de754c34f780e6befee5b3ff0893f8
-    - path: output/cnvkit/test2.paired_end.sorted.cnr
-      md5sum: 80318d06c6b095945a0fb0e85e887cbc
-    - path: output/cnvkit/test2.paired_end.sorted.cns
-      md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
-    - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
-      md5sum: 6ae6b3fce7299eedca6133d911c38fe1
-
-- name: cnvkit batch test_cnvkit_tumoronly_hybrid_bam
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
-  tags:
-    - cnvkit
-    - cnvkit/batch
-  files:
-    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
-      md5sum: 3d4d20f9f23b39970865d29ef239d20b
-    - path: output/cnvkit/reference_chr21.target-tmp.bed
-      md5sum: 657b25dbda8516624efa8cb2cf3716ca
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-      md5sum: 067115082c4af4b64d58c0dc3a3642e4
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
-      md5sum: f7caeca04aba28b125ce26b511f42afb
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
-      md5sum: d9bdb71ce807051369577ee7f807a40c
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
-      md5sum: 2b56aac606ba6183d018b30ca58afcec
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
-      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
-
-- name: cnvkit batch test_cnvkit_tumoronly_hybrid_cram
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
-  tags:
-    - cnvkit
-    - cnvkit/batch
-  files:
-    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
-      md5sum: 3d4d20f9f23b39970865d29ef239d20b
-    - path: output/cnvkit/reference_chr21.target-tmp.bed
-      md5sum: 657b25dbda8516624efa8cb2cf3716ca
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-      md5sum: 067115082c4af4b64d58c0dc3a3642e4
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
-      md5sum: f7caeca04aba28b125ce26b511f42afb
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
-      md5sum: d9bdb71ce807051369577ee7f807a40c
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
-      md5sum: 2b56aac606ba6183d018b30ca58afcec
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
-      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
-
-- name: cnvkit batch test_cnvkit_germline_hybrid_cram
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
-  tags:
-    - cnvkit
-    - cnvkit/batch
-  files:
-    - path: output/cnvkit/multi_intervals.antitarget.bed
-      md5sum: 3d4d20f9f23b39970865d29ef239d20b
-    - path: output/cnvkit/multi_intervals.target.bed
-      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
-    - path: output/cnvkit/reference.cnn
-      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-      md5sum: 067115082c4af4b64d58c0dc3a3642e4
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-      md5sum: 68b62b75cd91b2ffe5633686fb943490
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
-      md5sum: df196edd72613c59186f4d87df3dc4a4
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
-      md5sum: 3b4fc0cc73be78f978cfe2422470753e
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
-      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
-      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
-
-- name: cnvkit batch test_cnvkit_germline_hybrid_bam
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
-  tags:
-    - cnvkit
-    - cnvkit/batch
-  files:
-    - path: output/cnvkit/multi_intervals.antitarget.bed
-      md5sum: 3d4d20f9f23b39970865d29ef239d20b
-    - path: output/cnvkit/multi_intervals.target.bed
-      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
-    - path: output/cnvkit/reference.cnn
-      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-      md5sum: 067115082c4af4b64d58c0dc3a3642e4
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-      md5sum: 68b62b75cd91b2ffe5633686fb943490
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
-      md5sum: df196edd72613c59186f4d87df3dc4a4
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
-      md5sum: 3b4fc0cc73be78f978cfe2422470753e
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
-      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
-    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
-      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
diff --git a/tests/modules/cnvkit/reference/main.nf b/tests/modules/cnvkit/reference/main.nf
deleted file mode 100644
index a72ad56646a..00000000000
--- a/tests/modules/cnvkit/reference/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CNVKIT_REFERENCE } from '../../../../modules/cnvkit/reference/main.nf'
-
-workflow test_cnvkit_reference {
-
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    targets     = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-    antitargets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_antitarget_bed'], checkIfExists: true)
-
-    CNVKIT_REFERENCE ( fasta, targets, antitargets )
-}
diff --git a/tests/modules/cnvkit/reference/test.yml b/tests/modules/cnvkit/reference/test.yml
deleted file mode 100644
index a5baf0a2f7c..00000000000
--- a/tests/modules/cnvkit/reference/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: cnvkit reference test_cnvkit_reference
-  command: nextflow run ./tests/modules/cnvkit/reference -entry test_cnvkit_reference -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/reference/nextflow.config
-  tags:
-    - cnvkit/reference
-    - cnvkit
-  files:
-    - path: output/cnvkit/multi_intervals.reference.cnn
-      md5sum: 7c4a7902f5ab101b1f9d6038d331b3d9
diff --git a/tests/modules/cnvpytor/callcnvs/main.nf b/tests/modules/cnvpytor/callcnvs/main.nf
deleted file mode 100644
index 96d3325067a..00000000000
--- a/tests/modules/cnvpytor/callcnvs/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CNVPYTOR_CALLCNVS } from '../../../../modules/cnvpytor/callcnvs/main.nf'
-
-workflow test_cnvpytor_callcnvs {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
-    ]
-
-    CNVPYTOR_CALLCNVS ( input )
-}
diff --git a/tests/modules/cnvpytor/callcnvs/test.yml b/tests/modules/cnvpytor/callcnvs/test.yml
deleted file mode 100644
index fd07db4c21e..00000000000
--- a/tests/modules/cnvpytor/callcnvs/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: cnvpytor callcnvs test_cnvpytor_callcnvs
-  command: nextflow run tests/modules/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config
-  tags:
-    - cnvpytor
-    - cnvpytor/callcnvs
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
-
-- name: cnvpytor callcnvs test_cnvpytor_callcnvs stub
-  command: nextflow run tests/modules/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config -stub-run
-  tags:
-    - cnvpytor
-    - cnvpytor/callcnvs
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/cnvpytor/histogram/main.nf b/tests/modules/cnvpytor/histogram/main.nf
deleted file mode 100644
index 2178dee1f6b..00000000000
--- a/tests/modules/cnvpytor/histogram/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CNVPYTOR_HISTOGRAM } from '../../../../modules/cnvpytor/histogram/main.nf'
-
-workflow test_cnvpytor_histogram {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true),
-    ]
-
-    CNVPYTOR_HISTOGRAM ( input )
-}
diff --git a/tests/modules/cnvpytor/histogram/test.yml b/tests/modules/cnvpytor/histogram/test.yml
deleted file mode 100644
index f67901d4158..00000000000
--- a/tests/modules/cnvpytor/histogram/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: cnvpytor histogram test_cnvpytor_histogram
-  command: nextflow run tests/modules/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config
-  tags:
-    - cnvpytor
-    - cnvpytor/histogram
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
-
-- name: cnvpytor histogram test_cnvpytor_histogram stub
-  command: nextflow run tests/modules/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config -stub-run
-  tags:
-    - cnvpytor
-    - cnvpytor/histogram
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/cnvpytor/importreaddepth/main.nf b/tests/modules/cnvpytor/importreaddepth/main.nf
deleted file mode 100644
index 0d9be324fe3..00000000000
--- a/tests/modules/cnvpytor/importreaddepth/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CNVPYTOR_IMPORTREADDEPTH } from '../../../../modules/cnvpytor/importreaddepth/main.nf'
-
-
-workflow test_cnvpytor_importreaddepth {
-
-    input = [
-        [ id: 'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-
-    CNVPYTOR_IMPORTREADDEPTH (input, [], [])
-}
-
-workflow test_cnvpytor_importreaddepth_cram {
-
-    input = [
-        [ id: 'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    CNVPYTOR_IMPORTREADDEPTH (input, fasta, fai)
-}
diff --git a/tests/modules/cnvpytor/importreaddepth/test.yml b/tests/modules/cnvpytor/importreaddepth/test.yml
deleted file mode 100644
index a2530c26c12..00000000000
--- a/tests/modules/cnvpytor/importreaddepth/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth
-  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config
-  tags:
-    - cnvpytor
-    - cnvpytor/importreaddepth
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
-
-- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth stub
-  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config -stub-run
-  tags:
-    - cnvpytor
-    - cnvpytor/importreaddepth
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
-
-- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram
-  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config
-  tags:
-    - cnvpytor
-    - cnvpytor/importreaddepth
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
-
-- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram stub
-  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config -stub-run
-  tags:
-    - cnvpytor
-    - cnvpytor/importreaddepth
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/cnvpytor/partition/main.nf b/tests/modules/cnvpytor/partition/main.nf
deleted file mode 100644
index cd8063a46ee..00000000000
--- a/tests/modules/cnvpytor/partition/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CNVPYTOR_PARTITION } from '../../../../modules/cnvpytor/partition/main.nf'
-
-workflow test_cnvpytor_partition {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
-    ]
-
-    CNVPYTOR_PARTITION ( input )
-}
diff --git a/tests/modules/cnvpytor/partition/test.yml b/tests/modules/cnvpytor/partition/test.yml
deleted file mode 100644
index e24a1200b87..00000000000
--- a/tests/modules/cnvpytor/partition/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: cnvpytor partition test_cnvpytor_partition
-  command: nextflow run tests/modules/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config
-  tags:
-    - cnvpytor
-    - cnvpytor/partition
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
-
-- name: cnvpytor partition test_cnvpytor_partition stub
-  command: nextflow run tests/modules/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config -stub-run
-  tags:
-    - cnvpytor
-    - cnvpytor/partition
-  files:
-    - path: output/cnvpytor/test.pytor
-    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/cnvpytor/view/main.nf b/tests/modules/cnvpytor/view/main.nf
deleted file mode 100644
index 3b99c3140e1..00000000000
--- a/tests/modules/cnvpytor/view/main.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CNVPYTOR_VIEW } from '../../../../modules/cnvpytor/view/main.nf'
-
-workflow test_cnvpytor_view {
-
-    input = [
-        [ id:'test'], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
-    ]
-
-    bin_sizes = "10000 100000"
-
-    CNVPYTOR_VIEW ( input, bin_sizes, [] )
-}
-
-workflow test_cnvpytor_view_tsvout {
-
-    input = [
-        [ id:'test'], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
-    ]
-
-    output_suffix = "tsv"
-
-    CNVPYTOR_VIEW ( input, [], output_suffix )
-}
-
-workflow test_cnvpytor_view_stub {
-
-    input = [
-        [ id:'test'], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
-    ]
-
-    bin_sizes = []
-    output_suffix = []
-
-    CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
-}
diff --git a/tests/modules/cnvpytor/view/test.yml b/tests/modules/cnvpytor/view/test.yml
deleted file mode 100644
index ea8ab792199..00000000000
--- a/tests/modules/cnvpytor/view/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: cnvpytor view test_cnvpytor_view
-  command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view -c tests/config/nextflow.config
-  tags:
-    - cnvpytor
-    - cnvpytor/view
-  files:
-    - path: output/cnvpytor/test_10000.vcf
-    - path: output/cnvpytor/test_100000.vcf
-    - path: output/cnvpytor/versions.yml
-
-- name: cnvpytor view test_cnvpytor_view tsv
-  command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view_tsvout -c tests/config/nextflow.config
-  tags:
-    - cnvpytor
-    - cnvpytor/view
-  files:
-    - path: output/cnvpytor/test_1000.tsv
-    - path: output/cnvpytor/versions.yml
-
-- name: cnvpytor view test_cnvpytor_view stub
-  command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view_stub -c tests/config/nextflow.config  -stub-run
-  tags:
-    - cnvpytor
-    - cnvpytor/view
-  files:
-    - path: output/cnvpytor/test.vcf
-    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/controlfreec/assesssignificance/main.nf b/tests/modules/controlfreec/assesssignificance/main.nf
deleted file mode 100644
index e5ed1bf73d2..00000000000
--- a/tests/modules/controlfreec/assesssignificance/main.nf
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CONTROLFREEC_ASSESSSIGNIFICANCE } from '../../../../modules/controlfreec/assesssignificance/main.nf'
-include { CONTROLFREEC_FREEC              } from '../../../../modules/controlfreec/freec/main.nf'
-include { UNTAR                           }        from '../../../../modules/untar/main.nf'
-
-workflow test_controlfreec_assesssignificance {
-
-    input = [
-        [ id:'test', single_end:false, sex:'XX' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-
-    sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
-    CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
-}
-
-workflow test_controlfreec_assesssignificance_single {
-
-    input = [
-        [ id:'test', single_end:false, sex:'XX' ], // meta map
-        [],
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-
-    sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
-    CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
-}
diff --git a/tests/modules/controlfreec/assesssignificance/test.yml b/tests/modules/controlfreec/assesssignificance/test.yml
deleted file mode 100644
index 19e54acfe2a..00000000000
--- a/tests/modules/controlfreec/assesssignificance/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: controlfreec assesssignificance test_controlfreec_assesssignificance
-  command: nextflow run tests/modules/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance -c tests/config/nextflow.config
-  tags:
-    - controlfreec/assesssignificance
-    - controlfreec
-  files:
-    - path: output/controlfreec/test.p.value.txt
-      md5sum: 44e23b916535fbc1a3f47b57fad292df
-    - path: output/controlfreec/versions.yml
-
-- name: controlfreec assesssignificance test_controlfreec_assesssignificance_single
-  command: nextflow run tests/modules/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance_single -c tests/config/nextflow.config -stub-run
-  tags:
-    - controlfreec/assesssignificance
-    - controlfreec
-  files:
-    - path: output/controlfreec/test.p.value.txt
-    - path: output/controlfreec/versions.yml
diff --git a/tests/modules/controlfreec/freec/main.nf b/tests/modules/controlfreec/freec/main.nf
deleted file mode 100644
index 1f4a069b95b..00000000000
--- a/tests/modules/controlfreec/freec/main.nf
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf'
-include { UNTAR              }        from '../../../../modules/untar/main.nf'
-
-workflow test_controlfreec_freec {
-
-    input = [
-        [ id:'test', single_end:false, sex:'XX' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-}
-
-workflow test_controlfreec_freec_single {
-
-    input = [
-        [ id:'test2', single_end:false, sex:'XX' ], // meta map
-        [],
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-}
-
diff --git a/tests/modules/controlfreec/freec/test.yml b/tests/modules/controlfreec/freec/test.yml
deleted file mode 100644
index 1bd4e3a4265..00000000000
--- a/tests/modules/controlfreec/freec/test.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-- name: controlfreec test_controlfreec_freec
-  command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec -c tests/config/nextflow.config
-  tags:
-    - controlfreec
-    - controlfreec/freec
-  files:
-    - path: output/controlfreec/config.txt
-    - path: output/controlfreec/test.mpileup.gz_control.cpn
-      md5sum: 1768b571677c418560e5a8fe203bdc79
-    - path: output/controlfreec/test2.mpileup.gz_BAF.txt
-      md5sum: 3bb7437001cf061a77eaf87b8558c48d
-    - path: output/controlfreec/test2.mpileup.gz_CNVs
-      md5sum: 1f4f5834dbd1490afdb22f6d3091c4c9
-    - path: output/controlfreec/test2.mpileup.gz_info.txt
-      md5sum: 1a3055d35028525ccc9e693cc9f335e0
-    - path: output/controlfreec/test2.mpileup.gz_ratio.BedGraph
-      md5sum: 8ba455b232be20cdcc5bf1e4035e8032
-    - path: output/controlfreec/test2.mpileup.gz_ratio.txt
-      md5sum: b76b2434de710325069e37fb1e132760
-    - path: output/controlfreec/test2.mpileup.gz_sample.cpn
-      md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
-    - path: output/controlfreec/versions.yml
-
-- name: controlfreec test_controlfreec_freec_single
-  command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec_single -c tests/config/nextflow.config -stub-run
-  tags:
-    - controlfreec
-    - controlfreec/freec
-  files:
-    - path: output/controlfreec/config.txt
-    - path: output/controlfreec/test2_BAF.txt
-    - path: output/controlfreec/test2_CNVs
-    - path: output/controlfreec/test2_info.txt
-    - path: output/controlfreec/test2_ratio.BedGraph
-    - path: output/controlfreec/test2_ratio.txt
-    - path: output/controlfreec/test2_sample.cpn
-    - path: output/controlfreec/versions.yml
diff --git a/tests/modules/controlfreec/freec2bed/main.nf b/tests/modules/controlfreec/freec2bed/main.nf
deleted file mode 100644
index c1b0f04edd4..00000000000
--- a/tests/modules/controlfreec/freec2bed/main.nf
+++ /dev/null
@@ -1,75 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CONTROLFREEC_FREEC2BED } from '../../../../modules/controlfreec/freec2bed/main.nf'
-include { CONTROLFREEC_FREEC     } from '../../../../modules/controlfreec/freec/main.nf'
-include { UNTAR                  } from '../../../../modules/untar/main.nf'
-
-workflow test_controlfreec_freec2bed {
-
-    input = [
-        [ id:'test', single_end:false, sex:'XX' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-
-    CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
-}
-
-workflow test_controlfreec_freec2bed_single {
-
-      input = [
-        [ id:'test', single_end:false, sex:'XX' ], // meta map
-        [],
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-
-    CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
-}
diff --git a/tests/modules/controlfreec/freec2bed/test.yml b/tests/modules/controlfreec/freec2bed/test.yml
deleted file mode 100644
index 9abb3a545d7..00000000000
--- a/tests/modules/controlfreec/freec2bed/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: controlfreec freec2bed test_controlfreec_freec2bed
-  command: nextflow run tests/modules/controlfreec/freec2bed -entry test_controlfreec_freec2bed -c tests/config/nextflow.config
-  tags:
-    - controlfreec/freec2bed
-    - controlfreec
-  files:
-    - path: output/controlfreec/test.bed
-      md5sum: abe10b7ce94ba903503e697394c17297
-
-- name: controlfreec freec2bed test_controlfreec_freec2bed_single
-  command: nextflow run tests/modules/controlfreec/freec2bed -entry test_controlfreec_freec2bed_single -c tests/config/nextflow.config -stub-run
-  tags:
-    - controlfreec/freec2bed
-    - controlfreec
-  files:
-    - path: output/controlfreec/test.bed
diff --git a/tests/modules/controlfreec/freec2circos/main.nf b/tests/modules/controlfreec/freec2circos/main.nf
deleted file mode 100644
index 6b34edb6bb6..00000000000
--- a/tests/modules/controlfreec/freec2circos/main.nf
+++ /dev/null
@@ -1,75 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CONTROLFREEC_FREEC2CIRCOS } from '../../../../modules/controlfreec/freec2circos/main.nf'
-include { CONTROLFREEC_FREEC     } from '../../../../modules/controlfreec/freec/main.nf'
-include { UNTAR                  } from '../../../../modules/untar/main.nf'
-
-workflow test_controlfreec_freec2circos {
-
-    input = [
-        [ id:'test', single_end:false, sex:'XX' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-
-    CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
-}
-
-workflow test_controlfreec_freec2circos_single {
-
-    input = [
-        [ id:'test', single_end:false, sex:'XX' ], // meta map
-        [],
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-
-    CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
-}
diff --git a/tests/modules/controlfreec/freec2circos/test.yml b/tests/modules/controlfreec/freec2circos/test.yml
deleted file mode 100644
index c29111deb8f..00000000000
--- a/tests/modules/controlfreec/freec2circos/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: controlfreec freec2circos test_controlfreec_freec2circos
-  command: nextflow run tests/modules/controlfreec/freec2circos -entry test_controlfreec_freec2circos -c tests/config/nextflow.config
-  tags:
-    - controlfreec
-    - controlfreec/freec2circos
-  files:
-    - path: output/controlfreec/test.circos.txt
-      md5sum: 19cf35f2c36b46f717dc8342b8a5a645
-
-- name: controlfreec freec2circos test_controlfreec_freec2circos_single
-  command: nextflow run tests/modules/controlfreec/freec2circos -entry test_controlfreec_freec2circos_single -c tests/config/nextflow.config -stub-run
-  tags:
-    - controlfreec
-    - controlfreec/freec2circos
-  files:
-    - path: output/controlfreec/test.circos.txt
diff --git a/tests/modules/controlfreec/makegraph/main.nf b/tests/modules/controlfreec/makegraph/main.nf
deleted file mode 100644
index 543216e15b9..00000000000
--- a/tests/modules/controlfreec/makegraph/main.nf
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CONTROLFREEC_MAKEGRAPH } from '../../../../modules/controlfreec/makegraph/main.nf'
-include { CONTROLFREEC_FREEC     } from '../../../../modules/controlfreec/freec/main.nf'
-include { UNTAR                  } from '../../../../modules/untar/main.nf'
-
-workflow test_controlfreec_makegraph {
-
-    input = [
-        [ id:'test', single_end:false, sex:'XX' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-
-    makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
-    CONTROLFREEC_MAKEGRAPH ( makegraph_in )
-}
-
-workflow test_controlfreec_makegraph_single {
-
-    input = [
-        [ id:'test', single_end:false, sex:'XX' ], // meta map
-        [],
-        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
-        [],[],[],[]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-
-    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
-    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    UNTAR(chrfiles)
-    CONTROLFREEC_FREEC (input,
-                        fasta,
-                        fai,
-                        [],
-                        dbsnp,
-                        dbsnp_tbi,
-                        UNTAR.out.untar.map{ it[1] },
-                        [],
-                        target_bed,
-                        []
-                        )
-
-    makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
-    CONTROLFREEC_MAKEGRAPH ( makegraph_in )
-}
diff --git a/tests/modules/controlfreec/makegraph/test.yml b/tests/modules/controlfreec/makegraph/test.yml
deleted file mode 100644
index 02d1a165242..00000000000
--- a/tests/modules/controlfreec/makegraph/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: controlfreec makegraph test_controlfreec_makegraph
-  command: nextflow run tests/modules/controlfreec/makegraph -entry test_controlfreec_makegraph -c tests/config/nextflow.config
-  tags:
-    - controlfreec
-    - controlfreec/makegraph
-  files:
-    - path: output/controlfreec/test_BAF.png
-      md5sum: f9d977839e09c7e2472d970bd4aa834c
-    - path: output/controlfreec/test_ratio.log2.png
-      md5sum: b3c7916b1b4951a0cc3da20d8e9e0262
-    - path: output/controlfreec/test_ratio.png
-      md5sum: 1435b29536b3b1555b4c423f8f4fb000
-
-- name: controlfreec makegraph test_controlfreec_makegraph_single
-  command: nextflow run tests/modules/controlfreec/makegraph -entry test_controlfreec_makegraph_single -c tests/config/nextflow.config -stub-run
-  tags:
-    - controlfreec
-    - controlfreec/makegraph
-  files:
-    - path: output/controlfreec/test_BAF.png
-    - path: output/controlfreec/test_ratio.log2.png
-    - path: output/controlfreec/test_ratio.png
diff --git a/tests/modules/cooler/cload/main.nf b/tests/modules/cooler/cload/main.nf
deleted file mode 100644
index 170b7e1199d..00000000000
--- a/tests/modules/cooler/cload/main.nf
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { COOLER_CLOAD }                       from '../../../../modules/cooler/cload/main.nf'
-include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../modules/cooler/cload/main.nf'
-include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../modules/cooler/cload/main.nf'
-include { COOLER_DUMP }                        from '../../../../modules/cooler/dump/main.nf'
-include { COOLER_DUMP as COOLER_DUMP_PAIRS}    from '../../../../modules/cooler/dump/main.nf'
-include { COOLER_DUMP as COOLER_DUMP_TABIX}    from '../../../../modules/cooler/dump/main.nf'
-
-workflow test_cooler_cload_pairix {
-
-    input = [ [ id:'test_pairix', single_end:false ], // meta map
-             file(params.test_data['generic']['cooler']['test_pairix_pair_gz'], checkIfExists: true),
-             file(params.test_data['generic']['cooler']['test_pairix_pair_gz_px2'], checkIfExists: true)]
-
-    sizes    = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
-    bin_size = 2000000
-
-    COOLER_CLOAD ( input, bin_size, sizes )
-    COOLER_DUMP(COOLER_CLOAD.out.cool.map{[it[0], it[2]]}, [])
-
-}
-
-workflow test_cooler_cload_pairs {
-
-    input = [ [ id:'test_pairs', single_end:false ], // meta map
-             file(params.test_data['generic']['cooler']['test_pairs_pair'], checkIfExists: true),
-             []]
-
-    sizes    = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
-    bin_size = 2000000
-
-    COOLER_CLOAD_PAIRS ( input, bin_size, sizes )
-    COOLER_DUMP_PAIRS(COOLER_CLOAD_PAIRS.out.cool.map{[it[0], it[2]]}, [])
-
-}
-
-workflow test_cooler_cload_tabix {
-
-    input = [ [ id:'test_tabix', single_end:false ], // meta map
-             file(params.test_data['generic']['cooler']['test_tabix_pair_gz'], checkIfExists: true),
-             file(params.test_data['generic']['cooler']['test_tabix_pair_gz_tbi'], checkIfExists: true)]
-
-    sizes    = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
-    bin_size = 2000000
-
-    COOLER_CLOAD_TABIX ( input, bin_size, sizes )
-    COOLER_DUMP_TABIX(COOLER_CLOAD_TABIX.out.cool.map{[it[0], it[2]]}, [])
-
-}
diff --git a/tests/modules/cooler/cload/test.yml b/tests/modules/cooler/cload/test.yml
deleted file mode 100644
index f99f462411c..00000000000
--- a/tests/modules/cooler/cload/test.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-- name: cooler cload test_cooler_cload_pairix
-  command: nextflow run ./tests/modules/cooler/cload -entry test_cooler_cload_pairix -c ./tests/config/nextflow.config -c ./tests/modules/cooler/cload/nextflow.config
-  tags:
-    - cooler/cload
-    - cooler
-  files:
-    - path: output/cooler/test_pairix.2000000.cool
-    - path: output/cooler/test_pairix.bedpe
-      md5sum: 0cd85311089669688ec17468eae02111
-
-- name: cooler cload test_cooler_cload_pairs
-  command: nextflow run ./tests/modules/cooler/cload -entry test_cooler_cload_pairs -c ./tests/config/nextflow.config -c ./tests/modules/cooler/cload/nextflow.config
-  tags:
-    - cooler/cload
-    - cooler
-  files:
-    - path: output/cooler/test_pairs.2000000.cool
-    - path: output/cooler/test_pairs.bedpe
-      md5sum: 7f832733fc7853ebb1937b33e4c1e0de
-
-- name: cooler cload test_cooler_cload_tabix
-  command: nextflow run ./tests/modules/cooler/cload -entry test_cooler_cload_tabix -c ./tests/config/nextflow.config -c ./tests/modules/cooler/cload/nextflow.config
-  tags:
-    - cooler/cload
-    - cooler
-  files:
-    - path: output/cooler/test_tabix.2000000.cool
-    - path: output/cooler/test_tabix.bedpe
-      md5sum: 0cd85311089669688ec17468eae02111
diff --git a/tests/modules/cooler/digest/main.nf b/tests/modules/cooler/digest/main.nf
deleted file mode 100644
index 4dfa25be9bd..00000000000
--- a/tests/modules/cooler/digest/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { COOLER_DIGEST } from '../../../../modules/cooler/digest/main.nf'
-
-workflow test_cooler_digest {
-
-    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-    enzyme = "CviQI"
-
-    COOLER_DIGEST ( input, sizes, enzyme )
-}
diff --git a/tests/modules/cooler/digest/test.yml b/tests/modules/cooler/digest/test.yml
deleted file mode 100644
index 80430ed7df9..00000000000
--- a/tests/modules/cooler/digest/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: cooler digest test_cooler_digest
-  command: nextflow run ./tests/modules/cooler/digest -entry test_cooler_digest -c ./tests/config/nextflow.config -c ./tests/modules/cooler/digest/nextflow.config
-  tags:
-    - cooler/digest
-    - cooler
-  files:
-    - path: output/cooler/genome_CviQI.bed
-      md5sum: f02d3cfaf642b27d4cc197209845e096
diff --git a/tests/modules/cooler/dump/main.nf b/tests/modules/cooler/dump/main.nf
deleted file mode 100644
index d80ee0d76d7..00000000000
--- a/tests/modules/cooler/dump/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf'
-
-workflow test_cooler_dump {
-
-    input = [ [ id:'test' ], // meta map
-              file("https://raw.githubusercontent.com/open2c/cooler/master/tests/data/toy.asymm.16.cool", checkIfExists: true) ]
-
-    COOLER_DUMP ( input, [:] )
-}
diff --git a/tests/modules/cooler/dump/test.yml b/tests/modules/cooler/dump/test.yml
deleted file mode 100644
index 6f81c7a9ea0..00000000000
--- a/tests/modules/cooler/dump/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: cooler dump test_cooler_dump
-  command: nextflow run ./tests/modules/cooler/dump -entry test_cooler_dump -c ./tests/config/nextflow.config -c ./tests/modules/cooler/dump/nextflow.config
-  tags:
-    - cooler/dump
-    - cooler
-  files:
-    - path: output/cooler/test.bedpe
-      md5sum: 38e9b0b8cc74f55a15e8ab01023048bd
diff --git a/tests/modules/cooler/merge/main.nf b/tests/modules/cooler/merge/main.nf
deleted file mode 100644
index 81336984926..00000000000
--- a/tests/modules/cooler/merge/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { COOLER_MERGE } from '../../../../modules/cooler/merge/main.nf'
-include { COOLER_DUMP  } from '../../../../modules/cooler/dump/main.nf'
-
-workflow test_cooler_merge {
-
-    input = [
-        [ id:'test' ], // meta map
-        [
-            file(params.test_data['generic']['cooler']['test_merge_cool'], checkIfExists: true),
-            file(params.test_data['generic']['cooler']['test_merge_cool_cp2'], checkIfExists: true)
-        ]
-    ]
-
-    COOLER_MERGE ( input )
-    COOLER_DUMP ( COOLER_MERGE.out.cool, "" )
-}
diff --git a/tests/modules/cooler/merge/test.yml b/tests/modules/cooler/merge/test.yml
deleted file mode 100644
index c884ba5eee5..00000000000
--- a/tests/modules/cooler/merge/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: cooler merge test_cooler_merge
-  command: nextflow run ./tests/modules/cooler/merge -entry test_cooler_merge -c ./tests/config/nextflow.config -c ./tests/modules/cooler/merge/nextflow.config
-  tags:
-    - cooler/merge
-    - cooler
-  files:
-    - path: output/cooler/test.bedpe
-      md5sum: 0ce5e715bfc4674cdda02f2d7e7e3170
diff --git a/tests/modules/cooler/zoomify/main.nf b/tests/modules/cooler/zoomify/main.nf
deleted file mode 100644
index 42edadb8c60..00000000000
--- a/tests/modules/cooler/zoomify/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { COOLER_ZOOMIFY } from '../../../../modules/cooler/zoomify/main.nf'
-
-workflow test_cooler_zoomify {
-
-   input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['generic']['cooler']['test_merge_cool'], checkIfExists: true)
-    ]
-
-    COOLER_ZOOMIFY ( input )
-}
diff --git a/tests/modules/cooler/zoomify/test.yml b/tests/modules/cooler/zoomify/test.yml
deleted file mode 100644
index 3afdb8a6d7d..00000000000
--- a/tests/modules/cooler/zoomify/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: cooler zoomify test_cooler_zoomify
-  command: nextflow run ./tests/modules/cooler/zoomify -entry test_cooler_zoomify -c ./tests/config/nextflow.config -c ./tests/modules/cooler/zoomify/nextflow.config
-  tags:
-    - cooler
-    - cooler/zoomify
-  files:
-    - path: output/cooler/test.bedpe
-      md5sum: 0ce5e715bfc4674cdda02f2d7e7e3170
diff --git a/tests/modules/csvtk/concat/main.nf b/tests/modules/csvtk/concat/main.nf
deleted file mode 100644
index aee31679052..00000000000
--- a/tests/modules/csvtk/concat/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CSVTK_CONCAT } from '../../../../modules/csvtk/concat/main.nf'
-
-workflow test_csvtk_concat {
-
-    input = [ 
-        [ id:'test' ], // meta map
-        [ file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_hybrid.csv", checkIfExists: true),
-          file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_long.csv", checkIfExists: true),
-          file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_short.csv", checkIfExists: true) ]
-    ]
-
-    in_format = "tsv"
-    out_format = "csv"
-
-    CSVTK_CONCAT ( input, in_format, out_format )
-}
diff --git a/tests/modules/csvtk/concat/test.yml b/tests/modules/csvtk/concat/test.yml
deleted file mode 100644
index 11a2af67d5a..00000000000
--- a/tests/modules/csvtk/concat/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: csvtk concat
-  command: nextflow run ./tests/modules/csvtk/concat -entry test_csvtk_concat -c ./tests/config/nextflow.config -c ./tests/modules/csvtk/concat/nextflow.config
-  tags:
-    - csvtk
-    - csvtk/concat
-  files:
-    - path: output/csvtk/test.csv
-      md5sum: 917fe5d857f04b58e0f49c384d167cec
diff --git a/tests/modules/csvtk/split/main.nf b/tests/modules/csvtk/split/main.nf
deleted file mode 100644
index 31d24d61596..00000000000
--- a/tests/modules/csvtk/split/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CSVTK_SPLIT } from '../../../../modules/csvtk/split/main.nf'
-
-workflow test_csvtk_split_tsv {
-
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['generic']['tsv']['test_tsv'], checkIfExists: true) ]
-    ]
-    in_format = "tsv"
-    out_format = "tsv"
-    CSVTK_SPLIT ( input, in_format, out_format )
-}
-
-workflow test_csvtk_split_csv {
-
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['generic']['csv']['test_csv'], checkIfExists: true) ]
-    ]
-    in_format = "csv"
-    out_format = "csv"
-    CSVTK_SPLIT( input, in_format, out_format )
-}
diff --git a/tests/modules/csvtk/split/test.yml b/tests/modules/csvtk/split/test.yml
deleted file mode 100644
index bd13cca69d3..00000000000
--- a/tests/modules/csvtk/split/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: csvtk split test_csvtk_split_tsv
-  command: nextflow run ./tests/modules/csvtk/split -entry test_csvtk_split_tsv -c ./tests/config/nextflow.config -c ./tests/modules/csvtk/split/nextflow.config
-  tags:
-    - csvtk/split
-    - csvtk
-  files:
-    - path: output/csvtk/test-Ken.tsv
-      md5sum: 589a2add7f0b8e998d4959e5d883e7d5
-    - path: output/csvtk/test-Rob.tsv
-      md5sum: 6c5555d689c4e685d35d6e394ad6e1e6
-    - path: output/csvtk/test-Robert.tsv
-      md5sum: 45ae6da8111096746d1736d34220a3ec
-
-- name: csvtk split test_csvtk_split_csv
-  command: nextflow run ./tests/modules/csvtk/split -entry test_csvtk_split_csv -c ./tests/config/nextflow.config -c ./tests/modules/csvtk/split/nextflow.config
-  tags:
-    - csvtk/split
-    - csvtk
-  files:
-    - path: output/csvtk/test-Ken.csv
-      md5sum: 71a931dae6f15f5ddb0318c7d4afe81e
-    - path: output/csvtk/test-Rob.csv
-      md5sum: efc4bc507021043a3bf2fb0724c4a216
-    - path: output/csvtk/test-Robert.csv
-      md5sum: 8de2f076e64252c2abed69b9c2a3a386
diff --git a/tests/modules/custom/dumpsoftwareversions/main.nf b/tests/modules/custom/dumpsoftwareversions/main.nf
deleted file mode 100644
index a9e532d26d1..00000000000
--- a/tests/modules/custom/dumpsoftwareversions/main.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTQC                      } from '../../../../modules/fastqc/main.nf'
-include { MULTIQC                     } from '../../../../modules/multiqc/main.nf'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/custom/dumpsoftwareversions/main.nf'
-
-workflow fastqc1 {
-    take:
-    input
-
-    main:
-    FASTQC ( input )
-
-    emit:
-    versions = FASTQC.out.versions
-}
-
-workflow fastqc2 {
-    take:
-    input
-
-    main:
-    FASTQC ( input )
-
-    emit:
-    versions = FASTQC.out.versions
-    zip = FASTQC.out.zip
-}
-
-workflow test_custom_dumpsoftwareversions {
-    input = [
-        [ id: 'test', single_end: false ],
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    // Using subworkflows to ensure that the script can properly handle
-    // cases where subworkflows have a module with the same name.
-    fastqc1 ( input )
-    fastqc2 ( input )
-    MULTIQC ( fastqc2.out.zip.collect { it[1] }, [], [], [] )
-
-    fastqc1
-        .out
-        .versions
-        .mix(fastqc2.out.versions)
-        .mix(MULTIQC.out.versions)
-        .set { ch_software_versions }
-
-    CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
-}
diff --git a/tests/modules/custom/dumpsoftwareversions/test.yml b/tests/modules/custom/dumpsoftwareversions/test.yml
deleted file mode 100644
index 363a12182f4..00000000000
--- a/tests/modules/custom/dumpsoftwareversions/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: custom dumpsoftwareversions
-  command: nextflow run ./tests/modules/custom/dumpsoftwareversions -entry test_custom_dumpsoftwareversions -c ./tests/config/nextflow.config -c ./tests/modules/custom/dumpsoftwareversions/nextflow.config
-  tags:
-    - custom
-    - custom/dumpsoftwareversions
-  files:
-    - path: output/custom/software_versions.yml
-      contains:
-        - FASTQC
-        - MULTIQC
-      must_not_contain:
-        - fastqc1
-        - fastqc2
-    - path: output/custom/software_versions_mqc.yml
diff --git a/tests/modules/custom/getchromsizes/main.nf b/tests/modules/custom/getchromsizes/main.nf
deleted file mode 100644
index 0294b8747f1..00000000000
--- a/tests/modules/custom/getchromsizes/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CUSTOM_GETCHROMSIZES } from '../../../../modules/custom/getchromsizes/main.nf'
-
-workflow test_custom_getchromsizes {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    CUSTOM_GETCHROMSIZES ( input )
-}
-
-workflow test_custom_getchromsizes_bgzip {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) ]
-
-    CUSTOM_GETCHROMSIZES ( input )
-}
diff --git a/tests/modules/custom/getchromsizes/test.yml b/tests/modules/custom/getchromsizes/test.yml
deleted file mode 100644
index f9cc652626f..00000000000
--- a/tests/modules/custom/getchromsizes/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: custom getchromsizes
-  command: nextflow run ./tests/modules/custom/getchromsizes -entry test_custom_getchromsizes -c ./tests/config/nextflow.config -c ./tests/modules/custom/getchromsizes/nextflow.config
-  tags:
-    - custom
-    - custom/getchromsizes
-  files:
-    - path: output/custom/genome.fasta.fai
-      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
-    - path: output/custom/genome.fasta.sizes
-      md5sum: a57c401f27ae5133823fb09fb21c8a3c
-    - path: output/custom/versions.yml
-      md5sum: 3e4a23a0852f4ec34296224d87446d9a
-- name: custom getchromsizes_bgzip
-  command: nextflow run ./tests/modules/custom/getchromsizes -entry test_custom_getchromsizes_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/custom/getchromsizes/nextflow.config
-  tags:
-    - custom
-    - custom/getchromsizes
-  files:
-    - path: output/custom/genome.fasta.gz.fai
-      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
-    - path: output/custom/genome.fasta.gz.gzi
-      md5sum: 7dea362b3fac8e00956a4952a3d4f474
-    - path: output/custom/genome.fasta.gz.sizes
-      md5sum: a57c401f27ae5133823fb09fb21c8a3c
-    - path: output/custom/versions.yml
-      md5sum: 22871934dfac30a6109068fd79b2d0ba
diff --git a/tests/modules/custom/sratoolsncbisettings/main.nf b/tests/modules/custom/sratoolsncbisettings/main.nf
deleted file mode 100644
index 9f49f20e47a..00000000000
--- a/tests/modules/custom/sratoolsncbisettings/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../../modules/custom/sratoolsncbisettings/main.nf'
-
-workflow test_sratoolsncbisettings_with_good_existing {
-
-    file(params.settings_path).mkdirs()
-    def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
-    settings.copyTo(params.settings_file)
-
-    CUSTOM_SRATOOLSNCBISETTINGS()
-}
-
-workflow test_sratoolsncbisettings_with_bad_existing {
-
-    file(params.settings_path).mkdirs()
-    def settings = file(params.settings_file)
-    settings.text = '''
-    ## auto-generated configuration file - DO NOT EDIT ##
-
-    config/default = "false"
-    /repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
-    /repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
-    /repository/user/ad/public/apps/file/volumes/flatAd = "."
-    /repository/user/ad/public/apps/refseq/volumes/refseqAd = "."
-    /repository/user/ad/public/apps/sra/volumes/sraAd = "."
-    /repository/user/ad/public/apps/sraPileup/volumes/ad = "."
-    /repository/user/ad/public/apps/sraRealign/volumes/ad = "."
-    /repository/user/ad/public/apps/wgs/volumes/wgsAd = "."
-    /repository/user/ad/public/root = "."
-    /repository/user/default-path = "/root/ncbi"
-    '''.stripIndent()
-
-    CUSTOM_SRATOOLSNCBISETTINGS()
-}
-
-workflow test_sratoolsncbisettings_with_nonexisting {
-    def settings = file(params.settings_file)
-    settings.delete()
-
-    CUSTOM_SRATOOLSNCBISETTINGS()
-}
diff --git a/tests/modules/custom/sratoolsncbisettings/test.yml b/tests/modules/custom/sratoolsncbisettings/test.yml
deleted file mode 100644
index df3cd9363d7..00000000000
--- a/tests/modules/custom/sratoolsncbisettings/test.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_good_existing"
-  command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_good_existing -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow_mount.config
-  tags:
-    - "custom"
-    - "custom/sratoolsncbisettings"
-  files:
-    - path: "output/custom/user-settings.mkfg"
-      md5sum: 955e27aff2c277c2f1f0943a098888c1
-    - path: output/custom/versions.yml
-      contains:
-        - "sratools: 2.11.0"
-
-- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_bad_existing"
-  command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_bad_existing -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow_mount.config
-  tags:
-    - "custom"
-    - "custom/sratoolsncbisettings"
-  exit_code: 1
-  stdout:
-    contains:
-      - "Command error:"
-      - "missing the required entries"
-      - "/LIBS/GUID"
-      - "/libs/cloud/report_instance_identity"
-      - "Feel free to add the following"
-  files:
-    - path: "output/custom/user-settings.mkfg"
-      should_exist: false
-    - path: output/custom/versions.yml
-      should_exist: false
-
-- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_nonexisting"
-  command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_nonexisting -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow.config
-  tags:
-    - "custom"
-    - "custom/sratoolsncbisettings"
-  files:
-    - path: "output/custom/user-settings.mkfg"
-      contains:
-        - "/LIBS/GUID"
-        - "/libs/cloud/report_instance_identity"
-    - path: output/custom/versions.yml
-      contains:
-        - "sratools: 2.11.0"
diff --git a/tests/modules/cutadapt/main.nf b/tests/modules/cutadapt/main.nf
deleted file mode 100644
index a47feebba8d..00000000000
--- a/tests/modules/cutadapt/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CUTADAPT } from '../../../modules/cutadapt/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_cutadapt_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    CUTADAPT ( input )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_cutadapt_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    CUTADAPT ( input )
-}
-
diff --git a/tests/modules/cutadapt/test.yml b/tests/modules/cutadapt/test.yml
deleted file mode 100644
index 6fa0eb4fb2d..00000000000
--- a/tests/modules/cutadapt/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: cutadapt single-end
-  command: nextflow run ./tests/modules/cutadapt -entry test_cutadapt_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cutadapt/nextflow.config
-  tags:
-    - cutadapt
-  files:
-    - path: ./output/cutadapt/test.cutadapt.log
-    - path: ./output/cutadapt/test.trim.fastq.gz
-
-- name: cutadapt paired-end
-  command: nextflow run ./tests/modules/cutadapt -entry test_cutadapt_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cutadapt/nextflow.config
-  tags:
-    - cutadapt
-  files:
-    - path: ./output/cutadapt/test.cutadapt.log
-    - path: ./output/cutadapt/test_1.trim.fastq.gz
-    - path: ./output/cutadapt/test_2.trim.fastq.gz
diff --git a/tests/modules/damageprofiler/main.nf b/tests/modules/damageprofiler/main.nf
deleted file mode 100644
index 9207caf1504..00000000000
--- a/tests/modules/damageprofiler/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DAMAGEPROFILER } from '../../../modules/damageprofiler/main.nf'
-
-workflow test_damageprofiler {
-
-    input        = [ [ id:'test', single_end:false ], // meta map
-                   [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
-    fasta        = []
-    fai          = []
-    species_list = []
-
-
-    DAMAGEPROFILER ( input, fasta, fai, species_list )
-}
-
-workflow test_damageprofiler_reference {
-
-    input        = [ [ id:'test', single_end:false ], // meta map
-                   [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
-    fasta        = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai          = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    species_list = []
-
-    DAMAGEPROFILER ( input, fasta, fai, species_list )
-}
-
-workflow test_damageprofiler_specieslist {
-
-    input        = [ [ id:'test', single_end:false ], // meta map
-                   [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
-    fasta        = []
-    fai          = []
-    species_list = file(params.test_data['homo_sapiens']['genome']['genome_header'], checkIfExists: true)
-
-    DAMAGEPROFILER ( input, fasta, fai, species_list )
-}
diff --git a/tests/modules/damageprofiler/test.yml b/tests/modules/damageprofiler/test.yml
deleted file mode 100644
index 5760ee2c457..00000000000
--- a/tests/modules/damageprofiler/test.yml
+++ /dev/null
@@ -1,77 +0,0 @@
-- name: damageprofiler test_damageprofiler
-  command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config  -c ./tests/modules/damageprofiler/nextflow.config
-  tags:
-    - damageprofiler
-  files:
-    - path: output/damageprofiler/test/3pGtoA_freq.txt
-      md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
-    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
-      md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
-    - path: output/damageprofiler/test/5pCtoT_freq.txt
-      md5sum: 38b5d7c87ec2d8422bc5587095711c5f
-    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
-      md5sum: 05e041ff47e7c6d08ede51f5c81a2464
-    - path: output/damageprofiler/test/DNA_comp_genome.txt
-      md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
-    - path: output/damageprofiler/test/DNA_composition_sample.txt
-      md5sum: 16be9c91a06fa7defee376230b12862f
-    - path: output/damageprofiler/test/DamagePlot.pdf
-    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
-    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
-    - path: output/damageprofiler/test/DamageProfiler.log
-    - path: output/damageprofiler/test/Length_plot.pdf
-    - path: output/damageprofiler/test/Length_plot_combined_data.svg
-    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
-    - path: output/damageprofiler/test/dmgprof.json
-      md5sum: a011a47edaadb3a07527c329a6492570
-    - path: output/damageprofiler/test/editDistance.txt
-      md5sum: 7590dac007633ee11025cc99ec9f009b
-    - path: output/damageprofiler/test/edit_distance.pdf
-    - path: output/damageprofiler/test/edit_distance.svg
-    - path: output/damageprofiler/test/lgdistribution.txt
-      md5sum: 583fd98094de3fb462b133daeaadcf52
-    - path: output/damageprofiler/test/misincorporation.txt
-      md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
-
-- name: damageprofiler test_damageprofiler_reference
-  command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config  -c ./tests/modules/damageprofiler/nextflow.config
-  tags:
-    - damageprofiler
-  files:
-    - path: output/damageprofiler/test/3pGtoA_freq.txt
-      md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
-    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
-      md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
-    - path: output/damageprofiler/test/5pCtoT_freq.txt
-      md5sum: 38b5d7c87ec2d8422bc5587095711c5f
-    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
-      md5sum: 05e041ff47e7c6d08ede51f5c81a2464
-    - path: output/damageprofiler/test/DNA_comp_genome.txt
-      md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
-    - path: output/damageprofiler/test/DNA_composition_sample.txt
-      md5sum: 16be9c91a06fa7defee376230b12862f
-    - path: output/damageprofiler/test/DamagePlot.pdf
-    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
-    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
-    - path: output/damageprofiler/test/DamageProfiler.log
-    - path: output/damageprofiler/test/Length_plot.pdf
-    - path: output/damageprofiler/test/Length_plot_combined_data.svg
-    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
-    - path: output/damageprofiler/test/dmgprof.json
-      md5sum: a011a47edaadb3a07527c329a6492570
-    - path: output/damageprofiler/test/editDistance.txt
-      md5sum: 7590dac007633ee11025cc99ec9f009b
-    - path: output/damageprofiler/test/edit_distance.pdf
-    - path: output/damageprofiler/test/edit_distance.svg
-    - path: output/damageprofiler/test/lgdistribution.txt
-      md5sum: 583fd98094de3fb462b133daeaadcf52
-    - path: output/damageprofiler/test/misincorporation.txt
-      md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
-
-- name: damageprofiler test_damageprofiler_specieslist
-  command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config  -c ./tests/modules/damageprofiler/nextflow.config
-  tags:
-    - damageprofiler
-  files:
-    - path: output/damageprofiler/test/DamageProfiler.log
-      #contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
diff --git a/tests/modules/dastool/dastool/main.nf b/tests/modules/dastool/dastool/main.nf
deleted file mode 100644
index 9853e724b16..00000000000
--- a/tests/modules/dastool/dastool/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.enable.dsl = 2
-
-include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
-include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/dastool/fastatocontig2bin/main.nf'
-include { DASTOOL_DASTOOL } from '../../../../modules/dastool/dastool/main.nf'
-
-workflow test_dastool_dastool {
-
-    input_depth = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
-
-    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
-        .map { it -> [[ id:'test', single_end:false ], it] }
-        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
-        .set { input_metabat2 }
-
-    METABAT2_METABAT2 ( input_metabat2 )
-
-    DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
-
-    Channel.of([ [ id:'test', single_end:false ], // meta map
-                      file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)])
-        .join( DASTOOL_FASTATOCONTIG2BIN.out.fastatocontig2bin )
-        .set {input_dastool}
-
-
-    DASTOOL_DASTOOL ( input_dastool, [], [] )
-}
diff --git a/tests/modules/dastool/dastool/test.yml b/tests/modules/dastool/dastool/test.yml
deleted file mode 100644
index cda17bda686..00000000000
--- a/tests/modules/dastool/dastool/test.yml
+++ /dev/null
@@ -1,28 +0,0 @@
-- name: dastool dastool test_dastool_dastool
-  command: nextflow run tests/modules/dastool/dastool -entry test_dastool_dastool -c tests/config/nextflow.config
-  tags:
-    - dastool/dastool
-    - dastool
-  files:
-    - path: output/dastool/test.seqlength
-      md5sum: b815a5811008c36808a59b1d0dcfab24
-    - path: output/dastool/test.tsv
-      md5sum: 6e46c0be14dded7cb13af38f54feea47
-    - path: output/dastool/test_DASTool.log
-    - path: output/dastool/test_DASTool_contig2bin.tsv
-      md5sum: 6e46c0be14dded7cb13af38f54feea47
-    - path: output/dastool/test_DASTool_summary.tsv
-      md5sum: ab9dd3709a59a69bc66030b9e0ff3d5b
-    - path: output/dastool/test_proteins.faa
-    - path: output/dastool/test_proteins.faa.all.b6
-      md5sum: 39c11237ef22ac73109aaac267e185d0
-    - path: output/dastool/test_proteins.faa.archaea.scg
-      md5sum: e79d82eecee25821d1658ea4f082601d
-    - path: output/dastool/test_proteins.faa.bacteria.scg
-      md5sum: 8132cfb17cf398d41c036ead55c96ffe
-    - path: output/dastool/test_proteins.faa.findSCG.b6
-      md5sum: 48e90e12cd6c88d00608777dbc48a82a
-    - path: output/dastool/test_proteins.faa.scg.candidates.faa
-      md5sum: d94b7bed0f8aa9cf2824d72c548c537c
-    - path: output/dastool/versions.yml
-      md5sum: 004e04c6a38652df2e0c59c44e29c9de
diff --git a/tests/modules/dastool/fastatocontig2bin/main.nf b/tests/modules/dastool/fastatocontig2bin/main.nf
deleted file mode 100644
index 0178dbf9e92..00000000000
--- a/tests/modules/dastool/fastatocontig2bin/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP                                } from '../../../../modules/gunzip/main.nf'
-include { METABAT2_METABAT2                     } from '../../../../modules/metabat2/metabat2/main.nf'
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS  } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
-include { DASTOOL_FASTATOCONTIG2BIN                 } from '../../../../modules/dastool/fastatocontig2bin/main.nf'
-
-workflow test_dastool_fastatocontig2bin {
-
-    input_depth = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
-
-    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
-        .map { it -> [[ id:'test', single_end:false ], it] }
-        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
-        .set { input_metabat2 }
-
-    METABAT2_METABAT2 ( input_metabat2 )
-
-    DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
-}
-
-workflow test_dastool_fastatocontig2bin_ungzipped {
-
-    input_depth = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-
-    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
-
-    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
-        .map { it -> [[ id:'test', single_end:false ], it] }
-        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
-        .set { input_metabat2 }
-
-    METABAT2_METABAT2 ( input_metabat2 )
-
-    // TODO test unzipped input files
-    ch_input_2_fastatocontig2bin = GUNZIP( METABAT2_METABAT2.out.fasta  ).gunzip
-
-    DASTOOL_FASTATOCONTIG2BIN ( ch_input_2_fastatocontig2bin, "fa")
-}
diff --git a/tests/modules/dastool/fastatocontig2bin/test.yml b/tests/modules/dastool/fastatocontig2bin/test.yml
deleted file mode 100644
index 948814389ff..00000000000
--- a/tests/modules/dastool/fastatocontig2bin/test.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin
-  command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin -c tests/config/nextflow.config
-  tags:
-    - dastool
-    - dastool/fastatocontig2bin
-  files:
-    - path: output/dastool/test.tsv
-      md5sum: 6e46c0be14dded7cb13af38f54feea47
-    - path: output/dastool/versions.yml
-      md5sum: ff4b6f14bee4548bf09b5e602c306595
-
-- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin_ungzipped
-  command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin_ungzipped -c tests/config/nextflow.config
-  tags:
-    - dastool
-    - dastool/fastatocontig2bin
-  files:
-    - path: output/dastool/test.tsv
-      md5sum: 6e46c0be14dded7cb13af38f54feea47
-    - path: output/dastool/versions.yml
diff --git a/tests/modules/dastool/scaffolds2bin/main.nf b/tests/modules/dastool/scaffolds2bin/main.nf
deleted file mode 100644
index c45a6f2ba6b..00000000000
--- a/tests/modules/dastool/scaffolds2bin/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP                                } from '../../../../modules/gunzip/main.nf'
-include { METABAT2_METABAT2                     } from '../../../../modules/metabat2/metabat2/main.nf'
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS  } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
-include { DASTOOL_SCAFFOLDS2BIN                 } from '../../../../modules/dastool/scaffolds2bin/main.nf'
-
-workflow test_dastool_scaffolds2bin {
-
-    input_depth = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
-
-    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
-        .map { it -> [[ id:'test', single_end:false ], it] }
-        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
-        .set { input_metabat2 }
-
-    METABAT2_METABAT2 ( input_metabat2 )
-
-    DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
-}
-
-workflow test_dastool_scaffolds2bin_ungzipped {
-
-    input_depth = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-
-    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
-
-    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
-        .map { it -> [[ id:'test', single_end:false ], it] }
-        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
-        .set { input_metabat2 }
-
-    METABAT2_METABAT2 ( input_metabat2 )
-
-    // TODO test unzipped input files
-    ch_input_2_scaffolds2bin = GUNZIP( METABAT2_METABAT2.out.fasta  ).gunzip
-
-    DASTOOL_SCAFFOLDS2BIN ( ch_input_2_scaffolds2bin, "fa")
-}
diff --git a/tests/modules/dastool/scaffolds2bin/test.yml b/tests/modules/dastool/scaffolds2bin/test.yml
deleted file mode 100644
index 3d91c8c10af..00000000000
--- a/tests/modules/dastool/scaffolds2bin/test.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-- name: dastool scaffolds2bin test_dastool_scaffolds2bin
-  command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c tests/config/nextflow.config
-  tags:
-    - dastool
-    - dastool/scaffolds2bin
-  files:
-    - path: output/dastool/test.tsv
-      md5sum: 6e46c0be14dded7cb13af38f54feea47
-    - path: output/dastool/versions.yml
-      md5sum: d0831ed159eb5a1a1565d1d211012ad6
-- name: dastool scaffolds2bin test_dastool_scaffolds2bin_ungzipped
-  command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c tests/config/nextflow.config
-  tags:
-    - dastool
-    - dastool/scaffolds2bin
-  files:
-    - path: output/dastool/test.tsv
-      md5sum: 6e46c0be14dded7cb13af38f54feea47
-    - path: output/dastool/versions.yml
-      md5sum: da58e477b7f4c16a9ea495ec1a4a4d4f
diff --git a/tests/modules/dedup/main.nf b/tests/modules/dedup/main.nf
deleted file mode 100644
index 4a397eaa7c5..00000000000
--- a/tests/modules/dedup/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DEDUP } from '../../../modules/dedup/main.nf'
-
-workflow test_dedup {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
-
-    DEDUP ( input )
-}
diff --git a/tests/modules/dedup/test.yml b/tests/modules/dedup/test.yml
deleted file mode 100644
index 077aac0dc4d..00000000000
--- a/tests/modules/dedup/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: dedup test_dedup
-  command: nextflow run ./tests/modules/dedup -entry test_dedup -c ./tests/config/nextflow.config -c ./tests/modules/dedup/nextflow.config
-  tags:
-    - dedup
-  files:
-    - path: output/dedup/test.paired_end.dedup.json
-      md5sum: 2def0b54aba1fafa21b274f260de1b6f
-    - path: output/dedup/test.paired_end.hist
-      md5sum: df3492273a1db0d8152e35d9d5e38aa6
-    - path: output/dedup/test.paired_end.log
-      md5sum: 4b8855bd63b2f4b37da4cfb17e61fb00
-    - path: output/dedup/test.paired_end_rmdup.bam
-      md5sum: 8b0408fe3e258989095303a47e5b5061
diff --git a/tests/modules/deeparg/downloaddata/main.nf b/tests/modules/deeparg/downloaddata/main.nf
deleted file mode 100644
index 1074b0bcddb..00000000000
--- a/tests/modules/deeparg/downloaddata/main.nf
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DEEPARG_DOWNLOADDATA } from '../../../../modules/deeparg/downloaddata/main.nf'
-
-workflow test_deeparg_downloaddata {
-    DEEPARG_DOWNLOADDATA ( )
-}
diff --git a/tests/modules/deeparg/downloaddata/test.yml b/tests/modules/deeparg/downloaddata/test.yml
deleted file mode 100644
index c5c99de22e8..00000000000
--- a/tests/modules/deeparg/downloaddata/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: deeparg downloaddata test_deeparg_downloaddata
-  command: nextflow run tests/modules/deeparg/downloaddata -entry test_deeparg_downloaddata -c tests/config/nextflow.config
-  tags:
-    - deeparg
-    - deeparg/downloaddata
-  files:
-    - path: output/deeparg/db/
-    - path: output/deeparg/db/data/gg13/dataset.rev.2.bt2
-      md5sum: 99d90f132fc2795d5a527ce31f1c4d30
diff --git a/tests/modules/deeparg/predict/main.nf b/tests/modules/deeparg/predict/main.nf
deleted file mode 100644
index 2ada23740e2..00000000000
--- a/tests/modules/deeparg/predict/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DEEPARG_DOWNLOADDATA } from '../../../../modules/deeparg/downloaddata/main.nf'
-include { DEEPARG_PREDICT      } from '../../../../modules/deeparg/predict/main.nf'
-
-workflow test_deeparg_predict {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
-        'LS'
-    ]
-
-    DEEPARG_DOWNLOADDATA( )
-    DEEPARG_PREDICT ( input, DEEPARG_DOWNLOADDATA.out.db )
-
-}
diff --git a/tests/modules/deeparg/predict/test.yml b/tests/modules/deeparg/predict/test.yml
deleted file mode 100644
index e3a15411069..00000000000
--- a/tests/modules/deeparg/predict/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: deeparg predict test_deeparg_predict
-  command: nextflow run tests/modules/deeparg/predict -entry test_deeparg_predict -c tests/config/nextflow.config
-  tags:
-    - deeparg/predict
-    - deeparg
-  files:
-    - path: output/deeparg/test.align.daa
-      md5sum: c52d0af8362244f214da25bc45f2bf42
-    - path: output/deeparg/test.align.daa.tsv
-      md5sum: a4aa1da2db98274ede2b927fa8227e5a
-    - path: output/deeparg/test.mapping.ARG
-      md5sum: 0e049e99eab4c55666062df21707d5b9
-    - path: output/deeparg/test.mapping.potential.ARG
-      contains:
-        - "#ARG"
-    - path: output/deeparg/versions.yml
-      md5sum: e848ddab324e8c6fd18eaa6b2656f195
diff --git a/tests/modules/deepbgc/download/main.nf b/tests/modules/deepbgc/download/main.nf
deleted file mode 100644
index ecf3c9b6250..00000000000
--- a/tests/modules/deepbgc/download/main.nf
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DEEPBGC_DOWNLOAD } from '../../../../modules/deepbgc/download/main.nf'
-
-workflow test_deepbgc_download {
-
-    DEEPBGC_DOWNLOAD (  )
-}
diff --git a/tests/modules/deepbgc/download/test.yml b/tests/modules/deepbgc/download/test.yml
deleted file mode 100644
index bae68f67ed5..00000000000
--- a/tests/modules/deepbgc/download/test.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-- name: deepbgc download test_deepbgc_download
-  command: nextflow run ./tests/modules/deepbgc/download -entry test_deepbgc_download -c ./tests/config/nextflow.config  -c ./tests/modules/deepbgc/download/nextflow.config
-  tags:
-    - deepbgc
-    - deepbgc/download
-  files:
-    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_activity.pkl
-      md5sum: 90f0c010460e9df882cb057664a49f30
-    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_class.pkl
-      md5sum: f78a2eda240403d2f40643d42202f3ac
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_geneborder.pkl
-      md5sum: ca4be7031ae9f70780f17c616a4fa5b5
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_original.pkl
-      md5sum: 2ca2429bb9bc99a401d1093c376b37aa
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_retrained.pkl
-      md5sum: 65679a3b61c562ff4b84bdb574bb6d93
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/deepbgc.pkl
-      md5sum: 7e9218be79ba45bc9adb23bed3845dc1
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.clans.tsv
-      md5sum: a0a4590ffb2b33b83ef2b28f6ead886b
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm
-      md5sum: 79a3328e4c95b13949a4489b19959fc5
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3f
-      md5sum: cbca323cf8dd4e5e7c109114ec444162
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3i
-      md5sum: 5242332a3f6a60cd1ab634cd9331afd6
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3m
-      md5sum: 1fe946fa2b3bcde1d4b2bad732bce612
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3p
-      md5sum: 27b98a1ded123b6a1ef72db01927017c
diff --git a/tests/modules/deepbgc/pipeline/main.nf b/tests/modules/deepbgc/pipeline/main.nf
deleted file mode 100644
index a896fa51f50..00000000000
--- a/tests/modules/deepbgc/pipeline/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP } from '../../../modules/gunzip/main.nf'
-include { PRODIGAL } from '../../../modules/prodigal/main.nf'
-include { DEEPBGC_DOWNLOAD } from '../../../../modules/deepbgc/download/main.nf'
-include { DEEPBGC_PIPELINE } from '../../../../modules/deepbgc/pipeline/main.nf'
-
-workflow test_deepbgc_pipeline_gbk {
-
-    input = [
-        [ id:'test_gbk', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
-    ]
-
-    DEEPBGC_DOWNLOAD ()
-    GUNZIP ( input )
-    PRODIGAL ( GUNZIP.out.gunzip, 'gbk' )
-    DEEPBGC_PIPELINE ( PRODIGAL.out.gene_annotations, DEEPBGC_DOWNLOAD.out.db )
-}
-
-workflow test_deepbgc_pipeline_fa {
-
-    input = [
-        [ id:'test_fa', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
-    ]
-
-    DEEPBGC_DOWNLOAD ()
-    GUNZIP ( input )
-    DEEPBGC_PIPELINE ( GUNZIP.out.gunzip, DEEPBGC_DOWNLOAD.out.db )
-}
diff --git a/tests/modules/deepbgc/pipeline/test.yml b/tests/modules/deepbgc/pipeline/test.yml
deleted file mode 100644
index eea38831849..00000000000
--- a/tests/modules/deepbgc/pipeline/test.yml
+++ /dev/null
@@ -1,97 +0,0 @@
-- name: deepbgc pipeline test_deepbgc_pipeline_gbk
-  command: nextflow run ./tests/modules/deepbgc/pipeline -entry test_deepbgc_pipeline_gbk -c ./tests/config/nextflow.config  -c ./tests/modules/deepbgc/pipeline/nextflow.config
-  tags:
-    - deepbgc/pipeline
-    - deepbgc
-  files:
-    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_activity.pkl
-      md5sum: 90f0c010460e9df882cb057664a49f30
-    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_class.pkl
-      md5sum: f78a2eda240403d2f40643d42202f3ac
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_geneborder.pkl
-      md5sum: ca4be7031ae9f70780f17c616a4fa5b5
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_original.pkl
-      md5sum: 2ca2429bb9bc99a401d1093c376b37aa
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_retrained.pkl
-      md5sum: 65679a3b61c562ff4b84bdb574bb6d93
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/deepbgc.pkl
-      md5sum: 7e9218be79ba45bc9adb23bed3845dc1
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.clans.tsv
-      md5sum: a0a4590ffb2b33b83ef2b28f6ead886b
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm
-      md5sum: 79a3328e4c95b13949a4489b19959fc5
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3f
-      md5sum: cbca323cf8dd4e5e7c109114ec444162
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3i
-      md5sum: 5242332a3f6a60cd1ab634cd9331afd6
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3m
-      md5sum: 1fe946fa2b3bcde1d4b2bad732bce612
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3p
-      md5sum: 27b98a1ded123b6a1ef72db01927017c
-    - path: output/deepbgc/test_gbk/LOG.txt
-      contains: ["Saved DeepBGC result to:"]
-    - path: output/deepbgc/test_gbk/README.txt
-    - path: output/deepbgc/test_gbk/test_gbk.antismash.json
-      md5sum: 7dba3996cf38756b05e7612de8433c23
-    - path: output/deepbgc/test_gbk/test_gbk.bgc.gbk
-    - path: output/deepbgc/test_gbk/test_gbk.full.gbk
-    - path: output/gunzip/test1.contigs.fa
-      md5sum: 80c4d78f2810f6d9e90fa6da9bb9c4f9
-    - path: output/prodigal/test_gbk.faa
-      md5sum: b140ca303ff9ee32e615bfcc4b05038c
-    - path: output/prodigal/test_gbk.fna
-      md5sum: 28232dd696754fb95308874c9528296f
-    - path: output/prodigal/test_gbk.gbk
-      md5sum: b5c309b0296e7cdc21d1e71f33400f20
-    - path: output/prodigal/test_gbk_all.txt
-      md5sum: 8fe56fcf4d9e839e83be7523cd3efa02
-
-- name: deepbgc pipeline test_deepbgc_pipeline_fa
-  command: nextflow run ./tests/modules/deepbgc/pipeline -entry test_deepbgc_pipeline_fa -c ./tests/config/nextflow.config  -c ./tests/modules/deepbgc/pipeline/nextflow.config
-  tags:
-    - deepbgc/pipeline
-    - deepbgc
-  files:
-    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_activity.pkl
-      md5sum: 90f0c010460e9df882cb057664a49f30
-    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_class.pkl
-      md5sum: f78a2eda240403d2f40643d42202f3ac
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_geneborder.pkl
-      md5sum: ca4be7031ae9f70780f17c616a4fa5b5
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_original.pkl
-      md5sum: 2ca2429bb9bc99a401d1093c376b37aa
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_retrained.pkl
-      md5sum: 65679a3b61c562ff4b84bdb574bb6d93
-    - path: output/deepbgc/deepbgc_db/0.1.0/detector/deepbgc.pkl
-      md5sum: 7e9218be79ba45bc9adb23bed3845dc1
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.clans.tsv
-      md5sum: a0a4590ffb2b33b83ef2b28f6ead886b
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm
-      md5sum: 79a3328e4c95b13949a4489b19959fc5
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3f
-      md5sum: cbca323cf8dd4e5e7c109114ec444162
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3i
-      md5sum: 5242332a3f6a60cd1ab634cd9331afd6
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3m
-      md5sum: 1fe946fa2b3bcde1d4b2bad732bce612
-    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3p
-      md5sum: 27b98a1ded123b6a1ef72db01927017c
-    - path: output/deepbgc/test1.contigs/LOG.txt
-      contains: ["Saved DeepBGC result to:"]
-    - path: output/deepbgc/test1.contigs/README.txt
-    - path: output/deepbgc/test1.contigs/evaluation/test1.contigs.bgc.png
-      md5sum: f4a0fc6cd260e2d7ad16f7a1fa103f96
-    - path: output/deepbgc/test1.contigs/evaluation/test1.contigs.score.png
-      md5sum: 572e8882031f667580d8c8e13c2cbb91
-    - path: output/deepbgc/test1.contigs/test1.contigs.antismash.json
-      contains: ['"name": "DeepBGC"']
-    - path: output/deepbgc/test1.contigs/test1.contigs.bgc.gbk
-      md5sum: 7fc70dd034903622dae273bf71b402f2
-    - path: output/deepbgc/test1.contigs/test1.contigs.bgc.tsv
-      contains: ["sequence_id"]
-    - path: output/deepbgc/test1.contigs/test1.contigs.full.gbk
-      contains: ["LOCUS"]
-    - path: output/deepbgc/test1.contigs/test1.contigs.pfam.tsv
-      md5sum: 1179eb4e6df0c83aaeec18d7d34e7524
-    - path: output/gunzip/test1.contigs.fa
-      md5sum: 80c4d78f2810f6d9e90fa6da9bb9c4f9
diff --git a/tests/modules/deeptools/bamcoverage/main.nf b/tests/modules/deeptools/bamcoverage/main.nf
deleted file mode 100644
index 97a79508a28..00000000000
--- a/tests/modules/deeptools/bamcoverage/main.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DEEPTOOLS_BAMCOVERAGE } from '../../../../modules/deeptools/bamcoverage/main.nf'
-
-workflow test_deeptools_bamcoverage_bam {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-        ]
-
-    DEEPTOOLS_BAMCOVERAGE ( input, [], [] )
-}
-
-workflow test_deeptools_bamcoverage_cram {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
-        ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    DEEPTOOLS_BAMCOVERAGE ( input, fasta, fasta_fai)
-}
-
-workflow test_deeptools_bamcoverage_cram_no_fasta_fai {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
-        ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    DEEPTOOLS_BAMCOVERAGE ( input, fasta, [])
-}
diff --git a/tests/modules/deeptools/bamcoverage/test.yml b/tests/modules/deeptools/bamcoverage/test.yml
deleted file mode 100644
index 63ef6442007..00000000000
--- a/tests/modules/deeptools/bamcoverage/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: deeptools bamcoverage test_deeptools_bamcoverage_bam
-  command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c ./tests/config/nextflow.config  -c ./tests/modules/deeptools/bamcoverage/nextflow.config
-  tags:
-    - deeptools/bamcoverage
-    - deeptools
-  files:
-    - path: output/deeptools/test.bigWig
-      md5sum: 95fe9383a9e6c02aea6b785cf074274f
-
-- name: deeptools bamcoverage test_deeptools_bamcoverage_cram
-  command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c ./tests/config/nextflow.config  -c ./tests/modules/deeptools/bamcoverage/nextflow.config
-  tags:
-    - deeptools/bamcoverage
-    - deeptools
-  files:
-    - path: output/deeptools/test.bigWig
-      md5sum: 95fe9383a9e6c02aea6b785cf074274f
-
-- name: deeptools bamcoverage test_deeptools_bamcoverage_cram_no_fasta_fai
-  command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram_no_fasta_fai -c ./tests/config/nextflow.config  -c ./tests/modules/deeptools/bamcoverage/nextflow.config
-  tags:
-    - deeptools/bamcoverage
-    - deeptools
-  files:
-    - path: output/deeptools/test.bigWig
-      md5sum: 95fe9383a9e6c02aea6b785cf074274f
diff --git a/tests/modules/deeptools/computematrix/main.nf b/tests/modules/deeptools/computematrix/main.nf
deleted file mode 100644
index 35e49f5970b..00000000000
--- a/tests/modules/deeptools/computematrix/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DEEPTOOLS_COMPUTEMATRIX } from '../../../../modules/deeptools/computematrix/main.nf'
-
-workflow test_deeptools_computematrix {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_bigwig'], checkIfExists: true)
-            ]
-
-    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-
-    DEEPTOOLS_COMPUTEMATRIX ( input, bed )
-}
diff --git a/tests/modules/deeptools/computematrix/test.yml b/tests/modules/deeptools/computematrix/test.yml
deleted file mode 100644
index 88657de3ef0..00000000000
--- a/tests/modules/deeptools/computematrix/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: deeptools computematrix
-  command: nextflow run ./tests/modules/deeptools/computematrix -entry test_deeptools_computematrix -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/computematrix/nextflow.config
-  tags:
-    - deeptools
-    - deeptools/computematrix
-  files:
-    - path: output/deeptools/test.computeMatrix.mat.gz
-    - path: output/deeptools/test.computeMatrix.vals.mat.tab
-      md5sum: 19e22051cc44edb7db3e0f8345330d90
diff --git a/tests/modules/deeptools/plotfingerprint/main.nf b/tests/modules/deeptools/plotfingerprint/main.nf
deleted file mode 100644
index bcef970e966..00000000000
--- a/tests/modules/deeptools/plotfingerprint/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-params.fragment_size = 1000
-
-include { DEEPTOOLS_PLOTFINGERPRINT } from '../../../../modules/deeptools/plotfingerprint/main.nf'
-
-workflow test_deeptools_plotfingerprint {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-            ]
-
-    DEEPTOOLS_PLOTFINGERPRINT ( input )
-}
diff --git a/tests/modules/deeptools/plotfingerprint/test.yml b/tests/modules/deeptools/plotfingerprint/test.yml
deleted file mode 100644
index 11d4ae7b92f..00000000000
--- a/tests/modules/deeptools/plotfingerprint/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: deeptools plotfingerprint
-  command: nextflow run ./tests/modules/deeptools/plotfingerprint -entry test_deeptools_plotfingerprint -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/plotfingerprint/nextflow.config
-  tags:
-    - deeptools
-    - deeptools/plotfingerprint
-  files:
-    - path: output/deeptools/test.plotFingerprint.pdf
-    - path: output/deeptools/test.plotFingerprint.qcmetrics.txt
-      contains:
-        - "AUC"
-        - "0.24184576629880325"
-    - path: output/deeptools/test.plotFingerprint.raw.txt
-      md5sum: aff8e53de0ddd893aa9d8f9d4ce7e291
diff --git a/tests/modules/deeptools/plotheatmap/main.nf b/tests/modules/deeptools/plotheatmap/main.nf
deleted file mode 100644
index 86005b2cc96..00000000000
--- a/tests/modules/deeptools/plotheatmap/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DEEPTOOLS_PLOTHEATMAP } from '../../../../modules/deeptools/plotheatmap/main.nf'
-
-workflow test_deeptools_plotheatmap {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_computematrix_mat_gz'], checkIfExists: true)
-            ]
-
-    DEEPTOOLS_PLOTHEATMAP ( input )
-}
diff --git a/tests/modules/deeptools/plotheatmap/test.yml b/tests/modules/deeptools/plotheatmap/test.yml
deleted file mode 100644
index ddc468e29d0..00000000000
--- a/tests/modules/deeptools/plotheatmap/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: deeptools plotheatmap
-  command: nextflow run ./tests/modules/deeptools/plotheatmap -entry test_deeptools_plotheatmap -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/plotheatmap/nextflow.config
-  tags:
-    - deeptools
-    - deeptools/plotheatmap
-  files:
-    - path: output/deeptools/test.plotHeatmap.mat.tab
-    - path: output/deeptools/test.plotHeatmap.pdf
diff --git a/tests/modules/deeptools/plotprofile/main.nf b/tests/modules/deeptools/plotprofile/main.nf
deleted file mode 100644
index 63ee47cd795..00000000000
--- a/tests/modules/deeptools/plotprofile/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DEEPTOOLS_PLOTPROFILE } from '../../../../modules/deeptools/plotprofile/main.nf'
-
-workflow test_deeptools_plotprofile {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_computematrix_mat_gz'], checkIfExists: true)
-            ]
-
-    DEEPTOOLS_PLOTPROFILE ( input )
-}
diff --git a/tests/modules/deeptools/plotprofile/test.yml b/tests/modules/deeptools/plotprofile/test.yml
deleted file mode 100644
index 4b6c5b9afc4..00000000000
--- a/tests/modules/deeptools/plotprofile/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: deeptools plotprofile
-  command: nextflow run ./tests/modules/deeptools/plotprofile -entry test_deeptools_plotprofile -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/plotprofile/nextflow.config
-  tags:
-    - deeptools
-    - deeptools/plotprofile
-  files:
-    - path: output/deeptools/test.plotProfile.pdf
-    - path: output/deeptools/test.plotProfile.tab
-      md5sum: d561cb659a292cef973ea631c7d440cb
diff --git a/tests/modules/deepvariant/main.nf b/tests/modules/deepvariant/main.nf
deleted file mode 100644
index 3b1b90e636c..00000000000
--- a/tests/modules/deepvariant/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DEEPVARIANT                          } from '../../../modules/deepvariant/main.nf'
-include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../modules/deepvariant/main.nf'
-
-workflow test_deepvariant {
-
-    bam_tuple_ch = Channel.of([ [ id:'test', single_end:false ], // meta map
-                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                               []
-                                ])
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    DEEPVARIANT ( bam_tuple_ch, fasta, fai)
-}
-
-workflow test_deepvariant_cram_intervals {
-
-    cram_tuple_ch = Channel.of([[ id:'test', single_end:false ], // meta map
-                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                               file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-                            ])
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    DEEPVARIANT_INTERVALS ( cram_tuple_ch, fasta, fai)
-}
diff --git a/tests/modules/deepvariant/test.yml b/tests/modules/deepvariant/test.yml
deleted file mode 100644
index 30a0b1b32a4..00000000000
--- a/tests/modules/deepvariant/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: deepvariant test_deepvariant
-  command: nextflow run tests/modules/deepvariant -entry test_deepvariant -c tests/config/nextflow.config
-  tags:
-    - deepvariant
-  files:
-    - path: output/deepvariant/test_out.g.vcf.gz
-      md5sum: c4c65a3eaf62d6fbe0aba0a414318c8d
-    - path: output/deepvariant/test_out.vcf.gz
-      md5sum: ad964f68ac1d1b2720a9a4e0b6a3a389
-    - path: output/deepvariant/versions.yml
-      md5sum: 51572055ca5c07fc4001b25a9c273bf8
-
-- name: deepvariant test_deepvariant_cram_intervals
-  command: nextflow run tests/modules/deepvariant -entry test_deepvariant_cram_intervals -c tests/config/nextflow.config
-  tags:
-    - deepvariant
-  files:
-    - path: output/deepvariant/test_out.g.vcf.gz
-      md5sum: c4c65a3eaf62d6fbe0aba0a414318c8d
-    - path: output/deepvariant/test_out.vcf.gz
-      md5sum: ad964f68ac1d1b2720a9a4e0b6a3a389
-    - path: output/deepvariant/versions.yml
-      md5sum: 7d9293db0d44423b114abc7116feb967
diff --git a/tests/modules/delly/call/main.nf b/tests/modules/delly/call/main.nf
deleted file mode 100644
index 78dc7c37e9e..00000000000
--- a/tests/modules/delly/call/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DELLY_CALL } from '../../../../modules/delly/call/main.nf'
-
-workflow test_delly_call_bam {
-    input     = [ [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-                    []
-                ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    DELLY_CALL ( input, fasta, fai )
-}
-
-workflow test_delly_call_cram {
-    input     = [ [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                    []
-                ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    DELLY_CALL ( input, fasta, fai )
-}
-
-workflow test_delly_call_exclude_regions {
-    input     = [ [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-                ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    DELLY_CALL ( input, fasta, fai )
-}
diff --git a/tests/modules/delly/call/test.yml b/tests/modules/delly/call/test.yml
deleted file mode 100644
index c3490a76146..00000000000
--- a/tests/modules/delly/call/test.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-- name: delly call test_delly_call_bam
-  command: nextflow run ./tests/modules/delly/call -entry test_delly_call_bam -c ./tests/config/nextflow.config  -c ./tests/modules/delly/call/nextflow.config
-  tags:
-    - delly
-    - delly/call
-  files:
-    - path: output/delly/test.bcf
-      md5sum: 82be17d3b18b80ef5f37627bb579b07b
-    - path: output/delly/test.bcf.csi
-      md5sum: c198abfc14584c5ac69c004057927e0b
-
-- name: delly call test_delly_call_cram
-  command: nextflow run ./tests/modules/delly/call -entry test_delly_call_cram -c ./tests/config/nextflow.config  -c ./tests/modules/delly/call/nextflow.config
-  tags:
-    - delly
-    - delly/call
-  files:
-    - path: output/delly/test.bcf
-      md5sum: 4f6ae6b5800ae824ba35674f2903cd5c
-    - path: output/delly/test.bcf.csi
-      md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271
-
-- name: delly call test_delly_call_exclude_regions
-  command: nextflow run ./tests/modules/delly/call -entry test_delly_call_exclude_regions -c ./tests/config/nextflow.config  -c ./tests/modules/delly/call/nextflow.config
-  tags:
-    - delly
-    - delly/call
-  files:
-    - path: output/delly/test.bcf
-      md5sum: 4f6ae6b5800ae824ba35674f2903cd5c
-    - path: output/delly/test.bcf.csi
-      md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271
diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf
deleted file mode 100644
index ff669233d2d..00000000000
--- a/tests/modules/diamond/blastp/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
-include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf'
-
-workflow test_diamond_blastp {
-
-    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    out_ext = 'txt'
-    blast_columns = 'qseqid qlen'
-
-    DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
-}
-
-workflow test_diamond_blastp_daa {
-
-    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    out_ext = 'daa'
-    blast_columns = []
-
-    DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
-}
diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
deleted file mode 100644
index aff4e1c5637..00000000000
--- a/tests/modules/diamond/blastp/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: diamond blastp test_diamond_blastp
-  command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config
-  tags:
-    - diamond/blastp
-    - diamond
-  files:
-    - path: output/diamond/test.diamond_blastp.txt
-    - path: output/diamond/versions.yml
-
-- name: diamond blastp test_diamond_blastp_daa
-  command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config
-  tags:
-    - diamond/blastp
-    - diamond
-  files:
-    - path: output/diamond/test.diamond_blastp.daa
-    - path: output/diamond/versions.yml
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
deleted file mode 100644
index 8316aa9172c..00000000000
--- a/tests/modules/diamond/blastx/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
-include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf'
-
-workflow test_diamond_blastx {
-
-    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    out_ext = 'tfdfdt'  // Nonsense file extension to check default case.
-    blast_columns = 'qseqid qlen'
-
-    DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
-}
-
-workflow test_diamond_blastx_daa {
-
-    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    out_ext = 'daa'
-    blast_columns = []
-
-    DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
-}
diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml
deleted file mode 100644
index 9f62d2ef7e3..00000000000
--- a/tests/modules/diamond/blastx/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: diamond blastx test_diamond_blastx
-  command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config  -c ./tests/modules/diamond/blastx/nextflow.config
-  tags:
-    - diamond
-    - diamond/blastx
-  files:
-    - path: output/diamond/proteome.fasta.dmnd
-    - path: output/diamond/test.diamond_blastx.log
-      contains: ["queries aligned"]
-    - path: output/diamond/test.diamond_blastx.txt
-
-- name: diamond blastx test_diamond_blastx_daa
-  command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c ./tests/config/nextflow.config  -c ./tests/modules/diamond/blastx/nextflow.config
-  tags:
-    - diamond
-    - diamond/blastx
-  files:
-    - path: output/diamond/proteome.fasta.dmnd
-    - path: output/diamond/test.diamond_blastx.daa
-    - path: output/diamond/test.diamond_blastx.log
-      contains: ["queries aligned"]
diff --git a/tests/modules/diamond/makedb/main.nf b/tests/modules/diamond/makedb/main.nf
deleted file mode 100644
index d309de6d54a..00000000000
--- a/tests/modules/diamond/makedb/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
-
-workflow test_diamond_makedb {
-
-    input = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-
-    DIAMOND_MAKEDB ( input )
-}
diff --git a/tests/modules/diamond/makedb/test.yml b/tests/modules/diamond/makedb/test.yml
deleted file mode 100644
index cdddf735296..00000000000
--- a/tests/modules/diamond/makedb/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: diamond makedb test_diamond_makedb
-  command: nextflow run tests/modules/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config
-  tags:
-    - diamond/makedb
-    - diamond
-  files:
-    - path: output/diamond/proteome.fasta.dmnd
-      md5sum: fc28c50b202dd7a7c5451cddff2ba1f4
-    - path: output/diamond/versions.yml
diff --git a/tests/modules/dragmap/align/main.nf b/tests/modules/dragmap/align/main.nf
deleted file mode 100644
index 4376602c0a8..00000000000
--- a/tests/modules/dragmap/align/main.nf
+++ /dev/null
@@ -1,60 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DRAGMAP_HASHTABLE } from '../../../../modules/dragmap/hashtable/main.nf'
-include { DRAGMAP_ALIGN     } from '../../../../modules/dragmap/align/main.nf'
-
-workflow test_dragmap_align_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    DRAGMAP_HASHTABLE ( fasta )
-    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
-}
-
-workflow test_dragmap_align_single_end_sort {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    DRAGMAP_HASHTABLE ( fasta )
-    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
-}
-
-workflow test_dragmap_align_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    DRAGMAP_HASHTABLE ( fasta )
-    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
-}
-
-workflow test_dragmap_align_paired_end_sort {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    DRAGMAP_HASHTABLE ( fasta )
-    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
-}
diff --git a/tests/modules/dragmap/align/test.yml b/tests/modules/dragmap/align/test.yml
deleted file mode 100644
index b0196e554c8..00000000000
--- a/tests/modules/dragmap/align/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: dragmap align single-end
-  command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config
-  tags:
-    - dragmap
-    - dragmap/align
-  files:
-    - path: output/dragmap/test.bam
-    - path: output/dragmap/test.dragmap.log
-
-- name: dragmap align single-end_sort
-  command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config
-  tags:
-    - dragmap
-    - dragmap/align
-  files:
-    - path: output/dragmap/test.bam
-    - path: output/dragmap/test.dragmap.log
-
-- name: dragmap align paired-end
-  command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config
-  tags:
-    - dragmap
-    - dragmap/align
-  files:
-    - path: output/dragmap/test.bam
-    - path: output/dragmap/test.dragmap.log
-
-- name: dragmap align paired-end_sort
-  command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config
-  tags:
-    - dragmap
-    - dragmap/align
-  files:
-    - path: output/dragmap/test.bam
-    - path: output/dragmap/test.dragmap.log
diff --git a/tests/modules/dragmap/hashtable/main.nf b/tests/modules/dragmap/hashtable/main.nf
deleted file mode 100644
index 91b43caa96c..00000000000
--- a/tests/modules/dragmap/hashtable/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DRAGMAP_HASHTABLE } from '../../../../modules/dragmap/hashtable/main.nf'
-
-workflow test_dragmap_hashtable {
-    
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    DRAGMAP_HASHTABLE ( fasta )
-}
-
-// TODO Add test using alt-masked bed file
-// https://github.com/Illumina/dragmap#build-hash-table-using-an-alt-masked-bed-file
diff --git a/tests/modules/dragmap/hashtable/test.yml b/tests/modules/dragmap/hashtable/test.yml
deleted file mode 100644
index 0534bdc2ca9..00000000000
--- a/tests/modules/dragmap/hashtable/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: dragmap hashtable
-  command: nextflow run ./tests/modules/dragmap/hashtable -entry test_dragmap_hashtable -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/hashtable/nextflow.config
-  tags:
-    - dragmap
-    - dragmap/hashtable
-  files:
-    - path: output/dragmap/dragmap/hash_table.cfg
-    - path: output/dragmap/dragmap/hash_table.cfg.bin
-    - path: output/dragmap/dragmap/hash_table.cmp
-      md5sum: bc210e5358fd65656f9aea297b59ec7d
-    - path: output/dragmap/dragmap/hash_table_stats.txt
-    - path: output/dragmap/dragmap/reference.bin
-      md5sum: b6b5c12a42416b990cd2844de8f33c5d
-    - path: output/dragmap/dragmap/ref_index.bin
-      md5sum: 8470be9566ecee77eb4aea6a38922a66
-    - path: output/dragmap/dragmap/repeat_mask.bin
-      md5sum: 2439259a2fd32a1d0f4c53d585f3da3a
-    - path: output/dragmap/dragmap/str_table.bin
-      md5sum: 302e2b30993973527e69c6bcd1f093d0
diff --git a/tests/modules/dragonflye/main.nf b/tests/modules/dragonflye/main.nf
deleted file mode 100644
index 3d59bb21ebd..00000000000
--- a/tests/modules/dragonflye/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DRAGONFLYE  } from '../../../modules/dragonflye/main.nf'
-include { DRAGONFLYE as DRAGONFLYE_RAVEN   } from '../../../modules/dragonflye/main.nf'
-
-workflow test_dragonflye {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file("https://github.com/nf-core/test-datasets/raw/bacass/nanopore/subset15000.fq.gz", checkIfExists: true) ]
-            ]
-
-    DRAGONFLYE ( input )
-}
-
-workflow test_dragonflye_raven {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file("https://github.com/nf-core/test-datasets/raw/bacass/nanopore/subset15000.fq.gz", checkIfExists: true) ]
-            ]
-
-    DRAGONFLYE_RAVEN ( input )
-}
diff --git a/tests/modules/dragonflye/test.yml b/tests/modules/dragonflye/test.yml
deleted file mode 100644
index ef9121ba6ec..00000000000
--- a/tests/modules/dragonflye/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: dragonflye with miniasm
-  command: nextflow run ./tests/modules/dragonflye -entry test_dragonflye -c ./tests/config/nextflow.config -c ./tests/modules/dragonflye/nextflow.config
-  tags:
-    - dragonflye
-  files:
-    - path: output/dragonflye/miniasm.fasta
-      md5sum: 6b8903ba09592df99f43ed05fda488f6
-    - path: output/dragonflye/miniasm-unpolished.gfa
-      md5sum: 40ab03a417eafab0cb4ac2c32bd006e1
-    # MD5sum not reproducible (timestamp, contig order)
-    - path: output/dragonflye/contigs.fa
-    - path: output/dragonflye/dragonflye.log
-
-- name: dragonflye with raven
-  command: nextflow run ./tests/modules/dragonflye -entry test_dragonflye_raven -c ./tests/config/nextflow.config -c ./tests/modules/dragonflye/nextflow.config
-  tags:
-    - dragonflye
-  files:
-    - path: output/dragonflye/raven.fasta
-      md5sum: bd4ba5b0dda110a7ccbea9581c97a898
-    - path: output/dragonflye/raven-unpolished.gfa
-      md5sum: 62c21791dbf9b2c7375dc52d7bab5be2
-    # MD5sum not reproducible (timestamp, contig order)
-    - path: output/dragonflye/contigs.fa
-    - path: output/dragonflye/dragonflye.log
diff --git a/tests/modules/dshbio/exportsegments/main.nf b/tests/modules/dshbio/exportsegments/main.nf
deleted file mode 100644
index 0460950af99..00000000000
--- a/tests/modules/dshbio/exportsegments/main.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DSHBIO_EXPORTSEGMENTS } from '../../../../modules/dshbio/exportsegments/main.nf'
-
-workflow test_dshbio_exportsegments {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true) ]
-            ]
-
-    DSHBIO_EXPORTSEGMENTS ( input )
-}
-
-workflow test_dshbio_exportsegments_bgz {
-    input = [ [ id:'test_bgz' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa_bgz'], checkIfExists: true) ]
-            ]
-
-    DSHBIO_EXPORTSEGMENTS ( input )
-}
-
-workflow test_dshbio_exportsegments_gz {
-    input = [ [ id:'test_gz' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa_gz'], checkIfExists: true) ]
-            ]
-
-    DSHBIO_EXPORTSEGMENTS ( input )
-}
-
-workflow test_dshbio_exportsegments_zst {
-    input = [ [ id:'test_zst' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa_zst'], checkIfExists: true) ]
-            ]
-
-    DSHBIO_EXPORTSEGMENTS ( input )
-}
diff --git a/tests/modules/dshbio/exportsegments/test.yml b/tests/modules/dshbio/exportsegments/test.yml
deleted file mode 100644
index 85406f8f354..00000000000
--- a/tests/modules/dshbio/exportsegments/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: dshbio exportsegments
-  command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
-  tags:
-    - dshbio
-    - dshbio/exportsegments
-  files:
-    - path: ./output/dshbio/test.fa.gz
-      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
-
-- name: dshbio exportsegments bgz
-  command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_bgz -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
-  tags:
-    - dshbio
-    - dshbio/exportsegments
-  files:
-    - path: ./output/dshbio/test_bgz.fa.gz
-      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
-
-- name: dshbio exportsegments gz
-  command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_gz -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
-  tags:
-    - dshbio
-    - dshbio/exportsegments
-  files:
-    - path: ./output/dshbio/test_gz.fa.gz
-      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
-
-- name: dshbio exportsegments zst
-  command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_zst -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
-  tags:
-    - dshbio
-    - dshbio/exportsegments
-  files:
-    - path: ./output/dshbio/test_zst.fa.gz
-      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
diff --git a/tests/modules/dshbio/filterbed/main.nf b/tests/modules/dshbio/filterbed/main.nf
deleted file mode 100644
index 454a03be3d4..00000000000
--- a/tests/modules/dshbio/filterbed/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DSHBIO_FILTERBED } from '../../../../modules/dshbio/filterbed/main.nf'
-
-workflow test_dshbio_filterbed {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
-            ]
-
-    DSHBIO_FILTERBED ( input )
-}
diff --git a/tests/modules/dshbio/filterbed/test.yml b/tests/modules/dshbio/filterbed/test.yml
deleted file mode 100644
index 278fd5a375a..00000000000
--- a/tests/modules/dshbio/filterbed/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: dshbio filterbed
-  command: nextflow run ./tests/modules/dshbio/filterbed -entry test_dshbio_filterbed -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/filterbed/nextflow.config
-  tags:
-    - dshbio
-    - dshbio/filterbed
-  files:
-    - path: ./output/dshbio/test.filtered.bed.gz
-      md5sum: 163be0a88c70ca629fd516dbaadad96a
diff --git a/tests/modules/dshbio/filtergff3/main.nf b/tests/modules/dshbio/filtergff3/main.nf
deleted file mode 100644
index 7c803781cac..00000000000
--- a/tests/modules/dshbio/filtergff3/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DSHBIO_FILTERGFF3 } from '../../../../modules/dshbio/filtergff3/main.nf'
-
-workflow test_dshbio_filtergff3 {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ]
-            ]
-
-    DSHBIO_FILTERGFF3 ( input )
-}
diff --git a/tests/modules/dshbio/filtergff3/test.yml b/tests/modules/dshbio/filtergff3/test.yml
deleted file mode 100644
index 43238333c6b..00000000000
--- a/tests/modules/dshbio/filtergff3/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: dshbio filtergff3
-  command: nextflow run ./tests/modules/dshbio/filtergff3 -entry test_dshbio_filtergff3 -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/filtergff3/nextflow.config
-  tags:
-    - dshbio
-    - dshbio/filtergff3
-  files:
-    - path: ./output/dshbio/test.filtered.gff3.gz
-      md5sum: 89d320cf91c0ca8fd200cfa9688954e3
diff --git a/tests/modules/dshbio/splitbed/main.nf b/tests/modules/dshbio/splitbed/main.nf
deleted file mode 100644
index 517baad0ed4..00000000000
--- a/tests/modules/dshbio/splitbed/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DSHBIO_SPLITBED } from '../../../../modules/dshbio/splitbed/main.nf'
-
-workflow test_dshbio_splitbed {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
-            ]
-
-    DSHBIO_SPLITBED ( input )
-}
diff --git a/tests/modules/dshbio/splitbed/test.yml b/tests/modules/dshbio/splitbed/test.yml
deleted file mode 100644
index ab14648eb22..00000000000
--- a/tests/modules/dshbio/splitbed/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: dshbio splitbed
-  command: nextflow run ./tests/modules/dshbio/splitbed -entry test_dshbio_splitbed -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/splitbed/nextflow.config
-  tags:
-    - dshbio
-    - dshbio/splitbed
-  files:
-    - path: ./output/dshbio/test.1.bed.gz
-      md5sum: 967ba338f361740eb015304003ababe7
-    - path: ./output/dshbio/test.0.bed.gz
-      md5sum: 8b884d8cf5c57955f218f1c6dbf02d54
diff --git a/tests/modules/dshbio/splitgff3/main.nf b/tests/modules/dshbio/splitgff3/main.nf
deleted file mode 100644
index 03aa53947bf..00000000000
--- a/tests/modules/dshbio/splitgff3/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DSHBIO_SPLITGFF3 } from '../../../../modules/dshbio/splitgff3/main.nf'
-
-workflow test_dshbio_splitgff3 {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ]
-            ]
-
-    DSHBIO_SPLITGFF3 ( input )
-}
diff --git a/tests/modules/dshbio/splitgff3/test.yml b/tests/modules/dshbio/splitgff3/test.yml
deleted file mode 100644
index 6087ce111ee..00000000000
--- a/tests/modules/dshbio/splitgff3/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: dshbio splitgff3
-  command: nextflow run ./tests/modules/dshbio/splitgff3 -entry test_dshbio_splitgff3 -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/splitgff3/nextflow.config
-  tags:
-    - dshbio
-    - dshbio/splitgff3
-  files:
-    - path: ./output/dshbio/test.1.gff3.gz
-      md5sum: 0742895e81fe080c01f43f9dd616baae
-    - path: ./output/dshbio/test.0.gff3.gz
-      md5sum: 9aed611b89093f5e0db4e63cb56d8416
diff --git a/tests/modules/ectyper/main.nf b/tests/modules/ectyper/main.nf
deleted file mode 100644
index dd359fa23d3..00000000000
--- a/tests/modules/ectyper/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ECTYPER } from '../../../modules/ectyper/main.nf'
-
-workflow test_ectyper {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    ECTYPER ( input )
-}
diff --git a/tests/modules/ectyper/test.yml b/tests/modules/ectyper/test.yml
deleted file mode 100644
index 15e0327da0d..00000000000
--- a/tests/modules/ectyper/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: ectyper test_ectyper
-  command: nextflow run ./tests/modules/ectyper -entry test_ectyper -c ./tests/config/nextflow.config -c ./tests/modules/ectyper/nextflow.config
-  tags:
-    - ectyper
-  files:
-    - path: output/ectyper/blast_output_alleles.txt
-      md5sum: 27f3f5e84f7da451b2948d61589cdb06
-    - path: output/ectyper/ectyper.log
-      contains: ["Serotype", "RefSeq", "O-type", "finished"]
-    - path: output/ectyper/test.tsv
-      md5sum: ba923d7c7ee7d1047466aafc9a9df208
diff --git a/tests/modules/eido/convert/main.nf b/tests/modules/eido/convert/main.nf
deleted file mode 100644
index e3e49771be2..00000000000
--- a/tests/modules/eido/convert/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { EIDO_CONVERT } from '../../../../modules/eido/convert/main.nf'
-
-workflow test_eido_convert_nextflow_samplesheet {
-
-    nextflow_samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
-    format = "csv"
-    pep_input_base_dir = []
-
-    EIDO_CONVERT ( nextflow_samplesheet, format, pep_input_base_dir )
-}
-
-
-workflow test_eido_convert_pep_project {
-
-    pep_project = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
-    format = "csv"
-    pep_input_base_dir = []
-
-    EIDO_CONVERT ( pep_project, format, pep_input_base_dir )
-}
diff --git a/tests/modules/eido/convert/test.yml b/tests/modules/eido/convert/test.yml
deleted file mode 100644
index 8015c1149af..00000000000
--- a/tests/modules/eido/convert/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: eido convert test_eido_convert_nextflow_samplesheet
-  command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_nextflow_samplesheet -c ./tests/config/nextflow.config  -c ./tests/modules/eido/convert/nextflow.config
-  tags:
-    - eido/convert
-    - eido
-  files:
-    - path: output/eido/samplesheet_converted.csv
-      md5sum: 7aa4da4944650b9c7c451c5dfbeae663
-
-- name: eido convert test_eido_convert_pep_project
-  command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_pep_project -c ./tests/config/nextflow.config  -c ./tests/modules/eido/convert/nextflow.config
-  tags:
-    - eido/convert
-    - eido
-  files:
-    - path: output/eido/samplesheet_converted.csv
-      md5sum: 2191ccc9c9c1ac4577726ea24cdb9fda
diff --git a/tests/modules/eido/validate/main.nf b/tests/modules/eido/validate/main.nf
deleted file mode 100644
index d1e2d200430..00000000000
--- a/tests/modules/eido/validate/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { EIDO_VALIDATE } from '../../../../modules/eido/validate/main.nf'
-
-workflow test_eido_validate_on_nextflow_samplesheet {
-
-    samplesheet = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
-    schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
-    pep_input_base_dir = []
-
-    EIDO_VALIDATE ( samplesheet, schema, pep_input_base_dir )
-}
-
-workflow test_eido_validate_on_pep_config {
-
-    samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
-    schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
-    pep_input_base_dir = []
-
-    EIDO_VALIDATE ( samplesheet, schema, pep_input_base_dir )
-}
diff --git a/tests/modules/eido/validate/test.yml b/tests/modules/eido/validate/test.yml
deleted file mode 100644
index 03a4e5b2a35..00000000000
--- a/tests/modules/eido/validate/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: eido validate test_eido_validate_on_nextflow_samplesheet
-  command: nextflow run ./tests/modules/eido/validate -entry test_eido_validate_on_nextflow_samplesheet -c ./tests/config/nextflow.config  -c ./tests/modules/eido/validate/nextflow.config
-  tags:
-    - eido/validate
-    - eido
-  files:
-    - path: output/eido/validation.log
-      md5sum: 3a197c21ebf411aac7616bf9b4470de3
-
-- name: eido validate test_eido_validate_on_pep_config
-  command: nextflow run ./tests/modules/eido/validate -entry test_eido_validate_on_pep_config -c ./tests/config/nextflow.config  -c ./tests/modules/eido/validate/nextflow.config
-  tags:
-    - eido/validate
-    - eido
-  files:
-    - path: output/eido/validation.log
-      md5sum: 3a197c21ebf411aac7616bf9b4470de3
diff --git a/tests/modules/elprep/filter/main.nf b/tests/modules/elprep/filter/main.nf
deleted file mode 100644
index 0a8d43ca234..00000000000
--- a/tests/modules/elprep/filter/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ELPREP_FILTER } from '../../../../modules/elprep/filter/main.nf'
-
-workflow test_elprep_filter {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-    reference_elfasta = file(params.test_data['homo_sapiens']['genome']['genome_elfasta'], checkIfExists: true)
-    known_sites_elsites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_elsites'], checkIfExists: true)
-    target_regions_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-
-    ELPREP_FILTER ( input, true, true, [],  [], reference_elfasta, known_sites_elsites, target_regions_bed, [], [], true, true)
-}
diff --git a/tests/modules/elprep/filter/test.yml b/tests/modules/elprep/filter/test.yml
deleted file mode 100644
index 922d7a9b777..00000000000
--- a/tests/modules/elprep/filter/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: elprep filter test_elprep_filter
-  command: nextflow run tests/modules/elprep/filter -entry test_elprep_filter -c tests/config/nextflow.config
-  tags:
-    - elprep
-    - elprep/filter
-  files:
-    - path: output/elprep/test.activity_profile.igv
-    - path: output/elprep/test.assembly_regions.igv
-    - path: output/elprep/output/test.bam
-    - path: output/elprep/test.g.vcf.gz
-    - path: output/elprep/test.metrics.txt
-    - path: output/elprep/test.recall
-    - path: output/elprep/versions.yml
diff --git a/tests/modules/elprep/merge/main.nf b/tests/modules/elprep/merge/main.nf
deleted file mode 100644
index b4a40ce3fc5..00000000000
--- a/tests/modules/elprep/merge/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf'
-include { ELPREP_MERGE } from '../../../../modules/elprep/merge/main.nf'
-
-workflow test_elprep_merge {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-
-    ELPREP_SPLIT ( input )
-    ELPREP_MERGE ( ELPREP_SPLIT.out.bam )
-}
diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
deleted file mode 100644
index ad2ecfefd4f..00000000000
--- a/tests/modules/elprep/merge/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: elprep merge test_elprep_merge
-  command: nextflow run tests/modules/elprep/merge -entry test_elprep_merge -c tests/config/nextflow.config
-  tags:
-    - elprep
-    - elprep/merge
-  files:
-    - path: output/elprep/output/test.bam
-    - path: output/elprep/versions.yml
diff --git a/tests/modules/elprep/split/main.nf b/tests/modules/elprep/split/main.nf
deleted file mode 100644
index d5a111de8f3..00000000000
--- a/tests/modules/elprep/split/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf'
-
-workflow test_elprep_split {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-
-    ELPREP_SPLIT ( input )
-}
diff --git a/tests/modules/elprep/split/test.yml b/tests/modules/elprep/split/test.yml
deleted file mode 100644
index 2de3f99bd18..00000000000
--- a/tests/modules/elprep/split/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: elprep split test_elprep_split
-  command: nextflow run tests/modules/elprep/split -entry test_elprep_split -c tests/config/nextflow.config
-  tags:
-    - elprep
-    - elprep/split
-  files:
-    - path: output/elprep/output/splits/test-group00001.bam
-    - path: output/elprep/output/splits/test-unmapped.bam
-    - path: output/elprep/output/test-spread.bam
-    - path: output/elprep/versions.yml
diff --git a/tests/modules/emboss/seqret/main.nf b/tests/modules/emboss/seqret/main.nf
deleted file mode 100644
index d3c703a2ac3..00000000000
--- a/tests/modules/emboss/seqret/main.nf
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { EMBOSS_SEQRET } from '../../../../modules/emboss/seqret/main.nf'
-include { GUNZIP } from '../../../modules/gunzip/main.nf'
-
-workflow test_emboss_seqret_gb2embl {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
-    ]
-
-    GUNZIP ( input )
-    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'embl' )
-}
-
-workflow test_emboss_seqret_gb2gff {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
-    ]
-
-    GUNZIP ( input )
-    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'gff' )
-}
-
-workflow test_emboss_seqret_gb2pir {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
-    ]
-
-    GUNZIP ( input )
-    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'pir' )
-}
-
-workflow test_emboss_seqret_gb2fasta {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
-    ]
-
-    GUNZIP ( input )
-    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'fasta' )
-}
diff --git a/tests/modules/emboss/seqret/test.yml b/tests/modules/emboss/seqret/test.yml
deleted file mode 100644
index b98ccdbd1b6..00000000000
--- a/tests/modules/emboss/seqret/test.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-- name: emboss seqret test_emboss_seqret_gb2embl
-  command: nextflow run ./tests/modules/emboss/seqret -entry test_emboss_seqret_gb2embl -c ./tests/config/nextflow.config  -c ./tests/modules/emboss/seqret/nextflow.config
-  tags:
-    - emboss
-    - emboss/seqret
-  files:
-    - path: output/emboss/test.embl
-      md5sum: 4810933b1b2174f7067d9afa1da8b01b
-      contains: ["ID   NZ_CP069563;"] # Human-readable test for correct format and sequence
-
-- name: emboss seqret test_emboss_seqret_gb2gff
-  command: nextflow run ./tests/modules/emboss/seqret -entry test_emboss_seqret_gb2gff -c ./tests/config/nextflow.config  -c ./tests/modules/emboss/seqret/nextflow.config
-  tags:
-    - emboss
-    - emboss/seqret
-  files:
-    - path: output/emboss/test.gff
-      contains:
-        - "##gff-version 3" # Human-readable test for correct format
-        - ">NZ_CP069563" # Human-readable test for correct sequence
-
-- name: emboss seqret test_emboss_seqret_gb2pir
-  command: nextflow run ./tests/modules/emboss/seqret -entry test_emboss_seqret_gb2pir -c ./tests/config/nextflow.config  -c ./tests/modules/emboss/seqret/nextflow.config
-  tags:
-    - emboss
-    - emboss/seqret
-  files:
-    - path: output/emboss/test.pir
-      md5sum: 49f4a28533e970aa2438d8adf55a26bb
-      contains: [">D1;NZ_CP069563"] # Human-readable test for correct format and sequence
-
-- name: emboss seqret test_emboss_seqret_gb2fasta
-  command: nextflow run ./tests/modules/emboss/seqret -entry test_emboss_seqret_gb2fasta -c ./tests/config/nextflow.config  -c ./tests/modules/emboss/seqret/nextflow.config
-  tags:
-    - emboss
-    - emboss/seqret
-  files:
-    - path: output/emboss/test.fasta
-      md5sum: 0694275f05780aeb0b54d46687603f44
-      contains: [">NZ_CP069563"] # Human-readable test for correct format and sequence
diff --git a/tests/modules/emmtyper/main.nf b/tests/modules/emmtyper/main.nf
deleted file mode 100644
index ee96fc322f2..00000000000
--- a/tests/modules/emmtyper/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { EMMTYPER } from '../../../modules/emmtyper/main.nf'
-
-workflow test_emmtyper {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    EMMTYPER ( input )
-}
diff --git a/tests/modules/emmtyper/test.yml b/tests/modules/emmtyper/test.yml
deleted file mode 100644
index 81854eb6528..00000000000
--- a/tests/modules/emmtyper/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: emmtyper test_emmtyper
-  command: nextflow run ./tests/modules/emmtyper -entry test_emmtyper -c ./tests/config/nextflow.config -c ./tests/modules/emmtyper/nextflow.config
-  tags:
-    - emmtyper
-  files:
-    - path: output/emmtyper/test.tsv
-      md5sum: c727ba859adec9ca8ff0e091ecf79c62
diff --git a/tests/modules/endorspy/main.nf b/tests/modules/endorspy/main.nf
deleted file mode 100644
index 2f04c13a47d..00000000000
--- a/tests/modules/endorspy/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ENDORSPY } from '../../../modules/endorspy/main.nf'
-include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main.nf'
-include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT2 } from '../../../modules/samtools/flagstat/main.nf'
-include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf'
-include { SAMTOOLS_INDEX } from '../../../modules/samtools/index/main.nf'
-
-workflow test_endorspy {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-    
-
-    SAMTOOLS_FLAGSTAT ( input )
-    SAMTOOLS_VIEW ( input, [] )
-    SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
-    input2 = SAMTOOLS_VIEW.out.bam
-       .mix(SAMTOOLS_INDEX.out.bai)
-       .groupTuple(by:0)
-       .map{
-            def meta = it[0]
-            def bam = it[1][0]
-            def bai = it[1][1]
-
-            [meta, bam, bai]
-       }
-    SAMTOOLS_FLAGSTAT2 ( input2 )
-    ch_input_flagstat = SAMTOOLS_FLAGSTAT.out.flagstat.join(SAMTOOLS_FLAGSTAT2.out.flagstat)
-    ENDORSPY ( ch_input_flagstat )
-}
diff --git a/tests/modules/endorspy/test.yml b/tests/modules/endorspy/test.yml
deleted file mode 100644
index 1369227f404..00000000000
--- a/tests/modules/endorspy/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: endorspy test_endorspy
-  command: nextflow run ./tests/modules/endorspy -entry test_endorspy -c ./tests/config/nextflow.config  -c ./tests/modules/endorspy/nextflow.config
-  tags:
-    - endorspy
-  files:
-    - path: output/endorspy/test_endogenous_dna_mqc.json
-      md5sum: fe7bea111d966db321dcde7fbfb062b1
diff --git a/tests/modules/ensemblvep/main.nf b/tests/modules/ensemblvep/main.nf
deleted file mode 100644
index 8854d1a28c5..00000000000
--- a/tests/modules/ensemblvep/main.nf
+++ /dev/null
@@ -1,86 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf'
-
-include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../modules/ensemblvep/main.nf'
-include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../modules/ensemblvep/main.nf'
-include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../modules/ensemblvep/main.nf'
-include { ENSEMBLVEP as ENSEMBLVEP_VCF_BGZIP } from '../../../modules/ensemblvep/main.nf'
-include { ENSEMBLVEP as ENSEMBLVEP_VCF_GZIP  } from '../../../modules/ensemblvep/main.nf'
-
-workflow test_ensemblvep_fasta_json {
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    ENSEMBLVEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
-}
-
-workflow test_ensemblvep_fasta_tab {
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    ENSEMBLVEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
-}
-
-workflow test_ensemblvep_fasta_vcf {
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
-}
-
-workflow test_ensemblvep_fasta_vcf_bgzip {
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    ENSEMBLVEP_VCF_BGZIP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
-}
-
-workflow test_ensemblvep_fasta_vcf_gzip {
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    ENSEMBLVEP_VCF_GZIP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
-}
-
-workflow test_ensemblvep_fasta {
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
-}
-
-workflow test_ensemblvep_no_fasta {
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
-
-    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], [], [] )
-}
diff --git a/tests/modules/ensemblvep/test.yml b/tests/modules/ensemblvep/test.yml
deleted file mode 100644
index dedd56195b6..00000000000
--- a/tests/modules/ensemblvep/test.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-- name: ensemblvep test_ensemblvep_fasta_json
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_json -c ./tests/config/nextflow.config  -c ./tests/modules/ensemblvep/nextflow.config
-  tags:
-    - ensemblvep
-  files:
-    - path: output/ensemblvep/test.ann.json
-    - path: output/ensemblvep/test.summary.html
-
-- name: ensemblvep test_ensemblvep_fasta_tab
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_tab -c ./tests/config/nextflow.config  -c ./tests/modules/ensemblvep/nextflow.config
-  tags:
-    - ensemblvep
-  files:
-    - path: output/ensemblvep/test.ann.tab
-    - path: output/ensemblvep/test.summary.html
-
-- name: ensemblvep test_ensemblvep_fasta_vcf
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config  -c ./tests/modules/ensemblvep/nextflow.config
-  tags:
-    - ensemblvep
-  files:
-    - path: output/ensemblvep/test.ann.vcf
-    - path: output/ensemblvep/test.summary.html
-
-- name: ensemblvep test_ensemblvep_fasta_vcf_bgzip
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf_bgzip -c ./tests/config/nextflow.config  -c ./tests/modules/ensemblvep/nextflow.config
-  tags:
-    - ensemblvep
-  files:
-    - path: output/ensemblvep/test.ann.vcf.gz
-    - path: output/ensemblvep/test.summary.html
-
-- name: ensemblvep test_ensemblvep_fasta_vcf_gzip
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf_gzip -c ./tests/config/nextflow.config  -c ./tests/modules/ensemblvep/nextflow.config
-  tags:
-    - ensemblvep
-  files:
-    - path: output/ensemblvep/test.ann.vcf.gz
-    - path: output/ensemblvep/test.summary.html
-
-- name: ensemblvep test_ensemblvep_fasta
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/ensemblvep/nextflow.config
-  tags:
-    - ensemblvep
-  files:
-    - path: output/ensemblvep/test.ann.vcf
-    - path: output/ensemblvep/test.summary.html
-
-- name: ensemblvep test_ensemblvep_no_fasta
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/ensemblvep/nextflow.config
-  tags:
-    - ensemblvep
-  files:
-    - path: output/ensemblvep/test.ann.vcf
-    - path: output/ensemblvep/test.summary.html
-
-- name: ensemblvep test_ensemblvep_fasta_vcf_stub
-  command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config  -c ./tests/modules/ensemblvep/nextflow.config -stub
-  tags:
-    - ensemblvep
-  files:
-    - path: output/ensemblvep/test.ann.vcf
-    - path: output/ensemblvep/test.summary.html
diff --git a/tests/modules/entrezdirect/esearch/test.yml b/tests/modules/entrezdirect/esearch/test.yml
deleted file mode 100644
index 05372422f24..00000000000
--- a/tests/modules/entrezdirect/esearch/test.yml
+++ /dev/null
@@ -1,47 +0,0 @@
-- name: entrezdirect esearch test_entrezdirect_esearch_pubmed
-  command: nextflow run ./tests/modules/entrezdirect/esearch -entry test_entrezdirect_esearch_pubmed -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/esearch/nextflow.config
-  tags:
-    - entrezdirect/esearch
-    - entrezdirect
-  files:
-    - path: output/entrezdirect/test_pubmed.xml
-      contains:
-        - "<ENTREZ_DIRECT>"
-        - "<Db>pubmed</Db>"
-        - "<WebEnv>"
-        - "<QueryKey>"
-        - "<Step>"
-        - "<Count>"
-        - "</ENTREZ_DIRECT>"
-
-- name: entrezdirect esearch test_entrezdirect_esearch_genome
-  command: nextflow run ./tests/modules/entrezdirect/esearch -entry test_entrezdirect_esearch_genome -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/esearch/nextflow.config
-  tags:
-    - entrezdirect/esearch
-    - entrezdirect
-  files:
-    - path: output/entrezdirect/test_genome.xml
-      contains:
-        - "<ENTREZ_DIRECT>"
-        - "<Db>genome</Db>"
-        - "<WebEnv>"
-        - "<QueryKey>"
-        - "<Count>"
-        - "<Step>"
-        - "</ENTREZ_DIRECT>"
-
-- name: entrezdirect esearch test_entrezdirect_esearch_assembly
-  command: nextflow run ./tests/modules/entrezdirect/esearch -entry test_entrezdirect_esearch_assembly -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/esearch/nextflow.config
-  tags:
-    - entrezdirect/esearch
-    - entrezdirect
-  files:
-    - path: output/entrezdirect/test_assembly.xml
-      contains:
-        - "<ENTREZ_DIRECT>"
-        - "<Db>assembly</Db>"
-        - "<WebEnv>"
-        - "<QueryKey>"
-        - "<Count>"
-        - "<Step>"
-        - "</ENTREZ_DIRECT>"
diff --git a/tests/modules/entrezdirect/esummary/main.nf b/tests/modules/entrezdirect/esummary/main.nf
deleted file mode 100644
index 8308102cbfb..00000000000
--- a/tests/modules/entrezdirect/esummary/main.nf
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ENTREZDIRECT_ESUMMARY } from '../../../../modules/entrezdirect/esummary/main.nf'
-
-//
-// Test with SRA database
-//
-workflow test_entrezdirect_esummary_sra {
-
-    input = [
-        [ id:'test_sra' ], // meta map
-        uid = '5135484',
-        []
-    ]
-    database = 'sra'
-
-    ENTREZDIRECT_ESUMMARY ( input, database )
-}
-
-//
-// Test with Genome database
-//
-workflow test_entrezdirect_esummary_genome {
-
-    input = [
-        [ id:'test_genome' ], // meta map
-        uid = '768',
-        []
-    ]
-    database = 'genome'
-
-    ENTREZDIRECT_ESUMMARY ( input, database )
-}
-
-//
-// Test with Assembly database
-//
-workflow test_entrezdirect_esummary_assembly {
-
-    input = [
-        [ id:'test_assembly' ], // meta map
-        uid = '191021',
-        []
-    ]
-    database = 'assembly'
-
-    ENTREZDIRECT_ESUMMARY ( input, database )
-}
diff --git a/tests/modules/entrezdirect/esummary/test.yml b/tests/modules/entrezdirect/esummary/test.yml
deleted file mode 100644
index 06618ec6d44..00000000000
--- a/tests/modules/entrezdirect/esummary/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: entrezdirect esummary test_entrezdirect_esummary_sra
-  command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_sra -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/esummary/nextflow.config
-  tags:
-    - entrezdirect
-    - entrezdirect/esummary
-  files:
-    - path: output/entrezdirect/test_sra.xml
-      contains: ["WGS of ornithorhynchus anatinus"]
-
-- name: entrezdirect esummary test_entrezdirect_esummary_genome
-  command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_genome -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/esummary/nextflow.config
-  tags:
-    - entrezdirect
-    - entrezdirect/esummary
-  files:
-    - path: output/entrezdirect/test_genome.xml
-      contains: ["Hypsibius dujardini"]
-
-- name: entrezdirect esummary test_entrezdirect_esummary_assembly
-  command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_assembly -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/esummary/nextflow.config
-  tags:
-    - entrezdirect
-    - entrezdirect/esummary
-  files:
-    - path: output/entrezdirect/test_assembly.xml
-      contains: ["ContigN50"]
diff --git a/tests/modules/entrezdirect/xtract/main.nf b/tests/modules/entrezdirect/xtract/main.nf
deleted file mode 100644
index 93cd38491ba..00000000000
--- a/tests/modules/entrezdirect/xtract/main.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ENTREZDIRECT_ESUMMARY } from '../../../../modules/entrezdirect/esummary/main.nf'
-include { ENTREZDIRECT_XTRACT   } from '../../../../modules/entrezdirect/xtract/main.nf'
-
-//
-// Test with Assembly database
-//
-workflow test_entrezdirect_xtract_assembly {
-
-    input = [
-        [ id:'test_assembly' ], // meta map
-        uid = '191021',
-        []
-    ]
-    database = 'assembly'
-
-    pattern_in = 'DocumentSummary'
-    element_in = 'SpeciesName BioprojectAccn FtpPath_GenBank'
-    delim = ","
-
-    ENTREZDIRECT_ESUMMARY ( input, database )
-    ENTREZDIRECT_XTRACT ( ENTREZDIRECT_ESUMMARY.out.xml, pattern_in, element_in, delim )
-}
-
-//
-// Test with Genome database
-//
-workflow test_entrezdirect_xtract_genome {
-
-    input = [
-        [ id:'test_genome' ], // meta map
-        uid = '768',
-        []
-    ]
-    database = 'genome'
-
-    pattern_in = 'DocumentSummary'
-    element_in = 'TaxId Organism_Name Project_Accession Assembly_Accession'
-    delim = ","
-
-    ENTREZDIRECT_ESUMMARY ( input, database )
-    ENTREZDIRECT_XTRACT ( ENTREZDIRECT_ESUMMARY.out.xml, pattern_in, element_in, delim )
-}
diff --git a/tests/modules/entrezdirect/xtract/test.yml b/tests/modules/entrezdirect/xtract/test.yml
deleted file mode 100644
index a4b506168e3..00000000000
--- a/tests/modules/entrezdirect/xtract/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: entrezdirect xtract test_entrezdirect_xtract_assembly
-  command: nextflow run ./tests/modules/entrezdirect/xtract -entry test_entrezdirect_xtract_assembly -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/xtract/nextflow.config
-  tags:
-    - entrezdirect
-    - entrezdirect/xtract
-  files:
-    - path: output/entrezdirect/test_assembly.txt
-      md5sum: 17073db7c14890aef30f5e3f2d003d32
-
-- name: entrezdirect xtract test_entrezdirect_xtract_genome
-  command: nextflow run ./tests/modules/entrezdirect/xtract -entry test_entrezdirect_xtract_genome -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/xtract/nextflow.config
-  tags:
-    - entrezdirect
-    - entrezdirect/xtract
-  files:
-    - path: output/entrezdirect/test_genome.txt
-      md5sum: 931279db7c80c5bb9ed523815898a9cd
diff --git a/tests/modules/epang/main.nf b/tests/modules/epang/main.nf
deleted file mode 100644
index d2c64ad8bda..00000000000
--- a/tests/modules/epang/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { EPANG } from '../../../modules/epang/main.nf'
-
-workflow test_epang {
-    
-    input = [
-        [ id:'test', model:'LG' ], // meta map
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/query.alnfaa.gz', checkIfExists: true)
-    ]
-
-    EPANG ( 
-        input,
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/reference.alnfaa.gz', checkIfExists: true),
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/reference.newick', checkIfExists: true),
-        [],
-        [],
-        []
-    )
-}
diff --git a/tests/modules/epang/test.yml b/tests/modules/epang/test.yml
deleted file mode 100644
index b4b861c1a96..00000000000
--- a/tests/modules/epang/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: epang test_epang
-  command: nextflow run ./tests/modules/epang -entry test_epang -c ./tests/config/nextflow.config  -c ./tests/modules/epang/nextflow.config
-  tags:
-    - epang
-  files:
-    - path: output/epang/test.epa_info.log
-      contains:
-        - "INFO 3 Sequences done"
-    - path: output/epang/test.epa_result.jplace.gz
-      contains:
-        - '"placements":'
-        - '"metadata": {"invocation": "epa-ng --model LG --threads 2 --query query.alnfaa.gz --ref-msa reference.alnfaa.gz --tree reference.newick "}'
diff --git a/tests/modules/expansionhunter/main.nf b/tests/modules/expansionhunter/main.nf
deleted file mode 100644
index d0221234b97..00000000000
--- a/tests/modules/expansionhunter/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
-
-workflow test_expansionhunter {
-
-    input = [ [ id:'test', gender:'male' ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
-
-    EXPANSIONHUNTER ( input, fasta, variant_catalog )
-}
diff --git a/tests/modules/expansionhunter/test.yml b/tests/modules/expansionhunter/test.yml
deleted file mode 100644
index f9282f8c4c9..00000000000
--- a/tests/modules/expansionhunter/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: expansionhunter test_expansionhunter
-  command: nextflow run ./tests/modules/expansionhunter -entry test_expansionhunter -c ./tests/config/nextflow.config -c ./tests/modules/expansionhunter/nextflow.config
-  tags:
-    - expansionhunter
-  files:
-    - path: output/expansionhunter/test.vcf
-      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
diff --git a/tests/modules/faqcs/main.nf b/tests/modules/faqcs/main.nf
deleted file mode 100644
index eba4bb97206..00000000000
--- a/tests/modules/faqcs/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FAQCS } from '../../../modules/faqcs/main.nf'
-
-
-//
-// Test with single-end data
-//
-workflow test_fastp_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    FAQCS ( input )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_fastp_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    FAQCS ( input )
-}
-
diff --git a/tests/modules/faqcs/test.yml b/tests/modules/faqcs/test.yml
deleted file mode 100644
index ef50d30d145..00000000000
--- a/tests/modules/faqcs/test.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-- name: faqcs test_fastp_single_end
-  command: nextflow run tests/modules/faqcs -entry test_fastp_single_end -c tests/config/nextflow.config
-  tags:
-    - faqcs
-  files:
-    - path: output/faqcs/qa.test.base_content.txt
-      md5sum: f992603f01ca430c03c8aae02eba2f5d
-    - path: output/faqcs/qa.test.for_qual_histogram.txt
-      md5sum: a3d462ab84151e982f99f85f52c21de3
-    - path: output/faqcs/qa.test.length_count.txt
-      md5sum: 80915f09fbaf5884c32e95acab2d031c
-    - path: output/faqcs/test.base_content.txt
-      md5sum: f992603f01ca430c03c8aae02eba2f5d
-    - path: output/faqcs/test.fastp.log
-      md5sum: be79dc893f87de1f82faf749cdfb848c
-    - path: output/faqcs/test.for_qual_histogram.txt
-      md5sum: a3d462ab84151e982f99f85f52c21de3
-    - path: output/faqcs/test.length_count.txt
-      md5sum: 80915f09fbaf5884c32e95acab2d031c
-    - path: output/faqcs/test.stats.txt
-      md5sum: ea20e93706b2e4c676004253baa3cec6
-    - path: output/faqcs/test.trimmed.fastq.gz
-      md5sum: 875863b402f67403dac63ef59b9c9a8a
-    - path: output/faqcs/test_qc_report.pdf
-    - path: output/faqcs/versions.yml
-      md5sum: 2a38d7e7ab5299336e9669c393c9da6c
-
-- name: faqcs test_fastp_paired_end
-  command: nextflow run tests/modules/faqcs -entry test_fastp_paired_end -c tests/config/nextflow.config
-  tags:
-    - faqcs
-  files:
-    - path: output/faqcs/qa.test.base_content.txt
-      md5sum: 99aa9a775ccd8d6503f0cf80f775203c
-    - path: output/faqcs/qa.test.for_qual_histogram.txt
-      md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
-    - path: output/faqcs/qa.test.length_count.txt
-      md5sum: 420298983c762754d5b0ef32c9d5dad4
-    - path: output/faqcs/test.base_content.txt
-      md5sum: 99aa9a775ccd8d6503f0cf80f775203c
-    - path: output/faqcs/test.fastp.log
-      md5sum: be79dc893f87de1f82faf749cdfb848c
-    - path: output/faqcs/test.for_qual_histogram.txt
-      md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
-    - path: output/faqcs/test.length_count.txt
-      md5sum: 420298983c762754d5b0ef32c9d5dad4
-    - path: output/faqcs/test.stats.txt
-      md5sum: 9a693f8af94ab8c485519d9a523aa622
-    - path: output/faqcs/test_1.trimmed.fastq.gz
-      md5sum: 875863b402f67403dac63ef59b9c9a8a
-    - path: output/faqcs/test_2.trimmed.fastq.gz
-      md5sum: 375aeb74819ca3d72203135ac80df78c
-    - path: output/faqcs/test_qc_report.pdf
-    - path: output/faqcs/versions.yml
-      md5sum: 208d54c0cf6dfc54e719b81b990afac9
diff --git a/tests/modules/fargene/main.nf b/tests/modules/fargene/main.nf
deleted file mode 100644
index 471862e17e0..00000000000
--- a/tests/modules/fargene/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP } from '../../../modules/gunzip/main.nf'
-include { FARGENE } from '../../../modules/fargene/main.nf'
-
-workflow test_fargene {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) ]
-    hmm_model = 'class_a'
-
-    GUNZIP ( input )
-    FARGENE ( GUNZIP.out.gunzip, hmm_model )
-}
diff --git a/tests/modules/fargene/test.yml b/tests/modules/fargene/test.yml
deleted file mode 100644
index 3ca94bc0715..00000000000
--- a/tests/modules/fargene/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: fargene
-  command: nextflow run ./tests/modules/fargene -entry test_fargene -c ./tests/config/nextflow.config -c ./tests/modules/fargene/nextflow.config
-  tags:
-    - fargene
-  files:
-    - path: output/fargene/fargene_analysis.log
-    - path: output/fargene/test/hmmsearchresults/test1.contigs-class_A-hmmsearched.out
-    - path: output/fargene/test/results_summary.txt
-      md5sum: 690d351cfc52577263ef4cfab1c81f50
-    - path: output/fargene/test/tmpdir/test1.contigs-positives.out
-    - path: output/fargene/test/tmpdir/tmp.out
-    - path: output/gunzip/test1.contigs.fa
-      md5sum: 80c4d78f2810f6d9e90fa6da9bb9c4f9
diff --git a/tests/modules/fastani/main.nf b/tests/modules/fastani/main.nf
deleted file mode 100644
index 0395f6a9b94..00000000000
--- a/tests/modules/fastani/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTANI } from '../../../modules/fastani/main.nf'
-
-workflow test_fastani {
-
-    query = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    reference = file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
-
-    FASTANI ( [[ id:'test' ], query], reference )
-}
diff --git a/tests/modules/fastani/test.yml b/tests/modules/fastani/test.yml
deleted file mode 100644
index f3748d2548c..00000000000
--- a/tests/modules/fastani/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: fastani
-  command: nextflow run ./tests/modules/fastani -entry test_fastani -c ./tests/config/nextflow.config -c ./tests/modules/fastani/nextflow.config
-  tags:
-    - fastani
-  files:
-    - path: output/fastani/test.ani.txt
-      md5sum: 31d4f04e8cffe13080c86db3f9f3a589
diff --git a/tests/modules/fastawindows/main.nf b/tests/modules/fastawindows/main.nf
deleted file mode 100644
index 28d367d98bc..00000000000
--- a/tests/modules/fastawindows/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTAWINDOWS } from '../../../modules/fastawindows/main.nf'
-
-workflow test_fastawindows {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    FASTAWINDOWS ( input )
-}
diff --git a/tests/modules/fastawindows/test.yml b/tests/modules/fastawindows/test.yml
deleted file mode 100644
index 5cdd0e2c250..00000000000
--- a/tests/modules/fastawindows/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: fastawindows test_fastawindows
-  command: nextflow run ./tests/modules/fastawindows -entry test_fastawindows -c ./tests/config/nextflow.config  -c ./tests/modules/fastawindows/nextflow.config
-  tags:
-    - fastawindows
-  files:
-    - path: output/fastawindows/fw_out/test_freq_windows.tsv
-      md5sum: 237d50ac5ec2bef3142020d569fa5765
-    - path: output/fastawindows/fw_out/test_mononuc_windows.tsv
-      md5sum: a1b4437d0c71d9cfd676de6bda2633f0
-    - path: output/fastawindows/fw_out/test_dinuc_windows.tsv
-      md5sum: 696a9f2a4b2114dfbd6b414694f56a11
-    - path: output/fastawindows/fw_out/test_trinuc_windows.tsv
-      md5sum: dfb05b758f0474e937e2d6ba6fe46dae
-    - path: output/fastawindows/fw_out/test_tetranuc_windows.tsv
-      md5sum: e621537175ee8019360f8b6e8f4330b7
diff --git a/tests/modules/fastk/fastk/main.nf b/tests/modules/fastk/fastk/main.nf
deleted file mode 100644
index 944d434f415..00000000000
--- a/tests/modules/fastk/fastk/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf'
-
-workflow test_fastk_fastk_single_end {
-
-    input = [
-        [ id:'test' , single_end: true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-}
-
-workflow test_fastk_fastk_paired_end {
-
-    input = [
-        [ id:'test' , single_end: false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FASTK_FASTK ( input )
-}
diff --git a/tests/modules/fastk/fastk/test.yml b/tests/modules/fastk/fastk/test.yml
deleted file mode 100644
index fd3fdebef48..00000000000
--- a/tests/modules/fastk/fastk/test.yml
+++ /dev/null
@@ -1,45 +0,0 @@
-- name: fastk fastk test_fastk_fastk_single_end
-  command: nextflow run ./tests/modules/fastk/fastk -entry test_fastk_fastk_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/fastk/fastk/nextflow.config
-  tags:
-    - fastk
-    - fastk/fastk
-  files:
-    - path: output/fastk/.test_fk.ktab.1
-      md5sum: ceeacd0cb3aa69bf9b2a402830b40e26
-    - path: output/fastk/.test_fk.ktab.2
-      md5sum: f2629fd15b285aed3dc2d5fe546edf3f
-    - path: output/fastk/.test_fk.pidx.1
-      md5sum: 90bc384f61d2ecdb4586ab52ab04fddf
-    - path: output/fastk/.test_fk.prof.1
-      md5sum: ebd48923a724cf79934f0b2ed42ba73d
-    - path: output/fastk/test_fk.hist
-      md5sum: c80e12f7321e62dba4b437d7bff36ec0
-    - path: output/fastk/test_fk.ktab
-      md5sum: a605a58931a4b5029469e1c2575c8cee
-    - path: output/fastk/test_fk.prof
-      md5sum: 43d426c95d277b8148406624d513bd40
-
-- name: fastk fastk test_fastk_fastk_paired_end
-  command: nextflow run ./tests/modules/fastk/fastk -entry test_fastk_fastk_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/fastk/fastk/nextflow.config
-  tags:
-    - fastk
-    - fastk/fastk
-  files:
-    - path: output/fastk/.test_fk.ktab.1
-      md5sum: 7f28fb44940fda799797e3069f5d7263
-    - path: output/fastk/.test_fk.ktab.2
-      md5sum: c14a85c128926ace78372f09029977b1
-    - path: output/fastk/.test_fk.pidx.1
-      md5sum: e7e760f714070a4afefb38ffff559684
-    - path: output/fastk/.test_fk.pidx.2
-      md5sum: a549612bbdba2506eb3311237638c4b0
-    - path: output/fastk/.test_fk.prof.1
-      md5sum: 46a5fd9e297262b058f8c1fd062fcf56
-    - path: output/fastk/.test_fk.prof.2
-      md5sum: 80326a7406f41ccf2e51e341fc804132
-    - path: output/fastk/test_fk.hist
-      md5sum: 4f75b550d87ed4f26a2b10a05ac7e98c
-    - path: output/fastk/test_fk.ktab
-      md5sum: fddd5be0c36ad1d2131b8d8774f7657a
-    - path: output/fastk/test_fk.prof
-      md5sum: d3c7d8decd4ea6e298291b8be0e2de85
diff --git a/tests/modules/fastk/histex/main.nf b/tests/modules/fastk/histex/main.nf
deleted file mode 100644
index 74b46378181..00000000000
--- a/tests/modules/fastk/histex/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf'
-include { FASTK_HISTEX } from '../../../../modules/fastk/histex/main.nf'
-
-workflow test_fastk_histex {
-
-    input = [
-        [ id:'test' , single_end: true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-    FASTK_HISTEX ( FASTK_FASTK.out.hist )
-}
diff --git a/tests/modules/fastk/histex/test.yml b/tests/modules/fastk/histex/test.yml
deleted file mode 100644
index 8348af8fbf9..00000000000
--- a/tests/modules/fastk/histex/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: fastk histex test_fastk_histex
-  command: nextflow run ./tests/modules/fastk/histex -entry test_fastk_histex -c ./tests/config/nextflow.config  -c ./tests/modules/fastk/histex/nextflow.config
-  tags:
-    - fastk/histex
-    - fastk
-  files:
-    - path: output/fastk/test.hist
-      md5sum: e3f0c9e7641a46525123312008e4ae86
diff --git a/tests/modules/fastk/merge/main.nf b/tests/modules/fastk/merge/main.nf
deleted file mode 100644
index 1bed019e4fc..00000000000
--- a/tests/modules/fastk/merge/main.nf
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf'
-include { FASTK_MERGE } from '../../../../modules/fastk/merge/main.nf'
-
-workflow test_fastk_merge_hist_only {
-
-    input1 = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    input2= [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FASTK_FASTK ( Channel.of( input1, input2 ) )
-    FASTK_MERGE (
-        FASTK_FASTK.out.hist.groupTuple()
-            .join( FASTK_FASTK.out.ktab.groupTuple(), remainder: true )
-            .join( FASTK_FASTK.out.prof.groupTuple(), remainder: true )
-            .map { meta, hist, ktab, prof -> [meta, hist, ktab ? ktab.flatten() : [] , prof ? prof.flatten() : [] ] }
-    )
-}
-
-workflow test_fastk_merge_all_files {
-
-    input1 = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    input2= [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FASTK_FASTK ( Channel.of( input1, input2 ) )
-    FASTK_MERGE (
-        FASTK_FASTK.out.hist.groupTuple()
-            .join( FASTK_FASTK.out.ktab.groupTuple(), remainder: true )
-            .join( FASTK_FASTK.out.prof.groupTuple(), remainder: true )
-            .map { meta, hist, ktab, prof -> [meta, hist, ktab ? ktab.flatten() : [] , prof ? prof.flatten() : [] ] }
-    )
-}
diff --git a/tests/modules/fastk/merge/test.yml b/tests/modules/fastk/merge/test.yml
deleted file mode 100644
index 2c3fba2e72b..00000000000
--- a/tests/modules/fastk/merge/test.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-- name: fastk merge test_fastk_merge_hist_only
-  command: nextflow run ./tests/modules/fastk/merge -entry test_fastk_merge_hist_only -c ./tests/config/nextflow.config  -c ./tests/modules/fastk/merge/nextflow.config
-  tags:
-    - fastk/merge
-    - fastk
-  files:
-    - path: output/fastk/.test.ktab.1
-      md5sum: dff1e9d326aea87778645235cfa3380f
-    - path: output/fastk/.test.ktab.2
-      md5sum: 438e7807dcc2eb8120e1338838147600
-    - path: output/fastk/test.hist
-      md5sum: 75d41eb0e3f8af5456711a95966e2b00
-    - path: output/fastk/test.ktab
-      md5sum: 7d882f4e3542df1a2f5cb0858b12dc03
-
-- name: fastk merge test_fastk_merge_all_files
-  command: nextflow run ./tests/modules/fastk/merge -entry test_fastk_merge_all_files -c ./tests/config/nextflow.config  -c ./tests/modules/fastk/merge/nextflow.config
-  tags:
-    - fastk/merge
-    - fastk
-  files:
-    - path: output/fastk/.test.ktab.1
-      md5sum: dff1e9d326aea87778645235cfa3380f
-    - path: output/fastk/.test.ktab.2
-      md5sum: 438e7807dcc2eb8120e1338838147600
-    - path: output/fastk/.test.pidx.1
-      md5sum: 7553344778f6571192f04c7e659b967c
-    - path: output/fastk/.test.pidx.2
-      md5sum: 09bb65fb10db58d1fd5bb0a123fccfc6
-    - path: output/fastk/.test.prof.1
-      md5sum: 7f0f84a62c89063ec18c9b0e447afe93
-    - path: output/fastk/.test.prof.2
-      md5sum: 7f0f84a62c89063ec18c9b0e447afe93
-    - path: output/fastk/test.hist
-      md5sum: 75d41eb0e3f8af5456711a95966e2b00
-    - path: output/fastk/test.ktab
-      md5sum: 7d882f4e3542df1a2f5cb0858b12dc03
-    - path: output/fastk/test.prof
-      md5sum: d3c7d8decd4ea6e298291b8be0e2de85
diff --git a/tests/modules/fastp/main.nf b/tests/modules/fastp/main.nf
deleted file mode 100644
index 5073673a160..00000000000
--- a/tests/modules/fastp/main.nf
+++ /dev/null
@@ -1,86 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTP } from '../../../modules/fastp/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_fastp_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    save_trimmed_fail = false
-    save_merged       = false
-
-    FASTP ( input, save_trimmed_fail, save_merged )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_fastp_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    save_trimmed_fail = false
-    save_merged       = false
-
-    FASTP ( input, save_trimmed_fail, save_merged )
-}
-
-//
-// Test with intereleaved data
-//
-workflow test_fastp_interleaved {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ]
-            ]
-    save_trimmed_fail = false
-    save_merged       = false
-
-    FASTP ( input, save_trimmed_fail, save_merged )
-}
-
-//
-// Test with single-end data with saving trimming fails
-//
-workflow test_fastp_single_end_trim_fail {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    save_trimmed_fail = true
-    save_merged       = false
-
-    FASTP ( input, save_trimmed_fail, save_merged )
-}
-
-//
-// Test with paired-end data with saving trimming fails
-//
-workflow test_fastp_paired_end_trim_fail {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    save_trimmed_fail = true
-    save_merged       = false
-
-    FASTP ( input, save_trimmed_fail, save_merged )
-}
-
-//
-// Test with paired-end data with merging
-//
-workflow test_fastp_paired_end_merged {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    save_trimmed_fail = false
-    save_merged       = true
-
-    FASTP ( input, save_trimmed_fail, save_merged )
-}
diff --git a/tests/modules/fastp/test.yml b/tests/modules/fastp/test.yml
deleted file mode 100644
index d64b5506a2f..00000000000
--- a/tests/modules/fastp/test.yml
+++ /dev/null
@@ -1,191 +0,0 @@
-- name: fastp test_fastp_single_end
-  command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/fastp/nextflow.config
-  tags:
-    - fastp
-  files:
-    - path: output/fastp/test.fastp.fastq.gz
-      contains:
-        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
-        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
-        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
-        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
-        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
-        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
-    - path: output/fastp/test.fastp.html
-      contains:
-        - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
-        - "single end (151 cycles)"
-    - path: output/fastp/test.fastp.json
-      md5sum: 2616b6791fd89fb1cc2d16a73b9463b0
-    - path: output/fastp/test.fastp.log
-      contains:
-        - "Q20 bases: 12922(92.9841%)"
-        - "reads passed filter: 99"
-
-- name: fastp test_fastp_paired_end
-  command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/fastp/nextflow.config
-  tags:
-    - fastp
-  files:
-    - path: output/fastp/test.fastp.html
-      contains:
-        - "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
-        - "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
-    - path: output/fastp/test.fastp.json
-      contains:
-        - '"passed_filter_reads": 198'
-    - path: output/fastp/test.fastp.log
-      contains:
-        - "No adapter detected for read1"
-        - "Q30 bases: 12281(88.3716%)"
-    - path: output/fastp/test_1.fastp.fastq.gz
-      contains:
-        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
-        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
-        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
-        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
-        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
-        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
-    - path: output/fastp/test_2.fastp.fastq.gz
-      contains:
-        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
-        - "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
-        - "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
-        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/2"
-        - "GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT"
-        - "AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE"
-
-- name: fastp test_fastp_interleaved
-  command: nextflow run ./tests/modules/fastp -entry test_fastp_interleaved -c ./tests/config/nextflow.config  -c ./tests/modules/fastp/nextflow.config
-  tags:
-    - fastp
-  files:
-    - path: output/fastp/test.fastp.fastq.gz
-      contains:
-        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
-        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
-        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
-        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
-        - "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
-        - "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
-    - path: output/fastp/test.fastp.html
-      contains:
-        - "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
-        - "paired end (151 cycles + 151 cycles)"
-    - path: output/fastp/test.fastp.json
-      md5sum: 25ec85e3534f380ca2109c894671f1ed
-    - path: output/fastp/test.fastp.log
-      contains:
-        - "Q20 bases: 12922(92.9841%)"
-        - "reads passed filter: 198"
-
-- name: fastp test_fastp_single_end_trim_fail
-  command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config  -c ./tests/modules/fastp/nextflow.config
-  tags:
-    - fastp
-  files:
-    - path: output/fastp/test.fail.fastq.gz
-      contains:
-        - "@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/1 failed_quality_filter"
-        - "GTCTAATCATAATTTCTTGGTACAGGCTGGTATTGTTCATCTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTT"
-        - "AAA//E/EAA/E//E//E//E/E//AE/A/E//EAEA///AE//E///E/EEE6EEEAEEA///E/AEE/EAEE/E//E"
-    - path: output/fastp/test.fastp.fastq.gz
-      contains:
-        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
-        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
-        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
-        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
-        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
-        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
-    - path: output/fastp/test.fastp.html
-      contains:
-        - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
-        - "single end (151 cycles)"
-    - path: output/fastp/test.fastp.json
-      md5sum: 7e10b0b12fab5cff620fdeb1a32392f8
-    - path: output/fastp/test.fastp.log
-      contains:
-        - "Q20 bases: 12922(92.9841%)"
-        - "reads passed filter: 99"
-
-- name: fastp test_fastp_paired_end_trim_fail
-  command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config  -c ./tests/modules/fastp/nextflow.config
-  tags:
-    - fastp
-  files:
-    - path: output/fastp/test.fastp.html
-      contains:
-        - "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
-        - "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
-    - path: output/fastp/test.fastp.log
-      contains:
-        - "No adapter detected for read1"
-        - "Q30 bases: 12281(88.3716%)"
-    - path: output/fastp/test.fastp.json
-      contains:
-        - '"passed_filter_reads": 198'
-    - path: output/fastp/test_1.fastp.fastq.gz
-      contains:
-        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
-        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
-        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
-        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
-        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
-        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
-    - path: output/fastp/test_2.fastp.fastq.gz
-      contains:
-        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
-        - "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
-        - "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
-        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/2"
-        - "GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT"
-        - "AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE"
-    - path: output/fastp/test_1.fail.fastq.gz
-    - path: output/fastp/test_2.fail.fastq.gz
-      contains:
-        - "@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/2"
-        - "CTTAGGTCTTAGGATTGGCTGTATCAACCTTAAGCTTAAGTACACAATTTTGCATAGAATGTCCAATAA"
-        - "A//AA6EEAEEEEE6EEE/EEA/EA///AAE/EAEEEAE6AE/E/E/EEAAE/EAA/E/E/<EA//E/6"
-
-- name: fastp test_fastp_paired_end_merged
-  command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config  -c ./tests/modules/fastp/nextflow.config
-  tags:
-    - fastp
-  files:
-    - path: output/fastp/test.fastp.html
-      contains:
-        - "<div id='After_filtering__merged__quality'>"
-    - path: output/fastp/test.fastp.json
-      contains:
-        - '"merged_and_filtered": {'
-        - '"total_reads": 75'
-        - '"total_bases": 13683'
-    - path: output/fastp/test.fastp.log
-      contains:
-        - "Merged and filtered:"
-        - "total reads: 75"
-        - "total bases: 13683"
-    - path: output/fastp/test_1.fastp.fastq.gz
-      contains:
-        - "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1"
-        - "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC"
-        - "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE<AEEAEEEAEAEEEAEAEEAE/AEEEEAEEEEAEA"
-        - "@ERR5069949.324865 NS500628:121:HK3MMAFX2:1:11102:17526:14721/1"
-        - "CACAAACTCTAAAAGAATGTATAGGGTCAGCACCAAAAATACCAGCAGATAATAATGTTGCAAGTAGAACTTCGTGCAGATTAAAATTTTCATAAGCACTCTAAAGAAGTTGAATGTCTTCAAATTTCTTAACATTAGGGCCCACAACAAG"
-        - "AAAAAEA/A<EAA/AE/EE/EE//////EA/EEE/E/EEEE//E/6//EA//<AA/A/EEEAA/EEEE/EEEA/E/</AEE////AEEEE//<E//EAE/A///<EEE//<E<<EEE<///A//E/E/EEEAA/<A////<A/AEAAA//E"
-    - path: output/fastp/test_2.fastp.fastq.gz
-      contains:
-        - "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/2"
-        - "GTACAAAAATAGCCTAAGAAACAATAAACTAGCATTATACACTGAAGTGTATTACCAGTTATGAAGAAAATAGGGCAATACTCAACACACATAAAAACAATACCTCTGGCCAAAAACATGACAGTTGTAACTACACCTGAGTAGTTAGAAG"
-        - "AAAAAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEA/EAA</EEEEEEEEEE/AE//A/E<AE<AA<AEEE/AAEAAAEEAEEA<A6AEEA<EEAEEEEEEEAA//EE"
-        - "@ERR5069949.324865 NS500628:121:HK3MMAFX2:1:11102:17526:14721/2"
-        - "ATGAATCTGATGAATACATAGCTACTAATGGACCTCTTAAAGTGCGTGGTAGTTGTGATTAAAGCGGACACATACTTGCTAAACACTCTCTTCATGATGTC"
-        - "A/AAAEEEEA6AA6EE//EEA/EEEAE/EA/A////E</EEAA//EEA////EAE<///E/AEA</AAE/EA//E<EAAAE/AA//AEE//A/AE//</EE"
-    - path: output/fastp/test.merged.fastq.gz
-      contains:
-        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1 merged_150_37"
-        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGTGGTGCAGGTAATTGAGCAGGGTCGCCAATGTACACAT"
-        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAAEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEAAAAA"
-        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1 merged_77_0"
-        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
-        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
diff --git a/tests/modules/fastqc/main.nf b/tests/modules/fastqc/main.nf
deleted file mode 100644
index f7db9b7cc41..00000000000
--- a/tests/modules/fastqc/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTQC } from '../../../modules/fastqc/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_fastqc_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    FASTQC ( input )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_fastqc_paired_end {
-    input = [ [id: 'test', single_end: false], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    FASTQC ( input )
-}
diff --git a/tests/modules/fastqc/test.yml b/tests/modules/fastqc/test.yml
deleted file mode 100644
index fa830cbc0fa..00000000000
--- a/tests/modules/fastqc/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: fastqc single-end
-  command: nextflow run ./tests/modules/fastqc/ -entry test_fastqc_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastqc/nextflow.config -c ./tests/modules/fastqc/nextflow.config
-  tags:
-    - fastqc
-  files:
-    - path: ./output/fastqc/test_fastqc.html
-    - path: ./output/fastqc/test_fastqc.zip
-
-- name: fastqc paired-end
-  command: nextflow run ./tests/modules/fastqc/ -entry test_fastqc_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastqc/nextflow.config -c ./tests/modules/fastqc/nextflow.config
-  tags:
-    - fastqc
-  files:
-    - path: ./output/fastqc/test_1_fastqc.html
-    - path: ./output/fastqc/test_2_fastqc.html
-    - path: ./output/fastqc/test_2_fastqc.zip
-    - path: ./output/fastqc/test_1_fastqc.zip
diff --git a/tests/modules/fastqscan/main.nf b/tests/modules/fastqscan/main.nf
deleted file mode 100644
index b9a321fe4b0..00000000000
--- a/tests/modules/fastqscan/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTQSCAN } from '../../../modules/fastqscan/main.nf'
-
-workflow test_fastqscan {
-    
-    input = [ [ id:'test', single_end:true ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-
-    FASTQSCAN ( input )
-}
diff --git a/tests/modules/fastqscan/test.yml b/tests/modules/fastqscan/test.yml
deleted file mode 100644
index d538804c4dd..00000000000
--- a/tests/modules/fastqscan/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: fastqscan test_fastqscan
-  command: nextflow run ./tests/modules/fastqscan -entry test_fastqscan -c ./tests/config/nextflow.config -c ./tests/modules/fastqscan/nextflow.config
-  tags:
-    - fastqscan
-  files:
-    - path: output/fastqscan/test.json
-      md5sum: b9d59a36fe85e556b5a80573ea0b0266
diff --git a/tests/modules/fasttree/main.nf b/tests/modules/fasttree/main.nf
deleted file mode 100644
index e33228a90a8..00000000000
--- a/tests/modules/fasttree/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTTREE } from '../../../modules/fasttree/main.nf'
-
-workflow test_fasttree {
-    
-    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
-
-    FASTTREE ( input )
-}
diff --git a/tests/modules/fasttree/test.yml b/tests/modules/fasttree/test.yml
deleted file mode 100644
index 7e344cffe76..00000000000
--- a/tests/modules/fasttree/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: fasttree
-  command: nextflow run ./tests/modules/fasttree -entry test_fasttree -c ./tests/config/nextflow.config -c ./tests/modules/fasttree/nextflow.config
-  tags:
-    - fasttree
-  files:
-    - path: output/fasttree/fasttree_phylogeny.tre
-      md5sum: 63a886117535847c1e66fa4487f3b7d2
diff --git a/tests/modules/fcs/fcsadaptor/main.nf b/tests/modules/fcs/fcsadaptor/main.nf
deleted file mode 100644
index f86dd4301dc..00000000000
--- a/tests/modules/fcs/fcsadaptor/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FCS_FCSADAPTOR } from '../../../../modules/fcs/fcsadaptor/main.nf'
-
-workflow test_fcs_fcsadaptor {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
-    ]
-
-    FCS_FCSADAPTOR ( input )
-}
diff --git a/tests/modules/fcs/fcsadaptor/test.yml b/tests/modules/fcs/fcsadaptor/test.yml
deleted file mode 100644
index 85d931a9d36..00000000000
--- a/tests/modules/fcs/fcsadaptor/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: fcs fcsadaptor test_fcs_fcsadaptor
-  command: nextflow run ./tests/modules/fcs/fcsadaptor -entry test_fcs_fcsadaptor -c ./tests/config/nextflow.config  -c ./tests/modules/fcs/fcsadaptor/nextflow.config
-  tags:
-    - fcs/fcsadaptor
-    - fcs
-  files:
-    - path: output/fcs/test.cleaned_sequences.fa.gz
-      md5sum: 2f331e59b352418420a35236091bf93c
-    - path: output/fcs/test.fcs_adaptor.log
-      contains: ["Original command:", "Executing:", "INFO:cwltool:[workflow ] completed success"]
-    - path: output/fcs/test.fcs_adaptor_report.txt
-      md5sum: 27375be4671e01d2d2674ddd1d44414a
-    - path: output/fcs/test.pipeline_args.yaml
-      md5sum: 80effed2a75550a6a861c47f4c30449d
-    - path: output/fcs/test.skipped_trims.jsonl
diff --git a/tests/modules/ffq/main.nf b/tests/modules/ffq/main.nf
deleted file mode 100644
index 271e9afb201..00000000000
--- a/tests/modules/ffq/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FFQ } from '../../../modules/ffq/main.nf'
-
-workflow test_ffq_single_id {
-
-    FFQ ( [ 'SRR9990627' ] )
-}
-
-workflow test_ffq_multiple_ids {
-
-    FFQ ( [ 'SRR9990627', 'SRX7347523' ] )
-}
diff --git a/tests/modules/ffq/test.yml b/tests/modules/ffq/test.yml
deleted file mode 100644
index af85a370a9e..00000000000
--- a/tests/modules/ffq/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: ffq test_ffq_single_id
-  command: nextflow run ./tests/modules/ffq -entry test_ffq_single_id -c ./tests/config/nextflow.config  -c ./tests/modules/ffq/nextflow.config
-  tags:
-    - ffq
-  files:
-    - path: output/ffq/SRR9990627.json
-      md5sum: 68db6114ef348f721c139cd4c9534f73
-
-- name: ffq test_ffq_multiple_ids
-  command: nextflow run ./tests/modules/ffq -entry test_ffq_multiple_ids -c ./tests/config/nextflow.config  -c ./tests/modules/ffq/nextflow.config
-  tags:
-    - ffq
-  files:
-    - path: output/ffq/metadata.json
-      md5sum: af253a5587b54520f01a0ff5715b0c0a
diff --git a/tests/modules/fgbio/callmolecularconsensusreads/main.nf b/tests/modules/fgbio/callmolecularconsensusreads/main.nf
deleted file mode 100644
index e31fdf39761..00000000000
--- a/tests/modules/fgbio/callmolecularconsensusreads/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FGBIO_SORTBAM } from '../../../../modules/fgbio/sortbam/main.nf'
-include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../modules/fgbio/callmolecularconsensusreads/main.nf'
-
-workflow test_fgbio_callmolecularconsensusreads {
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
-    FGBIO_SORTBAM ( input )
-    FGBIO_CALLMOLECULARCONSENSUSREADS ( FGBIO_SORTBAM.out.bam  )
-}
diff --git a/tests/modules/fgbio/callmolecularconsensusreads/test.yml b/tests/modules/fgbio/callmolecularconsensusreads/test.yml
deleted file mode 100644
index 61ddb3824e2..00000000000
--- a/tests/modules/fgbio/callmolecularconsensusreads/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: fgbio callmolecularconsensusreads
-  command: nextflow run ./tests/modules/fgbio/callmolecularconsensusreads -entry test_fgbio_callmolecularconsensusreads -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/callmolecularconsensusreads/nextflow.config
-  tags:
-    - fgbio
-    - fgbio/callmolecularconsensusreads
-  files:
-    - path: output/fgbio/test_molreads.bam
-      md5sum: 6ae57429e3218f5eba9555d597b7c60f
-    - path: output/fgbio/test_out.bam
-      md5sum: d84e28fecc90c0752c543e934f10aa31
diff --git a/tests/modules/fgbio/fastqtobam/main.nf b/tests/modules/fgbio/fastqtobam/main.nf
deleted file mode 100644
index 794e66aafcd..00000000000
--- a/tests/modules/fgbio/fastqtobam/main.nf
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FGBIO_FASTQTOBAM } from '../../../../modules/fgbio/fastqtobam/main.nf'
-
-workflow test_fgbio_fastqtobam_paired_default {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FGBIO_FASTQTOBAM ( input )
-}
-
-
-workflow test_fgbio_fastqtobam_paired_cram {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FGBIO_FASTQTOBAM ( input )
-}
-
-workflow test_fgbio_fastqtobam_paired_bam {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FGBIO_FASTQTOBAM ( input )
-}
-
-workflow test_fgbio_fastqtobam_single {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
-        ]
-    ]
-
-    FGBIO_FASTQTOBAM ( input )
-}
-
-workflow test_fgbio_fastqtobam_paired_umi {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FGBIO_FASTQTOBAM ( input )
-}
-
-workflow test_fgbio_fastqtobam_paired_custom_samplename {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FGBIO_FASTQTOBAM ( input )
-}
diff --git a/tests/modules/fgbio/fastqtobam/test.yml b/tests/modules/fgbio/fastqtobam/test.yml
deleted file mode 100644
index d0ba9b5b19d..00000000000
--- a/tests/modules/fgbio/fastqtobam/test.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_default
-  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_default -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
-  tags:
-    - fgbio
-    - fgbio/fastqtobam
-  files:
-    - path: output/fgbio/test.bam
-      md5sum: 83cd60e01e5ab90ea3729431ce401add
-
-- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_cram
-  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_cram -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
-  tags:
-    - fgbio
-    - fgbio/fastqtobam
-  files:
-    - path: output/fgbio/test.cram
-
-- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_bam
-  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_bam -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
-  tags:
-    - fgbio
-    - fgbio/fastqtobam
-  files:
-    - path: output/fgbio/test.bam
-      md5sum: 83f879e3a302ca8a50dc9675be7a9216
-
-- name: fgbio fastqtobam test_fgbio_fastqtobam_single
-  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_single -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
-  tags:
-    - fgbio
-    - fgbio/fastqtobam
-  files:
-    - path: output/fgbio/test.bam
-      md5sum: c08fe1b035b972808f05128e37e8e669
-
-- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_umi
-  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_umi -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
-  tags:
-    - fgbio
-    - fgbio/fastqtobam
-  files:
-    - path: output/fgbio/test.bam
-      md5sum: 9510735554e5eff29244077a72075fb6
-
-- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_custom_samplename
-  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_custom_samplename -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
-  tags:
-    - fgbio
-    - fgbio/fastqtobam
-  files:
-    - path: output/fgbio/test.bam
-      md5sum: ab8d7d2d9c1559b19a501d120296ebe0
diff --git a/tests/modules/fgbio/groupreadsbyumi/main.nf b/tests/modules/fgbio/groupreadsbyumi/main.nf
deleted file mode 100644
index b9bb350aa49..00000000000
--- a/tests/modules/fgbio/groupreadsbyumi/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FGBIO_GROUPREADSBYUMI } from '../../../../modules/fgbio/groupreadsbyumi/main.nf'
-
-workflow test_fgbio_groupreadsbyumi {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_unsorted_tagged_bam'], checkIfExists: true)
-    ]
-
-    FGBIO_GROUPREADSBYUMI ( input, 'Adjacency' )
-}
diff --git a/tests/modules/fgbio/groupreadsbyumi/test.yml b/tests/modules/fgbio/groupreadsbyumi/test.yml
deleted file mode 100644
index 529a07e55d7..00000000000
--- a/tests/modules/fgbio/groupreadsbyumi/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: fgbio groupreadsbyumi test_fgbio_groupreadsbyumi
-  command: nextflow run ./tests/modules/fgbio/groupreadsbyumi -entry test_fgbio_groupreadsbyumi -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/groupreadsbyumi/nextflow.config
-  tags:
-    - fgbio
-    - fgbio/groupreadsbyumi
-  files:
-    - path: output/fgbio/test_umi-grouped.bam
-      md5sum: c7a9aee0b9b277c85d6a112d3021082d
-    - path: output/fgbio/test_umi_histogram.txt
-      md5sum: f2f29523bb7016e1a78fe634466cbfba
diff --git a/tests/modules/fgbio/sortbam/main.nf b/tests/modules/fgbio/sortbam/main.nf
deleted file mode 100644
index ada99d0f1da..00000000000
--- a/tests/modules/fgbio/sortbam/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FGBIO_SORTBAM } from '../../../../modules/fgbio/sortbam/main.nf'
-
-workflow test_fgbio_sortbam {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    FGBIO_SORTBAM ( input )
-}
diff --git a/tests/modules/fgbio/sortbam/test.yml b/tests/modules/fgbio/sortbam/test.yml
deleted file mode 100644
index 6789aed82c6..00000000000
--- a/tests/modules/fgbio/sortbam/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: fgbio sortbam
-  command: nextflow run ./tests/modules/fgbio/sortbam -entry test_fgbio_sortbam -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/sortbam/nextflow.config
-  tags:
-    - fgbio
-    - fgbio/sortbam
-  files:
-    - path: output/fgbio/test.bam
-      md5sum: 56987f74214cdc72ae840e0007ff4935
diff --git a/tests/modules/filtlong/main.nf b/tests/modules/filtlong/main.nf
deleted file mode 100644
index df7892aa04f..00000000000
--- a/tests/modules/filtlong/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FILTLONG } from '../../../modules/filtlong/main.nf'
-
-workflow test_filtlong {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              [],
-              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    FILTLONG ( input )
-}
-
-workflow test_filtlong_illumina_se {
-    
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    FILTLONG ( input )
-}
-
-workflow test_filtlong_illumina_pe {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    FILTLONG ( input )
-}
diff --git a/tests/modules/filtlong/test.yml b/tests/modules/filtlong/test.yml
deleted file mode 100644
index a4102a34acc..00000000000
--- a/tests/modules/filtlong/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: filtlong test_filtlong
-  command: nextflow run ./tests/modules/filtlong -entry test_filtlong -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
-  tags:
-    - filtlong
-  files:
-    - path: output/filtlong/test_lr.fastq.gz
-    - path: output/filtlong/test_lr.log
-      contains: ["Scoring long reads"]
-
-- name: filtlong test_filtlong_illumina_se
-  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
-  tags:
-    - filtlong
-  files:
-    - path: output/filtlong/test_lr.fastq.gz
-    - path: output/filtlong/test_lr.log
-      contains: ["Scoring long reads"]
-
-- name: filtlong test_filtlong_illumina_pe
-  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
-  tags:
-    - filtlong
-  files:
-    - path: output/filtlong/test_lr.fastq.gz
-    - path: output/filtlong/test_lr.log
-      contains: ["Scoring long reads"]
diff --git a/tests/modules/flash/main.nf b/tests/modules/flash/main.nf
deleted file mode 100644
index 4afcb8fcb24..00000000000
--- a/tests/modules/flash/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FLASH } from '../../../modules/flash/main.nf'
-
-workflow test_flash {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    FLASH ( input )
-}
diff --git a/tests/modules/flash/test.yml b/tests/modules/flash/test.yml
deleted file mode 100644
index e5ed49caf06..00000000000
--- a/tests/modules/flash/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: flash test_flash
-  command: nextflow run ./tests/modules/flash -entry test_flash -c ./tests/config/nextflow.config -c ./tests/modules/flash/nextflow.config
-  tags:
-    - flash
-  files:
-    - path: output/flash/test.notCombined_2.fastq.gz
-    - path: output/flash/test.extendedFrags.fastq.gz
-    - path: output/flash/test.notCombined_1.fastq.gz
diff --git a/tests/modules/flye/main.nf b/tests/modules/flye/main.nf
deleted file mode 100644
index c078c4da52e..00000000000
--- a/tests/modules/flye/main.nf
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FLYE } from '../../../modules/flye/main.nf'
-
-workflow test_flye_pacbio_raw {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
-    ]
-    mode = "--pacbio-raw"
-
-    FLYE ( input, mode )
-}
-
-workflow test_flye_pacbio_corr {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
-    ]
-    mode = "--pacbio-corr"
-
-    FLYE ( input, mode )
-}
-
-workflow test_flye_pacbio_hifi {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
-    ]
-    mode = "--pacbio-hifi"
-
-    FLYE ( input, mode )
-}
-
-workflow test_flye_nano_raw {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
-    ]
-    mode = "--nano-raw"
-
-    FLYE ( input, mode )
-}
-
-workflow test_flye_nano_corr {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
-    ]
-    mode = "--nano-corr"
-
-    FLYE ( input, mode )
-}
-
-workflow test_flye_nano_hq {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
-    ]
-    mode = "--nano-hq"
-
-    FLYE ( input, mode )
-}
diff --git a/tests/modules/flye/test.yml b/tests/modules/flye/test.yml
deleted file mode 100644
index 0c0f87662fb..00000000000
--- a/tests/modules/flye/test.yml
+++ /dev/null
@@ -1,85 +0,0 @@
-# According to the issue https://github.com/fenderglass/Flye/issues/164
-# Some fluctuations are expected because of the heuristics
-# Here we check the that test.assembly_info.txt contains at least one contig
-
-- name: flye test_flye_pacbio_raw
-  command: nextflow run ./tests/modules/flye -entry test_flye_pacbio_raw -c ./tests/config/nextflow.config  -c ./tests/modules/flye/nextflow.config -stub-run
-  tags:
-    - flye
-  files:
-    - path: output/flye/test.assembly.fasta.gz
-    - path: output/flye/test.assembly_graph.gfa.gz
-    - path: output/flye/test.assembly_graph.gv.gz
-    - path: output/flye/test.assembly_info.txt
-      contains: ["contig_1"]
-    - path: output/flye/test.flye.log
-    - path: output/flye/test.params.json
-
-- name: flye test_flye_pacbio_corr
-  command: nextflow run ./tests/modules/flye -entry test_flye_pacbio_corr -c ./tests/config/nextflow.config  -c ./tests/modules/flye/nextflow.config
-  tags:
-    - flye
-  files:
-    - path: output/flye/test.assembly.fasta.gz
-    - path: output/flye/test.assembly_graph.gfa.gz
-    - path: output/flye/test.assembly_graph.gv.gz
-    - path: output/flye/test.assembly_info.txt
-      contains: ["contig_1"]
-    - path: output/flye/test.flye.log
-    - path: output/flye/test.params.json
-      md5sum: 54b576cb6d4d27656878a7fd3657bde9
-
-- name: flye test_flye_pacbio_hifi
-  command: nextflow run ./tests/modules/flye -entry test_flye_pacbio_hifi -c ./tests/config/nextflow.config  -c ./tests/modules/flye/nextflow.config
-  tags:
-    - flye
-  files:
-    - path: output/flye/test.assembly.fasta.gz
-    - path: output/flye/test.assembly_graph.gfa.gz
-    - path: output/flye/test.assembly_graph.gv.gz
-    - path: output/flye/test.assembly_info.txt
-      contains: ["contig_1"]
-    - path: output/flye/test.flye.log
-    - path: output/flye/test.params.json
-      md5sum: 54b576cb6d4d27656878a7fd3657bde9
-
-- name: flye test_flye_nano_raw
-  command: nextflow run ./tests/modules/flye -entry test_flye_nano_raw -c ./tests/config/nextflow.config  -c ./tests/modules/flye/nextflow.config -stub-run
-  tags:
-    - flye
-  files:
-    - path: output/flye/test.assembly.fasta.gz
-    - path: output/flye/test.assembly_graph.gfa.gz
-    - path: output/flye/test.assembly_graph.gv.gz
-    - path: output/flye/test.assembly_info.txt
-      contains: ["contig_1"]
-    - path: output/flye/test.flye.log
-    - path: output/flye/test.params.json
-
-- name: flye test_flye_nano_corr
-  command: nextflow run ./tests/modules/flye -entry test_flye_nano_corr -c ./tests/config/nextflow.config  -c ./tests/modules/flye/nextflow.config
-  tags:
-    - flye
-  files:
-    - path: output/flye/test.assembly.fasta.gz
-    - path: output/flye/test.assembly_graph.gfa.gz
-    - path: output/flye/test.assembly_graph.gv.gz
-    - path: output/flye/test.assembly_info.txt
-      contains: ["contig_1"]
-    - path: output/flye/test.flye.log
-    - path: output/flye/test.params.json
-      md5sum: 54b576cb6d4d27656878a7fd3657bde9
-
-- name: flye test_flye_nano_hq
-  command: nextflow run ./tests/modules/flye -entry test_flye_nano_hq -c ./tests/config/nextflow.config  -c ./tests/modules/flye/nextflow.config
-  tags:
-    - flye
-  files:
-    - path: output/flye/test.assembly.fasta.gz
-    - path: output/flye/test.assembly_graph.gfa.gz
-    - path: output/flye/test.assembly_graph.gv.gz
-    - path: output/flye/test.assembly_info.txt
-      contains: ["contig_1"]
-    - path: output/flye/test.flye.log
-    - path: output/flye/test.params.json
-      md5sum: 54b576cb6d4d27656878a7fd3657bde9
diff --git a/tests/modules/fq/lint/main.nf b/tests/modules/fq/lint/main.nf
deleted file mode 100644
index 677d32f7fb9..00000000000
--- a/tests/modules/fq/lint/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FQ_LINT } from '../../../../modules/fq/lint/main.nf'
-
-workflow test_fq_lint_success {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FQ_LINT ( input )
-}
-
-workflow test_fq_lint_fail {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    FQ_LINT ( input )
-}
diff --git a/tests/modules/fq/lint/test.yml b/tests/modules/fq/lint/test.yml
deleted file mode 100644
index d3cfb0e46ed..00000000000
--- a/tests/modules/fq/lint/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: fq lint test_fq_lint_success
-  command: nextflow run ./tests/modules/fq/lint -entry test_fq_lint_success -c ./tests/config/nextflow.config  -c ./tests/modules/fq/lint/nextflow.config
-  tags:
-    - fq
-    - fq/lint
-  files:
-    - path: output/fq/test.fq_lint.txt
-      contains:
-        - "fq-lint start"
-        - "read 100 records"
-        - "fq-lint end"
-
-- name: fq lint test_fq_lint_fail
-  command: nextflow run ./tests/modules/fq/lint -entry test_fq_lint_fail -c ./tests/config/nextflow.config  -c ./tests/modules/fq/lint/nextflow.config
-  tags:
-    - fq
-    - fq/lint
-  exit_code: 1
diff --git a/tests/modules/freebayes/main.nf b/tests/modules/freebayes/main.nf
deleted file mode 100644
index 6ed708c5f82..00000000000
--- a/tests/modules/freebayes/main.nf
+++ /dev/null
@@ -1,102 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FREEBAYES } from '../../../modules/freebayes/main.nf'
-
-workflow test_freebayes {
-    targets     = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-              [],
-              [],
-              targets
-            ]
-    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai         = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    samples     = []
-    populations = []
-    cnv         = []
-
-    FREEBAYES (input, fasta, fai, samples, populations, cnv)
-}
-
-workflow test_freebayes_bed {
-
-    targets     = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-              [],
-              [],
-              targets
-            ]
-    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai         = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    samples     = []
-    populations = []
-    cnv         = []
-
-    FREEBAYES (input, fasta, fai, samples, populations, cnv)
-}
-
-workflow test_freebayes_cram {
-
-    targets     = []
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-              [],
-              [],
-              targets
-            ]
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai         = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    samples     = []
-    populations = []
-    cnv         = []
-
-    FREEBAYES (input, fasta, fai, samples, populations, cnv)
-}
-
-workflow test_freebayes_somatic {
-
-    targets     = []
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
-                targets
-            ]
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai         = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    samples     = []
-    populations = []
-    cnv         = []
-
-    FREEBAYES (input, fasta, fai, samples, populations, cnv)
-}
-
-workflow test_freebayes_somatic_cram_intervals {
-
-    targets     = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),
-                targets
-            ]
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai         = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    samples     = []
-    populations = []
-    cnv         = []
-
-    FREEBAYES (input, fasta, fai, samples, populations, cnv)
-}
diff --git a/tests/modules/freebayes/test.yml b/tests/modules/freebayes/test.yml
deleted file mode 100644
index c3c8e30b432..00000000000
--- a/tests/modules/freebayes/test.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-- name: freebayes test_freebayes
-  command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
-  tags:
-    - freebayes
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: f28d0b8e2ccedeac0e590ca2ecaac83d
-    - path: output/freebayes/versions.yml
-      md5sum: 53651eb835af65df829241257584a7d2
-
-- name: freebayes test_freebayes_bed
-  command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
-  tags:
-    - freebayes
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: 1927441d1b7a4c48cbb61821de300ad4
-    - path: output/freebayes/versions.yml
-      md5sum: becc93c8a0be580c09d55b955d60a5e1
-
-- name: freebayes test_freebayes_cram
-  command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
-  tags:
-    - freebayes
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: 9b8d1d51d779bbea4086c7f7a2ece641
-    - path: output/freebayes/versions.yml
-      md5sum: 2e5b266edfc6cab81353cfc72c00f67c
-
-- name: freebayes test_freebayes_somatic
-  command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
-  tags:
-    - freebayes
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: dcaa639912174055c1380913d6102c01
-    - path: output/freebayes/versions.yml
-      md5sum: 8fbdb4c052fb3e42b5508a966125fa05
-
-- name: freebayes test_freebayes_somatic_cram_intervals
-  command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
-  tags:
-    - freebayes
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: b0052a2b83c0ba1b9686d0c96e61712f
-    - path: output/freebayes/versions.yml
-      md5sum: af97e3dfdc086188739907c3460e49e0
diff --git a/tests/modules/gamma/gamma/main.nf b/tests/modules/gamma/gamma/main.nf
deleted file mode 100644
index 97e58be7e05..00000000000
--- a/tests/modules/gamma/gamma/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GAMMA_GAMMA } from '../../../../modules/gamma/gamma/main.nf'
-
-workflow test_unzip {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true),
-    ]
-
-    db = [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/ResGANNCBI_20210507_srst2.fasta", checkIfExists: true), ]
-
-    GAMMA_GAMMA ( input, db )
-}
-
-workflow test_gamma {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-
-    GAMMA_GAMMA ( input, db )
-}
diff --git a/tests/modules/gamma/gamma/test.yml b/tests/modules/gamma/gamma/test.yml
deleted file mode 100644
index 163eda5ff0b..00000000000
--- a/tests/modules/gamma/gamma/test.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-- name: gamma gamma test_unzip
-  command: nextflow run tests/modules/gamma/gamma -entry test_unzip -c tests/config/nextflow.config
-  tags:
-    - gamma/gamma
-    - gamma
-  files:
-    - path: output/gamma/test.fasta
-      md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce
-    - path: output/gamma/test.gamma
-      md5sum: 46165a89e10b7315d3a9b0aa6c561626
-    - path: output/gamma/test.psl
-      md5sum: f489ce4602ddbcb692d5781ee3fbf449
-    - path: output/gamma/versions.yml
-      md5sum: 8baafec7b3b87f788f69e30d317c9722
-
-- name: gamma gamma test_gamma
-  command: nextflow run tests/modules/gamma/gamma -entry test_gamma -c tests/config/nextflow.config
-  tags:
-    - gamma/gamma
-    - gamma
-  files:
-    - path: output/gamma/test.fasta
-      md5sum: df37b48466181311e0a679f3c5878484
-    - path: output/gamma/test.gamma
-      md5sum: 3256708fa517a65ed01d99e0e3c762ae
-    - path: output/gamma/test.psl
-      md5sum: 162a2757ed3b167ae1e0cdb24213f940
-    - path: output/gamma/versions.yml
-      md5sum: b75c2871d8cac2f8ac67c0fbd22babd6
diff --git a/tests/modules/gappa/examineassign/main.nf b/tests/modules/gappa/examineassign/main.nf
deleted file mode 100644
index c42a2033d61..00000000000
--- a/tests/modules/gappa/examineassign/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GAPPA_EXAMINEASSIGN } from '../../../../modules/gappa/examineassign/main.nf'
-
-workflow test_gappa_examineassign {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true)
-    ]
-    taxonomy = file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/gappa_taxonomy.tsv', checkIfExists: true)
-
-    GAPPA_EXAMINEASSIGN ( input, taxonomy )
-}
diff --git a/tests/modules/gappa/examineassign/test.yml b/tests/modules/gappa/examineassign/test.yml
deleted file mode 100644
index 21cbabe0844..00000000000
--- a/tests/modules/gappa/examineassign/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: gappa examineassign test_gappa_examineassign
-  command: nextflow run ./tests/modules/gappa/examineassign -entry test_gappa_examineassign -c ./tests/config/nextflow.config  -c ./tests/modules/gappa/examineassign/nextflow.config
-  tags:
-    - gappa
-    - gappa/examineassign
-  files:
-    - path: output/gappa/test.labelled_tree.newick
-      md5sum: 39de8a46303ea757f6eb94478db1ffe0
-    - path: output/gappa/test.per_query.tsv
-      md5sum: 16e1fbcc5f79588a0ed21e495cdd91ee
-    - path: output/gappa/test.profile.tsv
-      md5sum: ce604fa03604462358b69cfbff7c1593
-    - path: output/gappa/test.krona.profile
-      md5sum: 19110ac998eaa7532f2a92772cd35aa6
-    - path: output/gappa/test.sativa.tsv
-      md5sum: 28020fc2f8440fabb5ae83b0c7114cdb
-    - path: output/gappa/versions.yml
-      md5sum: a6a80882e5a6b76a412ba2378bb40b51
diff --git a/tests/modules/gappa/examinegraft/main.nf b/tests/modules/gappa/examinegraft/main.nf
deleted file mode 100644
index f137a32e90d..00000000000
--- a/tests/modules/gappa/examinegraft/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GAPPA_EXAMINEGRAFT } from '../../../../modules/gappa/examinegraft/main.nf'
-
-workflow test_gappa_examinegraft {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true)
-    ]
-
-    GAPPA_EXAMINEGRAFT ( input )
-}
diff --git a/tests/modules/gappa/examinegraft/test.yml b/tests/modules/gappa/examinegraft/test.yml
deleted file mode 100644
index 8caef0ac00f..00000000000
--- a/tests/modules/gappa/examinegraft/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: gappa examinegraft test_gappa_examinegraft
-  command: nextflow run ./tests/modules/gappa/examinegraft -entry test_gappa_examinegraft -c ./tests/config/nextflow.config  -c ./tests/modules/gappa/examinegraft/nextflow.config
-  tags:
-    - gappa
-    - gappa/examinegraft
-  files:
-    - path: output/gappa/test.epa_result.newick
-      md5sum: 97e54b6a9576a78b774fd63a050e5474
-    - path: output/gappa/versions.yml
-      contains:
-        - "0.8.0"
diff --git a/tests/modules/gappa/examineheattree/main.nf b/tests/modules/gappa/examineheattree/main.nf
deleted file mode 100644
index bee1449252b..00000000000
--- a/tests/modules/gappa/examineheattree/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GAPPA_EXAMINEHEATTREE } from '../../../../modules/gappa/examineheattree/main.nf'
-
-workflow test_gappa_examineheattree {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true)
-    ]
-
-    GAPPA_EXAMINEHEATTREE ( input )
-}
diff --git a/tests/modules/gappa/examineheattree/test.yml b/tests/modules/gappa/examineheattree/test.yml
deleted file mode 100644
index 3a0745fc245..00000000000
--- a/tests/modules/gappa/examineheattree/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: "gappa examineheattree"
-  command: nextflow run ./tests/modules/gappa/examineheattree -entry test_gappa_examineheattree -c ./tests/config/nextflow.config -c ./tests/modules/gappa/examineheattree/nextflow.config
-  tags:
-    - "gappa"
-    - "gappa/examineheattree"
-  files:
-    - path: output/gappa/test.tree.newick
-      md5sum: f055e11c9b44b6d3afb502aba99d9579
-    - path: output/gappa/test.tree.nexus
-      md5sum: e1cfdcb63f3a751677d0e78fb6b9230a
-    - path: output/gappa/test.tree.phyloxml
-      md5sum: ea35b07e4fd8d174fd6b2f204629cc4e
-    - path: output/gappa/test.tree.svg
-    - path: output/gappa/test.colours.txt
-      md5sum: 7704cd341c8693981253ba6d740c1061
-    - path: output/gappa/test.log
-    - path: output/gappa/versions.yml
-      md5sum: 1cfb752399307413b475438ab1997731
diff --git a/tests/modules/gatk/indelrealigner/main.nf b/tests/modules/gatk/indelrealigner/main.nf
deleted file mode 100644
index d4e01e128ff..00000000000
--- a/tests/modules/gatk/indelrealigner/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf'
-include { GATK_INDELREALIGNER } from '../../../../modules/gatk/indelrealigner/main.nf'
-
-
-workflow test_gatk_indelrealigner {
-
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    input_realignertargetcreator     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                ]
-
-    GATK_REALIGNERTARGETCREATOR ( input_realignertargetcreator, fasta, fai, dict, [] )
-
-    ch_intervals = GATK_REALIGNERTARGETCREATOR.out.intervals
-
-    ch_bams_indelrealigner = Channel.of([ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-                ])
-
-    ch_input_indelrealigner = ch_bams_indelrealigner.mix(ch_intervals).groupTuple(by: 0).map{ [it[0], it[1][0], it[2], it[1][1] ] }.dump(tag: "input")
-
-    GATK_INDELREALIGNER ( ch_input_indelrealigner, fasta, fai, dict, [] )
-}
diff --git a/tests/modules/gatk/indelrealigner/test.yml b/tests/modules/gatk/indelrealigner/test.yml
deleted file mode 100644
index b7f0c465f65..00000000000
--- a/tests/modules/gatk/indelrealigner/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: gatk indelrealigner test_gatk_indelrealigner
-  command: nextflow run ./tests/modules/gatk/indelrealigner -entry test_gatk_indelrealigner -c ./tests/config/nextflow.config  -c ./tests/modules/gatk/indelrealigner/nextflow.config
-  tags:
-    - gatk/indelrealigner
-    - gatk
-  files:
-    - path: output/gatk/test.realigned.bai
-      md5sum: 85a67df8827fe426e7f3a458134c0551
-    - path: output/gatk/test.realigned.bam
-      md5sum: ea1df6f7fcafc408fae4dc1574813d8a
-    - path: output/gatk/test.realigned.intervals
-      md5sum: 7aa7a1b235a510e6591e262382086bf8
diff --git a/tests/modules/gatk/realignertargetcreator/main.nf b/tests/modules/gatk/realignertargetcreator/main.nf
deleted file mode 100644
index 4b9f8effa74..00000000000
--- a/tests/modules/gatk/realignertargetcreator/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf'
-
-workflow test_gatk_realignertargetcreator {
-
-    input     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK_REALIGNERTARGETCREATOR ( input, fasta, fai, dict, [] )
-}
diff --git a/tests/modules/gatk/realignertargetcreator/test.yml b/tests/modules/gatk/realignertargetcreator/test.yml
deleted file mode 100644
index 0e247013444..00000000000
--- a/tests/modules/gatk/realignertargetcreator/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: gatk realignertargetcreator test_gatk_realignertargetcreator
-  command: nextflow run ./tests/modules/gatk/realignertargetcreator -entry test_gatk_realignertargetcreator -c ./tests/config/nextflow.config  -c ./tests/modules/gatk/realignertargetcreator/nextflow.config
-  tags:
-    - gatk
-    - gatk/realignertargetcreator
-  files:
-    - path: output/gatk/test.intervals
-      md5sum: 7aa7a1b235a510e6591e262382086bf8
diff --git a/tests/modules/gatk/unifiedgenotyper/main.nf b/tests/modules/gatk/unifiedgenotyper/main.nf
deleted file mode 100644
index 6d145e76073..00000000000
--- a/tests/modules/gatk/unifiedgenotyper/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/gatk/unifiedgenotyper/main.nf'
-
-workflow test_gatk_unifiedgenotyper {
-
-    input     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [], [], [], [])
-}
diff --git a/tests/modules/gatk/unifiedgenotyper/test.yml b/tests/modules/gatk/unifiedgenotyper/test.yml
deleted file mode 100644
index 498e79910bf..00000000000
--- a/tests/modules/gatk/unifiedgenotyper/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk unifiedgenotyper test_gatk_unifiedgenotyper
-  command: nextflow run ./tests/modules/gatk/unifiedgenotyper -entry test_gatk_unifiedgenotyper -c ./tests/config/nextflow.config  -c ./tests/modules/gatk/unifiedgenotyper/nextflow.config
-  tags:
-    - gatk
-    - gatk/unifiedgenotyper
-  files:
-    - path: output/gatk/test.vcf.gz
-      contains:
-        - "#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	test"
diff --git a/tests/modules/gatk4/applybqsr/main.nf b/tests/modules/gatk4/applybqsr/main.nf
deleted file mode 100644
index 66711574780..00000000000
--- a/tests/modules/gatk4/applybqsr/main.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_APPLYBQSR } from '../../../../modules/gatk4/applybqsr/main.nf'
-
-workflow test_gatk4_applybqsr {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-              []
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_APPLYBQSR ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_applybqsr_intervals {
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-              ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-  GATK4_APPLYBQSR ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_applybqsr_cram {
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-              ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-  GATK4_APPLYBQSR ( input, fasta, fai, dict )
-}
diff --git a/tests/modules/gatk4/applybqsr/test.yml b/tests/modules/gatk4/applybqsr/test.yml
deleted file mode 100644
index c3dd4eeff7c..00000000000
--- a/tests/modules/gatk4/applybqsr/test.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-- name: gatk4 applybqsr test_gatk4_applybqsr
-  command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/applybqsr
-  files:
-    - path: output/gatk4/test.bam
-      md5sum: e11b7eaf2034740a953626518e3c3d6e
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
-  command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/applybqsr
-  files:
-    - path: output/gatk4/test.bam
-      md5sum: e9e9aa753c106e43f936ad573e23d2e6
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 applybqsr test_gatk4_applybqsr_cram
-  command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/applybqsr
-  files:
-    - path: output/gatk4/test.cram
-      md5sum: bca9d234a5d484ce2a6f4826ca2ea308
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/applybqsrspark/main.nf b/tests/modules/gatk4/applybqsrspark/main.nf
deleted file mode 100644
index ee1f88dddfe..00000000000
--- a/tests/modules/gatk4/applybqsrspark/main.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_APPLYBQSR_SPARK } from '../../../../modules/gatk4/applybqsrspark/main.nf'
-
-workflow test_gatk4_applybqsr_spark {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-              []
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_APPLYBQSR_SPARK ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_applybqsr_spark_intervals {
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-              ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-  GATK4_APPLYBQSR_SPARK ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_applybqsr_spark_cram {
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-              ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-  GATK4_APPLYBQSR_SPARK ( input, fasta, fai, dict )
-}
diff --git a/tests/modules/gatk4/applybqsrspark/test.yml b/tests/modules/gatk4/applybqsrspark/test.yml
deleted file mode 100644
index b7b8c72dff0..00000000000
--- a/tests/modules/gatk4/applybqsrspark/test.yml
+++ /dev/null
@@ -1,28 +0,0 @@
-- name: gatk4 applybqsr test_gatk4_applybqsr_spark
-  command: nextflow run tests/modules/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsrspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/applybqsrspark
-  files:
-    - path: output/gatk4/test.bam
-      md5sum: 1901c819fcba0fdd5e2482e6dc8285ef
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals
-  command: nextflow run tests/modules/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsrspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/applybqsrspark
-  files:
-    - path: output/gatk4/test.bam
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram
-  command: nextflow run tests/modules/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsrspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/applybqsrspark
-  files:
-    - path: output/gatk4/test.cram
-      md5sum: 60f7c822a9f2833e11eb7bfd16e4421f
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/applyvqsr/main.nf b/tests/modules/gatk4/applyvqsr/main.nf
deleted file mode 100644
index c6e99d5c063..00000000000
--- a/tests/modules/gatk4/applyvqsr/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../modules/gatk4/applyvqsr/main.nf'
-include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../modules/gatk4/applyvqsr/main.nf'
-
-workflow test_gatk4_applyvqsr {
-    input = [ [ id:'test'], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_recal'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_recal_idx'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_tranches'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_APPLYVQSR_NO_ALLELSPECIFICITY ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_applyvqsr_allele_specific {
-    input = [ [ id:'test'], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal_idx'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_tranches'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY ( input, fasta, fai, dict)
-}
diff --git a/tests/modules/gatk4/applyvqsr/test.yml b/tests/modules/gatk4/applyvqsr/test.yml
deleted file mode 100644
index 5b367bcc858..00000000000
--- a/tests/modules/gatk4/applyvqsr/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: gatk4 applyvqsr test_gatk4_applyvqsr
-  command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
-  tags:
-    - gatk4/applyvqsr
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific
-  command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
-  tags:
-    - gatk4/applyvqsr
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/baserecalibrator/main.nf b/tests/modules/gatk4/baserecalibrator/main.nf
deleted file mode 100644
index 05c24ae319a..00000000000
--- a/tests/modules/gatk4/baserecalibrator/main.nf
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_BASERECALIBRATOR } from '../../../../modules/gatk4/baserecalibrator/main.nf'
-
-workflow test_gatk4_baserecalibrator {
-    input     = [ [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    []
-                  ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-    sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-    sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
-}
-
-workflow test_gatk4_baserecalibrator_cram {
-   input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                []
-              ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-    sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
-}
-
-workflow test_gatk4_baserecalibrator_intervals {
-    input     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-                ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-    sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-    sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
-}
-
-workflow test_gatk4_baserecalibrator_multiple_sites {
-    input     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                  []
-                ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-    sites =     [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)
-                ]
-    sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                ]
-
-  GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
-}
diff --git a/tests/modules/gatk4/baserecalibrator/test.yml b/tests/modules/gatk4/baserecalibrator/test.yml
deleted file mode 100644
index ec103dd4231..00000000000
--- a/tests/modules/gatk4/baserecalibrator/test.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-- name: gatk4 baserecalibrator test_gatk4_baserecalibrator
-  command: nextflow run ./tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibrator/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/baserecalibrator
-  files:
-    - path: output/gatk4/test.table
-      md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_cram
-  command: nextflow run ./tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibrator/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/baserecalibrator
-  files:
-    - path: output/gatk4/test.table
-      md5sum: 35d89a3811aa31711fc9815b6b80e6ec
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
-  command: nextflow run ./tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibrator/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/baserecalibrator
-  files:
-    - path: output/gatk4/test.table
-      md5sum: 9ecb5f00a2229291705addc09c0ec231
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_multiple_sites
-  command: nextflow run ./tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibrator/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/baserecalibrator
-  files:
-    - path: output/gatk4/test.table
-      md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/baserecalibratorspark/main.nf b/tests/modules/gatk4/baserecalibratorspark/main.nf
deleted file mode 100644
index 8419e16b724..00000000000
--- a/tests/modules/gatk4/baserecalibratorspark/main.nf
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_BASERECALIBRATOR_SPARK } from '../../../../modules/gatk4/baserecalibratorspark/main.nf'
-
-workflow test_gatk4_baserecalibrator_spark {
-    input     = [ [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    []
-                  ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-    sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-    sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_BASERECALIBRATOR_SPARK ( input, fasta, fai, dict, sites, sites_tbi )
-}
-
-workflow test_gatk4_baserecalibrator_spark_cram {
-   input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                []
-              ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-    sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_BASERECALIBRATOR_SPARK ( input, fasta, fai, dict, sites, sites_tbi )
-}
-
-workflow test_gatk4_baserecalibrator_spark_intervals {
-    input     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-                ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-    sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-    sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_BASERECALIBRATOR_SPARK ( input, fasta, fai, dict, sites, sites_tbi )
-}
-
-workflow test_gatk4_baserecalibrator_spark_multiple_sites {
-    input     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                  []
-                ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-    sites =     [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)
-                ]
-    sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                ]
-
-  GATK4_BASERECALIBRATOR_SPARK ( input, fasta, fai, dict, sites, sites_tbi )
-}
diff --git a/tests/modules/gatk4/baserecalibratorspark/test.yml b/tests/modules/gatk4/baserecalibratorspark/test.yml
deleted file mode 100644
index 6eb9d91d4df..00000000000
--- a/tests/modules/gatk4/baserecalibratorspark/test.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_spark
-  command: nextflow run ./tests/modules/gatk4/baserecalibratorspark -entry test_gatk4_baserecalibrator_spark -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibratorspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/baserecalibratorspark
-  files:
-    - path: output/gatk4/test.table
-      md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_spark_cram
-  command: nextflow run ./tests/modules/gatk4/baserecalibratorspark -entry test_gatk4_baserecalibrator_spark_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibratorspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/baserecalibratorspark
-  files:
-    - path: output/gatk4/test.table
-      md5sum: 35d89a3811aa31711fc9815b6b80e6ec
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_spark_intervals
-  command: nextflow run ./tests/modules/gatk4/baserecalibratorspark -entry test_gatk4_baserecalibrator_spark_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibratorspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/baserecalibratorspark
-  files:
-    - path: output/gatk4/test.table
-      md5sum: 9ecb5f00a2229291705addc09c0ec231
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_spark_multiple_sites
-  command: nextflow run ./tests/modules/gatk4/baserecalibratorspark -entry test_gatk4_baserecalibrator_spark_multiple_sites -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibratorspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/baserecalibratorspark
-  files:
-    - path: output/gatk4/test.table
-      md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/bedtointervallist/main.nf b/tests/modules/gatk4/bedtointervallist/main.nf
deleted file mode 100644
index 2dd72904f72..00000000000
--- a/tests/modules/gatk4/bedtointervallist/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/gatk4/bedtointervallist/main.nf'
-
-workflow test_gatk4_bedtointervallist {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
-            ]
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_BEDTOINTERVALLIST ( input, dict )
-}
diff --git a/tests/modules/gatk4/bedtointervallist/test.yml b/tests/modules/gatk4/bedtointervallist/test.yml
deleted file mode 100644
index d8eade5180c..00000000000
--- a/tests/modules/gatk4/bedtointervallist/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk4 bedtointervallist test_gatk4_bedtointervallist
-  command: nextflow run ./tests/modules/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/bedtointervallist/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/bedtointervallist
-  files:
-    - path: output/gatk4/test.interval_list
-      md5sum: e51101c9357fb2d59fd30e370eefa39c
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/calculatecontamination/main.nf b/tests/modules/gatk4/calculatecontamination/main.nf
deleted file mode 100644
index c6e085b1e5a..00000000000
--- a/tests/modules/gatk4/calculatecontamination/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_CALCULATECONTAMINATION                                              } from '../../../../modules/gatk4/calculatecontamination/main.nf'
-include { GATK4_CALCULATECONTAMINATION as GATK4_CALCULATECONTAMINATION_SEGMENTATION } from '../../../../modules/gatk4/calculatecontamination/main.nf'
-
-workflow test_gatk4_calculatecontamination_tumor_only {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
-              [] ]
-
-    GATK4_CALCULATECONTAMINATION ( input )
-}
-
-workflow test_gatk4_calculatecontamination_matched_pair {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ]
-
-    GATK4_CALCULATECONTAMINATION ( input )
-}
-
-workflow test_gatk4_calculatecontamination_segmentation {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ]
-
-    GATK4_CALCULATECONTAMINATION_SEGMENTATION ( input )
-}
diff --git a/tests/modules/gatk4/calculatecontamination/test.yml b/tests/modules/gatk4/calculatecontamination/test.yml
deleted file mode 100644
index a00e26f041c..00000000000
--- a/tests/modules/gatk4/calculatecontamination/test.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_tumor_only
-  command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/calculatecontamination
-  files:
-    - path: output/gatk4/test.contamination.table
-      md5sum: 46c708c943b453da89a3da08acfdb2a7
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair
-  command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/calculatecontamination
-  files:
-    - path: output/gatk4/test.contamination.table
-      md5sum: 46c708c943b453da89a3da08acfdb2a7
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation
-  command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/calculatecontamination
-  files:
-    - path: output/gatk4/test.contamination.table
-      md5sum: 46c708c943b453da89a3da08acfdb2a7
-    - path: output/gatk4/test.segmentation.table
-      md5sum: f4643d9319bde4efbfbe516d6fb13052
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/calibratedragstrmodel/main.nf b/tests/modules/gatk4/calibratedragstrmodel/main.nf
deleted file mode 100644
index 136a9742ce3..00000000000
--- a/tests/modules/gatk4/calibratedragstrmodel/main.nf
+++ /dev/null
@@ -1,66 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../modules/gatk4/calibratedragstrmodel/main.nf'
-
-workflow test_gatk4_calibratedragstrmodel_bam {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
-
-    GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
-}
-
-workflow test_gatk4_calibratedragstrmodel_cram {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
-
-    GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
-}
-
-workflow test_gatk4_calibratedragstrmodel_beds {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
-
-    GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
-}
-
diff --git a/tests/modules/gatk4/calibratedragstrmodel/test.yml b/tests/modules/gatk4/calibratedragstrmodel/test.yml
deleted file mode 100644
index 285d04caffb..00000000000
--- a/tests/modules/gatk4/calibratedragstrmodel/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_bam
-  command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_bam -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/calibratedragstrmodel
-  files:
-    - path: output/gatk4/test.txt
-      md5sum: e16fa32906c74bb18b93e98a86718ff1
-
-- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_cram
-  command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_cram -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/calibratedragstrmodel
-  files:
-    - path: output/gatk4/test.txt
-      md5sum: 81c7bf338886cb4d5c2cc07fc56afe44
-
-- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_beds
-  command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_beds -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/calibratedragstrmodel
-  files:
-    - path: output/gatk4/test.txt
-      md5sum: cb6a9acdee042302b54fd1f59b5f54ee
diff --git a/tests/modules/gatk4/cnnscorevariants/main.nf b/tests/modules/gatk4/cnnscorevariants/main.nf
deleted file mode 100644
index 1654c54a8e3..00000000000
--- a/tests/modules/gatk4/cnnscorevariants/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevariants/main.nf'
-
-workflow test_gatk4_cnnscorevariants {
-
-    input     = [ [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-                    [],
-                    []
-                ]
-    fasta  = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai    = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict   = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-    GATK4_CNNSCOREVARIANTS ( input, fasta, fai, dict, [], [] )
-}
diff --git a/tests/modules/gatk4/cnnscorevariants/test.yml b/tests/modules/gatk4/cnnscorevariants/test.yml
deleted file mode 100644
index eb2e681fc1e..00000000000
--- a/tests/modules/gatk4/cnnscorevariants/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk4 cnnscorevariants test_gatk4_cnnscorevariants
-  command: nextflow run ./tests/modules/gatk4/cnnscorevariants -entry test_gatk4_cnnscorevariants -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/cnnscorevariants/nextflow.config
-  tags:
-    - gatk4/cnnscorevariants
-    - gatk4
-  files:
-    - path: output/gatk4/test.cnn.vcf.gz
-      contains: ["##ALT=<ID=NON_REF,Description="]
-    - path: output/gatk4/test.cnn.vcf.gz.tbi
diff --git a/tests/modules/gatk4/collectreadcounts/main.nf b/tests/modules/gatk4/collectreadcounts/main.nf
deleted file mode 100644
index 9e69c018f45..00000000000
--- a/tests/modules/gatk4/collectreadcounts/main.nf
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_COLLECTREADCOUNTS } from '../../../../modules/gatk4/collectreadcounts/main.nf'
-
-workflow test_gatk4_collectreadcounts_hdf5 {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
-    ]
-
-    fasta = []
-    fai = []
-    dict = []
-
-    GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_collectreadcounts_tsv {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
-    ]
-
-    fasta = []
-    fai = []
-    dict = []
-
-    GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_collectreadcounts_cram {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
-}
-
diff --git a/tests/modules/gatk4/collectreadcounts/test.yml b/tests/modules/gatk4/collectreadcounts/test.yml
deleted file mode 100644
index 1652f021130..00000000000
--- a/tests/modules/gatk4/collectreadcounts/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_hdf5
-  command: nextflow run ./tests/modules/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_hdf5 -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/collectreadcounts/nextflow.config
-  tags:
-    - gatk4/collectreadcounts
-    - gatk4
-  files:
-    - path: output/gatk4/test.hdf5
-
-- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_tsv
-  command: nextflow run ./tests/modules/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_tsv -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/collectreadcounts/nextflow.config
-  tags:
-    - gatk4/collectreadcounts
-    - gatk4
-  files:
-    - path: output/gatk4/test.tsv
-      md5sum: 8e45a6164916c303387f39f02ce45841
-
-- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_cram
-  command: nextflow run ./tests/modules/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_cram -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/collectreadcounts/nextflow.config
-  tags:
-    - gatk4/collectreadcounts
-    - gatk4
-  files:
-    - path: output/gatk4/test.tsv
-      md5sum: d9a32039b7a84f5bb74e8382e5427670
diff --git a/tests/modules/gatk4/collectsvevidence/main.nf b/tests/modules/gatk4/collectsvevidence/main.nf
deleted file mode 100644
index 21761d6a870..00000000000
--- a/tests/modules/gatk4/collectsvevidence/main.nf
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/gatk4/collectsvevidence/main.nf'
-
-workflow test_gatk4_collectsvevidence_cram {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        [],
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
-}
-
-workflow test_gatk4_collectsvevidence_bam {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        [],
-        []
-    ]
-
-    fasta = []
-    fasta_fai = []
-    dict = []
-
-    GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
-}
-
-workflow test_gatk4_collectsvevidence_allele_count {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta = []
-    fasta_fai = []
-    dict = []
-
-    GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
-}
diff --git a/tests/modules/gatk4/collectsvevidence/test.yml b/tests/modules/gatk4/collectsvevidence/test.yml
deleted file mode 100644
index e08104cbf1c..00000000000
--- a/tests/modules/gatk4/collectsvevidence/test.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_cram
-  command: nextflow run ./tests/modules/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_cram -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/collectsvevidence/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/collectsvevidence
-  files:
-    - path: output/gatk4/test.pe.txt.gz
-      md5sum: 19f13dd0408204590b40239d14acbdde
-    - path: output/gatk4/test.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/test.sr.txt.gz
-      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
-    - path: output/gatk4/test.sr.txt.gz.tbi
-      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
-
-- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_bam
-  command: nextflow run ./tests/modules/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_bam -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/collectsvevidence/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/collectsvevidence
-  files:
-    - path: output/gatk4/test.pe.txt.gz
-      md5sum: 19f13dd0408204590b40239d14acbdde
-    - path: output/gatk4/test.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/test.sr.txt.gz
-      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
-    - path: output/gatk4/test.sr.txt.gz.tbi
-      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
-
-- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_allele_count
-  command: nextflow run ./tests/modules/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_allele_count -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/collectsvevidence/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/collectsvevidence
-  files:
-    - path: output/gatk4/test.ld.txt.gz
-      md5sum: c07747510deb2c2c886ee4e34d0a9c97
-    - path: output/gatk4/test.ld.txt.gz.tbi
-      md5sum: d1479eeb2217c2b8b4a84cf7237aca45
-    - path: output/gatk4/test.pe.txt.gz
-      md5sum: 19f13dd0408204590b40239d14acbdde
-    - path: output/gatk4/test.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/test.sr.txt.gz
-      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
-    - path: output/gatk4/test.sr.txt.gz.tbi
-      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
diff --git a/tests/modules/gatk4/combinegvcfs/main.nf b/tests/modules/gatk4/combinegvcfs/main.nf
deleted file mode 100644
index 50d42625168..00000000000
--- a/tests/modules/gatk4/combinegvcfs/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_COMBINEGVCFS } from '../../../../modules/gatk4/combinegvcfs/main.nf'
-
-workflow test_gatk4_combinegvcfs {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf'], checkIfExists: true) ],
-              [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_idx'], checkIfExists: true) ]              
-           ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)       
-
-    GATK4_COMBINEGVCFS ( input, fasta, fasta_fai, fasta_dict )
-}
-
diff --git a/tests/modules/gatk4/combinegvcfs/test.yml b/tests/modules/gatk4/combinegvcfs/test.yml
deleted file mode 100644
index 762a72f3bca..00000000000
--- a/tests/modules/gatk4/combinegvcfs/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk4 combinegvcfs test_gatk4_combinegvcfs
-  command: nextflow run tests/modules/gatk4/combinegvcfs -entry test_gatk4_combinegvcfs -c tests/config/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/combinegvcfs
-  files:
-    - path: output/gatk4/test.combined.g.vcf.gz
-      contains: ["VCFv4.2"]
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/composestrtablefile/main.nf b/tests/modules/gatk4/composestrtablefile/main.nf
deleted file mode 100644
index 8fccadb9dc3..00000000000
--- a/tests/modules/gatk4/composestrtablefile/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_COMPOSESTRTABLEFILE } from '../../../../modules/gatk4/composestrtablefile/main.nf'
-
-workflow test_gatk4_composestrtablefile {
-    
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_COMPOSESTRTABLEFILE ( fasta, fasta_fai, dict )
-}
diff --git a/tests/modules/gatk4/composestrtablefile/test.yml b/tests/modules/gatk4/composestrtablefile/test.yml
deleted file mode 100644
index 0a87372ad69..00000000000
--- a/tests/modules/gatk4/composestrtablefile/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: gatk4 composestrtablefile test_gatk4_composestrtablefile
-  command: nextflow run ./tests/modules/gatk4/composestrtablefile -entry test_gatk4_composestrtablefile -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/composestrtablefile/nextflow.config
-  tags:
-    - gatk4/composestrtablefile
-    - gatk4
-  files:
-    - path: output/gatk4/genome.zip
diff --git a/tests/modules/gatk4/createsequencedictionary/main.nf b/tests/modules/gatk4/createsequencedictionary/main.nf
deleted file mode 100644
index b304b0432a8..00000000000
--- a/tests/modules/gatk4/createsequencedictionary/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../modules/gatk4/createsequencedictionary/main.nf'
-
-workflow test_gatk4_createsequencedictionary {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    GATK4_CREATESEQUENCEDICTIONARY ( fasta )
-}
diff --git a/tests/modules/gatk4/createsequencedictionary/test.yml b/tests/modules/gatk4/createsequencedictionary/test.yml
deleted file mode 100644
index 3656e0e2931..00000000000
--- a/tests/modules/gatk4/createsequencedictionary/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk4 createsequencedictionary test_gatk4_createsequencedictionary
-  command: nextflow run ./tests/modules/gatk4/createsequencedictionary -entry test_gatk4_createsequencedictionary -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/createsequencedictionary/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/createsequencedictionary
-  files:
-    - path: output/gatk4/genome.dict
-      md5sum: 7362679f176e0f52add03c08f457f646
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/createsomaticpanelofnormals/main.nf b/tests/modules/gatk4/createsomaticpanelofnormals/main.nf
deleted file mode 100644
index 3316f73ac95..00000000000
--- a/tests/modules/gatk4/createsomaticpanelofnormals/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR           } from '../../../../modules/untar/main.nf'
-include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../modules/gatk4/createsomaticpanelofnormals/main.nf'
-
-workflow test_gatk4_createsomaticpanelofnormals {
-    db    = [[], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-
-    input = Channel.of([ id:'test'])
-              .combine(UNTAR.out.untar.map{ it[1] })
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_CREATESOMATICPANELOFNORMALS ( input, fasta, fastaidx, dict )
-}
diff --git a/tests/modules/gatk4/createsomaticpanelofnormals/test.yml b/tests/modules/gatk4/createsomaticpanelofnormals/test.yml
deleted file mode 100644
index 00d8cae9647..00000000000
--- a/tests/modules/gatk4/createsomaticpanelofnormals/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: gatk4 createsomaticpanelofnormals test_gatk4_createsomaticpanelofnormals
-  command: nextflow run ./tests/modules/gatk4/createsomaticpanelofnormals -entry test_gatk4_createsomaticpanelofnormals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/createsomaticpanelofnormals
-  files:
-    - path: output/gatk4/test.pon.vcf.gz
-    - path: output/gatk4/test.pon.vcf.gz.tbi
-      md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/estimatelibrarycomplexity/main.nf b/tests/modules/gatk4/estimatelibrarycomplexity/main.nf
deleted file mode 100644
index 398a6c7997e..00000000000
--- a/tests/modules/gatk4/estimatelibrarycomplexity/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../../modules/gatk4/estimatelibrarycomplexity/main.nf'
-
-workflow test_gatk4_estimatelibrarycomplexity {
-
-    input = [   [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_ESTIMATELIBRARYCOMPLEXITY ( input, fasta, fai, dict )
-}
diff --git a/tests/modules/gatk4/estimatelibrarycomplexity/test.yml b/tests/modules/gatk4/estimatelibrarycomplexity/test.yml
deleted file mode 100644
index cf5d187f904..00000000000
--- a/tests/modules/gatk4/estimatelibrarycomplexity/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: gatk4 estimatelibrarycomplexity test_gatk4_estimatelibrarycomplexity
-  command: nextflow run ./tests/modules/gatk4/estimatelibrarycomplexity -entry test_gatk4_estimatelibrarycomplexity -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/estimatelibrarycomplexity/nextflow.config
-  tags:
-    - gatk4/estimatelibrarycomplexity
-    - gatk4
-  files:
-    - path: output/gatk4/test.metrics
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/fastqtosam/main.nf b/tests/modules/gatk4/fastqtosam/main.nf
deleted file mode 100644
index 4f53c791101..00000000000
--- a/tests/modules/gatk4/fastqtosam/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_FASTQTOSAM } from '../../../../modules/gatk4/fastqtosam/main.nf'
-
-workflow test_gatk4_fastqtosam_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ]
-
-    GATK4_FASTQTOSAM ( input )
-}
-
-workflow test_gatk4_fastqtosam_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-            ]
-
-    GATK4_FASTQTOSAM ( input )
-}
diff --git a/tests/modules/gatk4/fastqtosam/test.yml b/tests/modules/gatk4/fastqtosam/test.yml
deleted file mode 100644
index f4b2c561909..00000000000
--- a/tests/modules/gatk4/fastqtosam/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
-  command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config  -c ./tests/modules/gatk4/fastqtosam/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/fastqtosam
-  files:
-    - path: output/gatk4/test.bam
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
-  command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config  -c ./tests/modules/gatk4/fastqtosam/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/fastqtosam
-  files:
-    - path: output/gatk4/test.bam
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/filtermutectcalls/main.nf b/tests/modules/gatk4/filtermutectcalls/main.nf
deleted file mode 100644
index 1a4ee377d22..00000000000
--- a/tests/modules/gatk4/filtermutectcalls/main.nf
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/gatk4/filtermutectcalls/main.nf'
-
-workflow test_gatk4_filtermutectcalls_base {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
-        [],
-        [],
-        [],
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_filtermutectcalls_with_files {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
-        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_artifact_prior_tar_gz'], checkIfExists: true) ],
-        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_segmentation_table'], checkIfExists: true) ],
-        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_contamination_table'], checkIfExists: true) ],
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_filtermutectcalls_use_val {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
-        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_artifact_prior_tar_gz'], checkIfExists: true) ],
-        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_segmentation_table'], checkIfExists: true) ],
-        [],
-        '20.0'
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_filtermutectcalls_base_stubs {
-
-    input = [
-         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
-        [],
-        [],
-        [],
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
-}
diff --git a/tests/modules/gatk4/filtermutectcalls/test.yml b/tests/modules/gatk4/filtermutectcalls/test.yml
deleted file mode 100644
index 35f23ca34a5..00000000000
--- a/tests/modules/gatk4/filtermutectcalls/test.yml
+++ /dev/null
@@ -1,46 +0,0 @@
-- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_base
-  command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_base -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/filtermutectcalls
-  files:
-    - path: output/gatk4/test.filtered.vcf.gz
-    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
-      md5sum: 55f228e5520c8b9fbac017d3a3a6c5fd
-    - path: output/gatk4/test.filtered.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_with_files
-  command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_with_files -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/filtermutectcalls
-  files:
-    - path: output/gatk4/test.filtered.vcf.gz
-    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
-      md5sum: 9ae27fbd04af1a2ea574e2ff1c3a683b
-    - path: output/gatk4/test.filtered.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_use_val
-  command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_use_val -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/filtermutectcalls
-  files:
-    - path: output/gatk4/test.filtered.vcf.gz
-    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
-      md5sum: 95cc3e37705bd3b97a292c5d46ab82f3
-    - path: output/gatk4/test.filtered.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_base_stubs
-  command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_base_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config -stub-run
-  tags:
-    - gatk4
-    - gatk4/filtermutectcalls
-  files:
-    - path: output/gatk4/test.filtered.vcf.gz
-    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
-    - path: output/gatk4/test.filtered.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/filtervarianttranches/main.nf b/tests/modules/gatk4/filtervarianttranches/main.nf
deleted file mode 100644
index 91dde3d425c..00000000000
--- a/tests/modules/gatk4/filtervarianttranches/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/gatk4/filtervarianttranches/main.nf'
-include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevariants/main.nf'
-include { GATK4_HAPLOTYPECALLER  } from '../../../../modules/gatk4/haplotypecaller/main.nf'
-workflow test_gatk4_filtervarianttranches {
-
-    resources = [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ]
-    resources_index  = [
-                    file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true),
-                ]
-
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true),
-                []
-            ]
-
-    fasta  = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai    = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict   = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_FILTERVARIANTTRANCHES (input , resources, resources_index, fasta, fai, dict)
-}
diff --git a/tests/modules/gatk4/filtervarianttranches/test.yml b/tests/modules/gatk4/filtervarianttranches/test.yml
deleted file mode 100644
index 03edd6d0bf2..00000000000
--- a/tests/modules/gatk4/filtervarianttranches/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk4 filtervarianttranches test_gatk4_filtervarianttranches
-  command: nextflow run ./tests/modules/gatk4/filtervarianttranches -entry test_gatk4_filtervarianttranches -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/filtervarianttranches/nextflow.config
-  tags:
-    - gatk4/filtervarianttranches
-    - gatk4
-  files:
-    - path: output/gatk4/test.filtered.vcf.gz
-    - path: output/gatk4/test.filtered.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/gatherbqsrreports/main.nf b/tests/modules/gatk4/gatherbqsrreports/main.nf
deleted file mode 100644
index 2693a06a0df..00000000000
--- a/tests/modules/gatk4/gatherbqsrreports/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_GATHERBQSRREPORTS } from '../../../../modules/gatk4/gatherbqsrreports/main.nf'
-
-workflow test_gatk4_gatherbqsrreports {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
-    ]
-
-    GATK4_GATHERBQSRREPORTS ( input )
-}
-
-workflow test_gatk4_gatherbqsrreports_multiple {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_baserecalibrator_table'], checkIfExists: true)
-        ]
-    ]
-
-    GATK4_GATHERBQSRREPORTS ( input )
-}
diff --git a/tests/modules/gatk4/gatherbqsrreports/test.yml b/tests/modules/gatk4/gatherbqsrreports/test.yml
deleted file mode 100644
index 2fb4917a962..00000000000
--- a/tests/modules/gatk4/gatherbqsrreports/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports
-  command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports -c tests/config/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/gatherbqsrreports
-  files:
-    - path: output/gatk4/test.table
-      md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple
-  command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c tests/config/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/gatherbqsrreports
-  files:
-    - path: output/gatk4/test.table
-      md5sum: 0c1257eececf95db8ca378272d0f21f9
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/gatherpileupsummaries/main.nf b/tests/modules/gatk4/gatherpileupsummaries/main.nf
deleted file mode 100644
index 2bd7e98c4d0..00000000000
--- a/tests/modules/gatk4/gatherpileupsummaries/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_GATHERPILEUPSUMMARIES } from '../../../../modules/gatk4/gatherpileupsummaries/main.nf'
-
-workflow test_gatk4_gatherpileupsummaries {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)]
-        //file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)]
-    ]
-
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_GATHERPILEUPSUMMARIES ( input, dict )
-}
diff --git a/tests/modules/gatk4/gatherpileupsummaries/test.yml b/tests/modules/gatk4/gatherpileupsummaries/test.yml
deleted file mode 100644
index efd02f52d21..00000000000
--- a/tests/modules/gatk4/gatherpileupsummaries/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk4 gatherpileupsummaries
-  command: nextflow run ./tests/modules/gatk4/gatherpileupsummaries -entry test_gatk4_gatherpileupsummaries -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/gatherpileupsummaries/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/gatherpileupsummaries
-  files:
-    - path: output/gatk4/test.pileupsummaries.table
-      md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/genomicsdbimport/main.nf b/tests/modules/gatk4/genomicsdbimport/main.nf
deleted file mode 100644
index 6d990f4e94a..00000000000
--- a/tests/modules/gatk4/genomicsdbimport/main.nf
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR           } from '../../../../modules/untar/main.nf'
-include { GATK4_GENOMICSDBIMPORT } from '../../../../modules/gatk4/genomicsdbimport/main.nf'
-
-workflow test_gatk4_genomicsdbimport_create_genomicsdb {
-
-    input = [ [ id:'test'], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) ,
-              file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ,
-              file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true) ,
-              [] ,
-              [] ]
-
-    run_intlist = false
-    run_updatewspace = false
-    input_map = false
-
-    GATK4_GENOMICSDBIMPORT ( input, run_intlist, run_updatewspace, input_map )
-}
-
-workflow test_gatk4_genomicsdbimport_get_intervalslist {
-    db    = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-
-    def input = Channel.of([ [ id:'test'], // meta map
-              [] ,
-              [] ,
-              [] ,
-              [] ])
-              .combine(UNTAR.out.untar.map{ it[1] })
-
-    run_intlist = true
-    run_updatewspace = false
-    input_map = false
-
-    GATK4_GENOMICSDBIMPORT ( input, run_intlist, run_updatewspace, input_map )
-}
-
-workflow test_gatk4_genomicsdbimport_update_genomicsdb {
-    db    = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-
-    def input = Channel.of([ [ id:'test'], // meta map
-              file( params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'] , checkIfExists: true) ,
-              file( params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz_tbi'] , checkIfExists: true) ,
-              [] ,
-              [] ])
-              .combine(UNTAR.out.untar.map{ it[1] })
-
-    run_intlist = false
-    run_updatewspace = true
-    input_map = false
-
-    GATK4_GENOMICSDBIMPORT ( input, run_intlist, run_updatewspace, input_map )
-
-}
diff --git a/tests/modules/gatk4/genomicsdbimport/test.yml b/tests/modules/gatk4/genomicsdbimport/test.yml
deleted file mode 100644
index 765cbfbe0bb..00000000000
--- a/tests/modules/gatk4/genomicsdbimport/test.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_create_genomicsdb
-  command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genomicsdbimport
-  files:
-    - path: output/gatk4/test/__tiledb_workspace.tdb
-    - path: output/gatk4/test/callset.json
-      md5sum: a7d07d1c86449bbb1091ff29368da07a
-    - path: output/gatk4/test/chr22$1$40001/.__consolidation_lock
-    - path: output/gatk4/test/chr22$1$40001/__array_schema.tdb
-    - path: output/gatk4/test/chr22$1$40001/genomicsdb_meta_dir/genomicsdb_column_bounds.json
-      md5sum: 2502f79658bc000578ebcfddfc1194c0
-    - path: output/gatk4/test/vcfheader.vcf
-      contains:
-        - "FORMAT=<ID=AD,Number=R,Type=Integer,Description="
-    - path: output/gatk4/test/vidmap.json
-      md5sum: 18d3f68bd2cb6f4474990507ff95017a
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist
-  command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genomicsdbimport
-  files:
-    - path: output/gatk4/test.interval_list
-      md5sum: 4c85812ac15fc1cd29711a851d23c0bf
-    - path: output/gatk4/versions.yml
-    - path: output/untar/versions.yml
-
-- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_update_genomicsdb
-  command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_update_genomicsdb -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genomicsdbimport
-  files:
-    - path: output/gatk4/test_genomicsdb/__tiledb_workspace.tdb
-    - path: output/gatk4/test_genomicsdb/callset.json
-      md5sum: 1ea31b59b9a218dd5681164aff4a5e07
-    - path: output/gatk4/test_genomicsdb/chr22$1$40001/.__consolidation_lock
-    - path: output/gatk4/test_genomicsdb/chr22$1$40001/__array_schema.tdb
-      md5sum: 6709e67921ae840bf61fbfb192554eda
-    - path: output/gatk4/test_genomicsdb/chr22$1$40001/genomicsdb_meta_dir/genomicsdb_column_bounds.json
-      md5sum: 2502f79658bc000578ebcfddfc1194c0
-    - path: output/gatk4/test_genomicsdb/vcfheader.vcf
-      md5sum: 3717f34ad68ff491f40a138410b2667a
-    - path: output/gatk4/test_genomicsdb/vidmap.json
-      md5sum: 18d3f68bd2cb6f4474990507ff95017a
-    - path: output/gatk4/versions.yml
-    - path: output/untar/versions.yml
diff --git a/tests/modules/gatk4/genotypegvcfs/main.nf b/tests/modules/gatk4/genotypegvcfs/main.nf
deleted file mode 100644
index cd7d3a03c25..00000000000
--- a/tests/modules/gatk4/genotypegvcfs/main.nf
+++ /dev/null
@@ -1,182 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_GENOTYPEGVCFS } from '../../../../modules/gatk4/genotypegvcfs/main.nf'
-include { UNTAR               } from '../../../../modules/untar/main.nf'
-
-// Basic parameters with uncompressed VCF input
-workflow test_gatk4_genotypegvcfs_vcf_input {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true),
-            [],
-            []
-        ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
-}
-
-// Basic parameters with compressed VCF input
-workflow test_gatk4_genotypegvcfs_gz_input {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            [],
-            []
-        ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
-}
-
-// Basic parameters + optional dbSNP
-workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            [],
-            []
-        ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi)
-}
-
-// Basic parameters + optional intervals
-workflow test_gatk4_genotypegvcfs_gz_input_intervals {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ,
-            []
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
-}
-
-// Basic parameters + optional dbSNP + optional intervals
-workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
-            []
-        ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )
-}
-
-// Basic parameters with GenomicsDB input
-workflow test_gatk4_genotypegvcfs_gendb_input {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.map{ it[1] }.collect()
-    gendb.add([])
-    gendb.add([])
-    gendb.add([])
-
-    input = Channel.of([ id:'test' ]).combine(gendb)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
-}
-
-// Basic parameters with GenomicsDB + optional dbSNP
-workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.map{ it[1] }.collect()
-    gendb.add([])
-    gendb.add([])
-    gendb.add([])
-    input = Channel.of([ id:'test' ]).combine(gendb)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi)
-}
-
-// Basic parameters with GenomicsDB + optional intervals
-workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.map{ it[1] }.collect()
-    gendb.add([])
-    gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
-    gendb.add([])
-
-    input = Channel.of([ id:'test' ]).combine(gendb)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [] )
-}
-
-// Basic parameters with GenomicsDB + optional dbSNP + optional intervals
-workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.map{ it[1] }.collect()
-    gendb.add([])
-    gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
-    gendb.add([])
-
-    input = Channel.of([ id:'test' ]).combine(gendb)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )
-}
diff --git a/tests/modules/gatk4/genotypegvcfs/test.yml b/tests/modules/gatk4/genotypegvcfs/test.yml
deleted file mode 100644
index ec8ee9511de..00000000000
--- a/tests/modules/gatk4/genotypegvcfs/test.yml
+++ /dev/null
@@ -1,119 +0,0 @@
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_vcf_input
-  command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input
-  command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp
-  command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_intervals
-  command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals
-  command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains: ["AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693"]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
-  command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp
-  command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_intervals
-  command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals
-  command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains: ["AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693"]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/getpileupsummaries/main.nf b/tests/modules/gatk4/getpileupsummaries/main.nf
deleted file mode 100644
index 2a53e35e284..00000000000
--- a/tests/modules/gatk4/getpileupsummaries/main.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf'
-
-
-workflow test_gatk4_getpileupsummaries_separate_sites {
-
-    input = [ [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) ]
-
-    variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    fasta = []
-    fai = []
-    dict = []
-    GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi)
-}
-
-workflow test_gatk4_getpileupsummaries_separate_sites_cram {
-
-    input = [ [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) ,
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true)
-        ]
-
-    variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi)
-}
diff --git a/tests/modules/gatk4/getpileupsummaries/test.yml b/tests/modules/gatk4/getpileupsummaries/test.yml
deleted file mode 100644
index 2529fbc511e..00000000000
--- a/tests/modules/gatk4/getpileupsummaries/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites
-  command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config
-  tags:
-    - gatk4/getpileupsummaries
-    - gatk4
-  files:
-    - path: output/gatk4/test.pileups.table
-      md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram
-  command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c tests/config/nextflow.config
-  tags:
-    - gatk4/getpileupsummaries
-    - gatk4
-  files:
-    - path: output/gatk4/test.pileups.table
-      md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/haplotypecaller/main.nf b/tests/modules/gatk4/haplotypecaller/main.nf
deleted file mode 100644
index 3ad3dfb5deb..00000000000
--- a/tests/modules/gatk4/haplotypecaller/main.nf
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_HAPLOTYPECALLER } from '../../../../modules/gatk4/haplotypecaller/main.nf'
-
-workflow test_gatk4_haplotypecaller {
-    input     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                  [],
-                  []
-                ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [])
-}
-
-workflow test_gatk4_haplotypecaller_cram {
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                [],
-                []
-              ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [])
-}
-
-workflow test_gatk4_haplotypecaller_intervals_dbsnp {
-   input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
-                []
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-    sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
-}
-
-workflow test_gatk4_haplotypecaller_dragstr_model {
-   input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                [],
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true)
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-    sites = []
-    sites_tbi = []
-
-    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
-}
diff --git a/tests/modules/gatk4/haplotypecaller/test.yml b/tests/modules/gatk4/haplotypecaller/test.yml
deleted file mode 100644
index 96270644495..00000000000
--- a/tests/modules/gatk4/haplotypecaller/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: gatk4 haplotypecaller test_gatk4_haplotypecaller
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
-  tags:
-    - gatk4/haplotypecaller
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.tbi
-
-- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
-  tags:
-    - gatk4/haplotypecaller
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.tbi
-
-- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
-  tags:
-    - gatk4/haplotypecaller
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.tbi
-
-- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_dragstr_model
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_dragstr_model -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
-  tags:
-    - gatk4/haplotypecaller
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.tbi
diff --git a/tests/modules/gatk4/indexfeaturefile/main.nf b/tests/modules/gatk4/indexfeaturefile/main.nf
deleted file mode 100644
index f61b57fc532..00000000000
--- a/tests/modules/gatk4/indexfeaturefile/main.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_INDEXFEATUREFILE } from '../../../../modules/gatk4/indexfeaturefile/main.nf'
-
-workflow test_gatk4_indexfeaturefile_bed {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) 
-    ]
-
-    GATK4_INDEXFEATUREFILE ( input )
-}
-
-workflow test_gatk4_indexfeaturefile_bed_gz {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
-    ]
-
-    GATK4_INDEXFEATUREFILE ( input )
-}
-
-workflow test_gatk4_indexfeaturefile_vcf {
-    
-    input = [ 
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) 
-    ]
-
-    GATK4_INDEXFEATUREFILE ( input )
-}
-
-workflow test_gatk4_indexfeaturefile_vcf_gz {
-    
-    input = [ 
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) 
-    ]
-
-    GATK4_INDEXFEATUREFILE ( input )
-}
diff --git a/tests/modules/gatk4/indexfeaturefile/test.yml b/tests/modules/gatk4/indexfeaturefile/test.yml
deleted file mode 100644
index 9187fa4a594..00000000000
--- a/tests/modules/gatk4/indexfeaturefile/test.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed
-  command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/indexfeaturefile
-  files:
-    - path: output/gatk4/genome.bed.idx
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed_gz
-  command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/indexfeaturefile
-  files:
-    - path: output/gatk4/genome.bed.gz.tbi
-      md5sum: 4bc51e2351a6e83f20e13be75861f941
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf
-  command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/indexfeaturefile
-  files:
-    - path: output/gatk4/test.genome.vcf.idx
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz
-  command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/indexfeaturefile
-  files:
-    - path: output/gatk4/test.genome.vcf.gz.tbi
-      md5sum: fedd68eaddf8d31257853d9da8325bd3
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/intervallisttobed/main.nf b/tests/modules/gatk4/intervallisttobed/main.nf
deleted file mode 100644
index 2963979fd3a..00000000000
--- a/tests/modules/gatk4/intervallisttobed/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_INTERVALLISTTOBED } from '../../../../modules/gatk4/intervallisttobed/main.nf'
-
-workflow test_gatk4_intervallisttobed {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true)
-    ]
-
-    GATK4_INTERVALLISTTOBED ( input )
-}
diff --git a/tests/modules/gatk4/intervallisttobed/test.yml b/tests/modules/gatk4/intervallisttobed/test.yml
deleted file mode 100644
index a148f745802..00000000000
--- a/tests/modules/gatk4/intervallisttobed/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk4 intervallisttobed
-  command: nextflow run ./tests/modules/gatk4/intervallisttobed -entry test_gatk4_intervallisttobed -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/intervallisttobed/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/intervallisttobed
-  files:
-    - path: output/gatk4/test.bed
-      md5sum: 9046675d01199fbbee79f2bc1c5dce52
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/intervallisttools/main.nf b/tests/modules/gatk4/intervallisttools/main.nf
deleted file mode 100644
index 535923fbafb..00000000000
--- a/tests/modules/gatk4/intervallisttools/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/gatk4/bedtointervallist/main.nf'
-include { GATK4_INTERVALLISTTOOLS } from '../../../../modules/gatk4/intervallisttools/main.nf'
-
-workflow test_gatk4_intervallisttools {
-
-    input = [
-        [ id:'test' ],
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    ]
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_BEDTOINTERVALLIST ( input, dict )
-    GATK4_INTERVALLISTTOOLS ( GATK4_BEDTOINTERVALLIST.out.interval_list )
-}
diff --git a/tests/modules/gatk4/intervallisttools/test.yml b/tests/modules/gatk4/intervallisttools/test.yml
deleted file mode 100644
index 89367a09e92..00000000000
--- a/tests/modules/gatk4/intervallisttools/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: gatk4 intervallisttools test_gatk4_intervallisttools
-  command: nextflow run ./tests/modules/gatk4/intervallisttools -entry test_gatk4_intervallisttools -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/intervallisttools/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/intervallisttools
-  files:
-    - path: output/gatk4/test.interval_list
-      md5sum: e51101c9357fb2d59fd30e370eefa39c
-    - path: output/gatk4/test_split/temp_0001_of_6/1scattered.interval_list
-      md5sum: 39385d38ac6cb7c05190026fc3b81411
-    - path: output/gatk4/test_split/temp_0002_of_6/2scattered.interval_list
-      md5sum: 59f1978c5f4ef3fce3b110816283d9f5
-    - path: output/gatk4/test_split/temp_0003_of_6/3scattered.interval_list
-      md5sum: 709fe81bfcf700bd80d96c62a71629fd
-    - path: output/gatk4/test_split/temp_0004_of_6/4scattered.interval_list
-      md5sum: c24044490cfedbcba61dbc646d3aa570
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/learnreadorientationmodel/main.nf b/tests/modules/gatk4/learnreadorientationmodel/main.nf
deleted file mode 100644
index dc6e8b89b5a..00000000000
--- a/tests/modules/gatk4/learnreadorientationmodel/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../modules/gatk4/learnreadorientationmodel/main.nf'
-
-workflow test_gatk4_learnreadorientationmodel {
-
-    input = [ [ id:'test' ], // meta map
-              [file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_f1r2_tar_gz'], checkIfExists: true)] ]
-
-    GATK4_LEARNREADORIENTATIONMODEL ( input )
-}
diff --git a/tests/modules/gatk4/learnreadorientationmodel/test.yml b/tests/modules/gatk4/learnreadorientationmodel/test.yml
deleted file mode 100644
index d3d64c50973..00000000000
--- a/tests/modules/gatk4/learnreadorientationmodel/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: gatk4 learnreadorientationmodel test_gatk4_learnreadorientationmodel
-  command: nextflow run ./tests/modules/gatk4/learnreadorientationmodel -entry test_gatk4_learnreadorientationmodel -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/learnreadorientationmodel/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/learnreadorientationmodel
-  files:
-    - path: output/gatk4/test.artifact-prior.tar.gz
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/leftalignandtrimvariants/main.nf b/tests/modules/gatk4/leftalignandtrimvariants/main.nf
deleted file mode 100644
index 1d890a54458..00000000000
--- a/tests/modules/gatk4/leftalignandtrimvariants/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../modules/gatk4/leftalignandtrimvariants/main.nf'
-
-workflow test_gatk4_leftalignandtrimvariants_interval {
-
-    input = [ [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_leftalignandtrimvariants_no_interval {
-
-    input = [ [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        []
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
-}
diff --git a/tests/modules/gatk4/leftalignandtrimvariants/test.yml b/tests/modules/gatk4/leftalignandtrimvariants/test.yml
deleted file mode 100644
index ff4ab0c464b..00000000000
--- a/tests/modules/gatk4/leftalignandtrimvariants/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_interval
-  command: nextflow run ./tests/modules/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_interval -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/leftalignandtrimvariants/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/leftalignandtrimvariants
-  files:
-    - path: output/gatk4/test.normalised.vcf.gz
-      contains:
-        - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
-    - path: output/gatk4/test.normalised.vcf.gz.tbi
-
-- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_no_interval
-  command: nextflow run ./tests/modules/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_no_interval -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/leftalignandtrimvariants/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/leftalignandtrimvariants
-  files:
-    - path: output/gatk4/test.normalised.vcf.gz
-      contains:
-        - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
-        - "MT192765.1\t10502\t.\tTAGATTATGACTGTGTCTCTTTTTGTTACATGCACCA\tTAGAT"
-    - path: output/gatk4/test.normalised.vcf.gz.tbi
diff --git a/tests/modules/gatk4/markduplicates/main.nf b/tests/modules/gatk4/markduplicates/main.nf
deleted file mode 100644
index e5ece314c3d..00000000000
--- a/tests/modules/gatk4/markduplicates/main.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_MARKDUPLICATES } from '../../../../modules/gatk4/markduplicates/main.nf'
-include { GATK4_MARKDUPLICATES as GATK4_MARKDUPLICATES_CRAM } from '../../../../modules/gatk4/markduplicates/main.nf'
-
-workflow test_gatk4_markduplicates {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    GATK4_MARKDUPLICATES ( input, [], [] )
-}
-
-workflow test_gatk4_markduplicates_multiple_bams {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
-            ] ]
-
-    GATK4_MARKDUPLICATES ( input, [], [] )
-}
-
-workflow test_gatk4_markduplicates_multiple_cram_output {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
-            ] ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    GATK4_MARKDUPLICATES_CRAM ( input, fasta, fai )
-}
diff --git a/tests/modules/gatk4/markduplicates/test.yml b/tests/modules/gatk4/markduplicates/test.yml
deleted file mode 100644
index 0d15297d389..00000000000
--- a/tests/modules/gatk4/markduplicates/test.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-- name: gatk4 markduplicates test_gatk4_markduplicates
-  command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicates/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/markduplicates
-  files:
-    - path: output/gatk4/test.bai
-      md5sum: 4ac375b5288501c832bc3e4773f06d39
-    - path: output/gatk4/test.bam
-      md5sum: c1a0d25c5f65514e72aa490326557a88
-    - path: output/gatk4/test.bam.metrics
-
-- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
-  command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicates/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/markduplicates
-  files:
-    - path: output/gatk4/test.bai
-      md5sum: 832fbc6b3c3266d024fc7131ffd1b45d
-    - path: output/gatk4/test.bam
-      md5sum: 36909e80bde1aa547fae6382fd35764d
-    - path: output/gatk4/test.bam.metrics
-      contains:
-        - "testN"
-        - "2820"
-
-- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_cram_output
-  command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_cram_output -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicates/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/markduplicates
-  files:
-    - path: output/gatk4/test.cram
-    - path: output/gatk4/test.cram.crai
-      md5sum: 53a329f0828210e317ad81b0e6ca4bc5
-    - path: output/gatk4/test.cram.metrics
-      contains:
-        - "testN"
-        - "2820"
diff --git a/tests/modules/gatk4/markduplicatesspark/main.nf b/tests/modules/gatk4/markduplicatesspark/main.nf
deleted file mode 100644
index 004fbb1e3f1..00000000000
--- a/tests/modules/gatk4/markduplicatesspark/main.nf
+++ /dev/null
@@ -1,57 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
-include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
-include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
-
-workflow test_gatk4_markduplicates_spark {
-    input = [ [ id:'test', single_end:false ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
-}
-
-// chr 22
-workflow test_gatk4_markduplicates_spark_multiple_bams {
-    input = [ [ id:'test', single_end:false ], // meta map
-            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
-            ] ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
-}
-
-// chr 22
-workflow test_gatk4_markduplicates_spark_multiple_bams_cram_out {
-    input = [ [ id:'test', single_end:false ], // meta map
-            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
-            ] ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_MARKDUPLICATES_SPARK_CRAM ( input, fasta, fai, dict )
-}
-
-// chr 22
-workflow test_gatk4_markduplicates_spark_multiple_bams_metrics {
-    input = [ [ id:'test', single_end:false ], // meta map
-            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
-            ] ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_MARKDUPLICATES_SPARK_METRICS ( input, fasta, fai, dict )
-}
diff --git a/tests/modules/gatk4/markduplicatesspark/test.yml b/tests/modules/gatk4/markduplicatesspark/test.yml
deleted file mode 100644
index 4ef9b9161a0..00000000000
--- a/tests/modules/gatk4/markduplicatesspark/test.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark
-  command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/markduplicatesspark
-  files:
-    - path: output/gatk4/test.bam
-      md5sum: dc1a09ac6371aab7c50d1a554baa06d3
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams
-  command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/markduplicatesspark
-  files:
-    - path: output/gatk4/test.bam
-      md5sum: 898cb0a6616897d8ada90bab53bf0837
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_cram_out
-  command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_cram_out -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/markduplicatesspark
-  files:
-    - path: output/gatk4/test.cram
-      md5sum: 2271016de5e4199736598f39d12d7587
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_metrics
-  command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_metrics -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/markduplicatesspark
-  files:
-    - path: output/gatk4/test.bam
-      md5sum: 898cb0a6616897d8ada90bab53bf0837
-    - path: output/gatk4/test.metrics
-      contains: ["## METRICS CLASS", "org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics"]
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/mergebamalignment/main.nf b/tests/modules/gatk4/mergebamalignment/main.nf
deleted file mode 100644
index d0949a523cf..00000000000
--- a/tests/modules/gatk4/mergebamalignment/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalignment/main.nf'
-
-workflow test_gatk4_mergebamalignment {
-    input    = [ [ id:'test' ], // meta map
-                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
-               ]
-    fasta    = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    dict     = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
-}
-
-workflow test_gatk4_mergebamalignment_stubs {
-     input    = [ [ id:'test' ], // meta map
-                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
-               ]
-    fasta    = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    dict     = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
-}
diff --git a/tests/modules/gatk4/mergebamalignment/test.yml b/tests/modules/gatk4/mergebamalignment/test.yml
deleted file mode 100644
index 01d9bf4617e..00000000000
--- a/tests/modules/gatk4/mergebamalignment/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: gatk4 mergebamalignment test_gatk4_mergebamalignment
-  command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/mergebamalignment
-  files:
-    - path: output/gatk4/test.bam
-      md5sum: e6f1b343700b7ccb94e81ae127433988
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
-  command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
-  tags:
-    - gatk4
-    - gatk4/mergebamalignment
-  files:
-    - path: output/gatk4/test.bam
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/mergemutectstats/main.nf b/tests/modules/gatk4/mergemutectstats/main.nf
deleted file mode 100644
index bf65a6a67e3..00000000000
--- a/tests/modules/gatk4/mergemutectstats/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_MERGEMUTECTSTATS } from '../../../../modules/gatk4/mergemutectstats/main.nf'
-
-workflow test_gatk4_mergemutectstats {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-         file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true)
-        ]
-
-    GATK4_MERGEMUTECTSTATS ( input )
-}
diff --git a/tests/modules/gatk4/mergemutectstats/test.yml b/tests/modules/gatk4/mergemutectstats/test.yml
deleted file mode 100644
index cc71854e6a6..00000000000
--- a/tests/modules/gatk4/mergemutectstats/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk4 mergemutectstats
-  command: nextflow run ./tests/modules/gatk4/mergemutectstats -entry test_gatk4_mergemutectstats -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergemutectstats/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/mergemutectstats
-  files:
-    - path: output/gatk4/test.vcf.gz.stats
-      md5sum: 17d2091015d04cbd4a26b7a67dc659e6
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/mergevcfs/main.nf b/tests/modules/gatk4/mergevcfs/main.nf
deleted file mode 100644
index 32569bdf46b..00000000000
--- a/tests/modules/gatk4/mergevcfs/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_MERGEVCFS } from '../../../../modules/gatk4/mergevcfs/main.nf'
-
-workflow test_gatk4_mergevcfs {
-    def input = []
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
-            ]
-
-    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_MERGEVCFS ( input, dict )
-}
-
-workflow test_gatk4_mergevcfs_no_dict {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
-            ]
-
-    GATK4_MERGEVCFS ( input, [] )
-}
-
-workflow test_gatk4_mergevcfs_no_dict_stubs {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
-            ]
-
-    GATK4_MERGEVCFS ( input, [] )
-}
diff --git a/tests/modules/gatk4/mergevcfs/test.yml b/tests/modules/gatk4/mergevcfs/test.yml
deleted file mode 100644
index 57400748d8e..00000000000
--- a/tests/modules/gatk4/mergevcfs/test.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-- name: gatk4 mergevcfs test_gatk4_mergevcfs
-  command: nextflow run ./tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergevcfs/nextflow.config
-  tags:
-    - gatk4/mergevcfs
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-      md5sum: 5b289bda88d3a3504f2e19ee8cff177c
-    - path: output/gatk4/test.vcf.gz.tbi
-      md5sum: a81673763b13086cfce9a23e72a35a16
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 mergevcfs test_gatk4_mergevcfs_no_dict
-  command: nextflow run ./tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs_no_dict -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergevcfs/nextflow.config
-  tags:
-    - gatk4/mergevcfs
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-      md5sum: 5b289bda88d3a3504f2e19ee8cff177c
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 mergevcfs test_gatk4_mergevcfs_no_dict_stubs
-  command: nextflow run ./tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs_no_dict_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergevcfs/nextflow.config -stub-run
-  tags:
-    - gatk4/mergevcfs
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf
deleted file mode 100644
index fa229effd4e..00000000000
--- a/tests/modules/gatk4/mutect2/main.nf
+++ /dev/null
@@ -1,142 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_MUTECT2                       } from '../../../../modules/gatk4/mutect2/main.nf'
-include { GATK4_MUTECT2 as GATK4_MUTECT2_PAIR } from '../../../../modules/gatk4/mutect2/main.nf'
-include { GATK4_MUTECT2 as GATK4_MUTECT2_MITO } from '../../../../modules/gatk4/mutect2/main.nf'
-include { GATK4_MUTECT2 as GATK4_MUTECT2_F1R2 } from '../../../../modules/gatk4/mutect2/main.nf'
-
-workflow test_gatk4_mutect2_tumor_normal_pair {
-    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
-                ],
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
-                ],
-              []
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
-    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_MUTECT2_PAIR ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
-}
-
-workflow test_gatk4_mutect2_tumor_normal_pair_f1r2 {
-    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
-                ],
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
-                ],
-              []
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
-    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
-}
-
-workflow test_gatk4_mutect2_tumor_single {
-    input = [ [ id:'test'], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
-              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
-              []
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
-    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
-}
-
-workflow test_gatk4_mutect2_cram_input {
-    input = [ [ id:'test'], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)],
-              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)],
-              []
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
-    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
-}
-
-workflow test_gatk4_mutect2_generate_pon {
-    input = [ [ id:'test'], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
-              []
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_MUTECT2 ( input, fasta, fai, dict, [], [], [], [] )
-}
-
-// mitochondria mode would ideally have some mitochondria test data
-// but since the mitochondria settings only increase detection sensitivity
-// we can use the chr22 data as a stand in as it is already a small dataset
-// the extra variants detected compared to generate_pon shows the mode is working
-workflow test_gatk4_mutect2_mitochondria {
-    input = [ [ id:'test'], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam'], checkIfExists: true)],
-              [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam_bai'], checkIfExists: true)],
-              [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] )
-}
-
-workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
-     input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
-                ],
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
-                ],
-              []
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
-    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
-}
diff --git a/tests/modules/gatk4/mutect2/test.yml b/tests/modules/gatk4/mutect2/test.yml
deleted file mode 100644
index 27fb40b9ce9..00000000000
--- a/tests/modules/gatk4/mutect2/test.yml
+++ /dev/null
@@ -1,83 +0,0 @@
-- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/mutect2
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.stats
-      md5sum: 17d2091015d04cbd4a26b7a67dc659e6
-    - path: output/gatk4/test.vcf.gz.tbi
-
-- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/mutect2
-  files:
-    - path: output/gatk4/test.f1r2.tar.gz
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.stats
-      md5sum: 17d2091015d04cbd4a26b7a67dc659e6
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/mutect2
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.stats
-      md5sum: 55ed641e16089afb33cdbc478e202d3d
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 mutect2 test_gatk4_mutect2_cram_input
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_cram_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/mutect2
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.stats
-      md5sum: 55ed641e16089afb33cdbc478e202d3d
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_generate_pon -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/mutect2
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.stats
-      md5sum: b569ce66bbffe9588b3d221e821023ee
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 mutect2 test_gatk4_mutect2_mitochondria
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_mitochondria -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/mutect2
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.stats
-      md5sum: fc6ea14ca2da346babe78161beea28c9
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
-  tags:
-    - gatk4
-    - gatk4/mutect2
-  files:
-    - path: output/gatk4/test.f1r2.tar.gz
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.stats
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/printsvevidence/main.nf b/tests/modules/gatk4/printsvevidence/main.nf
deleted file mode 100644
index 17a4d99ee1a..00000000000
--- a/tests/modules/gatk4/printsvevidence/main.nf
+++ /dev/null
@@ -1,116 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_PE } from '../../../../modules/gatk4/printsvevidence/main.nf'
-include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_SR } from '../../../../modules/gatk4/printsvevidence/main.nf'
-include { GATK4_COLLECTSVEVIDENCE                           } from '../../../../modules/gatk4/collectsvevidence/main.nf'
-
-workflow test_gatk4_printsvevidence {
-    
-    input = Channel.of(
-        [
-            [ id:'normal', single_end:false ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-            [],
-            []
-        ],
-        [
-            [ id:'tumour', single_end:false ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
-            [],
-            []
-        ]
-    )
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-
-    GATK4_COLLECTSVEVIDENCE(
-        input, 
-        fasta, 
-        fasta_fai, 
-        dict
-    )
-
-    pe_files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence
-                    .combine(GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index, by:0)
-    sr_files = GATK4_COLLECTSVEVIDENCE.out.split_read_evidence
-                    .combine(GATK4_COLLECTSVEVIDENCE.out.split_read_evidence_index, by:0)
-
-    GATK4_PRINTSVEVIDENCE_PE( 
-        pe_files,
-        [],
-        fasta,
-        fasta_fai,
-        dict
-    )
-
-    GATK4_PRINTSVEVIDENCE_SR( 
-        sr_files,
-        [],
-        fasta,
-        fasta_fai,
-        dict
-    )
-
-}
-
-workflow test_gatk4_printsvevidence_bed_no_fasta {
-    
-    input = Channel.of(
-        [
-            [ id:'normal', single_end:false ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-            [],
-            []
-        ],
-        [
-            [ id:'tumour', single_end:false ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
-            [],
-            []
-        ]
-    )
-
-    fasta = []
-    fasta_fai = []
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-
-    GATK4_COLLECTSVEVIDENCE(
-        input, 
-        fasta, 
-        fasta_fai, 
-        dict
-    )
-
-    pe_files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence
-                    .combine(GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index, by:0)
-    sr_files = GATK4_COLLECTSVEVIDENCE.out.split_read_evidence
-                    .combine(GATK4_COLLECTSVEVIDENCE.out.split_read_evidence_index, by:0)
-
-    GATK4_PRINTSVEVIDENCE_PE( 
-        pe_files,
-        bed,
-        fasta,
-        fasta_fai,
-        dict
-    )
-
-    GATK4_PRINTSVEVIDENCE_SR( 
-        sr_files,
-        bed,
-        fasta,
-        fasta_fai,
-        dict
-    )
-
-}
diff --git a/tests/modules/gatk4/printsvevidence/test.yml b/tests/modules/gatk4/printsvevidence/test.yml
deleted file mode 100644
index 880959a0840..00000000000
--- a/tests/modules/gatk4/printsvevidence/test.yml
+++ /dev/null
@@ -1,77 +0,0 @@
-- name: gatk4 printsvevidence test_gatk4_printsvevidence
-  command: nextflow run ./tests/modules/gatk4/printsvevidence -entry test_gatk4_printsvevidence -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/printsvevidence/nextflow.config
-  tags:
-    - gatk4/printsvevidence
-    - gatk4
-  files:
-    - path: output/gatk4/normal.pe.txt.gz
-      md5sum: 19f13dd0408204590b40239d14acbdde
-    - path: output/gatk4/normal.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/normal.sr.txt.gz
-      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
-    - path: output/gatk4/normal.sr.txt.gz.tbi
-      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
-    - path: output/gatk4/normal_print.pe.txt.gz
-      md5sum: 19f13dd0408204590b40239d14acbdde
-    - path: output/gatk4/normal_print.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/normal_print.sr.txt.gz
-      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
-    - path: output/gatk4/normal_print.sr.txt.gz.tbi
-      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
-    - path: output/gatk4/tumour.pe.txt.gz
-      md5sum: 11fb8aeeea29370d9d1b49448456da81
-    - path: output/gatk4/tumour.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/tumour.sr.txt.gz
-      md5sum: 3ce47a0e0abac1c2b291e73a2b57cba0
-    - path: output/gatk4/tumour.sr.txt.gz.tbi
-      md5sum: f2105270ba79ed645bac9842be79f411
-    - path: output/gatk4/tumour_print.pe.txt.gz
-      md5sum: 11fb8aeeea29370d9d1b49448456da81
-    - path: output/gatk4/tumour_print.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/tumour_print.sr.txt.gz
-      md5sum: 3ce47a0e0abac1c2b291e73a2b57cba0
-    - path: output/gatk4/tumour_print.sr.txt.gz.tbi
-      md5sum: f2105270ba79ed645bac9842be79f411
-
-- name: gatk4 printsvevidence test_gatk4_printsvevidence_bed_no_fasta
-  command: nextflow run ./tests/modules/gatk4/printsvevidence -entry test_gatk4_printsvevidence_bed_no_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/printsvevidence/nextflow.config
-  tags:
-    - gatk4/printsvevidence
-    - gatk4
-  files:
-    - path: output/gatk4/normal.pe.txt.gz
-      md5sum: 19f13dd0408204590b40239d14acbdde
-    - path: output/gatk4/normal.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/normal.sr.txt.gz
-      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
-    - path: output/gatk4/normal.sr.txt.gz.tbi
-      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
-    - path: output/gatk4/normal_print.pe.txt.gz
-      md5sum: 19f13dd0408204590b40239d14acbdde
-    - path: output/gatk4/normal_print.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/normal_print.sr.txt.gz
-      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
-    - path: output/gatk4/normal_print.sr.txt.gz.tbi
-      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
-    - path: output/gatk4/tumour.pe.txt.gz
-      md5sum: 11fb8aeeea29370d9d1b49448456da81
-    - path: output/gatk4/tumour.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/tumour.sr.txt.gz
-      md5sum: 3ce47a0e0abac1c2b291e73a2b57cba0
-    - path: output/gatk4/tumour.sr.txt.gz.tbi
-      md5sum: f2105270ba79ed645bac9842be79f411
-    - path: output/gatk4/tumour_print.pe.txt.gz
-      md5sum: 11fb8aeeea29370d9d1b49448456da81
-    - path: output/gatk4/tumour_print.pe.txt.gz.tbi
-      md5sum: 876170d2727a467263cbacecbd9979ee
-    - path: output/gatk4/tumour_print.sr.txt.gz
-      md5sum: 3ce47a0e0abac1c2b291e73a2b57cba0
-    - path: output/gatk4/tumour_print.sr.txt.gz.tbi
-      md5sum: f2105270ba79ed645bac9842be79f411
diff --git a/tests/modules/gatk4/reblockgvcf/main.nf b/tests/modules/gatk4/reblockgvcf/main.nf
deleted file mode 100644
index 2233a5c571a..00000000000
--- a/tests/modules/gatk4/reblockgvcf/main.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_REBLOCKGVCF } from '../../../../modules/gatk4/reblockgvcf/main.nf'
-
-workflow test_gatk4_reblockgvcf {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        []
-    ]
-
-    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_index = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict        = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, [], [] )
-}
-
-workflow test_gatk4_reblockgvcf_intervals {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    ]
-
-    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_index = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict        = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, [], [] )
-}
-
-workflow test_gatk4_reblockgvcf_dbsnp {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true),
-        []
-    ]
-
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict        = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-    dbsnp       = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi   = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, dbsnp, dbsnp_tbi )
-}
\ No newline at end of file
diff --git a/tests/modules/gatk4/reblockgvcf/test.yml b/tests/modules/gatk4/reblockgvcf/test.yml
deleted file mode 100644
index 623f58a69b7..00000000000
--- a/tests/modules/gatk4/reblockgvcf/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: gatk4 reblockgvcf test_gatk4_reblockgvcf
-  command: nextflow run ./tests/modules/gatk4/reblockgvcf -entry test_gatk4_reblockgvcf -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/reblockgvcf/nextflow.config
-  tags:
-    - gatk4/reblockgvcf
-    - gatk4
-  files:
-    - path: output/gatk4/test.rb.g.vcf.gz
-    - path: output/gatk4/test.rb.g.vcf.gz.tbi
-
-- name: gatk4 reblockgvcf test_gatk4_reblockgvcf_intervals
-  command: nextflow run ./tests/modules/gatk4/reblockgvcf -entry test_gatk4_reblockgvcf_intervals -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/reblockgvcf/nextflow.config
-  tags:
-    - gatk4/reblockgvcf
-    - gatk4
-  files:
-    - path: output/gatk4/test.rb.g.vcf.gz
-    - path: output/gatk4/test.rb.g.vcf.gz.tbi
-
-- name: gatk4 reblockgvcf test_gatk4_reblockgvcf_dbsnp
-  command: nextflow run ./tests/modules/gatk4/reblockgvcf -entry test_gatk4_reblockgvcf_dbsnp -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/reblockgvcf/nextflow.config
-  tags:
-    - gatk4/reblockgvcf
-    - gatk4
-  files:
-    - path: output/gatk4/test.rb.g.vcf.gz
-    - path: output/gatk4/test.rb.g.vcf.gz.tbi
diff --git a/tests/modules/gatk4/revertsam/main.nf b/tests/modules/gatk4/revertsam/main.nf
deleted file mode 100644
index 5b14d471920..00000000000
--- a/tests/modules/gatk4/revertsam/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_REVERTSAM } from '../../../../modules/gatk4/revertsam/main.nf'
-
-workflow test_gatk4_revertsam {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-            ]
-
-    GATK4_REVERTSAM ( input )
-}
-
-workflow test_gatk4_revertsam_stubs {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-            ]
-
-    GATK4_REVERTSAM ( input )
-}
diff --git a/tests/modules/gatk4/revertsam/test.yml b/tests/modules/gatk4/revertsam/test.yml
deleted file mode 100644
index fd26d06f8c2..00000000000
--- a/tests/modules/gatk4/revertsam/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: gatk4 revertsam test_gatk4_revertsam
-  command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/revertsam
-  files:
-    - path: output/gatk4/test.reverted.bam
-      md5sum: f783a88deb45c3a2c20ca12cbe1c5652
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 revertsam test_gatk4_revertsam_stubs
-  command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
-  tags:
-    - gatk4
-    - gatk4/revertsam
-  files:
-    - path: output/gatk4/test.reverted.bam
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/samtofastq/main.nf b/tests/modules/gatk4/samtofastq/main.nf
deleted file mode 100644
index 757b080fd1d..00000000000
--- a/tests/modules/gatk4/samtofastq/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_SAMTOFASTQ } from '../../../../modules/gatk4/samtofastq/main.nf'
-
-workflow test_gatk4_samtofastq_single_end {
-    input = [ [ id:'test', single_end: true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
-            ]
-
-    GATK4_SAMTOFASTQ ( input )
-}
-
-workflow test_gatk4_samtofastq_paired_end {
-    input = [ [ id:'test', single_end: false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
-            ]
-
-    GATK4_SAMTOFASTQ ( input )
-}
-
-workflow test_gatk4_samtofastq_paired_end_stubs {
-    input = [ [ id:'test', single_end: true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
-            ]
-
-    GATK4_SAMTOFASTQ ( input )
-}
diff --git a/tests/modules/gatk4/samtofastq/test.yml b/tests/modules/gatk4/samtofastq/test.yml
deleted file mode 100644
index bab7fc7ab45..00000000000
--- a/tests/modules/gatk4/samtofastq/test.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- name: gatk4 samtofastq test_gatk4_samtofastq_single_end
-  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/samtofastq
-  files:
-    - path: output/gatk4/test.fastq.gz
-      md5sum: 50ace41d4c24467f24f8b929540a7797
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end
-  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/samtofastq
-  files:
-    - path: output/gatk4/test_1.fastq.gz
-      md5sum: cfea607c9d75fd9ea9704780ad3a499c
-    - path: output/gatk4/test_2.fastq.gz
-      md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
-  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
-  tags:
-    - gatk4
-    - gatk4/samtofastq
-  files:
-    - path: output/gatk4/test_1.fastq.gz
-    - path: output/gatk4/test_2.fastq.gz
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/selectvariants/main.nf b/tests/modules/gatk4/selectvariants/main.nf
deleted file mode 100644
index 7005dcd363e..00000000000
--- a/tests/modules/gatk4/selectvariants/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_SELECTVARIANTS } from '../../../../modules/gatk4/selectvariants/main.nf'
-
-// Basic parameters with uncompressed VCF input
-workflow test_gatk4_selectvariants_vcf_input {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true)
-    ]
-
-    GATK4_SELECTVARIANTS ( input)
-}
-
-// Basic parameters with compressed VCF input
-workflow test_gatk4_selectvariants_gz_input {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    GATK4_SELECTVARIANTS ( input )
-}
diff --git a/tests/modules/gatk4/selectvariants/test.yml b/tests/modules/gatk4/selectvariants/test.yml
deleted file mode 100644
index 42d9dbd8677..00000000000
--- a/tests/modules/gatk4/selectvariants/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: gatk4 selectvariants test_gatk4_selectvariants_vcf_input
-  command: nextflow run tests/modules/gatk4/selectvariants -entry test_gatk4_selectvariants_vcf_input -c tests/config/nextflow.config
-  tags:
-    - gatk4/selectvariants
-    - gatk4
-  files:
-    - path: output/gatk4/test.selectvariants.vcf.gz
-    - path: output/gatk4/test.selectvariants.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 selectvariants test_gatk4_selectvariants_gz_input
-  command: nextflow run tests/modules/gatk4/selectvariants -entry test_gatk4_selectvariants_gz_input -c tests/config/nextflow.config
-  tags:
-    - gatk4/selectvariants
-    - gatk4
-  files:
-    - path: output/gatk4/test.selectvariants.vcf.gz
-    - path: output/gatk4/test.selectvariants.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/splitintervals/main.nf b/tests/modules/gatk4/splitintervals/main.nf
deleted file mode 100644
index f507ece5039..00000000000
--- a/tests/modules/gatk4/splitintervals/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_SPLITINTERVALS } from '../../../../modules/gatk4/splitintervals/main.nf'
-
-workflow test_gatk4_splitintervals_bed {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_SPLITINTERVALS ( input, fasta, fasta_fai, fasta_dict)
-}
-
-workflow test_gatk4_splitintervals_intervals {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_SPLITINTERVALS ( input, fasta, fasta_fai, fasta_dict)
-}
\ No newline at end of file
diff --git a/tests/modules/gatk4/splitintervals/test.yml b/tests/modules/gatk4/splitintervals/test.yml
deleted file mode 100644
index 741c6becf62..00000000000
--- a/tests/modules/gatk4/splitintervals/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: gatk4 splitintervals test_gatk4_splitintervals_bed
-  command: nextflow run tests/modules/gatk4/splitintervals -entry test_gatk4_splitintervals_bed -c tests/config/nextflow.config
-  tags:
-    - gatk4/splitintervals
-    - gatk4
-  files:
-    - path: output/gatk4/test/0000-scattered.interval_list
-      md5sum: c8d6b19e7a92535b6ce9608eae558faa
-    - path: output/gatk4/test/0001-scattered.interval_list
-      md5sum: b1877ad96aec308906594c50ebbe3ded
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 splitintervals test_gatk4_splitintervals_intervals
-  command: nextflow run tests/modules/gatk4/splitintervals -entry test_gatk4_splitintervals_intervals -c tests/config/nextflow.config
-  tags:
-    - gatk4/splitintervals
-    - gatk4
-  files:
-    - path: output/gatk4/test/0000-scattered.interval_list
-      md5sum: ebd6b34a335efc6732ff541936c6d2d5
-    - path: output/gatk4/test/0001-scattered.interval_list
-      md5sum: 9459b0e124fa84ec1e64ac4615bc9af7
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/splitncigarreads/main.nf b/tests/modules/gatk4/splitncigarreads/main.nf
deleted file mode 100644
index 31e45cec195..00000000000
--- a/tests/modules/gatk4/splitncigarreads/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_SPLITNCIGARREADS } from '../../../../modules/gatk4/splitncigarreads/main.nf'
-
-workflow test_gatk4_splitncigarreads {
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-                [],
-                []
-            ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_splitncigarreads_intervals {
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
-}
diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml
deleted file mode 100644
index 261f7bc3f57..00000000000
--- a/tests/modules/gatk4/splitncigarreads/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: gatk4 splitncigarreads test_gatk4_splitncigarreads
-  command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/splitncigarreads
-  files:
-    - path: output/gatk4/test.bam
-      md5sum: 37e5dbce8692b54c3292b539c91dfbd7
-    - path: output/gatk4/versions.yml
-- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
-  command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/splitncigarreads
-  files:
-    - path: output/gatk4/test.bam
-      md5sum: e5cd2fd1822298a9bf7bc8b8d42146af
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/variantfiltration/main.nf b/tests/modules/gatk4/variantfiltration/main.nf
deleted file mode 100644
index 221c469acd0..00000000000
--- a/tests/modules/gatk4/variantfiltration/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_VARIANTFILTRATION } from '../../../../modules/gatk4/variantfiltration/main.nf'
-
-// Basic parameters with uncompressed VCF input
-workflow test_gatk4_variantfiltration_vcf_input {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true)
-    ]
-
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    fasta_dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_VARIANTFILTRATION ( input, fasta, fasta_index, fasta_dict )
-}
-
-// Basic parameters with compressed VCF input
-workflow test_gatk4_variantfiltration_gz_input {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    fasta_dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_VARIANTFILTRATION ( input, fasta, fasta_index, fasta_dict )
-}
-
-
diff --git a/tests/modules/gatk4/variantfiltration/test.yml b/tests/modules/gatk4/variantfiltration/test.yml
deleted file mode 100644
index 0ab91091ee6..00000000000
--- a/tests/modules/gatk4/variantfiltration/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: gatk4 variantfiltration test_gatk4_variantfiltration_vcf_input
-  command: nextflow run ./tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/variantfiltration/nextflow.config
-  tags:
-    - gatk4/variantfiltration
-    - gatk4
-  files:
-    - path: output/gatk4/test.filtered.vcf.gz
-      contains:
-        [
-          "BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365",
-        ]
-    - path: output/gatk4/test.filtered.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 variantfiltration test_gatk4_variantfiltration_gz_input
-  command: nextflow run ./tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/variantfiltration/nextflow.config
-  tags:
-    - gatk4/variantfiltration
-    - gatk4
-  files:
-    - path: output/gatk4/test.filtered.vcf.gz
-      contains:
-        [
-          "BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365",
-        ]
-    - path: output/gatk4/test.filtered.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/variantrecalibrator/main.nf b/tests/modules/gatk4/variantrecalibrator/main.nf
deleted file mode 100644
index 6ece09ebb5a..00000000000
--- a/tests/modules/gatk4/variantrecalibrator/main.nf
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY   } from '../../../../modules/gatk4/variantrecalibrator/main.nf'
-include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../modules/gatk4/variantrecalibrator/main.nf'
-
-workflow test_gatk4_variantrecalibrator {
-
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
-            ]
-
-    resources_vcf = [
-                    file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-                ]
-    resources_tbi = [
-                    file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-                ]
-    labels = [
-                '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz',
-                '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz',
-                '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz',
-                '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz'
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY(input, resources_vcf, resources_tbi, labels, fasta, fai, dict)
-}
-
-workflow test_gatk4_variantrecalibrator_allele_specific {
-
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
-            ]
-
-    resources_vcf = [
-                    file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
-                ]
-    resources_tbi = [
-                    file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
-                ]
-    labels = [
-                '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz',
-                '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz',
-                '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz',
-                '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz'
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY(input, resources_vcf, resources_tbi, labels, fasta, fai, dict)
-}
diff --git a/tests/modules/gatk4/variantrecalibrator/test.yml b/tests/modules/gatk4/variantrecalibrator/test.yml
deleted file mode 100644
index 39931137ad1..00000000000
--- a/tests/modules/gatk4/variantrecalibrator/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator
-  command: nextflow run tests/modules/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator -c tests/config/nextflow.config -c ./tests/modules/gatk4/variantrecalibrator/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/variantrecalibrator
-  files:
-    - path: output/gatk4/test.recal
-      contains:
-        - "#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"
-    - path: output/gatk4/test.recal.idx
-    - path: output/gatk4/test.tranches
-      md5sum: c029e52fd63a893e1154cc9144a19eeb
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific
-  command: nextflow run tests/modules/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator_allele_specific -c tests/config/nextflow.config -c ./tests/modules/gatk4/variantrecalibrator/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/variantrecalibrator
-  files:
-    - path: output/gatk4/test.recal
-      contains:
-        - "#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"
-    - path: output/gatk4/test.recal.idx
-    - path: output/gatk4/test.tranches
-      md5sum: ad52fa69325c758f458a30ee5b43d6b5
-    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gecco/run/main.nf b/tests/modules/gecco/run/main.nf
deleted file mode 100644
index 42ff5f3d9da..00000000000
--- a/tests/modules/gecco/run/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GECCO_RUN } from '../../../../modules/gecco/run/main.nf'
-
-workflow test_gecco_run {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true),
-        []
-    ]
-    model_dir = []
-
-    GECCO_RUN ( input, model_dir )
-}
diff --git a/tests/modules/gecco/run/test.yml b/tests/modules/gecco/run/test.yml
deleted file mode 100644
index 0fe67e68005..00000000000
--- a/tests/modules/gecco/run/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: gecco run test_gecco_run
-  command: nextflow run ./tests/modules/gecco/run -entry test_gecco_run -c ./tests/config/nextflow.config  -c ./tests/modules/gecco/run/nextflow.config
-  tags:
-    - gecco/run
-    - gecco
-  files:
-    - path: output/gecco/NC_018507.1_cluster_1.gbk
-    - path: output/gecco/genome.clusters.tsv
-      md5sum: 6560ec765f6bbae50645896fd93b35cd
-    - path: output/gecco/genome.features.tsv
-      md5sum: 07492cf186003311ba9829056c65787f
-    - path: output/gecco/genome.genes.tsv
-      md5sum: 031a37dc603f8a5296f462608fd7bcc3
diff --git a/tests/modules/genescopefk/main.nf b/tests/modules/genescopefk/main.nf
deleted file mode 100644
index e61b6d89252..00000000000
--- a/tests/modules/genescopefk/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTK_FASTK  } from '../../../modules/fastk/fastk/main.nf'
-include { FASTK_HISTEX } from '../../../modules/fastk/histex/main.nf'
-include { GENESCOPEFK  } from '../../../modules/genescopefk/main.nf'
-
-workflow test_genescopefk {
-
-    input = [
-        [ id:'test' , single_end: true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-    FASTK_HISTEX ( FASTK_FASTK.out.hist )
-    GENESCOPEFK ( FASTK_HISTEX.out.hist )
-}
diff --git a/tests/modules/genescopefk/test.yml b/tests/modules/genescopefk/test.yml
deleted file mode 100644
index db4156ec132..00000000000
--- a/tests/modules/genescopefk/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: genescopefk test_genescopefk
-  command: nextflow run ./tests/modules/genescopefk -entry test_genescopefk -c ./tests/config/nextflow.config  -c ./tests/modules/genescopefk/nextflow.config
-  tags:
-    - genescopefk
-  files:
-    - path: output/genescopefk/test_linear_plot.png
-      md5sum: bb221e2e21a6c0d04dcb6ec8f1bf1cd7
-    - path: output/genescopefk/test_log_plot.png
-      md5sum: d71ad0c963775992043c8f3c55d27fc4
-    - path: output/genescopefk/test_model.txt
-      md5sum: 49e5a66cf02b53a3b20880bfabef2ee8
-    - path: output/genescopefk/test_summary.txt
-      md5sum: 34540dcc2ba4ab9530f8878bbdc0921c
-    - path: output/genescopefk/test_transformed_linear_plot.png
-      md5sum: 3c8e3ad315e6c15cdf51c87de277ec1f
-    - path: output/genescopefk/test_transformed_log_plot.png
-      md5sum: 90d983c6faa9b8a02a1d26b777feefc6
diff --git a/tests/modules/genmap/index/main.nf b/tests/modules/genmap/index/main.nf
deleted file mode 100644
index 061066400f3..00000000000
--- a/tests/modules/genmap/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf'
-
-workflow test_genmap_index {
-
-    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    GENMAP_INDEX ( input )
-}
diff --git a/tests/modules/genmap/index/test.yml b/tests/modules/genmap/index/test.yml
deleted file mode 100644
index ce2098ce712..00000000000
--- a/tests/modules/genmap/index/test.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-- name: genmap index test_genmap_index
-  command: nextflow run ./tests/modules/genmap/index -entry test_genmap_index -c ./tests/config/nextflow.config -c ./tests/modules/genmap/index/nextflow.config
-  tags:
-    - genmap
-    - genmap/index
-  files:
-    - path: output/genmap/genmap/index.ids.concat
-      md5sum: da6caa25f62c5407ccdfbcce1fa92408
-    - path: output/genmap/genmap/index.ids.limits
-      md5sum: f82636c5da188aec131d3a809473eff1
-    - path: output/genmap/genmap/index.info.concat
-      md5sum: 8ba5273aa9e58722bf45b9cc39fc6bfe
-    - path: output/genmap/genmap/index.info.limits
-      md5sum: 3522f2811f4ddf04598809fc84a1459e
-    - path: output/genmap/genmap/index.lf.drp
-      md5sum: dd85d6a23af2c7adf2695658e3056c08
-    - path: output/genmap/genmap/index.lf.drp.sbl
-      md5sum: f1d3ff8443297732862df21dc4e57262
-    - path: output/genmap/genmap/index.lf.drs
-      md5sum: 93b885adfe0da089cdf634904fd59f71
-    - path: output/genmap/genmap/index.lf.drv
-      md5sum: e06b605496bd91b32afa3c4f56d934ac
-    - path: output/genmap/genmap/index.lf.drv.sbl
-      md5sum: 8dd6bb7329a71449b0a1b292b5999164
-    - path: output/genmap/genmap/index.lf.pst
-      md5sum: e8daba34298e99e42942435286f9b3f0
-    - path: output/genmap/genmap/index.rev.lf.drp
-      md5sum: 5d9107e3aeec0721553dd661d4365fef
-    - path: output/genmap/genmap/index.rev.lf.drp.sbl
-      md5sum: f1d3ff8443297732862df21dc4e57262
-    - path: output/genmap/genmap/index.rev.lf.drs
-      md5sum: 93b885adfe0da089cdf634904fd59f71
-    - path: output/genmap/genmap/index.rev.lf.drv
-      md5sum: df7e795edc0a034577a9d2599fe8cfeb
-    - path: output/genmap/genmap/index.rev.lf.drv.sbl
-      md5sum: 8dd6bb7329a71449b0a1b292b5999164
-    - path: output/genmap/genmap/index.rev.lf.pst
-      md5sum: e8daba34298e99e42942435286f9b3f0
-    - path: output/genmap/genmap/index.sa.ind
-      md5sum: e21e5c7ce887cc8e3d0fa44ab1019cab
-    - path: output/genmap/genmap/index.sa.len
-      md5sum: 5dfc20cfe8ed9892451461a8d402f51c
-    - path: output/genmap/genmap/index.sa.val
-      md5sum: 400ee7f2fe93b2000ae3a5da5e509730
-    - path: output/genmap/genmap/index.txt.concat
-      md5sum: b4303962e0c176107945f3405370e6ae
-    - path: output/genmap/genmap/index.txt.limits
-      md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
diff --git a/tests/modules/genmap/mappability/main.nf b/tests/modules/genmap/mappability/main.nf
deleted file mode 100644
index eb6a34fadf0..00000000000
--- a/tests/modules/genmap/mappability/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENMAP_INDEX       } from '../../../../modules/genmap/index/main.nf'
-include { GENMAP_MAPPABILITY } from '../../../../modules/genmap/mappability/main.nf'
-
-workflow test_genmap_map {
-
-    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    GENMAP_INDEX ( input )
-    GENMAP_MAPPABILITY ( GENMAP_INDEX.out.index )
-}
diff --git a/tests/modules/genmap/mappability/test.yml b/tests/modules/genmap/mappability/test.yml
deleted file mode 100644
index 94c1d501078..00000000000
--- a/tests/modules/genmap/mappability/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: genmap mappability test_genmap_map
-  command: nextflow run ./tests/modules/genmap/mappability -entry test_genmap_map -c ./tests/config/nextflow.config -c ./tests/modules/genmap/mappability/nextflow.config
-  tags:
-    - genmap
-    - genmap/mappability
-  files:
-    - path: output/genmap/mappability.bedgraph
-      md5sum: c4203b84a84331282ef8660279f80b26
-    - path: output/genmap/mappability.txt
-      md5sum: 602d409493457f92b2e5f075f62ebe30
-    - path: output/genmap/mappability.wig
-      md5sum: fd2afb6512ab9e86f9a3b62f8b9d9088
diff --git a/tests/modules/genmod/annotate/main.nf b/tests/modules/genmod/annotate/main.nf
deleted file mode 100644
index 9e10c6b6995..00000000000
--- a/tests/modules/genmod/annotate/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENMOD_ANNOTATE } from '../../../../modules/genmod/annotate/main.nf'
-
-input = [
-    [ id:'test', single_end:false ], // meta map
-    file(params.test_data['homo_sapiens']['illumina']['genmod_vcf_gz'], checkIfExists: true)
-]
-
-workflow test_genmod_annotate {
-
-    GENMOD_ANNOTATE ( input )
-}
-
-workflow test_genmod_annotate_stub {
-
-    GENMOD_ANNOTATE ( input )
-}
diff --git a/tests/modules/genmod/annotate/test.yml b/tests/modules/genmod/annotate/test.yml
deleted file mode 100644
index f19e88e1700..00000000000
--- a/tests/modules/genmod/annotate/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: "genmod annotate"
-  command: nextflow run ./tests/modules/genmod/annotate -entry test_genmod_annotate -c ./tests/config/nextflow.config -c ./tests/modules/genmod/annotate/nextflow.config
-  tags:
-    - "genmod"
-    - "genmod/annotate"
-  files:
-    - path: "output/genmod/test_annotate.vcf"
-    - path: output/genmod/versions.yml
-
-- name: "genmod annotate stub"
-  command: nextflow run ./tests/modules/genmod/annotate -entry test_genmod_annotate_stub -c ./tests/config/nextflow.config -c ./tests/modules/genmod/annotate/nextflow.config -stub-run
-  tags:
-    - "genmod"
-    - "genmod/annotate"
-  files:
-    - path: "output/genmod/test_annotate.vcf"
-    - path: output/genmod/versions.yml
diff --git a/tests/modules/genmod/compound/main.nf b/tests/modules/genmod/compound/main.nf
deleted file mode 100644
index 01ddbe7b6d1..00000000000
--- a/tests/modules/genmod/compound/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENMOD_COMPOUND } from '../../../../modules/genmod/compound/main.nf'
-
-input = [
-    [ id:'test', single_end:false ], // meta map
-    file(params.test_data['homo_sapiens']['illumina']['genmod_score_vcf_gz'], checkIfExists: true)
-]
-fam = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
-config = file(params.test_data['homo_sapiens']['illumina']['rank_model'], checkIfExists: true)
-
-workflow test_genmod_compound {
-
-    GENMOD_COMPOUND ( input )
-}
-
-workflow test_genmod_compound_stub {
-
-    GENMOD_COMPOUND ( input )
-}
diff --git a/tests/modules/genmod/compound/test.yml b/tests/modules/genmod/compound/test.yml
deleted file mode 100644
index 3cb9e5d896c..00000000000
--- a/tests/modules/genmod/compound/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: "genmod compound"
-  command: nextflow run ./tests/modules/genmod/compound -entry test_genmod_compound -c ./tests/config/nextflow.config -c ./tests/modules/genmod/compound/nextflow.config
-  tags:
-    - "genmod"
-    - "genmod/compound"
-  files:
-    - path: output/genmod/test_compound.vcf
-    - path: output/genmod/versions.yml
-
-- name: "genmod compound stub"
-  command: nextflow run ./tests/modules/genmod/compound -entry test_genmod_compound_stub -c ./tests/config/nextflow.config -c ./tests/modules/genmod/compound/nextflow.config -stub-run
-  tags:
-    - "genmod"
-    - "genmod/compound"
-  files:
-    - path: output/genmod/test_compound.vcf
-    - path: output/genmod/versions.yml
diff --git a/tests/modules/genmod/models/main.nf b/tests/modules/genmod/models/main.nf
deleted file mode 100644
index 2566192e771..00000000000
--- a/tests/modules/genmod/models/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENMOD_MODELS   } from '../../../../modules/genmod/models/main.nf'
-
-input = [
-    [ id:'test', single_end:false ], // meta map
-    file(params.test_data['homo_sapiens']['illumina']['genmod_annotate_vcf_gz'], checkIfExists: true)
-]
-fam = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
-
-workflow test_genmod_models {
-
-    GENMOD_MODELS ( input, fam, [] )
-}
-
-workflow test_genmod_models_stub {
-
-    GENMOD_MODELS ( input, fam, [] )
-}
diff --git a/tests/modules/genmod/models/test.yml b/tests/modules/genmod/models/test.yml
deleted file mode 100644
index 21b48155c30..00000000000
--- a/tests/modules/genmod/models/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: "genmod models"
-  command: nextflow run ./tests/modules/genmod/models -entry test_genmod_models -c ./tests/config/nextflow.config -c ./tests/modules/genmod/models/nextflow.config
-  tags:
-    - "genmod"
-    - "genmod/models"
-  files:
-    - path: output/genmod/test_models.vcf
-    - path: output/genmod/versions.yml
-
-- name: "genmod models stub"
-  command: nextflow run ./tests/modules/genmod/models -entry test_genmod_models_stub -c ./tests/config/nextflow.config -c ./tests/modules/genmod/models/nextflow.config -stub-run
-  tags:
-    - "genmod"
-    - "genmod/models"
-  files:
-    - path: output/genmod/test_models.vcf
-    - path: output/genmod/versions.yml
diff --git a/tests/modules/genmod/score/main.nf b/tests/modules/genmod/score/main.nf
deleted file mode 100644
index 798569e1536..00000000000
--- a/tests/modules/genmod/score/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENMOD_SCORE    } from '../../../../modules/genmod/score/main.nf'
-
-input = [
-    [ id:'test', single_end:false ], // meta map
-    file(params.test_data['homo_sapiens']['illumina']['genmod_models_vcf_gz'], checkIfExists: true)
-]
-fam = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
-config = file(params.test_data['homo_sapiens']['illumina']['rank_model'], checkIfExists: true)
-
-workflow test_genmod_score {
-
-    GENMOD_SCORE    ( input, fam, config)
-}
-
-workflow test_genmod_score_stub {
-
-    GENMOD_SCORE    ( input, fam, config)
-}
diff --git a/tests/modules/genmod/score/test.yml b/tests/modules/genmod/score/test.yml
deleted file mode 100644
index 266a12aac72..00000000000
--- a/tests/modules/genmod/score/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: "genmod score"
-  command: nextflow run ./tests/modules/genmod/score -entry test_genmod_score -c ./tests/config/nextflow.config -c ./tests/modules/genmod/score/nextflow.config
-  tags:
-    - "genmod"
-    - "genmod/score"
-  files:
-    - path: output/genmod/test_score.vcf
-    - path: output/genmod/versions.yml
-
-- name: "genmod score stub"
-  command: nextflow run ./tests/modules/genmod/score -entry test_genmod_score_stub -c ./tests/config/nextflow.config -c ./tests/modules/genmod/score/nextflow.config -stub-run
-  tags:
-    - "genmod"
-    - "genmod/score"
-  files:
-    - path: output/genmod/test_score.vcf
-    - path: output/genmod/versions.yml
diff --git a/tests/modules/genomescope2/main.nf b/tests/modules/genomescope2/main.nf
deleted file mode 100644
index 5ceebfd6bd3..00000000000
--- a/tests/modules/genomescope2/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MERYL_COUNT     } from '../../../modules/meryl/count/main.nf'
-include { MERYL_HISTOGRAM } from '../../../modules/meryl/histogram/main.nf'
-include { GENOMESCOPE2    } from '../../../modules/genomescope2/main.nf'
-
-workflow test_genomescope2 {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    MERYL_COUNT ( input )
-    MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
-    GENOMESCOPE2 ( MERYL_HISTOGRAM.out.hist )
-}
diff --git a/tests/modules/genomescope2/test.yml b/tests/modules/genomescope2/test.yml
deleted file mode 100644
index 5b03f545fc2..00000000000
--- a/tests/modules/genomescope2/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: genomescope2 test_genomescope2
-  command: nextflow run tests/modules/genomescope2 -entry test_genomescope2 -c tests/config/nextflow.config
-  tags:
-    - genomescope2
-  files:
-    - path: output/genomescope2/test_linear_plot.png
-      md5sum: 94c165c5028156299a1d4d05766cac51
-    - path: output/genomescope2/test_log_plot.png
-      md5sum: 9d25ca463d92a0c73a893da7fd3979ba
-    - path: output/genomescope2/test_model.txt
-      md5sum: 3caf62f715f64a2f2b8fdff5d079cb84
-    - path: output/genomescope2/test_summary.txt
-      md5sum: 7452860e2cea99b85f3ff60daeac77f5
-    - path: output/genomescope2/test_transformed_linear_plot.png
-      md5sum: 99a64c1c18d8670f64cb863d4334abbb
-    - path: output/genomescope2/test_transformed_log_plot.png
-      md5sum: b4e029c9fb9987ca33b17392a691c1b4
-    - path: output/genomescope2/versions.yml
-      md5sum: 18afeb26f62a47f680b2bb3e27da9cbc
-    - path: output/meryl/test.hist
-      md5sum: f75362ab9cd70d96621b3690e952085f
-    - path: output/meryl/versions.yml
diff --git a/tests/modules/genotyphi/parse/main.nf b/tests/modules/genotyphi/parse/main.nf
deleted file mode 100644
index 761d18c1029..00000000000
--- a/tests/modules/genotyphi/parse/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MYKROBE_PREDICT } from '../../../../modules/mykrobe/predict/main.nf'
-include { GENOTYPHI_PARSE } from '../../../../modules/genotyphi/parse/main.nf'
-
-workflow test_mykrobe_predict {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    MYKROBE_PREDICT ( input, "typhi" )
-    GENOTYPHI_PARSE ( MYKROBE_PREDICT.out.json )
-}
diff --git a/tests/modules/genotyphi/parse/test.yml b/tests/modules/genotyphi/parse/test.yml
deleted file mode 100644
index 8d7e54fdc4c..00000000000
--- a/tests/modules/genotyphi/parse/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: genotyphi parse test_mykrobe_predict
-  command: nextflow run ./tests/modules/genotyphi/parse -entry test_mykrobe_predict -c ./tests/config/nextflow.config  -c ./tests/modules/genotyphi/parse/nextflow.config
-  tags:
-    - genotyphi/parse
-    - genotyphi
-  files:
-    - path: output/genotyphi/test_predictResults.tsv
-      contains: ["genome", "confidence", "supported", "test", "NA"]
-    - path: output/mykrobe/test.csv
-      contains: ["susceptibility", "genotype_model", "variants", "test.paired_end.bam"]
-    - path: output/mykrobe/test.json
-      contains: ["susceptibility", "kmer_count", "files", "test.paired_end.bam"]
diff --git a/tests/modules/genrich/main.nf b/tests/modules/genrich/main.nf
deleted file mode 100644
index 34db589e691..00000000000
--- a/tests/modules/genrich/main.nf
+++ /dev/null
@@ -1,79 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENRICH } from '../../../modules/genrich/main.nf'
-include { GENRICH as GENRICH_CTRL    } from '../../../modules/genrich/main.nf'
-include { GENRICH as GENRICH_ALL     } from '../../../modules/genrich/main.nf'
-include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf'
-
-workflow test_genrich {
-    input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ ]
-    blacklist = [ ]
-
-    save_pvalues    = false
-    save_pileup     = false
-    save_bed        = false
-    save_duplicates = false
-
-    GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
-}
-
-workflow test_genrich_ctrl {
-    input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
-    blacklist = [ ]
-
-    save_pvalues    = false
-    save_pileup     = false
-    save_bed        = false
-    save_duplicates = false
-
-    GENRICH_CTRL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
-}
-
-workflow test_genrich_all_outputs {
-    input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
-    blacklist = [ ]
-
-    save_pvalues    = true
-    save_pileup     = true
-    save_bed        = true
-    save_duplicates = true
-
-    GENRICH_ALL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
-}
-
-workflow test_genrich_blacklist {
-    input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ ]
-    blacklist = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
-
-    save_pvalues    = false
-    save_pileup     = false
-    save_bed        = false
-    save_duplicates = false
-
-    GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
-}
-
-workflow test_genrich_atacseq {
-    input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ ]
-    blacklist = [ ]
-
-    save_pvalues    = false
-    save_pileup     = false
-    save_bed        = false
-    save_duplicates = false
-
-    GENRICH_ATACSEQ ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
-}
-
diff --git a/tests/modules/genrich/test.yml b/tests/modules/genrich/test.yml
deleted file mode 100644
index 972335c46b6..00000000000
--- a/tests/modules/genrich/test.yml
+++ /dev/null
@@ -1,47 +0,0 @@
-- name: genrich test_genrich
-  command: nextflow run ./tests/modules/genrich -entry test_genrich -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
-  tags:
-    - genrich
-  files:
-    - path: output/genrich/test.narrowPeak
-      md5sum: 6afabdd3f691c7c84c66ff8a23984681
-
-- name: genrich test_genrich_ctrl
-  command: nextflow run ./tests/modules/genrich -entry test_genrich_ctrl -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
-  tags:
-    - genrich
-  files:
-    - path: output/genrich/test.narrowPeak
-      md5sum: 2fcc392360b317f5ebee88cdbc149e05
-
-- name: genrich test_genrich_all_outputs
-  command: nextflow run ./tests/modules/genrich -entry test_genrich_all_outputs -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
-  tags:
-    - genrich
-  files:
-    - path: output/genrich/test.duplicates.txt
-      md5sum: 159d557af7c23bc3cfb802d87fa96c34
-    - path: output/genrich/test.intervals.bed
-      md5sum: 4bea65caa3f4043d703af4b57161112e
-    - path: output/genrich/test.narrowPeak
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/genrich/test.pileup.bedGraph
-      md5sum: 03e53848de695b5794f32f15b2709203
-    - path: output/genrich/test.pvalues.bedGraph
-      md5sum: b14feef34b6d2379a173a734ca963cde
-
-- name: genrich test_genrich_blacklist
-  command: nextflow run ./tests/modules/genrich -entry test_genrich_blacklist -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
-  tags:
-    - genrich
-  files:
-    - path: output/genrich/test.narrowPeak
-      md5sum: 6afabdd3f691c7c84c66ff8a23984681
-
-- name: genrich test_genrich_atacseq
-  command: nextflow run ./tests/modules/genrich -entry test_genrich_atacseq -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
-  tags:
-    - genrich
-  files:
-    - path: output/genrich/test.narrowPeak
-      md5sum: ddea556b820f8be3695ffdf6c6f70aff
diff --git a/tests/modules/gfaffix/main.nf b/tests/modules/gfaffix/main.nf
deleted file mode 100644
index 333866c0bf0..00000000000
--- a/tests/modules/gfaffix/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GFAFFIX } from '../../../modules/gfaffix/main.nf'
-
-workflow test_gfaffix {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)]
-            ]
-
-    GFAFFIX ( input )
-}
diff --git a/tests/modules/gfaffix/test.yml b/tests/modules/gfaffix/test.yml
deleted file mode 100644
index d88db7c64f0..00000000000
--- a/tests/modules/gfaffix/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gfaffix
-  command: nextflow run ./tests/modules/gfaffix -entry test_gfaffix -c ./tests/config/nextflow.config -c ./tests/modules/gfaffix/nextflow.config
-  tags:
-    - gfaffix
-  files:
-    - path: output/gfaffix/test.gfaffix.gfa
-      md5sum: 7b51abeeab7706393957fcb66d31704a
-    - path: output/gfaffix/test.affixes.txt
-      md5sum: c3540baa386462552d7ebe4e4b7eda6a
diff --git a/tests/modules/gffread/main.nf b/tests/modules/gffread/main.nf
deleted file mode 100644
index 6ab7922bcc2..00000000000
--- a/tests/modules/gffread/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GFFREAD } from '../../../modules/gffread/main.nf'
-
-workflow test_gffread {
-    input = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
-
-    GFFREAD ( input )
-}
diff --git a/tests/modules/gffread/test.yml b/tests/modules/gffread/test.yml
deleted file mode 100644
index c5a16132e81..00000000000
--- a/tests/modules/gffread/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: gffread
-  command: nextflow run ./tests/modules/gffread/ -entry test_gffread -c ./tests/config/nextflow.config -c ./tests/modules/gffread/nextflow.config
-  tags:
-    - gffread
-  files:
-    - path: ./output/gffread/genome.out.gtf
-      md5sum: fcbf5744ed806e47768bc456fa043263
diff --git a/tests/modules/glimpse/chunk/main.nf b/tests/modules/glimpse/chunk/main.nf
deleted file mode 100644
index 9edb2783d5d..00000000000
--- a/tests/modules/glimpse/chunk/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GLIMPSE_CHUNK } from '../../../../modules/glimpse/chunk/main.nf'
-
-workflow test_glimpse_chunk {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)]
-    ]
-    GLIMPSE_CHUNK (input,"chr21")
-}
diff --git a/tests/modules/glimpse/chunk/test.yml b/tests/modules/glimpse/chunk/test.yml
deleted file mode 100644
index c8e9b6af70f..00000000000
--- a/tests/modules/glimpse/chunk/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: glimpse chunk test_glimpse_chunk
-  command: nextflow run ./tests/modules/glimpse/chunk -entry test_glimpse_chunk -c ./tests/config/nextflow.config  -c ./tests/modules/glimpse/chunk/nextflow.config
-  tags:
-    - glimpse
-    - glimpse/chunk
-  files:
-    - path: output/glimpse/test.txt
-      md5sum: c690cdcc7aa086bb85431bb2b193176f
diff --git a/tests/modules/glnexus/main.nf b/tests/modules/glnexus/main.nf
deleted file mode 100644
index aeb7c7e2e25..00000000000
--- a/tests/modules/glnexus/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GLNEXUS } from '../../../modules/glnexus/main.nf'
-
-workflow test_glnexus {
-    input = [
-        [ id:'test' ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true)
-        ]
-    ]
-
-    GLNEXUS ( input )
-}
diff --git a/tests/modules/glnexus/test.yml b/tests/modules/glnexus/test.yml
deleted file mode 100644
index bfca4529acf..00000000000
--- a/tests/modules/glnexus/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: glnexus test_glnexus
-  command: nextflow run ./tests/modules/glnexus -entry test_glnexus -c ./tests/config/nextflow.config -c ./tests/modules/glnexus/nextflow.config
-  tags:
-    - glnexus
-  files:
-    - path: output/glnexus/test.bcf
-      md5sum: 62b2cea9c1b92ac63645cb031eea46fc
diff --git a/tests/modules/goat/taxonsearch/main.nf b/tests/modules/goat/taxonsearch/main.nf
deleted file mode 100644
index 48f76f207ff..00000000000
--- a/tests/modules/goat/taxonsearch/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GOAT_TAXONSEARCH } from '../../../../modules/goat/taxonsearch/main.nf'
-
-//
-// Test with genus name (Canis)
-//
-workflow test_goat_taxonsearch_single_species {
-
-    input = [
-      [ id:'test_single_species' ], // meta map
-      taxon = 'Meles meles',
-      []
-  ]
-    GOAT_TAXONSEARCH ( input )
-}
-
-//
-// Test with genus (Drosophila, fruit flies) using NCBI taxonomy ID
-//
-workflow test_goat_taxonsearch_genus_id {
-
-    input = [
-      [ id:'test_genus_id' ], // meta map
-      taxon = '7215',
-      []
-  ]
-    GOAT_TAXONSEARCH ( input )
-}
-
-//
-// Test with multiple species from a taxa file
-//
-workflow test_goat_taxonsearch_species {
-
-    input = [
-      [ id:'test_species' ], // meta map
-      taxon = '',
-      file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/goat_taxonsearch/taxonomy_ids.txt', checkIfExists: true)
-  ]
-    GOAT_TAXONSEARCH ( input )
-}
diff --git a/tests/modules/goat/taxonsearch/test.yml b/tests/modules/goat/taxonsearch/test.yml
deleted file mode 100644
index db5ce3fb53f..00000000000
--- a/tests/modules/goat/taxonsearch/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: goat taxonsearch test_goat_taxonsearch_single_species
-  command: nextflow run ./tests/modules/goat/taxonsearch -entry test_goat_taxonsearch_single_species -c ./tests/config/nextflow.config  -c ./tests/modules/goat/taxonsearch/nextflow.config
-  tags:
-    - goat/taxonsearch
-    - goat
-  files:
-    - path: output/goat/test_single_species.tsv
-      md5sum: ed5b0afc7a6cf2f4b558882c10b35ef7
-
-- name: goat taxonsearch test_goat_taxonsearch_genus_id
-  command: nextflow run ./tests/modules/goat/taxonsearch -entry test_goat_taxonsearch_genus_id -c ./tests/config/nextflow.config  -c ./tests/modules/goat/taxonsearch/nextflow.config
-  tags:
-    - goat/taxonsearch
-    - goat
-  files:
-    - path: output/goat/test_genus_id.tsv
-      md5sum: 2cc41abbbc21b4b66f4d5126cfbba2bc
-
-- name: goat taxonsearch test_goat_taxonsearch_species
-  command: nextflow run ./tests/modules/goat/taxonsearch -entry test_goat_taxonsearch_species -c ./tests/config/nextflow.config  -c ./tests/modules/goat/taxonsearch/nextflow.config
-  tags:
-    - goat/taxonsearch
-    - goat
-  files:
-    - path: output/goat/test_species.tsv
-      md5sum: 7f5b36414820bd3ce2bfda06d98e479c
diff --git a/tests/modules/graphmap2/align/main.nf b/tests/modules/graphmap2/align/main.nf
deleted file mode 100644
index 96b951660f0..00000000000
--- a/tests/modules/graphmap2/align/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GRAPHMAP2_INDEX } from '../../../../modules/graphmap2/index/main.nf'
-include { GRAPHMAP2_ALIGN } from '../../../../modules/graphmap2/align/main.nf'
-
-workflow test_graphmap2_align {
-
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    GRAPHMAP2_INDEX ( fasta )
-    GRAPHMAP2_ALIGN ( input, fasta, GRAPHMAP2_INDEX.out.index )
-}
diff --git a/tests/modules/graphmap2/align/test.yml b/tests/modules/graphmap2/align/test.yml
deleted file mode 100644
index 90e52dd130a..00000000000
--- a/tests/modules/graphmap2/align/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: graphmap2 align
-  command: nextflow run ./tests/modules/graphmap2/align -entry test_graphmap2_align -c ./tests/config/nextflow.config -c ./tests/modules/graphmap2/align/nextflow.config
-  tags:
-    - graphmap2
-    - graphmap2/align
-  files:
-    - path: ./output/graphmap2/test.sam
diff --git a/tests/modules/graphmap2/index/main.nf b/tests/modules/graphmap2/index/main.nf
deleted file mode 100644
index 3c449c6b853..00000000000
--- a/tests/modules/graphmap2/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GRAPHMAP2_INDEX } from '../../../../modules/graphmap2/index/main.nf'
-
-workflow test_graphmap2_index {
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    GRAPHMAP2_INDEX ( fasta )
-}
diff --git a/tests/modules/graphmap2/index/test.yml b/tests/modules/graphmap2/index/test.yml
deleted file mode 100644
index 0bff487eb7f..00000000000
--- a/tests/modules/graphmap2/index/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: graphmap2 index
-  command: nextflow run ./tests/modules/graphmap2/index -entry test_graphmap2_index -c ./tests/config/nextflow.config -c ./tests/modules/graphmap2/index/nextflow.config
-  tags:
-    - graphmap2
-    - graphmap2/index
-  files:
-    - path: ./output/graphmap2/genome.fasta.gmidx
-      md5sum: 2973f9b7fa52c78899c73908f8afc6be
diff --git a/tests/modules/gstama/collapse/main.nf b/tests/modules/gstama/collapse/main.nf
deleted file mode 100644
index 3eb97767854..00000000000
--- a/tests/modules/gstama/collapse/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GSTAMA_COLLAPSE } from '../../../../modules/gstama/collapse/main.nf'
-
-workflow test_gstama_collapse {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['aligned'], checkIfExists: true)
-    ]
-    genome = file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true)
-
-    GSTAMA_COLLAPSE ( input, genome )
-}
diff --git a/tests/modules/gstama/collapse/test.yml b/tests/modules/gstama/collapse/test.yml
deleted file mode 100644
index 50d3775eb3c..00000000000
--- a/tests/modules/gstama/collapse/test.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-- name: gstama collapse test_gstama_collapse
-  command: nextflow run ./tests/modules/gstama/collapse -entry test_gstama_collapse -c ./tests/config/nextflow.config -c ./tests/modules/gstama/collapse/nextflow.config
-  tags:
-    - gstama
-    - gstama/collapse
-  files:
-    - path: output/gstama/test_tc_collapsed.bed
-      md5sum: e5105198ed970a33ae0ecaa7bff421d9
-    - path: output/gstama/test_tc_local_density_error.txt
-      md5sum: b917ac1f14eccd590b6881a686f324d5
-    - path: output/gstama/test_tc_polya.txt
-      md5sum: 628ea62b918fc4f31e109f724d714a66
-    - path: output/gstama/test_tc_read.txt
-      md5sum: d2685d7f24cd1611e0770a5ce25422fe
-    - path: output/gstama/test_tc_strand_check.txt
-      md5sum: 42cc52b2660b1e0b84e1c9ab37a965ec
-    - path: output/gstama/test_tc_trans_read.bed
-      md5sum: 0ca1a32f33ef05242d897d913802554b
-    - path: output/gstama/test_tc_trans_report.txt
-      md5sum: 33a86c15ca2acce36b2a5962f4c1adc4
-    - path: output/gstama/test_tc_varcov.txt
-      md5sum: 587fd899ff658eb66b1770a35283bfcb
-    - path: output/gstama/test_tc_variants.txt
-      md5sum: 5b1165e9f33faba4f7207013fc27257e
diff --git a/tests/modules/gstama/merge/main.nf b/tests/modules/gstama/merge/main.nf
deleted file mode 100644
index 4a9102a29da..00000000000
--- a/tests/modules/gstama/merge/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GSTAMA_MERGE } from '../../../../modules/gstama/merge/main'
-
-workflow test_gstama_merge {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['pacbio']['genemodel1'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['pacbio']['genemodel2'], checkIfExists: true)
-        ]
-    ]
-    filelist = file(params.test_data['homo_sapiens']['pacbio']['filelist'], checkIfExists: true)
-
-    GSTAMA_MERGE ( input, filelist )
-}
diff --git a/tests/modules/gstama/merge/test.yml b/tests/modules/gstama/merge/test.yml
deleted file mode 100644
index 1db35d15bc1..00000000000
--- a/tests/modules/gstama/merge/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: gstama merge test_gstama_merge
-  command: nextflow run ./tests/modules/gstama/merge -entry test_gstama_merge -c ./tests/config/nextflow.config -c ./tests/modules/gstama/merge/nextflow.config
-  tags:
-    - gstama
-    - gstama/merge
-  files:
-    - path: output/gstama/test_merged.bed
-      md5sum: 60ec34e1ff9655d4ce2e83d3f4bbf448
-    - path: output/gstama/test_merged_gene_report.txt
-      md5sum: 7029fd183dfd905a233403cfbe44722a
-    - path: output/gstama/test_merged_merge.txt
-      md5sum: 4279e59ed5739ce4f2f811568962893f
-    - path: output/gstama/test_merged_trans_report.txt
-      md5sum: 97d8346d9eb9da140941656c3a3325cd
diff --git a/tests/modules/gstama/polyacleanup/main.nf b/tests/modules/gstama/polyacleanup/main.nf
deleted file mode 100644
index 67b3fa876ac..00000000000
--- a/tests/modules/gstama/polyacleanup/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GSTAMA_POLYACLEANUP } from '../../../../modules/gstama/polyacleanup/main.nf'
-
-workflow test_gstama_polyacleanup {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
-    ]
-
-    GSTAMA_POLYACLEANUP ( input )
-}
diff --git a/tests/modules/gstama/polyacleanup/test.yml b/tests/modules/gstama/polyacleanup/test.yml
deleted file mode 100644
index 7f9f4260a35..00000000000
--- a/tests/modules/gstama/polyacleanup/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: gstama polyacleanup test_gstama_polyacleanup
-  command: nextflow run tests/modules/gstama/polyacleanup -entry test_gstama_polyacleanup -c tests/config/nextflow.config
-  tags:
-    - gstama
-    - gstama/polyacleanup
-  files:
-    - path: output/gstama/test_tama.fa.gz
-      md5sum: 9c768387478e5f966a42c369c0270b09
-    - path: output/gstama/test_tama_polya_flnc_report.txt.gz
-      md5sum: fe3606979ed11538aacd83159f4cff03
-    - path: output/gstama/test_tama_tails.fa.gz
-      md5sum: ba21256c0afe0bda71b3ee66b4c761bf
-    - path: output/gstama/versions.yml
-      md5sum: 07ebb812ae13a350d955fab7600b2542
diff --git a/tests/modules/gtdbtk/classifywf/main.nf b/tests/modules/gtdbtk/classifywf/main.nf
deleted file mode 100644
index 1517d7cc9a4..00000000000
--- a/tests/modules/gtdbtk/classifywf/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GTDBTK_CLASSIFYWF } from '../../../../modules/gtdbtk/classifywf/main.nf'
-
-process STUB_GTDBTK_DATABASE {
-    output:
-    tuple val("gtdbtk_r202_data"), path("database/*"), emit: database
-
-    stub:
-    """
-    mkdir database
-    touch database/gtdbtk_r202_data
-    """
-}
-
-workflow test_gtdbtk_classifywf {
-
-    STUB_GTDBTK_DATABASE()
-
-    input = [ 
-        [ id:'test', single_end:false, assembler:'SPADES' ],
-        [ 
-            file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
-        ]
-    ]
-	
-    GTDBTK_CLASSIFYWF ( input, STUB_GTDBTK_DATABASE.out.database )
-}
diff --git a/tests/modules/gtdbtk/classifywf/test.yml b/tests/modules/gtdbtk/classifywf/test.yml
deleted file mode 100644
index e24f1e1790d..00000000000
--- a/tests/modules/gtdbtk/classifywf/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: gtdbtk classifywf
-  command: nextflow run ./tests/modules/gtdbtk/classifywf -entry test_gtdbtk_classifywf -c ./tests/config/nextflow.config -stub-run -c ./tests/modules/gtdbtk/classifywf/nextflow.config
-  tags:
-    - gtdbtk
-    - gtdbtk/classifywf
-  files:
-    - path: output/gtdbtk/gtdbtk.SPADES-test.stub.summary.tsv
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/gubbins/main.nf b/tests/modules/gubbins/main.nf
deleted file mode 100644
index 342150b383f..00000000000
--- a/tests/modules/gubbins/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUBBINS } from '../../../modules/gubbins/main.nf'
-
-workflow test_gubbins { 
-    input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
-
-    GUBBINS ( input )
-}
diff --git a/tests/modules/gubbins/test.yml b/tests/modules/gubbins/test.yml
deleted file mode 100644
index 6c85260dbec..00000000000
--- a/tests/modules/gubbins/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: gubbins
-  command: nextflow run ./tests/modules/gubbins -entry test_gubbins -c ./tests/config/nextflow.config -c ./tests/modules/gubbins/nextflow.config
-  tags:
-    - gubbins
-  files:
-    - path: output/gubbins/all_sites.filtered_polymorphic_sites.fasta
-      md5sum: 4cbfd93868d8ed7d4d8b099eba137134
-    - path: output/gubbins/all_sites.recombination_predictions.embl
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/gubbins/all_sites.recombination_predictions.gff
-      md5sum: f95871e79968340cb82532e2c9b0c92b
-    - path: output/gubbins/all_sites.branch_base_reconstruction.embl
-      md5sum: 9e051646d630f528fff58f1f73286006
-    - path: output/gubbins/all_sites.summary_of_snp_distribution.vcf
-      md5sum: 276e62e888ea811577c8ffb2da0b3aff
-    - path: output/gubbins/all_sites.per_branch_statistics.csv
-      md5sum: 25e4fdb6681c3709a9add1d5632bbf3e
-    - path: output/gubbins/all_sites.filtered_polymorphic_sites.phylip
-      md5sum: 0a77f397a7797c5c3386832745b0c97a
-    - path: output/gubbins/all_sites.final_tree.tre
-      md5sum: 6cb251b58307aab11cb4b48792d6cda1
-    - path: output/gubbins/all_sites.node_labelled.final_tree.tre
-      md5sum: e01f965a15924b4f97603b8011c8d3f7
diff --git a/tests/modules/gunc/downloaddb/main.nf b/tests/modules/gunc/downloaddb/main.nf
deleted file mode 100644
index 3e3126f538d..00000000000
--- a/tests/modules/gunc/downloaddb/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNC_DOWNLOADDB } from '../../../../modules/gunc/downloaddb/main.nf'
-
-workflow test_gunc_downloaddb {
-
-    input = 'progenomes'
-
-    GUNC_DOWNLOADDB ( input )
-}
diff --git a/tests/modules/gunc/downloaddb/test.yml b/tests/modules/gunc/downloaddb/test.yml
deleted file mode 100644
index 4e1c23f836a..00000000000
--- a/tests/modules/gunc/downloaddb/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: gunc downloaddb
-  command: nextflow run ./tests/modules/gunc/downloaddb -entry test_gunc_downloaddb -c ./tests/config/nextflow.config -c ./tests/modules/gunc/downloaddb/nextflow.config
-  tags:
-    - gunc
-    - gunc/downloaddb
-  files:
-    - path: output/gunc/gunc_db_progenomes2.1.dmnd
-      md5sum: 447c9330056b02f29f30fe81fe4af4eb
diff --git a/tests/modules/gunc/run/main.nf b/tests/modules/gunc/run/main.nf
deleted file mode 100644
index 28ecd35fea6..00000000000
--- a/tests/modules/gunc/run/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNC_RUN        } from '../../../../modules/gunc/run/main.nf'
-include { GUNC_DOWNLOADDB } from '../../../../modules/gunc/downloaddb/main.nf'
-
-workflow test_gunc_run {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
-    ]
-
-    GUNC_DOWNLOADDB ( 'progenomes' )
-    GUNC_RUN ( input, GUNC_DOWNLOADDB.out.db )
-}
diff --git a/tests/modules/gunc/run/test.yml b/tests/modules/gunc/run/test.yml
deleted file mode 100644
index 5bcef868cc9..00000000000
--- a/tests/modules/gunc/run/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: gunc run
-  command: nextflow run ./tests/modules/gunc/run -entry test_gunc_run -c ./tests/config/nextflow.config -c ./tests/modules/gunc/run/nextflow.config
-  tags:
-    - gunc
-    - gunc/run
-  files:
-    - path: output/gunc/GUNC.progenomes_2.1.maxCSS_level.tsv
-      md5sum: 0420c1a9f2c50fefaee9fab5d80a551a
diff --git a/tests/modules/gunzip/main.nf b/tests/modules/gunzip/main.nf
deleted file mode 100644
index 3d41a4a2055..00000000000
--- a/tests/modules/gunzip/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP } from '../../../modules/gunzip/main.nf'
-
-workflow test_gunzip {
-    input = [ [],
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ]
-
-    GUNZIP ( input )
-}
diff --git a/tests/modules/gunzip/test.yml b/tests/modules/gunzip/test.yml
deleted file mode 100644
index 70e95d6bc0a..00000000000
--- a/tests/modules/gunzip/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: gunzip
-  command: nextflow run ./tests/modules/gunzip -entry test_gunzip -c ./tests/config/nextflow.config -c ./tests/modules/gunzip/nextflow.config
-  tags:
-    - gunzip
-  files:
-    - path: ./output/gunzip/test_1.fastq
-      md5sum: 4161df271f9bfcd25d5845a1e220dbec
diff --git a/tests/modules/gvcftools/extractvariants/main.nf b/tests/modules/gvcftools/extractvariants/main.nf
deleted file mode 100644
index b614072f5b3..00000000000
--- a/tests/modules/gvcftools/extractvariants/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GVCFTOOLS_EXTRACTVARIANTS } from '../../../../modules/gvcftools/extractvariants/main.nf'
-
-workflow test_gvcftools_extractvariants {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true)
-    ]
-
-    GVCFTOOLS_EXTRACTVARIANTS ( input )
-}
-
-workflow test_gvcftools_extractvariants_uncompressed {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
-    ]
-
-    GVCFTOOLS_EXTRACTVARIANTS ( input )
-}
diff --git a/tests/modules/gvcftools/extractvariants/test.yml b/tests/modules/gvcftools/extractvariants/test.yml
deleted file mode 100644
index 9b8e7f3ebcf..00000000000
--- a/tests/modules/gvcftools/extractvariants/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: gvcftools extractvariants test_gvcftools_extractvariants
-  command: nextflow run ./tests/modules/gvcftools/extractvariants -entry test_gvcftools_extractvariants -c ./tests/config/nextflow.config  -c ./tests/modules/gvcftools/extractvariants/nextflow.config
-  tags:
-    - gvcftools
-    - gvcftools/extractvariants
-  files:
-    - path: output/gvcftools/test.vcf.gz
-
-- name: gvcftools extractvariants test_gvcftools_extractvariants_uncompressed
-  command: nextflow run ./tests/modules/gvcftools/extractvariants -entry test_gvcftools_extractvariants_uncompressed -c ./tests/config/nextflow.config  -c ./tests/modules/gvcftools/extractvariants/nextflow.config
-  tags:
-    - gvcftools
-    - gvcftools/extractvariants
-  files:
-    - path: output/gvcftools/test.vcf.gz
diff --git a/tests/modules/hamronization/abricate/main.nf b/tests/modules/hamronization/abricate/main.nf
deleted file mode 100644
index 111824697e1..00000000000
--- a/tests/modules/hamronization/abricate/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HAMRONIZATION_ABRICATE } from '../../../../modules/hamronization/abricate/main.nf'
-
-workflow test_hamronization_abricate {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true),
-    ]
-
-    HAMRONIZATION_ABRICATE ( input, 'tsv', '1.0.1', '2021-Mar-27' )
-}
diff --git a/tests/modules/hamronization/abricate/test.yml b/tests/modules/hamronization/abricate/test.yml
deleted file mode 100644
index 7d18db2e574..00000000000
--- a/tests/modules/hamronization/abricate/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: hamronization abricate test_hamronization_abricate
-  command: nextflow run ./tests/modules/hamronization/abricate -entry test_hamronization_abricate -c ./tests/config/nextflow.config  -c ./tests/modules/hamronization/abricate/nextflow.config
-  tags:
-    - hamronization/abricate
-    - hamronization
-  files:
-    - path: output/hamronization/test.tsv
-      contains:
-        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"
diff --git a/tests/modules/hamronization/amrfinderplus/main.nf b/tests/modules/hamronization/amrfinderplus/main.nf
deleted file mode 100644
index cb477847457..00000000000
--- a/tests/modules/hamronization/amrfinderplus/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-include { HAMRONIZATION_AMRFINDERPLUS } from '../../../../modules/hamronization/amrfinderplus/main.nf'
-
-workflow test_hamronization_amrfinderplus {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true)
-    ]
-
-    HAMRONIZATION_AMRFINDERPLUS ( input, 'tsv', '3.10.30', '2022-05-26.1' )
-}
diff --git a/tests/modules/hamronization/amrfinderplus/test.yml b/tests/modules/hamronization/amrfinderplus/test.yml
deleted file mode 100644
index 8d77d6feeda..00000000000
--- a/tests/modules/hamronization/amrfinderplus/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: hamronization amrfinderplus test_hamronization_amrfinderplus
-  command: nextflow run ./tests/modules/hamronization/amrfinderplus -entry test_hamronization_amrfinderplus -c ./tests/config/nextflow.config  -c ./tests/modules/hamronization/amrfinderplus/nextflow.config
-  tags:
-    - hamronization
-    - hamronization/amrfinderplus
-  files:
-    - path: output/hamronization/test.tsv
-      contains:
-        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"
diff --git a/tests/modules/hamronization/deeparg/main.nf b/tests/modules/hamronization/deeparg/main.nf
deleted file mode 100644
index 3f674bbc0c9..00000000000
--- a/tests/modules/hamronization/deeparg/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf'
-
-workflow test_hamronization_deeparg {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
-    ]
-
-    HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2'  )
-}
diff --git a/tests/modules/hamronization/deeparg/test.yml b/tests/modules/hamronization/deeparg/test.yml
deleted file mode 100644
index a9bd1315d51..00000000000
--- a/tests/modules/hamronization/deeparg/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: hamronization deeparg test_hamronization_deeparg
-  command: nextflow run tests/modules/hamronization/deeparg -entry test_hamronization_deeparg -c tests/config/nextflow.config
-  tags:
-    - hamronization
-    - hamronization/deeparg
-  files:
-    - path: output/hamronization/test.tsv
-      contains:
-        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"
diff --git a/tests/modules/hamronization/fargene/main.nf b/tests/modules/hamronization/fargene/main.nf
deleted file mode 100644
index f54a4534c30..00000000000
--- a/tests/modules/hamronization/fargene/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP                } from '../../../modules/gunzip/main.nf'
-include { FARGENE               } from '../../../modules/fargene/main.nf'
-include { HAMRONIZATION_FARGENE } from '../../../../modules/hamronization/fargene/main.nf'
-
-workflow test_hamronization_fargene {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) ]
-    hmm_model = 'class_a'
-
-    GUNZIP ( input )
-    FARGENE ( GUNZIP.out.gunzip, hmm_model )
-
-    HAMRONIZATION_FARGENE ( FARGENE.out.hmm, 'tsv', '0.1', '0.1' )
-}
diff --git a/tests/modules/hamronization/fargene/test.yml b/tests/modules/hamronization/fargene/test.yml
deleted file mode 100644
index 27c42aa4ca2..00000000000
--- a/tests/modules/hamronization/fargene/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: hamronization fargene test_hamronization_fargene
-  command: nextflow run ./tests/modules/hamronization/fargene -entry test_hamronization_fargene -c ./tests/config/nextflow.config  -c ./tests/modules/hamronization/fargene/nextflow.config
-  tags:
-    - hamronization
-    - hamronization/fargene
-  files:
-    - path: output/hamronization/test.tsv
diff --git a/tests/modules/hamronization/rgi/main.nf b/tests/modules/hamronization/rgi/main.nf
deleted file mode 100644
index 1940e4a3f47..00000000000
--- a/tests/modules/hamronization/rgi/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-include { RGI_MAIN } from '../../../../modules/rgi/main/main.nf'
-include { HAMRONIZATION_RGI } from '../../../../modules/hamronization/rgi/main.nf'
-
-workflow test_hamronization_rgi {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
-    ]
-
-    RGI_MAIN ( input )
-    HAMRONIZATION_RGI ( RGI_MAIN.out.tsv, 'tsv', '1.0.2', '3.2.3' )
-}
diff --git a/tests/modules/hamronization/rgi/test.yml b/tests/modules/hamronization/rgi/test.yml
deleted file mode 100644
index e11c0ea1318..00000000000
--- a/tests/modules/hamronization/rgi/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: hamronization rgi
-  command: nextflow run ./tests/modules/hamronization/rgi -entry test_hamronization_rgi -c ./tests/config/nextflow.config  -c ./tests/modules/hamronization/rgi/nextflow.config
-  tags:
-    - hamronization
-    - hamronization/rgi
-  files:
-    - path: output/hamronization/test.tsv
-      contains:
-        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"
diff --git a/tests/modules/hamronization/summarize/main.nf b/tests/modules/hamronization/summarize/main.nf
deleted file mode 100644
index aeb46991bbf..00000000000
--- a/tests/modules/hamronization/summarize/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HAMRONIZATION_DEEPARG                                 } from '../../../../modules/hamronization/deeparg/main.nf'
-include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../modules/hamronization/deeparg/main.nf'
-include { HAMRONIZATION_SUMMARIZE                               } from '../../../../modules/hamronization/summarize/main.nf'
-
-workflow test_hamronization_summarize {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
-    ]
-
-    input2 = [
-        [ id:'test2', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
-    ]
-
-    HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2'  )
-    HAMRONIZATION_DEEPARG_SECOND ( input2, 'tsv', '1.0.2', '2' )
-
-    ch_deeparg_run_one = HAMRONIZATION_DEEPARG.out.tsv
-    ch_deeparg_run_two = HAMRONIZATION_DEEPARG_SECOND.out.tsv
-
-    ch_deeparg_run_one
-        .mix( ch_deeparg_run_two )
-        .map{
-            [ it[1] ]
-        }
-        .collect()
-        .set { ch_input_for_summarize }
-
-    HAMRONIZATION_SUMMARIZE ( ch_input_for_summarize , 'json' )
-}
diff --git a/tests/modules/hamronization/summarize/test.yml b/tests/modules/hamronization/summarize/test.yml
deleted file mode 100644
index 7dca7477f59..00000000000
--- a/tests/modules/hamronization/summarize/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: hamronization summarize test_hamronization_summarize
-  command: nextflow run ./tests/modules/hamronization/summarize -entry test_hamronization_summarize -c ./tests/config/nextflow.config  -c ./tests/modules/hamronization/summarize/nextflow.config
-  tags:
-    - hamronization
-    - hamronization/summarize
-  files:
-    - path: output/hamronization/hamronization_combined_report.json
-      md5sum: ab0c899664398193a25a699b92f960b9
-    - path: output/hamronization/test.tsv
-      md5sum: e886d665bf9fc266be8193859863d2f4
-    - path: output/hamronization/test2.tsv
-      md5sum: 2d94ecb8be8d9036877e47a81ae92a41
diff --git a/tests/modules/haplocheck/main.nf b/tests/modules/haplocheck/main.nf
deleted file mode 100644
index 9699c33c516..00000000000
--- a/tests/modules/haplocheck/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HAPLOCHECK } from '../../../modules/haplocheck/main.nf'
-
-workflow test_haplocheck {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_mito_vcf'], checkIfExists: true)
-    ]
-
-    HAPLOCHECK ( input )
-}
diff --git a/tests/modules/haplocheck/test.yml b/tests/modules/haplocheck/test.yml
deleted file mode 100644
index 69a816fcb27..00000000000
--- a/tests/modules/haplocheck/test.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-- name: haplocheck test_haplocheck
-  command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config
-  tags:
-    - haplocheck
-  files:
-    - path: output/haplocheck/test.html
-      md5sum: 59d69052c86edff0301816956eaf4d5f
-    - path: output/haplocheck/test.raw.txt
-      md5sum: 69f4e5b28a59b97fc19eb8e8b650d9d5
-    - path: output/haplocheck/versions.yml
-      md5sum: 94e2fa3ceb3946487319f92cea08c942
-
-- name: haplocheck test_haplocheck using stubs
-  command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config -stub-run
-  tags:
-    - haplocheck
-  files:
-    - path: output/haplocheck/test.html
-    - path: output/haplocheck/test.raw.txt
-    - path: output/haplocheck/versions.yml
diff --git a/tests/modules/haplogrep2/classify/main.nf b/tests/modules/haplogrep2/classify/main.nf
deleted file mode 100644
index 89f45f36127..00000000000
--- a/tests/modules/haplogrep2/classify/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HAPLOGREP2_CLASSIFY } from '../../../../modules/haplogrep2/classify/main.nf'
-
-workflow test_haplogrep2_classify {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_mito_vcf'], checkIfExists: true)
-    ]
-    format = 'vcf'
-
-    HAPLOGREP2_CLASSIFY ( input,format )
-}
diff --git a/tests/modules/haplogrep2/classify/test.yml b/tests/modules/haplogrep2/classify/test.yml
deleted file mode 100644
index 547c9fab907..00000000000
--- a/tests/modules/haplogrep2/classify/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: haplogrep2 classify
-  command: nextflow run ./tests/modules/haplogrep2/classify -entry test_haplogrep2_classify -c ./tests/config/nextflow.config -c ./tests/modules/haplogrep2/classify/nextflow.config
-  tags:
-    - haplogrep2
-    - haplogrep2/classify
-  files:
-    - path: output/haplogrep2/test.txt
-    - path: output/haplogrep2/versions.yml
-
-- name: haplogrep2 classify stubs
-  command: nextflow run ./tests/modules/haplogrep2/classify -stub-run -entry test_haplogrep2_classify -c ./tests/config/nextflow.config -c ./tests/modules/haplogrep2/classify/nextflow.config
-  tags:
-    - haplogrep2
-    - haplogrep2/classify
-  files:
-    - path: output/haplogrep2/test.txt
-    - path: output/haplogrep2/versions.yml
diff --git a/tests/modules/happy/happy/main.nf b/tests/modules/happy/happy/main.nf
deleted file mode 100644
index 515a657bb5c..00000000000
--- a/tests/modules/happy/happy/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HAPPY_HAPPY } from '../../../../modules/happy/happy/main.nf'
-
-workflow test_happy_vcf {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
-    ]
-
-    fasta = Channel.value([
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    ])
-
-    HAPPY_HAPPY ( input, fasta )
-}
-
-workflow test_happy_gvcf {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
-    ]
-
-    fasta = Channel.value([
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    ])
-
-    HAPPY_HAPPY ( input, fasta )
-}
diff --git a/tests/modules/happy/happy/test.yml b/tests/modules/happy/happy/test.yml
deleted file mode 100644
index 89a1f0124f2..00000000000
--- a/tests/modules/happy/happy/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: happy happy test_happy_vcf
-  command: nextflow run tests/modules/happy/happy -entry test_happy_vcf -c tests/config/nextflow.config
-  tags:
-    - happy
-    - happy/happy
-  files:
-    - path: output/happy/test.extended.csv
-      md5sum: ef79c7c789ef4f146ca2e50dafaf22b3
-    - path: output/happy/test.runinfo.json
-    - path: output/happy/test.summary.csv
-      md5sum: f8aa5d36d3c48dede2f607fd565894ad
-    - path: output/happy/versions.yml
-      md5sum: 82243bf6dbdc71aa63211ee2a89f47f2
-
-- name: happy happy test_happy_gvcf
-  command: nextflow run tests/modules/happy/happy -entry test_happy_gvcf -c tests/config/nextflow.config
-  tags:
-    - happy
-    - happy/happy
-  files:
-    - path: output/happy/test.extended.csv
-      md5sum: 3d5c21b67a259a3f6dcb088d55b86cd3
-    - path: output/happy/test.runinfo.json
-    - path: output/happy/test.summary.csv
-      md5sum: 03044e9bb5a0c6f0947b7e910fc8a558
-    - path: output/happy/versions.yml
-      md5sum: 551fa216952d6f5de78e6e453b92aaab
diff --git a/tests/modules/happy/prepy/main.nf b/tests/modules/happy/prepy/main.nf
deleted file mode 100644
index 0b511104e9d..00000000000
--- a/tests/modules/happy/prepy/main.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HAPPY_PREPY } from '../../../../modules/happy/prepy/main.nf'
-
-workflow test_happy_prepy_vcf {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
-    ]
-
-    fasta = Channel.value([
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    ])
-
-    HAPPY_PREPY ( input, fasta )
-}
-
-workflow test_happy_prepy_gvcf {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
-    ]
-
-    fasta = Channel.value([
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    ])
-
-    HAPPY_PREPY ( input, fasta )
-}
diff --git a/tests/modules/happy/prepy/test.yml b/tests/modules/happy/prepy/test.yml
deleted file mode 100644
index a0a45c3899d..00000000000
--- a/tests/modules/happy/prepy/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: happy prepy test_happy_prepy_vcf
-  command: nextflow run tests/modules/happy/prepy -entry test_happy_prepy_vcf -c tests/config/nextflow.config
-  tags:
-    - happy/prepy
-    - happy
-  files:
-    - path: output/happy/test.vcf.gz
-    - path: output/happy/versions.yml
-      md5sum: 814d20f1f29f23a3d21012748a5d6393
-
-- name: happy prepy test_happy_prepy_gvcf
-  command: nextflow run tests/modules/happy/prepy -entry test_happy_prepy_gvcf -c tests/config/nextflow.config
-  tags:
-    - happy/prepy
-    - happy
-  files:
-    - path: output/happy/test.vcf.gz
-    - path: output/happy/versions.yml
-      md5sum: 970a54de46e68ef6d5228a26eaa4c8e7
diff --git a/tests/modules/hicap/main.nf b/tests/modules/hicap/main.nf
deleted file mode 100644
index 82c515de49b..00000000000
--- a/tests/modules/hicap/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HICAP } from '../../../modules/hicap/main.nf'
-
-workflow test_hicap {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
-    ]
-    database_dir = []
-    model_fp = []
-
-    HICAP ( input, database_dir, model_fp )
-}
diff --git a/tests/modules/hicap/test.yml b/tests/modules/hicap/test.yml
deleted file mode 100644
index 0cce28c70f9..00000000000
--- a/tests/modules/hicap/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: hicap test_hicap
-  command: nextflow run ./tests/modules/hicap -entry test_hicap -c ./tests/config/nextflow.config -c ./tests/modules/hicap/nextflow.config
-  tags:
-    - hicap
-  files:
-    - path: output/hicap/genome.gbk
-      md5sum: 562d026956903354ac80721f501335d4
-    - path: output/hicap/genome.svg
-      md5sum: 4fb94871dd0fdd8b4496049668176631
-    - path: output/hicap/genome.tsv
diff --git a/tests/modules/hifiasm/main.nf b/tests/modules/hifiasm/main.nf
deleted file mode 100644
index f0e2a0f4499..00000000000
--- a/tests/modules/hifiasm/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HIFIASM } from '../../../modules/hifiasm/main.nf'
-
-/*
- * Test with long reads only
- */
-workflow test_hifiasm_hifi_only {
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
-    ]
-
-    HIFIASM ( input, [], [], false )
-}
-
-/*
- * Test with parental reads for phasing
- */
-workflow test_hifiasm_with_parental_reads {
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
-    ]
-    paternal_kmer_dump = file(params.test_data['homo_sapiens']['illumina']['test_yak'], checkIfExists: true)
-    maternal_kmer_dump = file(params.test_data['homo_sapiens']['illumina']['test2_yak'], checkIfExists: true)
-
-    HIFIASM ( input, paternal_kmer_dump, maternal_kmer_dump, true )
-}
diff --git a/tests/modules/hifiasm/test.yml b/tests/modules/hifiasm/test.yml
deleted file mode 100644
index f7e3e6ae1f9..00000000000
--- a/tests/modules/hifiasm/test.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-- name: hifiasm test_hifiasm_hifi_only
-  command: nextflow run ./tests/modules/hifiasm -entry test_hifiasm_hifi_only -c ./tests/config/nextflow.config -c ./tests/modules/hifiasm/nextflow.config
-  tags:
-    - hifiasm
-  files:
-    - path: output/hifiasm/test.asm.bp.hap1.p_ctg.gfa
-      md5sum: 73b0c1b01d445db91c269034b8660501
-    - path: output/hifiasm/test.asm.bp.hap2.p_ctg.gfa
-      md5sum: 76847b7835185ab92611a820467c0066
-    - path: output/hifiasm/test.asm.bp.p_utg.gfa
-      md5sum: 97446fb95de214835c36b10a90838486
-    - path: output/hifiasm/test.asm.bp.r_utg.gfa
-      md5sum: 97446fb95de214835c36b10a90838486
-    - path: output/hifiasm/test.asm.ec.bin
-    - path: output/hifiasm/test.asm.ovlp.reverse.bin
-    - path: output/hifiasm/test.asm.ovlp.source.bin
-
-- name: hifiasm test_hifiasm_with_parental_reads
-  command: nextflow run ./tests/modules/hifiasm -entry test_hifiasm_with_parental_reads -c ./tests/config/nextflow.config -c ./tests/modules/hifiasm/nextflow.config
-  tags:
-    - hifiasm
-  files:
-    - path: output/hifiasm/test.asm.dip.hap1.p_ctg.gfa
-      md5sum: 16907b1aea2081884deb9d039dd14038
-    - path: output/hifiasm/test.asm.dip.hap2.p_ctg.gfa
-      md5sum: d283479bf72a31d0cc34f880535d0bd4
-    - path: output/hifiasm/test.asm.dip.p_utg.gfa
-      md5sum: 97446fb95de214835c36b10a90838486
-    - path: output/hifiasm/test.asm.dip.r_utg.gfa
-      md5sum: 97446fb95de214835c36b10a90838486
-    - path: output/hifiasm/test.asm.ec.bin
-    - path: output/hifiasm/test.asm.ovlp.reverse.bin
-    - path: output/hifiasm/test.asm.ovlp.source.bin
diff --git a/tests/modules/hisat2/align/main.nf b/tests/modules/hisat2/align/main.nf
deleted file mode 100644
index 17b47c93606..00000000000
--- a/tests/modules/hisat2/align/main.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf'
-include { HISAT2_BUILD              } from '../../../../modules/hisat2/build/main.nf'
-include { HISAT2_ALIGN              } from '../../../../modules/hisat2/align/main.nf'
-
-workflow test_hisat2_align_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-
-    HISAT2_EXTRACTSPLICESITES ( gtf )
-    HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
-    HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
-}
-
-workflow test_hisat2_align_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-
-    HISAT2_EXTRACTSPLICESITES ( gtf )
-    HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
-    HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
-}
diff --git a/tests/modules/hisat2/align/test.yml b/tests/modules/hisat2/align/test.yml
deleted file mode 100644
index a99b2f9422a..00000000000
--- a/tests/modules/hisat2/align/test.yml
+++ /dev/null
@@ -1,53 +0,0 @@
-- name: hisat2 align test_hisat2_align_single_end
-  command: nextflow run ./tests/modules/hisat2/align -entry test_hisat2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/hisat2/align/nextflow.config
-  tags:
-    - hisat2
-    - hisat2/align
-  files:
-    - path: output/hisat2/test.hisat2.summary.log
-      md5sum: 7b8a9e61b7646da1089b041333c41a87
-    - path: output/hisat2/genome.splice_sites.txt
-    - path: output/hisat2/test.bam
-    - path: output/hisat2/hisat2/genome.5.ht2
-      md5sum: 91198831aaba993acac1734138c5f173
-    - path: output/hisat2/hisat2/genome.7.ht2
-      md5sum: 9013eccd91ad614d7893c739275a394f
-    - path: output/hisat2/hisat2/genome.1.ht2
-      md5sum: 057cfa8a22b97ee9cff4c8d342498803
-    - path: output/hisat2/hisat2/genome.2.ht2
-      md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: output/hisat2/hisat2/genome.6.ht2
-      md5sum: 265e1284ce85686516fae5d35540994a
-    - path: output/hisat2/hisat2/genome.3.ht2
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: output/hisat2/hisat2/genome.8.ht2
-      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
-    - path: output/hisat2/hisat2/genome.4.ht2
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
-
-- name: hisat2 align test_hisat2_align_paired_end
-  command: nextflow run ./tests/modules/hisat2/align -entry test_hisat2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/hisat2/align/nextflow.config
-  tags:
-    - hisat2
-    - hisat2/align
-  files:
-    - path: output/hisat2/test.hisat2.summary.log
-      md5sum: 9839b31db795958cc4b70711a3414e9c
-    - path: output/hisat2/genome.splice_sites.txt
-    - path: output/hisat2/test.bam
-    - path: output/hisat2/hisat2/genome.5.ht2
-      md5sum: 91198831aaba993acac1734138c5f173
-    - path: output/hisat2/hisat2/genome.7.ht2
-      md5sum: 9013eccd91ad614d7893c739275a394f
-    - path: output/hisat2/hisat2/genome.1.ht2
-      md5sum: 057cfa8a22b97ee9cff4c8d342498803
-    - path: output/hisat2/hisat2/genome.2.ht2
-      md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: output/hisat2/hisat2/genome.6.ht2
-      md5sum: 265e1284ce85686516fae5d35540994a
-    - path: output/hisat2/hisat2/genome.3.ht2
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: output/hisat2/hisat2/genome.8.ht2
-      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
-    - path: output/hisat2/hisat2/genome.4.ht2
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
diff --git a/tests/modules/hisat2/build_test/main.nf b/tests/modules/hisat2/build_test/main.nf
deleted file mode 100644
index a0c14dc863d..00000000000
--- a/tests/modules/hisat2/build_test/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf'
-include { HISAT2_BUILD              } from '../../../../modules/hisat2/build/main.nf'
-
-workflow test_hisat2_build {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-
-    HISAT2_EXTRACTSPLICESITES ( gtf )
-    HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
-}
diff --git a/tests/modules/hisat2/build_test/test.yml b/tests/modules/hisat2/build_test/test.yml
deleted file mode 100644
index 34c036d041f..00000000000
--- a/tests/modules/hisat2/build_test/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: hisat2 build test_hisat2_build
-  command: nextflow run ./tests/modules/hisat2/build_test -entry test_hisat2_build -c ./tests/config/nextflow.config -c ./tests/modules/hisat2/build/nextflow.config
-  tags:
-    - hisat2
-    - hisat2/build
-  files:
-    - path: output/hisat2/genome.splice_sites.txt
-    - path: output/hisat2/hisat2/genome.5.ht2
-      md5sum: 91198831aaba993acac1734138c5f173
-    - path: output/hisat2/hisat2/genome.7.ht2
-      md5sum: 9013eccd91ad614d7893c739275a394f
-    - path: output/hisat2/hisat2/genome.1.ht2
-      md5sum: 057cfa8a22b97ee9cff4c8d342498803
-    - path: output/hisat2/hisat2/genome.2.ht2
-      md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: output/hisat2/hisat2/genome.6.ht2
-      md5sum: 265e1284ce85686516fae5d35540994a
-    - path: output/hisat2/hisat2/genome.3.ht2
-      md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: output/hisat2/hisat2/genome.8.ht2
-      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
-    - path: output/hisat2/hisat2/genome.4.ht2
-      md5sum: c25be5f8b0378abf7a58c8a880b87626
diff --git a/tests/modules/hisat2/extractsplicesites/main.nf b/tests/modules/hisat2/extractsplicesites/main.nf
deleted file mode 100644
index e947717ee4a..00000000000
--- a/tests/modules/hisat2/extractsplicesites/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf'
-
-workflow test_hisat2_extractsplicesites {
-    gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-
-    HISAT2_EXTRACTSPLICESITES ( gtf )
-}
diff --git a/tests/modules/hisat2/extractsplicesites/test.yml b/tests/modules/hisat2/extractsplicesites/test.yml
deleted file mode 100644
index 2571af944f0..00000000000
--- a/tests/modules/hisat2/extractsplicesites/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: hisat2 extractsplicesites test_hisat2_extractsplicesites
-  command: nextflow run ./tests/modules/hisat2/extractsplicesites -entry test_hisat2_extractsplicesites -c ./tests/config/nextflow.config -c ./tests/modules/hisat2/extractsplicesites/nextflow.config
-  tags:
-    - hisat2
-    - hisat2/extractsplicesites
-  files:
-    - path: output/hisat2/genome.splice_sites.txt
diff --git a/tests/modules/hmmcopy/gccounter/main.nf b/tests/modules/hmmcopy/gccounter/main.nf
deleted file mode 100644
index 05728bf52f0..00000000000
--- a/tests/modules/hmmcopy/gccounter/main.nf
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMCOPY_GCCOUNTER } from '../../../../modules/hmmcopy/gccounter/main.nf'
-
-workflow test_hmmcopy_gccounter {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    HMMCOPY_GCCOUNTER (fasta)
-}
diff --git a/tests/modules/hmmcopy/gccounter/test.yml b/tests/modules/hmmcopy/gccounter/test.yml
deleted file mode 100644
index 1cd20273bb1..00000000000
--- a/tests/modules/hmmcopy/gccounter/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: hmmcopy gccounter test_hmmcopy_gccounter
-  command: nextflow run ./tests/modules/hmmcopy/gccounter -entry test_hmmcopy_gccounter -c ./tests/config/nextflow.config -c ./tests/modules/hmmcopy/gccounter/nextflow.config
-  tags:
-    - hmmcopy
-    - hmmcopy/gccounter
-  files:
-    - path: output/hmmcopy/genome.gc.wig
-      md5sum: 59ad14bc5aaa903187d7b248c9490deb
diff --git a/tests/modules/hmmcopy/generatemap/main.nf b/tests/modules/hmmcopy/generatemap/main.nf
deleted file mode 100644
index 381420d35bd..00000000000
--- a/tests/modules/hmmcopy/generatemap/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMCOPY_GENERATEMAP } from '../../../../modules/hmmcopy/generatemap/main.nf'
-
-workflow test_hmmcopy_generatemap {
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    HMMCOPY_GENERATEMAP ( fasta )
-}
diff --git a/tests/modules/hmmcopy/generatemap/test.yml b/tests/modules/hmmcopy/generatemap/test.yml
deleted file mode 100644
index 274e5d0f5ea..00000000000
--- a/tests/modules/hmmcopy/generatemap/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: hmmcopy generatemap test_hmmcopy_generatemap
-  command: nextflow run tests/modules/hmmcopy/generatemap -entry test_hmmcopy_generatemap -c tests/config/nextflow.config
-  tags:
-    - hmmcopy
-    - hmmcopy/generatemap
-  files:
-    - path: output/hmmcopy/genome.fasta.map.bw
-      md5sum: 7ad68224a1e40287978284c387e8eb70
-    - path: output/hmmcopy/versions.yml
-      md5sum: f950580f94d8a2d88332c477972cb9f0
diff --git a/tests/modules/hmmcopy/mapcounter/main.nf b/tests/modules/hmmcopy/mapcounter/main.nf
deleted file mode 100644
index c364f0f7234..00000000000
--- a/tests/modules/hmmcopy/mapcounter/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMCOPY_MAPCOUNTER } from '../../../../modules/hmmcopy/mapcounter/main.nf'
-include { HMMCOPY_GENERATEMAP } from '../../../../modules/hmmcopy/generatemap/main.nf'
-workflow test_hmmcopy_mapcounter {
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    HMMCOPY_GENERATEMAP( fasta )
-
-    HMMCOPY_MAPCOUNTER ( HMMCOPY_GENERATEMAP.out.bigwig )
-}
diff --git a/tests/modules/hmmcopy/mapcounter/test.yml b/tests/modules/hmmcopy/mapcounter/test.yml
deleted file mode 100644
index 204800a1381..00000000000
--- a/tests/modules/hmmcopy/mapcounter/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: hmmcopy mapcounter test_hmmcopy_mapcounter
-  command: nextflow run tests/modules/hmmcopy/mapcounter -entry test_hmmcopy_mapcounter -c tests/config/nextflow.config
-  tags:
-    - hmmcopy/mapcounter
-    - hmmcopy
-  files:
-    - path: output/hmmcopy/genome.fasta.map.bw
-      md5sum: 7ad68224a1e40287978284c387e8eb70
-    - path: output/hmmcopy/genome.fasta.map.map.wig
-      md5sum: e2d39dc204ed31c1ce372d633a42560f
-    - path: output/hmmcopy/versions.yml
-      md5sum: 8361e3c0f8b96cf84834678cf988a209
diff --git a/tests/modules/hmmcopy/readcounter/main.nf b/tests/modules/hmmcopy/readcounter/main.nf
deleted file mode 100644
index 21737aabaed..00000000000
--- a/tests/modules/hmmcopy/readcounter/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf'
-
-workflow test_hmmcopy_readcounter {
-
-    input = [ [ id:'test'], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)]
-            ]
-    HMMCOPY_READCOUNTER ( input )
-}
diff --git a/tests/modules/hmmcopy/readcounter/test.yml b/tests/modules/hmmcopy/readcounter/test.yml
deleted file mode 100644
index e13b0b8dadc..00000000000
--- a/tests/modules/hmmcopy/readcounter/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: hmmcopy readcounter test_hmmcopy_readcounter
-  command: nextflow run tests/modules/hmmcopy/readcounter -entry test_hmmcopy_readcounter -c tests/config/nextflow.config
-  tags:
-    - hmmcopy
-    - hmmcopy/readcounter
-  files:
-    - path: output/hmmcopy/test.wig
-      md5sum: 4682778422b9a2510a3cb70bd13ccd08
-    - path: output/hmmcopy/versions.yml
-      md5sum: 624a85e6a1bc61abc33cac03aea33a1e
diff --git a/tests/modules/hmmer/eslalimask/main.nf b/tests/modules/hmmer/eslalimask/main.nf
deleted file mode 100644
index 6a37b345028..00000000000
--- a/tests/modules/hmmer/eslalimask/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMER_HMMALIGN             } from '../../../../modules/hmmer/hmmalign/main.nf'
-include { HMMER_ESLALIMASK as RFMASK } from '../../../../modules/hmmer/eslalimask/main.nf'
-
-workflow test_hmmer_rfmask {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in tests/config/test_data.config
-    ]
-
-    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
-
-    HMMER_HMMALIGN ( input, hmm )
-
-    RFMASK ( HMMER_HMMALIGN.out.sthlm, [] )
-}
diff --git a/tests/modules/hmmer/eslalimask/test.yml b/tests/modules/hmmer/eslalimask/test.yml
deleted file mode 100644
index 3bb676662f9..00000000000
--- a/tests/modules/hmmer/eslalimask/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: hmmer eslalimask test_hmmer_rfmask
-  command: nextflow run ./tests/modules/hmmer/eslalimask -entry test_hmmer_rfmask -c ./tests/config/nextflow.config  -c ./tests/modules/hmmer/eslalimask/nextflow.config
-  tags:
-    - hmmer
-    - hmmer/eslalimask
-  files:
-    - path: output/rfmask/test.masked.sthlm.gz
-      contains:
-        - "GS CP025268.1:223601-225154 DE Escherichia coli"
-        - "=GC RF"
-    - path: output/rfmask/versions.yml
-      contains:
-        - "easel:"
diff --git a/tests/modules/hmmer/eslreformat/main.nf b/tests/modules/hmmer/eslreformat/main.nf
deleted file mode 100644
index aa1d3d690f3..00000000000
--- a/tests/modules/hmmer/eslreformat/main.nf
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMER_HMMALIGN                                 } from '../../../../modules/hmmer/hmmalign/main.nf'
-include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_AFA     } from '../../../../modules/hmmer/eslreformat/main.nf'
-include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_PHYLIP  } from '../../../../modules/hmmer/eslreformat/main.nf'
-include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_UNALIGN } from '../../../../modules/hmmer/eslreformat/main.nf'
-
-workflow test_hmmer_eslreformat_afa {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in tests/config/test_data.config
-    ]
-
-    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
-
-    HMMER_HMMALIGN ( input, hmm )
-
-    HMMER_ESLREFORMAT_AFA ( HMMER_HMMALIGN.out.sthlm )
-}
-
-workflow test_hmmer_eslreformat_phylip {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in tests/config/test_data.config
-    ]
-
-    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
-
-    HMMER_HMMALIGN ( input, hmm )
-
-    HMMER_ESLREFORMAT_PHYLIP ( HMMER_HMMALIGN.out.sthlm )
-}
-
-workflow test_hmmer_eslreformat_unalign {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in tests/config/test_data.config
-    ]
-
-    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
-
-    HMMER_HMMALIGN ( input, hmm )
-
-    HMMER_ESLREFORMAT_UNALIGN ( HMMER_HMMALIGN.out.sthlm )
-}
diff --git a/tests/modules/hmmer/eslreformat/test.yml b/tests/modules/hmmer/eslreformat/test.yml
deleted file mode 100644
index b625c5f2bf8..00000000000
--- a/tests/modules/hmmer/eslreformat/test.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-- name: hmmer eslreformat test_hmmer_eslreformat_afa
-  command: nextflow run ./tests/modules/hmmer/eslreformat -entry test_hmmer_eslreformat_afa -c ./tests/config/nextflow.config  -c ./tests/modules/hmmer/eslreformat/nextflow.config
-  tags:
-    - hmmer/eslreformat
-    - hmmer
-  files:
-    - path: output/hmmer/test.afa.gz
-      contains:
-        - ">CP025268.1"
-        - "aaa---UUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUG"
-    - path: output/hmmer/versions.yml
-      contains:
-        - "easel:"
-- name: hmmer eslreformat test_hmmer_eslreformat_phylip
-  command: nextflow run ./tests/modules/hmmer/eslreformat -entry test_hmmer_eslreformat_phylip -c ./tests/config/nextflow.config  -c ./tests/modules/hmmer/eslreformat/nextflow.config
-  tags:
-    - hmmer/eslreformat
-    - hmmer
-  files:
-    - path: output/hmmer/test.phylip.gz
-      contains:
-        - "CP025268.1 AAA---UUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUG"
-    - path: output/hmmer/versions.yml
-      contains:
-        - "easel:"
-- name: hmmer eslreformat test_hmmer_eslreformat_unalign
-  command: nextflow run ./tests/modules/hmmer/eslreformat -entry test_hmmer_eslreformat_unalign -c ./tests/config/nextflow.config  -c ./tests/modules/hmmer/eslreformat/nextflow.config
-  tags:
-    - hmmer/eslreformat
-    - hmmer
-  files:
-    - path: output/hmmer/test.afa.gz
-      contains:
-        - ">CP025268.1"
-        - "aaaUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUG"
-    - path: output/hmmer/versions.yml
-      contains:
-        - "easel:"
diff --git a/tests/modules/hmmer/hmmalign/main.nf b/tests/modules/hmmer/hmmalign/main.nf
deleted file mode 100644
index 7e48d00a338..00000000000
--- a/tests/modules/hmmer/hmmalign/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMER_HMMALIGN as HMMER_HMMALIGN        } from '../../../../modules/hmmer/hmmalign/main.nf'
-include { HMMER_HMMALIGN as HMMER_HMMALIGN_PREFIX } from '../../../../modules/hmmer/hmmalign/main.nf'
-
-workflow test_hmmer_hmmalign {
-
-    input = [
-        [ id:'test' ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in tests/config/test_data.config
-    ]
-
-    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
-
-    HMMER_HMMALIGN ( input, hmm )
-}
-
-workflow test_hmmer_hmmalign_prefix {
-
-    input = [
-        [ id:'test' ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in tests/config/test_data.config
-    ]
-
-    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
-
-    HMMER_HMMALIGN_PREFIX ( input, hmm )
-}
diff --git a/tests/modules/hmmer/hmmalign/test.yml b/tests/modules/hmmer/hmmalign/test.yml
deleted file mode 100644
index becf51dde71..00000000000
--- a/tests/modules/hmmer/hmmalign/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: hmmer hmmalign test_hmmer_hmmalign
-  command: nextflow run ./tests/modules/hmmer/hmmalign -entry test_hmmer_hmmalign -c ./tests/config/nextflow.config -c ./tests/modules/hmmer/hmmalign/nextflow.config
-  tags:
-    - hmmer
-    - hmmer/hmmalign
-  files:
-    - path: output/hmmer/test.sthlm.gz
-      md5sum: ddaa8b96291edf4e1a929a224329161b
-- name: hmmer hmmalign test_hmmer_hmmalign_prefix
-  command: nextflow run ./tests/modules/hmmer/hmmalign -entry test_hmmer_hmmalign_prefix -c ./tests/config/nextflow.config -c ./tests/modules/hmmer/hmmalign/nextflow.config
-  tags:
-    - hmmer
-    - hmmer/hmmalign
-  files:
-    - path: output/hmmer/test.prefix.sthlm.gz
-      md5sum: ddaa8b96291edf4e1a929a224329161b
diff --git a/tests/modules/hmmer/hmmbuild/main.nf b/tests/modules/hmmer/hmmbuild/main.nf
deleted file mode 100644
index 15fb04c6af9..00000000000
--- a/tests/modules/hmmer/hmmbuild/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMER_HMMBUILD } from '../../../../modules/hmmer/hmmbuild/main.nf'
-
-workflow test_hmmer_hmmbuild {
-    
-    input = [
-        [ id: 'PF14720' ],      // meta map
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true)
-    ]
-
-    HMMER_HMMBUILD ( input, [] )
-}
diff --git a/tests/modules/hmmer/hmmbuild/test.yml b/tests/modules/hmmer/hmmbuild/test.yml
deleted file mode 100644
index 04bd14e8616..00000000000
--- a/tests/modules/hmmer/hmmbuild/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: hmmer hmmbuild test_hmmer_hmmbuild
-  command: nextflow run ./tests/modules/hmmer/hmmbuild -entry test_hmmer_hmmbuild -c ./tests/config/nextflow.config  -c ./tests/modules/hmmer/hmmbuild/nextflow.config
-  tags:
-    - hmmer
-    - hmmer/hmmbuild
-  files:
-    - path: output/hmmer/PF14720.hmm.gz
-      contains:
-        - "LENG  80"
-    - path: output/hmmer/versions.yml
-      contains:
-        - "hmmer:"
diff --git a/tests/modules/hmmer/hmmsearch/main.nf b/tests/modules/hmmer/hmmsearch/main.nf
deleted file mode 100644
index b181a529ca3..00000000000
--- a/tests/modules/hmmer/hmmsearch/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMER_HMMSEARCH } from '../../../../modules/hmmer/hmmsearch/main.nf'
-
-workflow test_hmmer_hmmsearch {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true),
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz', checkIfExists: true),
-        false,
-        false,
-        false
-    ]
-
-    HMMER_HMMSEARCH ( input )
-}
-
-workflow test_hmmer_hmmsearch_optional {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true),
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz', checkIfExists: true),
-        true,
-        true,
-        true
-    ]
-
-    HMMER_HMMSEARCH ( input )
-}
diff --git a/tests/modules/hmmer/hmmsearch/test.yml b/tests/modules/hmmer/hmmsearch/test.yml
deleted file mode 100644
index dd3e16eff5e..00000000000
--- a/tests/modules/hmmer/hmmsearch/test.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- name: hmmer hmmsearch test_hmmer_hmmsearch
-  command: nextflow run tests/modules/hmmer/hmmsearch -entry test_hmmer_hmmsearch -c tests/config/nextflow.config
-  tags:
-    - hmmer/hmmsearch
-    - hmmer
-  files:
-    - path: output/hmmer/test.txt.gz
-      contains:
-        - "[ok]"
-    - path: output/hmmer/versions.yml
-      md5sum: ed0808c10abd205c6bd0fb01f45259bb
-
-- name: hmmer hmmsearch test_hmmer_hmmsearch_optional
-  command: nextflow run tests/modules/hmmer/hmmsearch -entry test_hmmer_hmmsearch_optional -c tests/config/nextflow.config
-  tags:
-    - hmmer/hmmsearch
-    - hmmer
-  files:
-    - path: output/hmmer/test.sto.gz
-      md5sum: d3121aa33455074c566fb7f8fdcda7b0
-    - path: output/hmmer/test.domtbl.gz
-      contains:
-        - "# [ok]"
-    - path: output/hmmer/test.tbl.gz
-      contains:
-        - "# [ok]"
-    - path: output/hmmer/test.txt.gz
-      contains:
-        - "[ok]"
-    - path: output/hmmer/versions.yml
-      md5sum: ebdcb08ae540e840f7b5c4c75a3a2993
diff --git a/tests/modules/hmtnote/main.nf b/tests/modules/hmtnote/main.nf
deleted file mode 100644
index 9bee719c415..00000000000
--- a/tests/modules/hmtnote/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMTNOTE } from '../../../modules/hmtnote/main.nf'
-
-workflow test_hmtnote {
-    
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-            ]
-
-    HMTNOTE ( input)
-}
diff --git a/tests/modules/hmtnote/test.yml b/tests/modules/hmtnote/test.yml
deleted file mode 100644
index 10b7225fa2a..00000000000
--- a/tests/modules/hmtnote/test.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-- name: hmtnote test_hmtnote
-  command: nextflow run ./tests/modules/hmtnote -entry test_hmtnote -c ./tests/config/nextflow.config -c ./tests/modules/hmtnote/nextflow.config
-  tags:
-    - hmtnote
-  files:
-    - path: output/hmtnote/test_annotated.vcf
diff --git a/tests/modules/homer/annotatepeaks/main.nf b/tests/modules/homer/annotatepeaks/main.nf
deleted file mode 100644
index ab8f6f8f19a..00000000000
--- a/tests/modules/homer/annotatepeaks/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HOMER_ANNOTATEPEAKS } from '../../../../modules/homer/annotatepeaks/main.nf'
-
-workflow test_homer_annotatepeaks {
-    input = [ [ id:'test'],
-              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gtf   = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-    HOMER_ANNOTATEPEAKS ( input, fasta, gtf )
-}
diff --git a/tests/modules/homer/annotatepeaks/test.yml b/tests/modules/homer/annotatepeaks/test.yml
deleted file mode 100644
index 52fd99a3928..00000000000
--- a/tests/modules/homer/annotatepeaks/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: homer annotatepeaks test_homer_annotatepeaks
-  command: nextflow run ./tests/modules/homer/annotatepeaks -entry test_homer_annotatepeaks -c ./tests/config/nextflow.config -c ./tests/modules/homer/annotatepeaks/nextflow.config
-  tags:
-    - homer
-    - homer/annotatepeaks
-  files:
-    - path: output/homer/test.annotatePeaks.txt
diff --git a/tests/modules/homer/findpeaks/main.nf b/tests/modules/homer/findpeaks/main.nf
deleted file mode 100644
index 0e7e8ed6d4f..00000000000
--- a/tests/modules/homer/findpeaks/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
-include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main.nf'
-
-workflow test_homer_findpeaks {
-    input = [[id:'test'],
-             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    HOMER_MAKETAGDIRECTORY (input, fasta)
-    HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
-}
-
diff --git a/tests/modules/homer/findpeaks/test.yml b/tests/modules/homer/findpeaks/test.yml
deleted file mode 100644
index b5225404820..00000000000
--- a/tests/modules/homer/findpeaks/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: homer findpeaks
-  command: nextflow run ./tests/modules/homer/findpeaks -entry test_homer_findpeaks -c ./tests/config/nextflow.config -c ./tests/modules/homer/findpeaks/nextflow.config
-  tags:
-    - homer
-    - homer/findpeaks
-  files:
-    - path: output/homer/test.peaks.txt
-      md5sum: 86e15beaa4b439585786478e58418c0c
diff --git a/tests/modules/homer/maketagdirectory/main.nf b/tests/modules/homer/maketagdirectory/main.nf
deleted file mode 100644
index 7de693e6a1b..00000000000
--- a/tests/modules/homer/maketagdirectory/main.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include {
-    HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BED
-    HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BAM
-} from '../../../../modules/homer/maketagdirectory/main.nf'
-
-workflow test_homer_maketagdirectory_bed {
-    input = [[id:'test'],
-             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    HOMER_MAKETAGDIRECTORY_BED (input, fasta)
-}
-
-
-workflow test_homer_maketagdirectory_meta {
-    input =
-        [[[ id:'test1'],
-          [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]],
-         [[ id:'test2'],
-          [file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    meta_input = [[id: 'meta_test']] + [ input.collect{it[1]}.flatten() ]
-
-    HOMER_MAKETAGDIRECTORY_BED (meta_input, fasta)
-}
-
-workflow test_homer_maketagdirectory_bam {
-    input = [[id:'test'],
-             [file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    HOMER_MAKETAGDIRECTORY_BAM (input, fasta)
-}
diff --git a/tests/modules/homer/maketagdirectory/test.yml b/tests/modules/homer/maketagdirectory/test.yml
deleted file mode 100644
index 970ca90676e..00000000000
--- a/tests/modules/homer/maketagdirectory/test.yml
+++ /dev/null
@@ -1,50 +0,0 @@
-- name: homer maketagdirectory bed
-  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory_bed -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
-  tags:
-    - homer
-    - homer/maketagdirectory
-  files:
-    - path: output/homer/test_tagdir/MT192765.1.tags.tsv
-      md5sum: e29522171ca2169b57396495f8b97485
-    - path: output/homer/test_tagdir/tagAutocorrelation.txt
-      md5sum: 62b107c4971b94126fb89a0bc2800455
-    - path: output/homer/test_tagdir/tagCountDistribution.txt
-      md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
-    - path: output/homer/test_tagdir/tagInfo.txt
-      md5sum: c9bb2ca53bb101d74c1ec92d2b0ad26e
-    - path: output/homer/test_tagdir/tagLengthDistribution.txt
-      md5sum: e5aa2b9843ca9c04ace297280aed6af4
-
-- name: homer maketagdirectory meta
-  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory_meta -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
-  tags:
-    - homer
-    - homer/maketagdirectory
-  files:
-    - path: output/homer/meta_test_tagdir/MT192765.1.tags.tsv
-      md5sum: e29522171ca2169b57396495f8b97485
-    - path: output/homer/meta_test_tagdir/tagAutocorrelation.txt
-      md5sum: 62b107c4971b94126fb89a0bc2800455
-    - path: output/homer/meta_test_tagdir/tagCountDistribution.txt
-      md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
-    - path: output/homer/meta_test_tagdir/tagInfo.txt
-      md5sum: cb907ebf9afc042bb61196d624e793c8
-    - path: output/homer/meta_test_tagdir/tagLengthDistribution.txt
-      md5sum: e5aa2b9843ca9c04ace297280aed6af4
-
-- name: homer maketagdirectory bam
-  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory_bam -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
-  tags:
-    - homer
-    - homer/maketagdirectory
-  files:
-    - path: output/homer/test_tagdir/MT192765.1.tags.tsv
-      md5sum: 365808c4751ef6dd7085ac52037a22bc
-    - path: output/homer/test_tagdir/tagAutocorrelation.txt
-      md5sum: 8b396f2aef1cdd3af4fab57b142d3250
-    - path: output/homer/test_tagdir/tagCountDistribution.txt
-      md5sum: afc6d007096c3872bbe84c9dc8edb832
-    - path: output/homer/test_tagdir/tagInfo.txt
-      md5sum: aebf6ff15fd0a238ee6a94d623c578ca
-    - path: output/homer/test_tagdir/tagLengthDistribution.txt
-      md5sum: 44f231adb2a705ae81950808c55cf248
diff --git a/tests/modules/homer/makeucscfile/main.nf b/tests/modules/homer/makeucscfile/main.nf
deleted file mode 100644
index 986c9c14d34..00000000000
--- a/tests/modules/homer/makeucscfile/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
-include { HOMER_MAKEUCSCFILE } from '../../../../modules/homer/makeucscfile/main.nf'
-
-workflow test_homer_makeucscfile {
-    input = [[id:'test'],
-             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    HOMER_MAKETAGDIRECTORY (input, fasta)
-    HOMER_MAKEUCSCFILE ( HOMER_MAKETAGDIRECTORY.out.tagdir )
-}
-
diff --git a/tests/modules/homer/makeucscfile/test.yml b/tests/modules/homer/makeucscfile/test.yml
deleted file mode 100644
index e6ccb9fa164..00000000000
--- a/tests/modules/homer/makeucscfile/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: homer makeucscfile
-  command: nextflow run ./tests/modules/homer/makeucscfile -entry test_homer_makeucscfile -c ./tests/config/nextflow.config -c ./tests/modules/homer/makeucscfile/nextflow.config
-  tags:
-    - homer
-    - homer/makeucscfile
-  files:
-    - path: output/homer/test.bedGraph.gz
diff --git a/tests/modules/homer/pos2bed/main.nf b/tests/modules/homer/pos2bed/main.nf
deleted file mode 100644
index bcfdc0bc0fa..00000000000
--- a/tests/modules/homer/pos2bed/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
-include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main.nf'
-include { HOMER_POS2BED } from '../../../../modules/homer/pos2bed/main.nf'
-
-workflow test_homer_pos2bed {
-    input = [[id:'test'],
-             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    HOMER_MAKETAGDIRECTORY (input, fasta)
-    HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
-
-    HOMER_POS2BED ( HOMER_FINDPEAKS.out.txt )
-}
diff --git a/tests/modules/homer/pos2bed/test.yml b/tests/modules/homer/pos2bed/test.yml
deleted file mode 100644
index 6aad55bc9cd..00000000000
--- a/tests/modules/homer/pos2bed/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: "homer pos2bed"
-  command: nextflow run ./tests/modules/homer/pos2bed -entry test_homer_pos2bed -c ./tests/config/nextflow.config -c ./tests/modules/homer/pos2bed/nextflow.config
-  tags:
-    - "homer"
-    - "homer/pos2bed"
-  files:
-    - path: output/homer/test.bed
-      md5sum: 5d6ddd9c7e621a66f6f045b9b5abecb4
-    - path: output/homer/versions.yml
-      md5sum: 1485f4b2d76484e8fe3310e2505de2fd
diff --git a/tests/modules/hpsuissero/main.nf b/tests/modules/hpsuissero/main.nf
deleted file mode 100644
index f66fcd9368e..00000000000
--- a/tests/modules/hpsuissero/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HPSUISSERO } from '../../../modules/hpsuissero/main.nf'
-
-workflow test_hpsuissero {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
-    ]
-
-    HPSUISSERO ( input )
-}
diff --git a/tests/modules/hpsuissero/test.yml b/tests/modules/hpsuissero/test.yml
deleted file mode 100644
index 33b26eb2234..00000000000
--- a/tests/modules/hpsuissero/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: hpsuissero test_hpsuissero
-  command: nextflow run tests/modules/hpsuissero -entry test_hpsuissero -c tests/config/nextflow.config
-  tags:
-    - hpsuissero
-  files:
-    - path: output/hpsuissero/test_serotyping_res.tsv
-      md5sum: 559dd2ca386eeb58f3975e3204ce9d43
-    - path: output/hpsuissero/versions.yml
-      md5sum: f65438e63a74ac6ee365bfdbbd3f996a
diff --git a/tests/modules/ichorcna/createpon/main.nf b/tests/modules/ichorcna/createpon/main.nf
deleted file mode 100644
index 0e86fb92c4a..00000000000
--- a/tests/modules/ichorcna/createpon/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ICHORCNA_CREATEPON } from '../../../../modules/ichorcna/createpon/main.nf'
-
-workflow test_ichorcna_createpon {
-
-    input = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
-
-    gcwig   = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
-    mapwig  = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
-
-    centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
-
-    ICHORCNA_CREATEPON ( input, gcwig, mapwig, centromere )
-}
-
-workflow test_ichorcna_createpon2 {
-
-    input = [file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true),
-             file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315_T2.ctDNA.reads.wig", checkIfExists: true)]
-
-    gcwig   = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
-    mapwig  = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
-
-    centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
-
-    ICHORCNA_CREATEPON ( input, gcwig, mapwig, centromere )
-}
diff --git a/tests/modules/ichorcna/createpon/test.yml b/tests/modules/ichorcna/createpon/test.yml
deleted file mode 100644
index c8fe63c86bf..00000000000
--- a/tests/modules/ichorcna/createpon/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: ichorcna createpon test_ichorcna_createpon
-  command: nextflow run tests/modules/ichorcna/createpon -entry test_ichorcna_createpon -c tests/config/nextflow.config
-  tags:
-    - ichorcna/createpon
-    - ichorcna
-  files:
-    - path: output/ichorcna/PoN_median.txt
-      contains: ["seqnames"]
-    - path: output/ichorcna/versions.yml
-      md5sum: 59a2121301113cc013bfae65935e07f1
-
-- name: ichorcna createpon test_ichorcna_createpon2
-  command: nextflow run tests/modules/ichorcna/createpon -entry test_ichorcna_createpon2 -c tests/config/nextflow.config
-  tags:
-    - ichorcna/createpon
-    - ichorcna
-  files:
-    - path: output/ichorcna/PoN_median.txt
-      contains: ["seqnames"]
-    - path: output/ichorcna/versions.yml
-      md5sum: 31a5fcc0075dbe747f7736efbdb99644
diff --git a/tests/modules/ichorcna/run/main.nf b/tests/modules/ichorcna/run/main.nf
deleted file mode 100644
index 8a830f62451..00000000000
--- a/tests/modules/ichorcna/run/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ICHORCNA_RUN } from '../../../../modules/ichorcna/run/main.nf'
-include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf'
-include { HMMCOPY_GCCOUNTER } from '../../../../modules/hmmcopy/gccounter/main.nf'
-include { HMMCOPY_MAPCOUNTER } from '../../../../modules/hmmcopy/mapcounter/main.nf'
-include { HMMCOPY_GENERATEMAP } from '../../../../modules/hmmcopy/generatemap/main.nf'
-
-workflow test_ichorcna_run_no_panel {
-
-    input = [ [ id:'test'], // meta map
-              file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
-            ]
-
-    gcwig   = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
-    mapwig  = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
-
-    panel_of_normals = []
-    centromere = []
-
-    ICHORCNA_RUN ( input, gcwig, mapwig, panel_of_normals, centromere)
-}
-
-workflow test_ichorcna_run_inc_panel {
-
-    input = [ [ id:'test'], // meta map
-              file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
-            ]
-
-    gcwig   = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
-    mapwig  = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
-
-    panel_of_normals = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds", checkIfExists: true)
-
-    centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
-
-    ICHORCNA_RUN ( input, gcwig, mapwig, panel_of_normals, centromere)
-}
diff --git a/tests/modules/ichorcna/run/test.yml b/tests/modules/ichorcna/run/test.yml
deleted file mode 100644
index 4be837743b1..00000000000
--- a/tests/modules/ichorcna/run/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: ichorcna run test_ichorcna_run_no_panel
-  command: nextflow run tests/modules/ichorcna/run -entry test_ichorcna_run_no_panel -c tests/config/nextflow.config
-  tags:
-    - ichorcna
-    - ichorcna/run
-  files:
-    - path: output/ichorcna/test.cna.seg
-      contains: ["Corrected_Copy_Number"]
-    - path: output/ichorcna/test.params.txt
-      md5sum: e39a579cdcc9576679f06dc5c22605a7
-    - path: output/ichorcna/versions.yml
-      md5sum: effb37e19bec3609417aaccad4b6a294
-
-- name: ichorcna run test_ichorcna_run_inc_panel
-  command: nextflow run tests/modules/ichorcna/run -entry test_ichorcna_run_inc_panel -c tests/config/nextflow.config
-  tags:
-    - ichorcna
-    - ichorcna/run
-  files:
-    - path: output/ichorcna/test.cna.seg
-      contains: ["Corrected_Copy_Number"]
-    - path: output/ichorcna/test.params.txt
-      md5sum: 0b97e0269cd0b571f5a85890f6ddb181
-    - path: output/ichorcna/versions.yml
-      md5sum: fc9d96de0a1c15cea59208305b14e535
diff --git a/tests/modules/idr/main.nf b/tests/modules/idr/main.nf
deleted file mode 100644
index ed3bf289ead..00000000000
--- a/tests/modules/idr/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { IDR } from '../../../modules/idr/main.nf'
-
-workflow test_idr_narrowpeak {
-
-    input = [
-        file(params.test_data['homo_sapiens']['illumina']['test_narrowpeak'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_narrowpeak'], checkIfExists: true)
-    ]
-
-    IDR ( input, 'narrowPeak', 'test' )
-}
-
-workflow test_idr_broadpeak {
-
-    input = [
-        file(params.test_data['homo_sapiens']['illumina']['test_broadpeak'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_broadpeak'], checkIfExists: true)
-    ]
-
-    IDR ( input, 'broadPeak', 'test' )
-}
-
-workflow test_idr_noprefix {
-
-    input = [
-        file(params.test_data['homo_sapiens']['illumina']['test_narrowpeak'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_narrowpeak'], checkIfExists: true)
-    ]
-
-    IDR ( input, 'narrowPeak', '' )
-}
diff --git a/tests/modules/idr/test.yml b/tests/modules/idr/test.yml
deleted file mode 100644
index 9d5ef2a7cfa..00000000000
--- a/tests/modules/idr/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: idr test_idr_narrowpeak
-  command: nextflow run ./tests/modules/idr -entry test_idr_narrowpeak -c ./tests/config/nextflow.config -c ./tests/modules/idr/nextflow.config
-  tags:
-    - idr
-  files:
-    - path: output/idr/test.idrValues.txt
-      md5sum: 09be837cc6abbc3eb5958b74802eea55
-    - path: output/idr/test.idrValues.txt.png
-      md5sum: 4a7143ccc0ccadb37c2317bf626e6d96
-    - path: output/idr/test.log.txt
-      md5sum: 6443507ac66b9d3b64bc56b78328083e
-
-- name: idr test_idr_broadpeak
-  command: nextflow run ./tests/modules/idr -entry test_idr_broadpeak -c ./tests/config/nextflow.config -c ./tests/modules/idr/nextflow.config
-  tags:
-    - idr
-  files:
-    - path: output/idr/test.idrValues.txt
-      md5sum: 387441c716815e4caec3e70a2cc11a4a
-    - path: output/idr/test.idrValues.txt.png
-      md5sum: 7204083ca5b920b4215a5991c12cb4e7
-    - path: output/idr/test.log.txt
-      md5sum: e6917133112b5cec135c182ffac19237
-
-- name: idr test_idr_noprefix
-  command: nextflow run ./tests/modules/idr -entry test_idr_noprefix -c ./tests/config/nextflow.config -c ./tests/modules/idr/nextflow.config
-  tags:
-    - idr
-  files:
-    - path: output/idr/idrValues.txt
-      md5sum: 09be837cc6abbc3eb5958b74802eea55
-    - path: output/idr/idrValues.txt.png
-      md5sum: 4a7143ccc0ccadb37c2317bf626e6d96
-    - path: output/idr/log.txt
-      md5sum: 6443507ac66b9d3b64bc56b78328083e
diff --git a/tests/modules/imputeme/vcftoprs/main.nf b/tests/modules/imputeme/vcftoprs/main.nf
deleted file mode 100644
index dccc06e0e25..00000000000
--- a/tests/modules/imputeme/vcftoprs/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { IMPUTEME_VCFTOPRS } from '../../../../modules/imputeme/vcftoprs/main.nf'
-
-workflow test_imputeme_vcftoprs {
-    
-    input = [ 
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
-    ]
-
-    IMPUTEME_VCFTOPRS ( input )
-}
diff --git a/tests/modules/imputeme/vcftoprs/test.yml b/tests/modules/imputeme/vcftoprs/test.yml
deleted file mode 100644
index 89f2d540724..00000000000
--- a/tests/modules/imputeme/vcftoprs/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: imputeme vcftoprs test_imputeme_vcftoprs
-  command: nextflow run ./tests/modules/imputeme/vcftoprs -entry test_imputeme_vcftoprs -c ./tests/config/nextflow.config -c ./tests/modules/imputeme/vcftoprs/nextflow.config
-  tags:
-    - imputeme
-    - imputeme/vcftoprs
-  files:
-    - path: output/imputeme/output.json
-      contains: ['type_2_diabetes_32541925":{"GRS":[24.01]']
diff --git a/tests/modules/instrain/profile/main.nf b/tests/modules/instrain/profile/main.nf
deleted file mode 100644
index ce054725efa..00000000000
--- a/tests/modules/instrain/profile/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { INSTRAIN_PROFILE } from '../../../../modules/instrain/profile/main.nf'
-
-workflow test_instrain_profile {
-    
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-        ]
-    ]
-    genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    INSTRAIN_PROFILE ( input , genome_fasta , [] , [] )
-}
diff --git a/tests/modules/instrain/profile/test.yml b/tests/modules/instrain/profile/test.yml
deleted file mode 100644
index c256d1018ce..00000000000
--- a/tests/modules/instrain/profile/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: "instrain"
-  command: nextflow run ./tests/modules/instrain/profile -entry test_instrain_profile -c ./tests/config/nextflow.config -c ./tests/modules/instrain/profile/nextflow.config
-  tags:
-    - instrain
-    - instrain/profile
-  files:
-    - path: output/instrain/versions.yml
-    - path: output/instrain/test.IS/output/test.IS_SNVs.tsv
-      md5sum: 1d753903af5a25be540dcff255e25a1f
diff --git a/tests/modules/iqtree/main.nf b/tests/modules/iqtree/main.nf
deleted file mode 100644
index 2d73bd52c77..00000000000
--- a/tests/modules/iqtree/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { IQTREE } from '../../../modules/iqtree/main.nf'
-
-workflow test_iqtree {
-    
-    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
-
-    IQTREE ( input, '' )
-}
diff --git a/tests/modules/iqtree/test.yml b/tests/modules/iqtree/test.yml
deleted file mode 100644
index 291472b09ac..00000000000
--- a/tests/modules/iqtree/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: iqtree test workflow
-  command: nextflow run ./tests/modules/iqtree -entry test_iqtree -c ./tests/config/nextflow.config -c ./tests/modules/iqtree/nextflow.config
-  tags:
-    - iqtree
-  files:
-    - path: output/iqtree/informative_sites.fas.treefile
-      contains:
-        - "(sample1:0.002"
-        - "(sample2:0.005"
-        - "sample3:0.0005"
-        - "sample4:0.001"
diff --git a/tests/modules/ismapper/main.nf b/tests/modules/ismapper/main.nf
deleted file mode 100644
index abb180f746c..00000000000
--- a/tests/modules/ismapper/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ISMAPPER } from '../../../modules/ismapper/main.nf'
-
-workflow test_ismapper {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
-        file("https://github.com/jhawkey/IS_mapper/raw/master/test/inputs/S_suis_P17.gbk", checkIfExists: true),
-        file("https://github.com/jhawkey/IS_mapper/raw/master/test/inputs/ISSsu3.fasta", checkIfExists: true)
-    ]
-
-    ISMAPPER ( input )
-}
diff --git a/tests/modules/ismapper/test.yml b/tests/modules/ismapper/test.yml
deleted file mode 100644
index b4f64448356..00000000000
--- a/tests/modules/ismapper/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: ismapper test_ismapper
-  command: nextflow run ./tests/modules/ismapper -entry test_ismapper -c ./tests/config/nextflow.config -c ./tests/modules/ismapper/nextflow.config
-  tags:
-    - ismapper
-  files:
-    - path: output/ismapper/results/test/ISSsu3/test_ISSsu3_left_final.fastq
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/ismapper/results/test/ISSsu3/test_ISSsu3_right_final.fastq
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/ismapper/results/test/ISSsu3/test__AM946016.1_closest.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/ismapper/results/test/ISSsu3/test__AM946016.1_intersect.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/ismapper/results/test/ISSsu3/test__AM946016.1_table.txt
-      md5sum: 9e05cda3990cb841db2bfb6e6e04a1f5
-    - path: output/ismapper/results/test/ISSsu3/test_left_AM946016.1_finalcov.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/ismapper/results/test/ISSsu3/test_left_AM946016.1_merged.sorted.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/ismapper/results/test/ISSsu3/test_left_AM946016.1_unpaired.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/ismapper/results/test/ISSsu3/test_right_AM946016.1_finalcov.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/ismapper/results/test/ISSsu3/test_right_AM946016.1_merged.sorted.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/ismapper/results/test/ISSsu3/test_right_AM946016.1_unpaired.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/isoseq3/cluster/main.nf b/tests/modules/isoseq3/cluster/main.nf
deleted file mode 100644
index 958b03a6b2c..00000000000
--- a/tests/modules/isoseq3/cluster/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ISOSEQ3_CLUSTER } from '../../../../modules/isoseq3/cluster/main.nf'
-
-workflow test_isoseq3_cluster {
-
-    input = [
-            [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['pacbio']['refine'], checkIfExists: true),
-        ]
-
-    ISOSEQ3_CLUSTER ( input )
-}
diff --git a/tests/modules/isoseq3/cluster/test.yml b/tests/modules/isoseq3/cluster/test.yml
deleted file mode 100644
index 2df3024cba0..00000000000
--- a/tests/modules/isoseq3/cluster/test.yml
+++ /dev/null
@@ -1,28 +0,0 @@
-- name: isoseq3 cluster test_isoseq3_cluster
-  command: nextflow run ./tests/modules/isoseq3/cluster -entry test_isoseq3_cluster -c ./tests/config/nextflow.config -c ./tests/modules/isoseq3/cluster/nextflow.config
-  tags:
-    - isoseq3
-    - isoseq3/cluster
-  files:
-    - path: output/isoseq3/test.transcripts.bam
-      md5sum: eb36697688099c757ef4196f54ad7d7a
-    - path: output/isoseq3/test.transcripts.bam.pbi
-      md5sum: db70cee03421822e9b8f9fb6b228f461
-    - path: output/isoseq3/test.transcripts.cluster
-      md5sum: d5059d856763fc5591332980bfc0d57b
-    - path: output/isoseq3/test.transcripts.cluster_report.csv
-      md5sum: 342d97dc10aedf80a45977edcb491c62
-    - path: output/isoseq3/test.transcripts.hq.bam
-      md5sum: 4c5f4ffb429107c9c9578419e07d6987
-    - path: output/isoseq3/test.transcripts.hq.bam.pbi
-      md5sum: 39ac3e957c8d55b0ce3f425d63baa154
-    - path: output/isoseq3/test.transcripts.lq.bam
-      md5sum: 710ca4bc58ac039d76775460e1c822a0
-    - path: output/isoseq3/test.transcripts.lq.bam.pbi
-      md5sum: 9b32036553bf3dced3065e6d0f36aef9
-    - path: output/isoseq3/test.transcripts.singletons.bam
-      md5sum: 0288577406b9d1e7356de9b4d7c2bb7c
-    - path: output/isoseq3/test.transcripts.singletons.bam.pbi
-      md5sum: 8e0e0681179c0c36209b49fa60783841
-    - path: output/isoseq3/test.transcripts.transcriptset.xml
-      contains: ["PacBio.DataSet.TranscriptSet"]
diff --git a/tests/modules/isoseq3/refine/main.nf b/tests/modules/isoseq3/refine/main.nf
deleted file mode 100644
index 45dd1560f11..00000000000
--- a/tests/modules/isoseq3/refine/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ISOSEQ3_REFINE } from '../../../../modules/isoseq3/refine/main'
-
-workflow test_isoseq3_refine {
-
-    input = [
-            [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['pacbio']['lima'], checkIfExists: true),
-    ]
-    primers = file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true)
-
-    ISOSEQ3_REFINE ( input, primers )
-}
diff --git a/tests/modules/isoseq3/refine/test.yml b/tests/modules/isoseq3/refine/test.yml
deleted file mode 100644
index 82180ed970b..00000000000
--- a/tests/modules/isoseq3/refine/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: isoseq3 refine test_isoseq3_refine
-  command: nextflow run ./tests/modules/isoseq3/refine -entry test_isoseq3_refine -c ./tests/config/nextflow.config -c ./tests/modules/isoseq3/refine/nextflow.config
-  tags:
-    - isoseq3
-    - isoseq3/refine
-  files:
-    - path: output/isoseq3/test.refine.bam
-      md5sum: e8387afd5f66a7f6a89f90a0dcf3b823
-    - path: output/isoseq3/test.refine.bam.pbi
-      md5sum: 8097cad9e472f2f79de6de5fe3dcc822
-    - path: output/isoseq3/test.refine.consensusreadset.xml
-      contains: ["pbds:ConsensusReadSet"]
-    - path: output/isoseq3/test.refine.filter_summary.json
-      md5sum: 87f8bdd5c60741f47b8a991e002f7ef3
-    - path: output/isoseq3/test.refine.report.csv
-      md5sum: d42a139e5d9b08396bdb087c01243ea9
diff --git a/tests/modules/ivar/consensus/main.nf b/tests/modules/ivar/consensus/main.nf
deleted file mode 100644
index 27ac83f9917..00000000000
--- a/tests/modules/ivar/consensus/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { IVAR_CONSENSUS } from '../../../../modules/ivar/consensus/main.nf'
-
-workflow test_ivar_consensus {
-
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_mpileup = false
-
-    IVAR_CONSENSUS ( input, fasta, save_mpileup)
-}
-
-workflow test_ivar_consensus_mpileup {
-
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    save_mpileup = true
-
-    IVAR_CONSENSUS ( input, fasta, save_mpileup)
-}
diff --git a/tests/modules/ivar/consensus/test.yml b/tests/modules/ivar/consensus/test.yml
deleted file mode 100644
index c045eebbebf..00000000000
--- a/tests/modules/ivar/consensus/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: ivar consensus test_ivar_consensus
-  command: nextflow run ./tests/modules/ivar/consensus -entry test_ivar_consensus -c ./tests/config/nextflow.config -c ./tests/modules/ivar/consensus/nextflow.config
-  tags:
-    - ivar
-    - ivar/consensus
-  files:
-    - path: output/ivar/test.fa
-      md5sum: 9e21a64818f4302b4dece5480fa5e8b8
-    - path: output/ivar/test.qual.txt
-      md5sum: 68b329da9893e34099c7d8ad5cb9c940
-
-- name: ivar consensus test_ivar_consensus_mpileup
-  command: nextflow run ./tests/modules/ivar/consensus -entry test_ivar_consensus_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/ivar/consensus/nextflow.config
-  tags:
-    - ivar
-    - ivar/consensus
-  files:
-    - path: output/ivar/test.fa
-      md5sum: 9e21a64818f4302b4dece5480fa5e8b8
-    - path: output/ivar/test.qual.txt
-      md5sum: 68b329da9893e34099c7d8ad5cb9c940
-    - path: output/ivar/test.mpileup
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/ivar/trim/main.nf b/tests/modules/ivar/trim/main.nf
deleted file mode 100644
index 15d0e73956d..00000000000
--- a/tests/modules/ivar/trim/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { IVAR_TRIM } from '../../../../modules/ivar/trim/main.nf'
-
-workflow test_ivar_trim {
-    input = [ [ id:'test'],
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) 
-            ]
-    bed_file   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-
-    IVAR_TRIM ( input, bed_file )
-}
diff --git a/tests/modules/ivar/trim/test.yml b/tests/modules/ivar/trim/test.yml
deleted file mode 100644
index 0be18ba801c..00000000000
--- a/tests/modules/ivar/trim/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: ivar trim
-  command: nextflow run ./tests/modules/ivar/trim -entry test_ivar_trim -c ./tests/config/nextflow.config -c ./tests/modules/ivar/trim/nextflow.config
-  tags:
-    - ivar
-    - ivar/trim
-  files:
-    - path: output/ivar/test.bam
-      md5sum: 12cff17d43b1efdba8120a6bff5311e3
diff --git a/tests/modules/ivar/variants/main.nf b/tests/modules/ivar/variants/main.nf
deleted file mode 100644
index 2d8e77c5dca..00000000000
--- a/tests/modules/ivar/variants/main.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { IVAR_VARIANTS } from '../../../../modules/ivar/variants/main.nf'
-
-workflow test_ivar_variants_no_gff_no_mpileup {
-
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    gff   = []
-    save_mpileup = false
-
-    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
-}
-
-workflow test_ivar_variants_no_gff_with_mpileup {
-
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    gff   = []
-    save_mpileup = true
-
-    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
-}
-
-workflow test_ivar_variants_with_gff_with_mpileup {
-
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    gff   = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
-    save_mpileup = true
-
-    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
-}
diff --git a/tests/modules/ivar/variants/test.yml b/tests/modules/ivar/variants/test.yml
deleted file mode 100644
index 00e6e2c031d..00000000000
--- a/tests/modules/ivar/variants/test.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-- name: ivar variants no gff no mpileup
-  command: nextflow run ./tests/modules/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/ivar/variants/nextflow.config
-  tags:
-    - ivar
-    - ivar/variants
-  files:
-    - path: output/ivar/test.tsv
-      md5sum: 728f1430f2402861396d9953465ac706
-
-- name: ivar variants no gff with mpileup
-  command: nextflow run ./tests/modules/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c ./tests/config/nextflow.config --save_mpileup -c ./tests/modules/ivar/variants/nextflow.config
-  tags:
-    - ivar
-    - ivar/variants
-  files:
-    - path: output/ivar/test.tsv
-      md5sum: 728f1430f2402861396d9953465ac706
-    - path: output/ivar/test.mpileup
-      md5sum: 56c4cd5a4ecb7d6364878818f46ae256
-
-- name: ivar variants with gff with mpileup
-  command: nextflow run ./tests/modules/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c ./tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup -c ./tests/modules/ivar/variants/nextflow.config
-  tags:
-    - ivar
-    - ivar/variants
-  files:
-    - path: output/ivar/test.tsv
-      md5sum: 7b59146132a60da58444bebffc3c2577
-    - path: output/ivar/test.mpileup
-      md5sum: 56c4cd5a4ecb7d6364878818f46ae256
diff --git a/tests/modules/jupyternotebook/main.nf b/tests/modules/jupyternotebook/main.nf
deleted file mode 100644
index 1db9d812f0e..00000000000
--- a/tests/modules/jupyternotebook/main.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { JUPYTERNOTEBOOK } from '../../../modules/jupyternotebook/main.nf'
-include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../modules/jupyternotebook/main.nf'
-include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../modules/jupyternotebook/main.nf'
-
-workflow test_jupyternotebook {
-
-    input = [ [ id:'test_jupyter' ], // meta map
-              file(params.test_data['generic']['notebooks']['ipython_md'], checkIfExists: true) ]
-
-    JUPYTERNOTEBOOK ( input, [:], [])
-
-}
-
-workflow test_jupyternotebook_parametrize {
-
-    input = [ [ id:'test_jupyter' ], // meta map
-              file(params.test_data['generic']['notebooks']['ipython_md'], checkIfExists: true) ]
-
-    JUPYTERNOTEBOOK_PARAMETRIZE(
-        input,
-        [input_filename: "hello.txt", n_iter: 12],
-        file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
-    )
-
-}
-
-workflow test_jupyternotebook_parametrize_ipynb {
-
-    input = [ [ id:'test_jupyter' ], // meta map
-              file(params.test_data['generic']['notebooks']['ipython_ipynb'], checkIfExists: true) ]
-
-    JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB(
-        input,
-        [input_filename: "hello.txt", n_iter: 12],
-        file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
-    )
-
-}
-
diff --git a/tests/modules/jupyternotebook/test.yml b/tests/modules/jupyternotebook/test.yml
deleted file mode 100644
index 31fdfdbbf9d..00000000000
--- a/tests/modules/jupyternotebook/test.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-- name: jupyternotebook test_jupyternotebook
-  command: nextflow run ./tests/modules/jupyternotebook -entry test_jupyternotebook -c ./tests/config/nextflow.config -c ./tests/modules/jupyternotebook/nextflow.config
-  tags:
-    - jupyternotebook
-  files:
-    - path: output/jupyternotebook/test_jupyter.html
-      contains:
-        - "n_iter = 10"
-
-- name: jupyternotebook test_jupyternotebook_parametrize
-  command: nextflow run ./tests/modules/jupyternotebook -entry test_jupyternotebook_parametrize -c ./tests/config/nextflow.config -c ./tests/modules/jupyternotebook/nextflow.config
-  tags:
-    - jupyternotebook
-  files:
-    - path: output/jupyternotebook/artifacts/artifact.txt
-      md5sum: 8ddd8be4b179a529afa5f2ffae4b9858
-    - path: output/jupyternotebook/test_jupyter.html
-      contains:
-        - "n_iter = 12"
-
-- name: jupyternotebook test_jupyternotebook_parametrize_ipynb
-  command: nextflow run ./tests/modules/jupyternotebook -entry test_jupyternotebook_parametrize_ipynb -c ./tests/config/nextflow.config -c ./tests/modules/jupyternotebook/nextflow.config
-  tags:
-    - jupyternotebook
-  files:
-    - path: output/jupyternotebook/artifacts/artifact.txt
-      md5sum: 8ddd8be4b179a529afa5f2ffae4b9858
-    - path: output/jupyternotebook/test_jupyter.html
-      contains:
-        - "n_iter = 12"
diff --git a/tests/modules/kaiju/kaiju/main.nf b/tests/modules/kaiju/kaiju/main.nf
deleted file mode 100644
index 10849ff8ab9..00000000000
--- a/tests/modules/kaiju/kaiju/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR       } from '../../../../modules/untar/main.nf'
-include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf'
-
-workflow test_kaiju_kaiju_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
-}
-
-workflow test_kaiju_kaiju_paired_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-    ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
-
-}
diff --git a/tests/modules/kaiju/kaiju/test.yml b/tests/modules/kaiju/kaiju/test.yml
deleted file mode 100644
index 72eb64c56a6..00000000000
--- a/tests/modules/kaiju/kaiju/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: kaiju kaiju test_kaiju_kaiju_single_end
-  command: nextflow run tests/modules/kaiju/kaiju -entry test_kaiju_kaiju_single_end -c tests/config/nextflow.config
-  tags:
-    - kaiju/kaiju
-    - kaiju
-  files:
-    - path: output/kaiju/test.tsv
-      contains: ["C\tERR5069949.2257580\t2697049"]
-    - path: output/kaiju/versions.yml
-      md5sum: 7e218c0ea00a71dd3a5ec5aaf28804f4
-
-- name: kaiju kaiju test_kaiju_kaiju_paired_end
-  command: nextflow run tests/modules/kaiju/kaiju -entry test_kaiju_kaiju_paired_end -c tests/config/nextflow.config
-  tags:
-    - kaiju/kaiju
-    - kaiju
-  files:
-    - path: output/kaiju/test.tsv
-      contains: ["C\tERR5069949.2257580\t2697049"]
-    - path: output/kaiju/versions.yml
-      md5sum: a74215f6f69979ae046fb1d65c56ac67
diff --git a/tests/modules/kaiju/kaiju2krona/main.nf b/tests/modules/kaiju/kaiju2krona/main.nf
deleted file mode 100644
index aabefd1fc33..00000000000
--- a/tests/modules/kaiju/kaiju2krona/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR } from '../../../../modules/untar/main.nf'
-include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf'
-include { KAIJU_KAIJU2KRONA } from '../../../../modules/kaiju/kaiju2krona/main.nf'
-
-workflow test_kaiju_kaiju2krona {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
-    KAIJU_KAIJU2KRONA ( KAIJU_KAIJU.out.results , UNTAR.out.untar.map{ it[1] } )
-}
diff --git a/tests/modules/kaiju/kaiju2krona/test.yml b/tests/modules/kaiju/kaiju2krona/test.yml
deleted file mode 100644
index a9bb294ce27..00000000000
--- a/tests/modules/kaiju/kaiju2krona/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: kaiju kaiju2krona test_kaiju_kaiju2krona
-  command: nextflow run ./tests/modules/kaiju/kaiju2krona -entry test_kaiju_kaiju2krona -c ./tests/config/nextflow.config  -c ./tests/modules/kaiju/kaiju2krona/nextflow.config
-  tags:
-    - kaiju/kaiju2krona
-    - kaiju
-  files:
-    - path: output/kaiju/test.txt
-      md5sum: 68b2309d37767e444193fa6cea7c0494
diff --git a/tests/modules/kaiju/kaiju2table/main.nf b/tests/modules/kaiju/kaiju2table/main.nf
deleted file mode 100644
index b7169ba51ec..00000000000
--- a/tests/modules/kaiju/kaiju2table/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR             } from '../../../../modules/untar/main.nf'
-include { KAIJU_KAIJU       } from '../../../../modules/kaiju/kaiju/main.nf'
-include { KAIJU_KAIJU2TABLE } from '../../../../modules/kaiju/kaiju2table/main.nf'
-
-workflow test_kaiju_kaiju_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
-    taxon_rank = "species"
-
-    ch_db = UNTAR ( db )
-    KAIJU_KAIJU ( input, ch_db.untar.map{ it[1] } )
-    KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_db.untar.map{ it[1] }, taxon_rank )
-}
diff --git a/tests/modules/kaiju/kaiju2table/test.yml b/tests/modules/kaiju/kaiju2table/test.yml
deleted file mode 100644
index 47d99c89b4e..00000000000
--- a/tests/modules/kaiju/kaiju2table/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: kaiju kaiju2table test_kaiju_kaiju_single_end
-  command: nextflow run tests/modules/kaiju/kaiju2table -entry test_kaiju_kaiju_single_end -c tests/config/nextflow.config
-  tags:
-    - kaiju
-    - kaiju/kaiju2table
-  files:
-    - path: output/kaiju/test.txt
-      md5sum: 0d9f8fd36fcf2888296ae12632c5f0a8
-    - path: output/kaiju/versions.yml
diff --git a/tests/modules/kallisto/index/main.nf b/tests/modules/kallisto/index/main.nf
deleted file mode 100644
index 8ecd6d526c6..00000000000
--- a/tests/modules/kallisto/index/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KALLISTO_INDEX } from '../../../../modules/kallisto/index/main.nf'
-
-workflow test_kallisto_index {
-
-    def input = []
-    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    KALLISTO_INDEX ( input )
-}
diff --git a/tests/modules/kallisto/index/test.yml b/tests/modules/kallisto/index/test.yml
deleted file mode 100644
index 31732e3e9df..00000000000
--- a/tests/modules/kallisto/index/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: kallisto index test_kallisto_index
-  command: nextflow run ./tests/modules/kallisto/index -entry test_kallisto_index -c ./tests/config/nextflow.config -c ./tests/modules/kallisto/index/nextflow.config
-  tags:
-    - kallisto
-    - kallisto/index
-  files:
-    - path: output/kallisto/kallisto
-      md5sum: bf8a58d329dddc96f0c32f7823bc0310
-
-- name: kallisto index test_kallisto_index stub
-  command: nextflow run ./tests/modules/kallisto/index -entry test_kallisto_index -c ./tests/config/nextflow.config -c ./tests/modules/kallisto/index/nextflow.config -stub-run
-  tags:
-    - kallisto
-    - kallisto/index
-  files:
-    - path: output/kallisto/kallisto
diff --git a/tests/modules/kallistobustools/count/main.nf b/tests/modules/kallistobustools/count/main.nf
deleted file mode 100644
index 1dd55cb3f6b..00000000000
--- a/tests/modules/kallistobustools/count/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KALLISTOBUSTOOLS_REF   } from '../../../../modules/kallistobustools/ref/main.nf'
-include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf'
-
-workflow test_kallistobustools_count {
-
-    input   = [
-        [id:'test'], // meta map
-        [ 
-          file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    sc_workflow = "standard"
-    technology  = "10XV3"
-
-    KALLISTOBUSTOOLS_REF(fasta, gtf, sc_workflow)
-    KALLISTOBUSTOOLS_COUNT ( 
-      input, 
-      KALLISTOBUSTOOLS_REF.out.index, 
-      KALLISTOBUSTOOLS_REF.out.t2g, 
-      KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] },   // when empty the module doesn't run unless something is passed. 
-      KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] }, // when empty the module doesn't run unless something is passed.
-      technology 
-    )
-}
diff --git a/tests/modules/kallistobustools/count/test.yml b/tests/modules/kallistobustools/count/test.yml
deleted file mode 100644
index 21d7d73a361..00000000000
--- a/tests/modules/kallistobustools/count/test.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-- name: kallistobustools count test_kallistobustools_count
-  command: nextflow run ./tests/modules/kallistobustools/count -entry test_kallistobustools_count -c ./tests/config/nextflow.config  -c ./tests/modules/kallistobustools/count/nextflow.config
-  tags:
-    - kallistobustools/count
-    - kallistobustools
-  files:
-    - path: output/kallistobustools/cdna.fa
-    - path: output/kallistobustools/kb_ref_out.idx
-    - path: output/kallistobustools/t2g.txt
-    - path: output/kallistobustools/test.count/10x_version3_whitelist.txt
-      md5sum: 3d36d0a4021fd292b265e2b5e72aaaf3
-    - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/barcodes.tsv
-      md5sum: 8a41142de30df61fbb9551b29dd05a83
-    - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/genes.tsv
-      md5sum: 1b31f05f9b20a4c0ac3e07b9e3ff3a14
-    - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/matrix.mtx
-      md5sum: 5b7bff2d19fc90168733f4ac812c7d7b
-    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.barcodes.txt
-      md5sum: 8d7ef602416818a598f5680a707756a7
-    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.genes.txt
-      md5sum: fe6d5501923867b514a0447aa4b4995f
-    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.mtx
-      md5sum: 0a84dc5a7570b5821da4eef6b5769a0c
-    - path: output/kallistobustools/test.count/inspect.json
-      md5sum: b853330f160e06fc8af170a837384ef5
-    - path: output/kallistobustools/test.count/kb_info.json
-    - path: output/kallistobustools/test.count/matrix.ec
-    - path: output/kallistobustools/test.count/output.bus
-      md5sum: f5d8efa83f107826824292cbbdb4e37b
-    - path: output/kallistobustools/test.count/output.unfiltered.bus
-      md5sum: dcbc651dc64eb38ae14e0b90795b30d2
-    - path: output/kallistobustools/test.count/run_info.json
-    - path: output/kallistobustools/test.count/transcripts.txt
diff --git a/tests/modules/kallistobustools/ref/main.nf b/tests/modules/kallistobustools/ref/main.nf
deleted file mode 100644
index 09ea68ea8fa..00000000000
--- a/tests/modules/kallistobustools/ref/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KALLISTOBUSTOOLS_REF } from '../../../../modules/kallistobustools/ref/main.nf'
-
-workflow test_kallistobustools_ref_standard {
-
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    workflow    = "standard"
-
-    KALLISTOBUSTOOLS_REF(fasta, gtf, workflow)
-}
-
-workflow test_kallistobustools_ref_lamanno {
-
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    workflow    = "lamanno"
-
-    KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
-}
-
-workflow test_kallistobustools_ref_nucleus {
-
-    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    workflow    = "nucleus"
-
-    KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
-}
-
diff --git a/tests/modules/kallistobustools/ref/test.yml b/tests/modules/kallistobustools/ref/test.yml
deleted file mode 100644
index 1e8fd6c4d04..00000000000
--- a/tests/modules/kallistobustools/ref/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: kallistobustools ref test_kallistobustools_ref_standard
-  command: nextflow run ./tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_standard -c ./tests/config/nextflow.config -c ./tests/modules/kallistobustools/ref/nextflow.config
-  tags:
-    - kallistobustools/ref
-    - kallistobustools
-  files:
-    - path: output/kallistobustools/cdna.fa
-    - path: output/kallistobustools/kb_ref_out.idx
-    - path: output/kallistobustools/t2g.txt
-
-- name: kallistobustools ref test_kallistobustools_ref_lamanno
-  command: nextflow run ./tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c ./tests/config/nextflow.config -c ./tests/modules/kallistobustools/ref/nextflow.config
-  tags:
-    - kallistobustools/ref
-    - kallistobustools
-  files:
-    - path: output/kallistobustools/cdna.fa
-    - path: output/kallistobustools/cdna_t2c.txt
-    - path: output/kallistobustools/intron.fa
-    - path: output/kallistobustools/intron_t2c.txt
-    - path: output/kallistobustools/kb_ref_out.idx
-    - path: output/kallistobustools/t2g.txt
-
-- name: kallistobustools ref test_kallistobustools_ref_nucleus
-  command: nextflow run ./tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c ./tests/config/nextflow.config -c ./tests/modules/kallistobustools/ref/nextflow.config
-  tags:
-    - kallistobustools/ref
-    - kallistobustools
-  files:
-    - path: output/kallistobustools/cdna.fa
-    - path: output/kallistobustools/cdna_t2c.txt
-    - path: output/kallistobustools/intron.fa
-    - path: output/kallistobustools/intron_t2c.txt
-    - path: output/kallistobustools/kb_ref_out.idx
-    - path: output/kallistobustools/t2g.txt
diff --git a/tests/modules/kat/hist/main.nf b/tests/modules/kat/hist/main.nf
deleted file mode 100644
index 88136749ba8..00000000000
--- a/tests/modules/kat/hist/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KAT_HIST } from '../../../../modules/kat/hist/main.nf'
-
-workflow test_kat_hist_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    KAT_HIST ( input )
-}
-
-workflow test_kat_hist_paired_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test2_2_fastq_gz'], checkIfExists: true),
-        ]
-    ]
-
-    KAT_HIST ( input )
-}
diff --git a/tests/modules/kat/hist/test.yml b/tests/modules/kat/hist/test.yml
deleted file mode 100644
index 391a3a21f55..00000000000
--- a/tests/modules/kat/hist/test.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-- name: kat hist test_kat_hist_single_end
-  command: nextflow run tests/modules/kat/hist -entry test_kat_hist_single_end -c tests/config/nextflow.config
-  tags:
-    - kat/hist
-    - kat
-  files:
-    - path: output/kat/test.hist
-      md5sum: c6eba52b3a2653a684577a8ae20b74c1
-    - path: output/kat/test.hist-hash.jf27
-    - path: output/kat/test.hist.dist_analysis.json
-      # md5sum: 52a5a2d91c71b940f36f1f0a7fd5ef10 # This is variable for an unknown reason
-      contains:
-        - "nb_peaks"
-        - "global_minima"
-        - "global_maxima"
-        - "mean_freq"
-        - "est_genome_size"
-        - "est_het_rate"
-    - path: output/kat/test.hist.png
-      md5sum: 49861ef1a265e0edde3550b39c64a274
-    - path: output/kat/versions.yml
-
-- name: kat hist test_kat_hist_paired_end
-  command: nextflow run tests/modules/kat/hist -entry test_kat_hist_paired_end -c tests/config/nextflow.config
-  tags:
-    - kat/hist
-    - kat
-  files:
-    - path: output/kat/test.hist
-      md5sum: 91429091e74b1718051591d83a1ccb5d
-    - path: output/kat/test.hist.dist_analysis.json
-      # md5sum: 8b0dabeaff4ba706b33aa8964d687e13  # This is variable for an unknown reason
-      contains:
-        - "nb_peaks"
-        - "global_minima"
-        - "global_maxima"
-        - "mean_freq"
-        - "est_genome_size"
-        - "est_het_rate"
-    - path: output/kat/test.hist.png
-      md5sum: e20774d0d2b979cb6ead7b7fb5ad36d9
-    - path: output/kat/versions.yml
diff --git a/tests/modules/khmer/normalizebymedian/main.nf b/tests/modules/khmer/normalizebymedian/main.nf
deleted file mode 100644
index c439c40f6e3..00000000000
--- a/tests/modules/khmer/normalizebymedian/main.nf
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQTK_MERGEPE                                           } from '../../../../modules/seqtk/mergepe/main.nf'
-include { KHMER_NORMALIZEBYMEDIAN                                 } from '../../../../modules/khmer/normalizebymedian/main.nf'
-include { KHMER_NORMALIZEBYMEDIAN as KHMER_NORMALIZEBYMEDIAN_ARGS } from '../../../../modules/khmer/normalizebymedian/main.nf'
-
-workflow test_khmer_normalizebymedian_only_pe {
-    
-    pe_reads = [
-        [ id:'khmer_test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
-        ]
-    ]
-
-    SEQTK_MERGEPE(pe_reads)
-
-    KHMER_NORMALIZEBYMEDIAN ( SEQTK_MERGEPE.out.reads.collect { it[1] }, [], 'only_pe' )
-}
-
-workflow test_khmer_normalizebymedian_only_se {
-    
-    se_reads = [
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
-    ]
-
-    KHMER_NORMALIZEBYMEDIAN ( [], se_reads, 'only_se' )
-}
-
-workflow test_khmer_normalizebymedian_mixed {
-    
-    pe_reads = [
-        [ id:'khmer_test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
-        ]
-    ]
-    se_reads = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-
-    SEQTK_MERGEPE(pe_reads)
-
-    KHMER_NORMALIZEBYMEDIAN ( SEQTK_MERGEPE.out.reads.map { it[1] }, se_reads, 'mixed' )
-}
-
-workflow test_khmer_normalizebymedian_multiple_pe {
-    
-    pe_reads = [
-        [ id:'khmer_test0', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
-        ],
-        [ id:'khmer_test1', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
-        ]
-    ]
-    se_reads = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-
-    SEQTK_MERGEPE(pe_reads)
-
-    KHMER_NORMALIZEBYMEDIAN ( SEQTK_MERGEPE.out.reads.collect { it[1] }, se_reads, 'multiple_pe' )
-}
-
-workflow test_khmer_normalizebymedian_args {
-    
-    pe_reads = [
-        [ id:'khmer_test0', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
-        ]
-    ]
-    se_reads = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-
-    SEQTK_MERGEPE(pe_reads)
-
-    KHMER_NORMALIZEBYMEDIAN_ARGS ( SEQTK_MERGEPE.out.reads.collect { it[1] }, se_reads, 'args' )
-}
diff --git a/tests/modules/khmer/normalizebymedian/test.yml b/tests/modules/khmer/normalizebymedian/test.yml
deleted file mode 100644
index f4d687efb3c..00000000000
--- a/tests/modules/khmer/normalizebymedian/test.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-#                nf-core modules create-test-yml khmer/normalizebymedian
-- name: khmer normalizebymedian only pe reads
-  command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_only_pe -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
-  tags:
-    - khmer
-    - khmer/normalizebymedian
-  files:
-    - path: output/khmer/only_pe.fastq.gz
-    # md5sum not stable even locally with docker (gzip done by tool)
-    # md5sum: 75e05f2e80cf4bd0b534d4b73f7c059c
-
-- name: khmer normalizebymedian only se reads
-  command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_only_se -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
-  tags:
-    - khmer
-    - khmer/normalizebymedian
-  files:
-    - path: output/khmer/only_se.fastq.gz
-
-- name: khmer normalizebymedian mixed reads
-  command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_mixed -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
-  tags:
-    - khmer
-    - khmer/normalizebymedian
-  files:
-    - path: output/khmer/mixed.fastq.gz
-
-- name: khmer normalizebymedian multiple pe reads
-  command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_multiple_pe -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
-  tags:
-    - khmer
-    - khmer/normalizebymedian
-  files:
-    - path: output/khmer/multiple_pe.fastq.gz
-
-- name: khmer normalizebymedian args
-  command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_args -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
-  tags:
-    - khmer
-    - khmer/normalizebymedian
-  files:
-    - path: output/khmer/args.fastq.gz
diff --git a/tests/modules/khmer/uniquekmers/main.nf b/tests/modules/khmer/uniquekmers/main.nf
deleted file mode 100644
index cfd6de9f483..00000000000
--- a/tests/modules/khmer/uniquekmers/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KHMER_UNIQUEKMERS } from '../../../../modules/khmer/uniquekmers/main.nf'
-
-workflow test_khmer_uniquekmers {
-
-    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    KHMER_UNIQUEKMERS ( input, 50 )
-}
diff --git a/tests/modules/khmer/uniquekmers/test.yml b/tests/modules/khmer/uniquekmers/test.yml
deleted file mode 100644
index ad4e8a54035..00000000000
--- a/tests/modules/khmer/uniquekmers/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: khmer uniquekmers test_khmer_uniquekmers
-  command: nextflow run ./tests/modules/khmer/uniquekmers -entry test_khmer_uniquekmers -c ./tests/config/nextflow.config  -c ./tests/modules/khmer/uniquekmers/nextflow.config
-  tags:
-    - khmer
-    - khmer/uniquekmers
-  files:
-    - path: output/khmer/kmers.txt
-      md5sum: 496ebf23653a01c7a42d743e47c19f65
-    - path: output/khmer/report.txt
-      md5sum: ee489abd3b244dea3640649e1790d55e
diff --git a/tests/modules/kleborate/main.nf b/tests/modules/kleborate/main.nf
deleted file mode 100644
index bce31225908..00000000000
--- a/tests/modules/kleborate/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KLEBORATE } from '../../../modules/kleborate/main.nf'
-
-workflow test_kleborate {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
-        ]
-    ]
-
-    KLEBORATE ( input )
-}
diff --git a/tests/modules/kleborate/test.yml b/tests/modules/kleborate/test.yml
deleted file mode 100644
index 413ac2aea09..00000000000
--- a/tests/modules/kleborate/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: kleborate
-  command: nextflow run ./tests/modules/kleborate -entry test_kleborate -c ./tests/config/nextflow.config -c ./tests/modules/kleborate/nextflow.config
-  tags:
-    - kleborate
-  files:
-    - path: output/kleborate/test.results.txt
-      contains: ["strain", "genome", "scaffolds"]
diff --git a/tests/modules/kraken2/kraken2/main.nf b/tests/modules/kraken2/kraken2/main.nf
deleted file mode 100644
index 4a3593e40f6..00000000000
--- a/tests/modules/kraken2/kraken2/main.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR           } from '../../../../modules/untar/main.nf'
-include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
-
-workflow test_kraken2_kraken2_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
-}
-
-workflow test_kraken2_kraken2_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
-}
-
-workflow test_kraken2_kraken2_classifyreads {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, true )
-}
diff --git a/tests/modules/kraken2/kraken2/test.yml b/tests/modules/kraken2/kraken2/test.yml
deleted file mode 100644
index af1e6e0dd30..00000000000
--- a/tests/modules/kraken2/kraken2/test.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-- name: kraken2 kraken2 test_kraken2_kraken2_single_end
-  command: nextflow run tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_single_end -c tests/config/nextflow.config
-  tags:
-    - kraken2
-    - kraken2/kraken2
-  files:
-    - path: output/kraken2/test.classified.fastq.gz
-    - path: output/kraken2/test.kraken2.report.txt
-      md5sum: 4227755fe40478b8d7dc8634b489761e
-    - path: output/kraken2/test.unclassified.fastq.gz
-    - path: output/kraken2/versions.yml
-      md5sum: 6e3ad947ac8dee841a89216071c181cc
-    - path: output/untar/versions.yml
-
-- name: kraken2 kraken2 test_kraken2_kraken2_paired_end
-  command: nextflow run tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_paired_end -c tests/config/nextflow.config
-  tags:
-    - kraken2
-    - kraken2/kraken2
-  files:
-    - path: output/kraken2/test.classified_1.fastq.gz
-    - path: output/kraken2/test.classified_2.fastq.gz
-    - path: output/kraken2/test.kraken2.report.txt
-      md5sum: 4227755fe40478b8d7dc8634b489761e
-    - path: output/kraken2/test.unclassified_1.fastq.gz
-    - path: output/kraken2/test.unclassified_2.fastq.gz
-    - path: output/kraken2/versions.yml
-      md5sum: 604482fe7a4519f890fae9c8beb1bd6e
-    - path: output/untar/versions.yml
-
-- name: kraken2 kraken2 test_kraken2_kraken2_classifyreads
-  command: nextflow run tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_classifyreads -c tests/config/nextflow.config
-  tags:
-    - kraken2
-    - kraken2/kraken2
-  files:
-    - path: output/kraken2/test.kraken2.classifiedreads.txt
-      md5sum: e7a90531f0d8d777316515c36fe4cae0
-    - path: output/kraken2/test.kraken2.report.txt
-      md5sum: 4227755fe40478b8d7dc8634b489761e
-    - path: output/kraken2/versions.yml
-      md5sum: 3488c304259e83c5bea573403293fce9
-    - path: output/untar/versions.yml
diff --git a/tests/modules/krakentools/combinekreports/main.nf b/tests/modules/krakentools/combinekreports/main.nf
deleted file mode 100644
index 6a1f829084d..00000000000
--- a/tests/modules/krakentools/combinekreports/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR } from '../../../../modules/untar/main'
-include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main'
-include { KRAKENTOOLS_COMBINEKREPORTS } from '../../../../modules/krakentools/combinekreports/main.nf'
-
-workflow test_krakentools_combinekreports {
-
-    input = Channel.of(
-        [[ id:'test', single_end:false ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
-        [[ id:'test2', single_end:false ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
-    )
-
-
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, false )
-
-    KRAKENTOOLS_COMBINEKREPORTS ( KRAKEN2_KRAKEN2.out.report.map{ [[id:"test"], it[1]] }.groupTuple().dump())
-}
diff --git a/tests/modules/krakentools/combinekreports/test.yml b/tests/modules/krakentools/combinekreports/test.yml
deleted file mode 100644
index 5fb864dcd59..00000000000
--- a/tests/modules/krakentools/combinekreports/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: krakentools combinekreports test_krakentools_combinekreports
-  command: nextflow run ./tests/modules/krakentools/combinekreports -entry test_krakentools_combinekreports -c ./tests/config/nextflow.config  -c ./tests/modules/krakentools/combinekreports/nextflow.config
-  tags:
-    - krakentools
-    - krakentools/combinekreports
-  files:
-    - path: output/krakentools/test.txt
-      contains:
-        - "#Number of Samples: 2"
diff --git a/tests/modules/krakentools/kreport2krona/main.nf b/tests/modules/krakentools/kreport2krona/main.nf
deleted file mode 100644
index c9c626fdf16..00000000000
--- a/tests/modules/krakentools/kreport2krona/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR } from '../../../../modules/untar/main'
-include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main'
-include { KRAKENTOOLS_KREPORT2KRONA } from '../../../../modules/krakentools/kreport2krona/main'
-
-workflow test_krakentools_kreport2krona {
-
-    input = Channel.of([ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ])
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, false )
-    KRAKENTOOLS_KREPORT2KRONA ( KRAKEN2_KRAKEN2.out.report )
-}
diff --git a/tests/modules/krakentools/kreport2krona/test.yml b/tests/modules/krakentools/kreport2krona/test.yml
deleted file mode 100644
index 6525e915352..00000000000
--- a/tests/modules/krakentools/kreport2krona/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: krakentools kreport2krona test_krakentools_kreport2krona
-  command: nextflow run ./tests/modules/krakentools/kreport2krona -entry test_krakentools_kreport2krona -c ./tests/config/nextflow.config  -c ./tests/modules/krakentools/kreport2krona/nextflow.config
-  tags:
-    - krakentools/kreport2krona
-    - krakentools
-  files:
-    - path: output/krakentools/test.txt
-      md5sum: c89a9db7acbdba9dea0fe246bcaa85c1
diff --git a/tests/modules/krona/kronadb/main.nf b/tests/modules/krona/kronadb/main.nf
deleted file mode 100644
index ed95585400a..00000000000
--- a/tests/modules/krona/kronadb/main.nf
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KRONA_KRONADB } from '../../../../modules/krona/kronadb/main.nf'
-
-workflow test_krona_kronadb {
-    KRONA_KRONADB ( )
-}
diff --git a/tests/modules/krona/kronadb/test.yml b/tests/modules/krona/kronadb/test.yml
deleted file mode 100644
index 1d61640f778..00000000000
--- a/tests/modules/krona/kronadb/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: krona kronadb test_krona_kronadb
-  command: nextflow run ./tests/modules/krona/kronadb -entry test_krona_kronadb -c ./tests/config/nextflow.config -c ./tests/modules/krona/kronadb/nextflow.config
-  tags:
-    - krona
-    - krona/kronadb
-  files:
-    - path: output/krona/taxonomy/taxonomy.tab
diff --git a/tests/modules/krona/ktimporttaxonomy/main.nf b/tests/modules/krona/ktimporttaxonomy/main.nf
deleted file mode 100644
index 7b39ee821ff..00000000000
--- a/tests/modules/krona/ktimporttaxonomy/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_READS  } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
-include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
-
-workflow test_krona_ktimporttaxonomy_reads {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['metagenome']['classified_reads_assignment'], checkIfExists: true)
-    ]
-    taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
-
-    KRONA_KTIMPORTTAXONOMY_READS ( input, taxonomy )
-}
-
-workflow test_krona_ktimporttaxonomy_report {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true)
-    ]
-    taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
-
-    KRONA_KTIMPORTTAXONOMY_REPORT ( input, taxonomy )
-}
diff --git a/tests/modules/krona/ktimporttaxonomy/test.yml b/tests/modules/krona/ktimporttaxonomy/test.yml
deleted file mode 100644
index 2a16e29092c..00000000000
--- a/tests/modules/krona/ktimporttaxonomy/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_reads
-  command: nextflow run ./tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_reads -c ./tests/config/nextflow.config  -c ./tests/modules/krona/ktimporttaxonomy/nextflow.config
-  tags:
-    - krona/ktimporttaxonomy
-    - krona
-  files:
-    - path: output/krona/test.html
-      contains: ["Krona is a flexible tool for exploring the relative proportions of"]
-
-- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_report
-  command: nextflow run ./tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_report -c ./tests/config/nextflow.config  -c ./tests/modules/krona/ktimporttaxonomy/nextflow.config
-  tags:
-    - krona/ktimporttaxonomy
-    - krona
-  files:
-    - path: output/krona/test.html
-      contains: ["Krona is a flexible tool for exploring the relative proportions of"]
diff --git a/tests/modules/krona/ktimporttext/main.nf b/tests/modules/krona/ktimporttext/main.nf
deleted file mode 100644
index 3d288b7b5d0..00000000000
--- a/tests/modules/krona/ktimporttext/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KRONA_KTIMPORTTEXT } from '../../../../modules/krona/ktimporttext/main.nf'
-
-workflow test_krona_ktimporttext_multi {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/ktimporttext.txt', checkIfExists: true), // krona default test file
-            file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true), //Kraken2 report file
-            file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/kaiju_out4krona.txt', checkIfExists: true) // Kaiju output 4 krona
-        ]
-    ]
-
-    KRONA_KTIMPORTTEXT ( input )
-}
-
-workflow test_krona_ktimporttext_single {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file('http://krona.sourceforge.net/examples/text.txt', checkIfExists: true) // krona default test file
-        ]
-    ]
-
-    KRONA_KTIMPORTTEXT ( input )
-}
diff --git a/tests/modules/krona/ktimporttext/test.yml b/tests/modules/krona/ktimporttext/test.yml
deleted file mode 100644
index 93ae12daff3..00000000000
--- a/tests/modules/krona/ktimporttext/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: krona ktimporttext test_krona_ktimporttext_multi
-  command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_multi -c tests/config/nextflow.config
-  tags:
-    - krona
-    - krona/ktimporttext
-  files:
-    - path: output/krona/test.html
-      contains:
-        - "DOCTYPE html PUBLIC"
-
-- name: krona ktimporttext test_krona_ktimporttext_single
-  command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_single -c tests/config/nextflow.config
-  tags:
-    - krona
-    - krona/ktimporttext
-  files:
-    - path: output/krona/test.html
-      contains:
-        - "DOCTYPE html PUBLIC"
diff --git a/tests/modules/krona/ktupdatetaxonomy/main.nf b/tests/modules/krona/ktupdatetaxonomy/main.nf
deleted file mode 100644
index d2d18f3145c..00000000000
--- a/tests/modules/krona/ktupdatetaxonomy/main.nf
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KRONA_KTUPDATETAXONOMY } from '../../../../modules/krona/ktupdatetaxonomy/main.nf'
-
-workflow test_krona_ktupdatetaxonomy {
-    KRONA_KTUPDATETAXONOMY ( )
-}
diff --git a/tests/modules/krona/ktupdatetaxonomy/test.yml b/tests/modules/krona/ktupdatetaxonomy/test.yml
deleted file mode 100644
index b50fe8f29e4..00000000000
--- a/tests/modules/krona/ktupdatetaxonomy/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: krona ktupdatetaxonomy test_krona_ktupdatetaxonomy
-  command: nextflow run ./tests/modules/krona/ktupdatetaxonomy -entry test_krona_ktupdatetaxonomy -c ./tests/config/nextflow.config -c ./tests/modules/krona/ktupdatetaxonomy/nextflow.config
-  tags:
-    - krona
-    - krona/ktupdatetaxonomy
-  files:
-    - path: output/krona/taxonomy/taxonomy.tab
diff --git a/tests/modules/last/dotplot/main.nf b/tests/modules/last/dotplot/main.nf
deleted file mode 100644
index 3353821d76b..00000000000
--- a/tests/modules/last/dotplot/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LAST_DOTPLOT } from '../../../../modules/last/dotplot/main.nf'
-
-workflow test_last_dotplot {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
-
-    LAST_DOTPLOT ( input, "png" )
-}
diff --git a/tests/modules/last/dotplot/test.yml b/tests/modules/last/dotplot/test.yml
deleted file mode 100644
index c2a9910f3c5..00000000000
--- a/tests/modules/last/dotplot/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: last dotplot test_last_dotplot
-  command: nextflow run ./tests/modules/last/dotplot -entry test_last_dotplot -c ./tests/config/nextflow.config -c ./tests/modules/last/dotplot/nextflow.config
-  tags:
-    - last/dotplot
-    - last
-  files:
-    - path: output/last/test.png
-      md5sum: 6189aaf96f522cdb664869724997bbcd
diff --git a/tests/modules/last/lastal/main.nf b/tests/modules/last/lastal/main.nf
deleted file mode 100644
index 76e124c38f6..00000000000
--- a/tests/modules/last/lastal/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR       } from '../../../../modules/untar/main.nf'
-include { LAST_LASTAL } from '../../../../modules/last/lastal/main.nf'
-
-workflow test_last_lastal_with_dummy_param_file {
-
-    input = [ [ id:'contigs', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
-              [] ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    LAST_LASTAL ( input, UNTAR.out.untar.map{ it[1] })
-}
-
-workflow test_last_lastal_with_real_param_file {
-
-    input      = [ [ id:'contigs', single_end:false ], // meta map
-                   file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
-                   file(params.test_data['sarscov2']['genome']['contigs_genome_par'], checkIfExists: true) ]
-    db         = [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    LAST_LASTAL ( input, UNTAR.out.untar.map{ it[1] })
-}
diff --git a/tests/modules/last/lastal/test.yml b/tests/modules/last/lastal/test.yml
deleted file mode 100644
index f75e4ac521e..00000000000
--- a/tests/modules/last/lastal/test.yml
+++ /dev/null
@@ -1,45 +0,0 @@
-- name: last lastal test_last_lastal_with_dummy_param_file
-  command: nextflow run ./tests/modules/last/lastal -entry test_last_lastal_with_dummy_param_file -c ./tests/config/nextflow.config -c ./tests/modules/last/lastal/nextflow.config
-  tags:
-    - last
-    - last/lastal
-  files:
-    - path: output/last/contigs.genome.maf.gz
-      md5sum: 670f4fa1a94b23690cdb6fc603813c75
-    - path: output/untar/lastdb/genome.bck
-      md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
-    - path: output/untar/lastdb/genome.des
-      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
-    - path: output/untar/lastdb/genome.prj
-      md5sum: 489715f14b0fea6273822696e72357f9
-    - path: output/untar/lastdb/genome.sds
-      md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
-    - path: output/untar/lastdb/genome.ssp
-      md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
-    - path: output/untar/lastdb/genome.suf
-      md5sum: 1895efa8653e8e9bd3605cff0408ed33
-    - path: output/untar/lastdb/genome.tis
-      md5sum: b7c40f06b1309dc6f37849eeb86dfd22
-
-- name: last lastal test_last_lastal_with_real_param_file
-  command: nextflow run ./tests/modules/last/lastal -entry test_last_lastal_with_real_param_file -c ./tests/config/nextflow.config -c ./tests/modules/last/lastal/nextflow.config
-  tags:
-    - last
-    - last/lastal
-  files:
-    - path: output/last/contigs.genome.maf.gz
-      md5sum: b0202b013e1caa9163516cd4ff4fbdbc
-    - path: output/untar/lastdb/genome.bck
-      md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
-    - path: output/untar/lastdb/genome.des
-      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
-    - path: output/untar/lastdb/genome.prj
-      md5sum: 489715f14b0fea6273822696e72357f9
-    - path: output/untar/lastdb/genome.sds
-      md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
-    - path: output/untar/lastdb/genome.ssp
-      md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
-    - path: output/untar/lastdb/genome.suf
-      md5sum: 1895efa8653e8e9bd3605cff0408ed33
-    - path: output/untar/lastdb/genome.tis
-      md5sum: b7c40f06b1309dc6f37849eeb86dfd22
diff --git a/tests/modules/last/lastdb/main.nf b/tests/modules/last/lastdb/main.nf
deleted file mode 100644
index d1c7b79acb0..00000000000
--- a/tests/modules/last/lastdb/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LAST_LASTDB } from '../../../../modules/last/lastdb/main.nf'
-
-workflow test_last_lastdb {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-            ]
-
-    LAST_LASTDB ( input )
-}
-
-workflow test_last_lastdb_gzipped_input {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ]
-
-    LAST_LASTDB ( input )
-}
diff --git a/tests/modules/last/lastdb/test.yml b/tests/modules/last/lastdb/test.yml
deleted file mode 100644
index ece44cf382a..00000000000
--- a/tests/modules/last/lastdb/test.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-- name: last lastdb test_last_lastdb
-  command: nextflow run ./tests/modules/last/lastdb -entry test_last_lastdb -c ./tests/config/nextflow.config -c ./tests/modules/last/lastdb/nextflow.config
-  tags:
-    - last/lastdb
-    - last
-  files:
-    - path: output/last/lastdb/test.bck
-      md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
-    - path: output/last/lastdb/test.des
-      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
-    - path: output/last/lastdb/test.prj
-      md5sum: 6948d17d2a10e470ea545f659930a543
-    - path: output/last/lastdb/test.sds
-      md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
-    - path: output/last/lastdb/test.ssp
-      md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
-    - path: output/last/lastdb/test.suf
-      md5sum: 1895efa8653e8e9bd3605cff0408ed33
-    - path: output/last/lastdb/test.tis
-      md5sum: b7c40f06b1309dc6f37849eeb86dfd22
-
-- name: last lastdb test_last_lastdb_gzipped_input
-  command: nextflow run ./tests/modules/last/lastdb -entry test_last_lastdb_gzipped_input -c ./tests/config/nextflow.config -c ./tests/modules/last/lastdb/nextflow.config
-  tags:
-    - last/lastdb
-    - last
-  files:
-    - path: output/last/lastdb/test.bck
-      md5sum: 8692b1229b1fff1c2d39c4c610ff842b
-    - path: output/last/lastdb/test.des
-      md5sum: 26ab49015cc572172b9efa50fc5190bc
-    - path: output/last/lastdb/test.prj
-      md5sum: d253fc4320d9b4d7fcfc43b2734412ee
-    - path: output/last/lastdb/test.sds
-      md5sum: cad9927d4bd161257e98165ad755d8e4
-    - path: output/last/lastdb/test.ssp
-      md5sum: 574c8a080247c2af9b5c46ff70936186
-    - path: output/last/lastdb/test.suf
-      md5sum: 8c406111b398631e51ca79d99b0ee897
-    - path: output/last/lastdb/test.tis
-      md5sum: d57a3a5f7e3e036807356c15bd3aad97
diff --git a/tests/modules/last/mafconvert/main.nf b/tests/modules/last/mafconvert/main.nf
deleted file mode 100644
index c87f6e6aa28..00000000000
--- a/tests/modules/last/mafconvert/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LAST_MAFCONVERT } from '../../../../modules/last/mafconvert/main.nf'
-
-workflow test_last_mafconvert {
-    
-    input = [ [ id:'contigs.genome' ], // meta map
-              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
-
-    LAST_MAFCONVERT ( input, "psl" )
-}
diff --git a/tests/modules/last/mafconvert/test.yml b/tests/modules/last/mafconvert/test.yml
deleted file mode 100644
index 86a80f20936..00000000000
--- a/tests/modules/last/mafconvert/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: last mafconvert test_last_mafconvert
-  command: nextflow run ./tests/modules/last/mafconvert -entry test_last_mafconvert -c ./tests/config/nextflow.config -c ./tests/modules/last/mafconvert/nextflow.config
-  tags:
-    - last/mafconvert
-    - last
-  files:
-    - path: output/last/contigs.genome.psl.gz
-      md5sum: 807889fbc4129884ae74c4ecf8804dde
diff --git a/tests/modules/last/mafswap/main.nf b/tests/modules/last/mafswap/main.nf
deleted file mode 100644
index 5cc94932347..00000000000
--- a/tests/modules/last/mafswap/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LAST_MAFSWAP } from '../../../../modules/last/mafswap/main.nf'
-
-workflow test_last_mafswap {
-
-    input = [ [ id:'contigs.genome' ], // meta map
-              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
-
-    LAST_MAFSWAP ( input )
-}
diff --git a/tests/modules/last/mafswap/test.yml b/tests/modules/last/mafswap/test.yml
deleted file mode 100644
index a0865e00725..00000000000
--- a/tests/modules/last/mafswap/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: last mafswap test_last_mafswap
-  command: nextflow run ./tests/modules/last/mafswap -entry test_last_mafswap -c ./tests/config/nextflow.config -c ./tests/modules/last/mafswap/nextflow.config
-  tags:
-    - last
-    - last/mafswap
-  files:
-    - path: output/last/contigs.genome.swapped.maf.gz
-      md5sum: b98c5ff297878a19f1ab4f1a5e354678
diff --git a/tests/modules/last/postmask/main.nf b/tests/modules/last/postmask/main.nf
deleted file mode 100644
index 9bbb10e9fa2..00000000000
--- a/tests/modules/last/postmask/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LAST_POSTMASK } from '../../../../modules/last/postmask/main.nf'
-
-workflow test_last_postmask {
-
-    input = [ [ id:'contigs.genome' ], // meta map
-              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
-
-    LAST_POSTMASK ( input )
-}
diff --git a/tests/modules/last/postmask/test.yml b/tests/modules/last/postmask/test.yml
deleted file mode 100644
index 81ae7f736a3..00000000000
--- a/tests/modules/last/postmask/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: last postmask test_last_postmask
-  command: nextflow run ./tests/modules/last/postmask -entry test_last_postmask -c ./tests/config/nextflow.config -c ./tests/modules/last/postmask/nextflow.config
-  tags:
-    - last
-    - last/postmask
-  files:
-    - path: output/last/contigs.genome.postmask.maf.gz
-      md5sum: 3a0f42e76da9549748983ac4d7ff7473
diff --git a/tests/modules/last/split/main.nf b/tests/modules/last/split/main.nf
deleted file mode 100644
index f4ece4f21ef..00000000000
--- a/tests/modules/last/split/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LAST_SPLIT } from '../../../../modules/last/split/main.nf'
-
-workflow test_last_split {
-    
-    input = [ [ id:'contigs.genome' ], // meta map
-              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
-
-    LAST_SPLIT ( input )
-}
diff --git a/tests/modules/last/split/test.yml b/tests/modules/last/split/test.yml
deleted file mode 100644
index 57eb345f50e..00000000000
--- a/tests/modules/last/split/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: last split test_last_split
-  command: nextflow run ./tests/modules/last/split -entry test_last_split -c ./tests/config/nextflow.config -c ./tests/modules/last/split/nextflow.config
-  tags:
-    - last
-    - last/split
-  files:
-    - path: output/last/contigs.genome.split.maf.gz
-      md5sum: 2a177444f63c9294767a67a0247f0f05
diff --git a/tests/modules/last/train/main.nf b/tests/modules/last/train/main.nf
deleted file mode 100644
index 2e10735e34f..00000000000
--- a/tests/modules/last/train/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR      } from '../../../../modules/untar/main.nf'
-include { LAST_TRAIN } from '../../../../modules/last/train/main.nf'
-
-workflow test_last_train {
-
-    db =         [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
-    input =      [ [ id:'contigs' ], // meta map
-                   file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
-    UNTAR ( db )
-    LAST_TRAIN ( input, UNTAR.out.untar.map{ it[1] } )
-}
diff --git a/tests/modules/last/train/test.yml b/tests/modules/last/train/test.yml
deleted file mode 100644
index 8641600beda..00000000000
--- a/tests/modules/last/train/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: last train test_last_train
-  command: nextflow run ./tests/modules/last/train -entry test_last_train -c ./tests/config/nextflow.config -c ./tests/modules/last/train/nextflow.config
-  tags:
-    - last/train
-    - last
-  files:
-    - path: output/last/contigs.genome.par
-      contains:
-        - "score matrix"
-    - path: output/untar/lastdb/genome.bck
-      md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
-    - path: output/untar/lastdb/genome.des
-      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
-    - path: output/untar/lastdb/genome.prj
-      md5sum: 489715f14b0fea6273822696e72357f9
-    - path: output/untar/lastdb/genome.sds
-      md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
-    - path: output/untar/lastdb/genome.ssp
-      md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
-    - path: output/untar/lastdb/genome.suf
-      md5sum: 1895efa8653e8e9bd3605cff0408ed33
-    - path: output/untar/lastdb/genome.tis
-      md5sum: b7c40f06b1309dc6f37849eeb86dfd22
diff --git a/tests/modules/leehom/main.nf b/tests/modules/leehom/main.nf
deleted file mode 100644
index 1615d2e14b0..00000000000
--- a/tests/modules/leehom/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LEEHOM } from '../../../modules/leehom/main.nf'
-include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf'
-
-workflow test_leehom_bam {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-
-    fasta = []
-
-    SAMTOOLS_VIEW ( input, fasta )
-    LEEHOM ( SAMTOOLS_VIEW.out.bam )
-}
-
-workflow test_leehom_se_fq {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-
-    LEEHOM ( input )
-}
-
-workflow test_leehom_pe_fq {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              [
-                  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-              ] ]
-
-    LEEHOM ( input )
-}
diff --git a/tests/modules/leehom/test.yml b/tests/modules/leehom/test.yml
deleted file mode 100644
index 98257492025..00000000000
--- a/tests/modules/leehom/test.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-- name: leehom test_leehom_bam
-  command: nextflow run ./tests/modules/leehom -entry test_leehom_bam -c ./tests/config/nextflow.config -c ./tests/modules/leehom/nextflow.config
-  tags:
-    - leehom
-  files:
-    - path: output/leehom/test.bam
-    - path: output/samtools/test.bam
-    - path: output/leehom/test.log
-      md5sum: d1f5da273eb69f41babda510797c7671
-
-- name: leehom test_leehom_se_fq
-  command: nextflow run ./tests/modules/leehom -entry test_leehom_se_fq -c ./tests/config/nextflow.config -c ./tests/modules/leehom/nextflow.config
-  tags:
-    - leehom
-  files:
-    - path: output/leehom/test.fail.fq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/leehom/test.fq.gz
-      md5sum: ed10c4bbf5c3082ca68823535b91e1e2
-    - path: output/leehom/test.log
-      md5sum: 59aa280cb72dfbea05ba913cb89db143
-
-- name: leehom test_leehom_pe_fq
-  command: nextflow run ./tests/modules/leehom -entry test_leehom_pe_fq -c ./tests/config/nextflow.config -c ./tests/modules/leehom/nextflow.config
-  tags:
-    - leehom
-  files:
-    - path: output/leehom/test.fail.fq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/leehom/test.fq.gz
-      md5sum: 84929b78e3f89371ecd3b4c915b9ec33
-    - path: output/leehom/test.log
-      md5sum: 800b5a88dc0822886bfbb271029e2a4a
-    - path: output/leehom/test_r1.fail.fq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/leehom/test_r1.fq.gz
-      md5sum: e9258420fa712e8536106995a7d1d97a
-    - path: output/leehom/test_r2.fail.fq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/leehom/test_r2.fq.gz
-      md5sum: 27230bcc5eae81ec5c1701798d39c1af
diff --git a/tests/modules/legsta/main.nf b/tests/modules/legsta/main.nf
deleted file mode 100644
index 606d8209548..00000000000
--- a/tests/modules/legsta/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LEGSTA } from '../../../modules/legsta/main.nf'
-
-workflow test_legsta {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
-    ]
-
-    LEGSTA ( input )
-}
diff --git a/tests/modules/legsta/test.yml b/tests/modules/legsta/test.yml
deleted file mode 100644
index 8ac28a7e270..00000000000
--- a/tests/modules/legsta/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: legsta test_legsta
-  command: nextflow run tests/modules/legsta -entry test_legsta -c tests/config/nextflow.config
-  tags:
-    - legsta
-  files:
-    - path: output/legsta/test.tsv
-      md5sum: c493bdd19335de4828aa8b4e3ce7e1f8
-    - path: output/legsta/versions.yml
-      md5sum: d16c5f6fd68d2bcc2c71954e3342aabe
diff --git a/tests/modules/lima/main.nf b/tests/modules/lima/main.nf
deleted file mode 100644
index 7501def9d32..00000000000
--- a/tests/modules/lima/main.nf
+++ /dev/null
@@ -1,60 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LIMA } from '../../../modules/lima/main.nf'
-
-workflow test_lima_bam {
-
-    input = [
-                [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['pacbio']['ccs'],     checkIfExists: true),
-            ]
-    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
-
-    LIMA ( input, primers )
-}
-
-workflow test_lima_fa {
-
-    input = [
-                [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'],  checkIfExists: true),
-            ]
-    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
-
-    LIMA ( input, primers )
-}
-
-workflow test_lima_fa_gz {
-
-    input = [
-                [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], checkIfExists: true),
-            ]
-    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'],   checkIfExists: true) ]
-
-    LIMA ( input, primers )
-}
-
-workflow test_lima_fq {
-
-    input = [
-                [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'],  checkIfExists: true),
-            ]
-    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
-
-    LIMA ( input, primers )
-}
-
-workflow test_lima_fq_gz {
-
-    input = [
-                [ id:'test' ], // meta map
-                file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true),
-            ]
-    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'],   checkIfExists: true) ]
-
-    LIMA ( input, primers )
-}
diff --git a/tests/modules/lima/test.yml b/tests/modules/lima/test.yml
deleted file mode 100644
index 2278cc90484..00000000000
--- a/tests/modules/lima/test.yml
+++ /dev/null
@@ -1,91 +0,0 @@
-- name: lima test_lima_bam
-  command: nextflow run ./tests/modules/lima -entry test_lima_bam -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
-  tags:
-    - lima
-  files:
-    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam
-      md5sum: 14b51d7f44e30c05a5b14e431a992097
-    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi
-      md5sum: 6ae7f057304ad17dd9d5f565d72d3f7b
-    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.consensusreadset.xml
-      contains: ["ConsensusReadSet"]
-    - path: output/lima/test.fl.json
-      contains: ["ConsensusReadSet"]
-    - path: output/lima/test.fl.lima.clips
-      md5sum: fa03bc75bd78b2648a139fd67c69208f
-    - path: output/lima/test.fl.lima.counts
-      md5sum: 842c6a23ca2de504ced4538ad5111da1
-    - path: output/lima/test.fl.lima.guess
-      md5sum: d3675af3ca8a908ee9e3c231668392d3
-    - path: output/lima/test.fl.lima.report
-      md5sum: dc073985322ae0a003ccc7e0fa4db5e6
-    - path: output/lima/test.fl.lima.summary
-      md5sum: bcbcaaaca418bdeb91141c81715ca420
-
-- name: lima test_lima_fa
-  command: nextflow run ./tests/modules/lima -entry test_lima_fa -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
-  tags:
-    - lima
-  files:
-    - path: output/lima/test.fl.lima.clips
-      md5sum: 1012bc8874a14836f291bac48e8482a4
-    - path: output/lima/test.fl.lima.counts
-      md5sum: a4ceaa408be334eaa711577e95f8730e
-    - path: output/lima/test.fl.lima.guess
-      md5sum: 651e5f2b438b8ceadb3e06a2177e1818
-    - path: output/lima/test.fl.lima.report
-      md5sum: bd4a8bde17471563cf91aab4c787911d
-    - path: output/lima/test.fl.lima.summary
-      md5sum: 03be2311ba4afb878d8e547ab38c11eb
-
-- name: lima test_lima_fa_gz
-  command: nextflow run ./tests/modules/lima -entry test_lima_fa_gz -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
-  tags:
-    - lima
-  files:
-    - path: output/lima/test.fl.lima.clips
-      md5sum: 1012bc8874a14836f291bac48e8482a4
-    - path: output/lima/test.fl.lima.counts
-      md5sum: a4ceaa408be334eaa711577e95f8730e
-    - path: output/lima/test.fl.lima.guess
-      md5sum: 651e5f2b438b8ceadb3e06a2177e1818
-    - path: output/lima/test.fl.lima.report
-      md5sum: bd4a8bde17471563cf91aab4c787911d
-    - path: output/lima/test.fl.lima.summary
-      md5sum: 03be2311ba4afb878d8e547ab38c11eb
-
-- name: lima test_lima_fq
-  command: nextflow run ./tests/modules/lima -entry test_lima_fq -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
-  tags:
-    - lima
-  files:
-    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq
-      md5sum: ef395f689c5566f501e300bb83d7a5f2
-    - path: output/lima/test.fl.lima.clips
-      md5sum: 5c16ef8122f6f1798acc30eb8a30828c
-    - path: output/lima/test.fl.lima.counts
-      md5sum: 767b687e6eda7b24cd0e577f527eb2f0
-    - path: output/lima/test.fl.lima.guess
-      md5sum: 31b988aab6bda84867e704b9edd8a763
-    - path: output/lima/test.fl.lima.report
-      md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd
-    - path: output/lima/test.fl.lima.summary
-      md5sum: e91d3c386aaf4effa63f33ee2eb7da2a
-
-- name: lima test_lima_fq_gz
-  command: nextflow run ./tests/modules/lima -entry test_lima_fq_gz -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
-  tags:
-    - lima
-  files:
-    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq.gz
-      md5sum: 32c11db85f69a1b4454b6bbd794b6df2
-    - path: output/lima/test.fl.lima.clips
-      md5sum: 5c16ef8122f6f1798acc30eb8a30828c
-    - path: output/lima/test.fl.lima.counts
-      md5sum: 767b687e6eda7b24cd0e577f527eb2f0
-    - path: output/lima/test.fl.lima.guess
-      md5sum: 31b988aab6bda84867e704b9edd8a763
-    - path: output/lima/test.fl.lima.report
-      md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd
-    - path: output/lima/test.fl.lima.summary
-      md5sum: e91d3c386aaf4effa63f33ee2eb7da2a
diff --git a/tests/modules/lissero/main.nf b/tests/modules/lissero/main.nf
deleted file mode 100644
index 339576c34d9..00000000000
--- a/tests/modules/lissero/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LISSERO } from '../../../modules/lissero/main.nf'
-
-workflow test_lissero {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("https://github.com/MDU-PHL/LisSero/raw/master/tests/test_seq/NC_002973.fna", checkIfExists: true) ]
-
-    LISSERO ( input )
-}
diff --git a/tests/modules/lissero/test.yml b/tests/modules/lissero/test.yml
deleted file mode 100644
index 688cfa825d4..00000000000
--- a/tests/modules/lissero/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: lissero test_lissero
-  command: nextflow run ./tests/modules/lissero -entry test_lissero -c ./tests/config/nextflow.config -c ./tests/modules/lissero/nextflow.config
-  tags:
-    - lissero
-  files:
-    - path: output/lissero/test.tsv
-      contains: ["ID", "SEROTYPE", "FULL"]
diff --git a/tests/modules/lofreq/call/main.nf b/tests/modules/lofreq/call/main.nf
deleted file mode 100644
index 70da4ea59d2..00000000000
--- a/tests/modules/lofreq/call/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LOFREQ_CALL } from '../../../../modules/lofreq/call/main.nf'
-
-workflow test_lofreq_call {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    LOFREQ_CALL ( input, fasta )
-}
diff --git a/tests/modules/lofreq/call/test.yml b/tests/modules/lofreq/call/test.yml
deleted file mode 100644
index c84d08fbcf8..00000000000
--- a/tests/modules/lofreq/call/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: lofreq call test_lofreq_call
-  command: nextflow run ./tests/modules/lofreq/call -entry test_lofreq_call -c ./tests/config/nextflow.config -c ./tests/modules/lofreq/call/nextflow.config
-  tags:
-    - lofreq
-    - lofreq/call
-  files:
-    - path: output/lofreq/test.vcf.gz
-      contains:
-        [
-          '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
-        ]
diff --git a/tests/modules/lofreq/callparallel/main.nf b/tests/modules/lofreq/callparallel/main.nf
deleted file mode 100644
index 24ab2db3ba6..00000000000
--- a/tests/modules/lofreq/callparallel/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LOFREQ_CALLPARALLEL } from '../../../../modules/lofreq/callparallel/main.nf'
-
-workflow test_lofreq_callparallel {
-    
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    LOFREQ_CALLPARALLEL ( input, fasta, fai )
-}
diff --git a/tests/modules/lofreq/callparallel/test.yml b/tests/modules/lofreq/callparallel/test.yml
deleted file mode 100644
index c21eeaa711f..00000000000
--- a/tests/modules/lofreq/callparallel/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: lofreq callparallel test_lofreq_callparallel
-  command: nextflow run ./tests/modules/lofreq/callparallel -entry test_lofreq_callparallel -c ./tests/config/nextflow.config -c ./tests/modules/lofreq/callparallel/nextflow.config
-  tags:
-    - lofreq/callparallel
-    - lofreq
-  files:
-    - path: output/lofreq/test.vcf.gz
-      contains:
-        [
-          '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
-        ]
diff --git a/tests/modules/lofreq/filter/main.nf b/tests/modules/lofreq/filter/main.nf
deleted file mode 100644
index bd2a7f54fac..00000000000
--- a/tests/modules/lofreq/filter/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LOFREQ_FILTER } from '../../../../modules/lofreq/filter/main.nf'
-
-workflow test_lofreq_filter {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
-
-    LOFREQ_FILTER ( input )
-}
diff --git a/tests/modules/lofreq/filter/test.yml b/tests/modules/lofreq/filter/test.yml
deleted file mode 100644
index d3ee3812aa0..00000000000
--- a/tests/modules/lofreq/filter/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: lofreq filter test_lofreq_filter
-  command: nextflow run ./tests/modules/lofreq/filter -entry test_lofreq_filter -c ./tests/config/nextflow.config -c ./tests/modules/lofreq/filter/nextflow.config
-  tags:
-    - lofreq
-    - lofreq/filter
-  files:
-    - path: output/lofreq/test.vcf.gz
-      md5sum: 1914d9bc5d855ff11fe89da7d795e57a
diff --git a/tests/modules/lofreq/indelqual/main.nf b/tests/modules/lofreq/indelqual/main.nf
deleted file mode 100644
index 71652ce14b1..00000000000
--- a/tests/modules/lofreq/indelqual/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-
-include { LOFREQ_INDELQUAL } from '../../../../modules/lofreq/indelqual/main.nf'
-
-workflow test_lofreq_indelqual {
-    
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    LOFREQ_INDELQUAL ( input, fasta )
-}
diff --git a/tests/modules/lofreq/indelqual/test.yml b/tests/modules/lofreq/indelqual/test.yml
deleted file mode 100644
index 6fffb523b72..00000000000
--- a/tests/modules/lofreq/indelqual/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: lofreq indelqual
-  command: nextflow run ./tests/modules/lofreq/indelqual -entry test_lofreq_indelqual -c ./tests/config/nextflow.config -c ./tests/modules/lofreq/indelqual/nextflow.config
-  tags:
-    - lofreq
-    - lofreq/indelqual
-  files:
-    - path: output/lofreq/test.indelqual.bam
-      md5sum: 18de975638c2633069bfe1a41ebc5ff7
diff --git a/tests/modules/macrel/contigs/main.nf b/tests/modules/macrel/contigs/main.nf
deleted file mode 100644
index a613dcc42c9..00000000000
--- a/tests/modules/macrel/contigs/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MACREL_CONTIGS } from '../../../../modules/macrel/contigs/main.nf'
-
-workflow test_macrel_contigs {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) 
-    ]
-
-    MACREL_CONTIGS ( input )
-}
diff --git a/tests/modules/macrel/contigs/test.yml b/tests/modules/macrel/contigs/test.yml
deleted file mode 100644
index af272605457..00000000000
--- a/tests/modules/macrel/contigs/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: macrel contigs test_macrel_contigs
-  command: nextflow run ./tests/modules/macrel/contigs -entry test_macrel_contigs -c ./tests/config/nextflow.config -c ./tests/modules/macrel/contigs/nextflow.config
-  tags:
-    - macrel/contigs
-    - macrel
-  files:
-    - path: output/macrel/test/README.md
-      md5sum: fa3706dfc95d0538a52c4d0d824be5fb
-    - path: output/macrel/test/test.all_orfs.faa.gz
-    - path: output/macrel/test/test.prediction.gz
-    - path: output/macrel/test/test.smorfs.faa.gz
-      md5sum: 79704c6120c2f794518301af6f9b963d
-    - path: output/macrel/test/test_log.txt
-      md5sum: 6fdba143dce759597eb9f80e5d968729
-    - path: output/macrel/versions.yml
-      md5sum: be8bf0d0647751c635c3736655f29f85
diff --git a/tests/modules/macs2/callpeak/main.nf b/tests/modules/macs2/callpeak/main.nf
deleted file mode 100644
index 070469dd329..00000000000
--- a/tests/modules/macs2/callpeak/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MACS2_CALLPEAK } from '../../../../modules/macs2/callpeak/main.nf'
-include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL    } from '../../../../modules/macs2/callpeak/main.nf'
-include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED     } from '../../../../modules/macs2/callpeak/main.nf'
-
-workflow test_macs2_callpeak_bed {
-    input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['pacbio']['genemodel1'], checkIfExists: true)],
-                  []]
-
-    MACS2_CALLPEAK_BED ( input, 4000 )
-}
-
-workflow test_macs2_callpeak {
-    input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
-                  []]
-
-    MACS2_CALLPEAK ( input, 40000 )
-}
-
-workflow test_macs2_callpeak_ctrl {
-    input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
-                  [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-
-    MACS2_CALLPEAK_CTRL ( input, 40000 )
-}
diff --git a/tests/modules/macs2/callpeak/test.yml b/tests/modules/macs2/callpeak/test.yml
deleted file mode 100644
index 43c99140509..00000000000
--- a/tests/modules/macs2/callpeak/test.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-- name: macs2 callpeak test_macs2_callpeak_bed
-  command: nextflow run ./tests/modules/macs2/callpeak -entry test_macs2_callpeak_bed -c ./tests/config/nextflow.config -c ./tests/modules/macs2/callpeak/nextflow.config
-  tags:
-    - macs2
-    - macs2/callpeak
-  files:
-    - path: output/macs2/test_peaks.narrowPeak
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/macs2/test_peaks.xls
-      md5sum: 762383e3a35e1f9ac3834fd6b2926092
-    - path: output/macs2/test_summits.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-
-- name: macs2 callpeak test_macs2_callpeak
-  command: nextflow run ./tests/modules/macs2/callpeak -entry test_macs2_callpeak -c ./tests/config/nextflow.config -c ./tests/modules/macs2/callpeak/nextflow.config
-  tags:
-    - macs2
-    - macs2/callpeak
-  files:
-    - path: output/macs2/test_peaks.narrowPeak
-      md5sum: 2e4da1c1704595e12aaf99cc715ad70c
-    - path: output/macs2/test_peaks.xls
-      md5sum: 5d65cb3dbd5421ea3bb5b490a100e9a4
-    - path: output/macs2/test_summits.bed
-      md5sum: 26f0f97b6c14dbca129e947a58067c82
-
-- name: macs2 callpeak test_macs2_callpeak_ctrl
-  command: nextflow run ./tests/modules/macs2/callpeak -entry test_macs2_callpeak_ctrl -c ./tests/config/nextflow.config -c ./tests/modules/macs2/callpeak/nextflow.config
-  tags:
-    - macs2
-    - macs2/callpeak
-  files:
-    - path: output/macs2/test_peaks.narrowPeak
-      md5sum: 653e1108cc57ca07d0f60fc0f4fb8ba3
-    - path: output/macs2/test_peaks.xls
-      md5sum: bf86546faa7b581b5209c29b22046a0a
-    - path: output/macs2/test_summits.bed
-      md5sum: 4f3c7c53a1d730d90d1b3dd9d3197af4
diff --git a/tests/modules/mafft/main.nf b/tests/modules/mafft/main.nf
deleted file mode 100644
index 7f50b35aef9..00000000000
--- a/tests/modules/mafft/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MAFFT } from '../../../modules/mafft/main.nf'
-
-workflow test_mafft {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
-    ]
-
-    MAFFT ( input )
-}
diff --git a/tests/modules/mafft/test.yml b/tests/modules/mafft/test.yml
deleted file mode 100644
index cd40caa7171..00000000000
--- a/tests/modules/mafft/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: mafft test_mafft
-  command: nextflow run tests/modules/mafft -entry test_mafft -c tests/config/nextflow.config
-  tags:
-    - mafft
-  files:
-    - path: output/mafft/test.fas
-      md5sum: 23426611f4a0df532b6708f072bd445b
-    - path: output/mafft/versions.yml
-      md5sum: b1b5ab3728ae17401808335f1c8f8215
diff --git a/tests/modules/malt/build_test/main.nf b/tests/modules/malt/build_test/main.nf
deleted file mode 100644
index 6b8de805bb5..00000000000
--- a/tests/modules/malt/build_test/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNZIP } from '../../../../modules/unzip/main.nf'
-include { MALT_BUILD } from '../../../../modules/malt/build/main.nf'
-
-workflow test_malt_build {
-    fastas        = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    seq_type      = "DNA"
-    map_accession = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/nucl_acc2tax-Jul2019.abin.zip", checkIfExists: true) ]
-    mapping_type  = 'ref'
-    mapping_db    = 'taxonomy'
-
-    UNZIP ( map_accession )
-    MALT_BUILD ( fastas, seq_type, UNZIP.out.unzipped_archive.map{ it[1] }, "ref", "taxonomy" )
-}
diff --git a/tests/modules/malt/build_test/test.yml b/tests/modules/malt/build_test/test.yml
deleted file mode 100644
index 33361c85ec2..00000000000
--- a/tests/modules/malt/build_test/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: malt build test_malt_build
-  command: nextflow run ./tests/modules/malt/build -entry test_malt_build -c ./tests/config/nextflow.config  -c ./tests/modules/malt/build/nextflow.config
-  tags:
-    - malt
-    - malt/build
-  files:
-    - path: output/malt/malt-build.log
-      contains:
-        - "Peak memory"
-    - path: output/malt/malt_index/index0.idx
-      md5sum: 1954f2c00b418d00112829b0a6adb8ce
-    - path: output/malt/malt_index/ref.db
-      md5sum: 1fb74eccd5400fb23454454da1bd4c0c
-    - path: output/malt/malt_index/ref.idx
-      md5sum: 7dea362b3fac8e00956a4952a3d4f474
-    - path: output/malt/malt_index/ref.inf
-      md5sum: b146842067cf278ef1d23e6c2e7c0c35
-    - path: output/malt/malt_index/table0.db
-    - path: output/malt/malt_index/table0.idx
-    - path: output/malt/malt_index/taxonomy.idx
-      md5sum: 13aa81314892b5537319fca2a63a2c31
-    - path: output/malt/malt_index/taxonomy.map
-      md5sum: 1e972302ae6d705b8abb377cfafd380a
-    - path: output/malt/malt_index/taxonomy.tre
-      md5sum: 79c2322475a8eebc57607ff36c1e4728
-    - path: output/unzip/nucl_acc2tax-Jul2019.abin/nucl_acc2tax-Jul2019.abin
-      md5sum: b2deb1df50ebcec4de71a6beec6226d7
diff --git a/tests/modules/malt/run/main.nf b/tests/modules/malt/run/main.nf
deleted file mode 100644
index 28db0e92f8a..00000000000
--- a/tests/modules/malt/run/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNZIP      } from '../../../../modules/unzip/main.nf'
-include { MALT_BUILD } from  '../../../../modules/malt/build/main.nf'
-include { MALT_RUN   } from '../../../../modules/malt/run/main.nf'
-
-workflow test_malt_run {
-
-    fastas        = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    seq_type      = "DNA"
-    map_accession = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/nucl_acc2tax-Jul2019.abin.zip", checkIfExists: true) ]
-    mapping_type  = 'ref'
-    mapping_db    = 'taxonomy'
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    mode = "BlastN"
-
-    UNZIP ( map_accession )
-    MALT_BUILD ( fastas, seq_type, UNZIP.out.unzipped_archive.map{ it[1] }, "ref", "taxonomy" )
-    MALT_RUN ( input, mode, MALT_BUILD.out.index )
-}
-
diff --git a/tests/modules/malt/run/test.yml b/tests/modules/malt/run/test.yml
deleted file mode 100644
index eae96004d68..00000000000
--- a/tests/modules/malt/run/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: malt run test_malt_run
-  command: nextflow run ./tests/modules/malt/run -entry test_malt_run -c ./tests/config/nextflow.config  -c ./tests/modules/malt/run/nextflow.config
-  tags:
-    - malt/run
-    - malt
-  files:
-    - path: output/malt/test-malt-run.log
-      contains:
-        - "Peak memory"
-    - path: output/malt/test_1.rma6
diff --git a/tests/modules/maltextract/main.nf b/tests/modules/maltextract/main.nf
deleted file mode 100644
index ed1e32c9b38..00000000000
--- a/tests/modules/maltextract/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNZIP as UNZIP_MALT        } from '../../../modules/unzip/main.nf'
-include { UNZIP as UNZIP_MALTEXTRACT }  from '../../../modules/unzip/main.nf'
-include { MALT_BUILD                 } from  '../../../modules/malt/build/main.nf'
-include { MALT_RUN                   } from '../../../modules/malt/run/main.nf'
-include { MALTEXTRACT                } from '../../../modules/maltextract/main.nf'
-
-workflow test_maltextract {
-
-    fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff = []
-    seq_type = "DNA"
-    map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    mode = "BlastN"
-    taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
-    ncbi_dir = [ [], file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true) ]
-
-    UNZIP_MALT ( map_db )
-    UNZIP_MALTEXTRACT ( ncbi_dir )
-    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive.map{ it[1] } )
-    MALT_RUN ( input, mode, MALT_BUILD.out.index )
-    ch_input_to_maltextract = MALT_RUN.out.rma6.map{ it[1] }
-    MALTEXTRACT ( ch_input_to_maltextract, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive.map{ it[1] })
-}
diff --git a/tests/modules/maltextract/test.yml b/tests/modules/maltextract/test.yml
deleted file mode 100644
index 6802fe8b937..00000000000
--- a/tests/modules/maltextract/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: maltextract
-  command: nextflow run ./tests/modules/maltextract -entry test_maltextract -c ./tests/config/nextflow.config -c ./tests/modules/maltextract/nextflow.config
-  tags:
-    - maltextract
-  files:
-    - path: output/maltextract/results/error.txt
-    - path: output/maltextract/results/log.txt
-      contains:
-        - "INFO: Peak memory"
diff --git a/tests/modules/manta/convertinversion/main.nf b/tests/modules/manta/convertinversion/main.nf
deleted file mode 100644
index 6997b5c9cf9..00000000000
--- a/tests/modules/manta/convertinversion/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MANTA_CONVERTINVERSION } from '../../../../modules/manta/convertinversion/main.nf'
-include { MANTA_TUMORONLY        } from '../../../../modules/manta/tumoronly/main.nf'
-
-workflow test_manta_convertinversion {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        [], []
-    ]
-
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    MANTA_TUMORONLY ( input, fasta, fai )
-
-    MANTA_CONVERTINVERSION ( MANTA_TUMORONLY.out.tumor_sv_vcf, fasta )
-}
diff --git a/tests/modules/manta/convertinversion/test.yml b/tests/modules/manta/convertinversion/test.yml
deleted file mode 100644
index 33330b20a7f..00000000000
--- a/tests/modules/manta/convertinversion/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: manta convertinversion test_manta_convertinversion
-  command: nextflow run ./tests/modules/manta/convertinversion -entry test_manta_convertinversion -c ./tests/config/nextflow.config  -c ./tests/modules/manta/convertinversion/nextflow.config
-  tags:
-    - manta
-    - manta/convertinversion
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.tumor_sv.vcf.gz
-    - path: output/manta/test.tumor_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.vcf.gz
-    - path: output/manta/test.vcf.gz.tbi
-      md5sum: e7180bb953d2bd657c420a5f76a7164d
diff --git a/tests/modules/manta/germline/main.nf b/tests/modules/manta/germline/main.nf
deleted file mode 100644
index 5f6687b2749..00000000000
--- a/tests/modules/manta/germline/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
-
-workflow test_manta_germline {
-    input = [
-        [ id:'test'], // meta map
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)],
-        [],[]
-    ]
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    MANTA_GERMLINE ( input, fasta, fai )
-}
-
-workflow test_manta_germline_target_bed {
-    input = [
-        [ id:'test'], // meta map
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)],
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
-    ]
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    MANTA_GERMLINE ( input, fasta, fai )
-}
-
-workflow test_manta_germline_target_bed_jointcalling {
-    input = [
-        [ id:'test'], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)],
-        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
-    ]
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    MANTA_GERMLINE ( input, fasta, fai )
-}
diff --git a/tests/modules/manta/germline/test.yml b/tests/modules/manta/germline/test.yml
deleted file mode 100644
index 7ded24adc58..00000000000
--- a/tests/modules/manta/germline/test.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-- name: manta germline
-  command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config
-  tags:
-    - manta
-    - manta/germline
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-    - path: output/manta/test.diploid_sv.vcf.gz
-    - path: output/manta/test.diploid_sv.vcf.gz.tbi
-- name: manta germline target bed
-  command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config
-  tags:
-    - manta
-    - manta/germline
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-    - path: output/manta/test.diploid_sv.vcf.gz
-    - path: output/manta/test.diploid_sv.vcf.gz.tbi
-- name: manta germline target bed jointcalling
-  command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline_target_bed_jointcalling -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config
-  tags:
-    - manta
-    - manta/germline
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-    - path: output/manta/test.diploid_sv.vcf.gz
-    - path: output/manta/test.diploid_sv.vcf.gz.tbi
diff --git a/tests/modules/manta/somatic/main.nf b/tests/modules/manta/somatic/main.nf
deleted file mode 100644
index b32a273ef69..00000000000
--- a/tests/modules/manta/somatic/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MANTA_SOMATIC } from '../../../../modules/manta/somatic/main.nf'
-
-workflow test_manta_somatic {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        [], []
-    ]
-
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    MANTA_SOMATIC ( input, fasta, fai )
-}
-
-workflow test_manta_somatic_target_bed {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true),
-    ]
-
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    MANTA_SOMATIC ( input, fasta, fai )
-}
diff --git a/tests/modules/manta/somatic/test.yml b/tests/modules/manta/somatic/test.yml
deleted file mode 100644
index d701a210d94..00000000000
--- a/tests/modules/manta/somatic/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: manta somatic test_manta_somatic
-  command: nextflow run ./tests/modules/manta/somatic -entry test_manta_somatic -c ./tests/config/nextflow.config -c ./tests/modules/manta/somatic/nextflow.config
-  tags:
-    - manta/somatic
-    - manta
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.diploid_sv.vcf.gz
-    - path: output/manta/test.diploid_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.somatic_sv.vcf.gz
-    - path: output/manta/test.somatic_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
diff --git a/tests/modules/manta/tumoronly/main.nf b/tests/modules/manta/tumoronly/main.nf
deleted file mode 100644
index dbe079140e4..00000000000
--- a/tests/modules/manta/tumoronly/main.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MANTA_TUMORONLY } from '../../../../modules/manta/tumoronly/main.nf'
-
-workflow test_manta_tumoronly {
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        [], []
-    ]
-
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    MANTA_TUMORONLY ( input, fasta, fai )
-}
-
-workflow test_manta_tumoronly_target_bed {
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    MANTA_TUMORONLY ( input, fasta, fai )
-}
diff --git a/tests/modules/manta/tumoronly/test.yml b/tests/modules/manta/tumoronly/test.yml
deleted file mode 100644
index c56e23fa19a..00000000000
--- a/tests/modules/manta/tumoronly/test.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-- name: manta tumoronly
-  command: nextflow run ./tests/modules/manta/tumoronly -entry test_manta_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/manta/tumoronly/nextflow.config
-  tags:
-    - manta
-    - manta/tumoronly
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-    - path: output/manta/test.tumor_sv.vcf.gz
-    - path: output/manta/test.tumor_sv.vcf.gz.tbi
-- name: manta tumoronly target bed
-  command: nextflow run ./tests/modules/manta/tumoronly -entry test_manta_tumoronly_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/manta/tumoronly/nextflow.config
-  tags:
-    - manta
-    - manta/tumoronly
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-    - path: output/manta/test.tumor_sv.vcf.gz
-    - path: output/manta/test.tumor_sv.vcf.gz.tbi
diff --git a/tests/modules/mapdamage2/main.nf b/tests/modules/mapdamage2/main.nf
deleted file mode 100644
index b7e4d23b06e..00000000000
--- a/tests/modules/mapdamage2/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MAPDAMAGE2 } from '../../../modules/mapdamage2/main.nf'
-
-workflow test_mapdamage2 {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) 
-            ]                            
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    
-    MAPDAMAGE2 ( input, fasta )
-}
diff --git a/tests/modules/mapdamage2/test.yml b/tests/modules/mapdamage2/test.yml
deleted file mode 100644
index 96c8b2dae24..00000000000
--- a/tests/modules/mapdamage2/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: mapdamage2 test_mapdamage2
-  command: nextflow run ./tests/modules/mapdamage2 -entry test_mapdamage2 -c ./tests/config/nextflow.config -c ./tests/modules/mapdamage2/nextflow.config
-  tags:
-    - mapdamage2
-  files:
-    - path: output/mapdamage2/results_test.paired_end.sorted/3pGtoA_freq.txt
-      md5sum: 3b300b8d2842441675cb2b56740801f0
-    - path: output/mapdamage2/results_test.paired_end.sorted/5pCtoT_freq.txt
-      md5sum: 4c27465cd02e1fb8bf6fb2b01e98446d
-    - path: output/mapdamage2/results_test.paired_end.sorted/Fragmisincorporation_plot.pdf
-    - path: output/mapdamage2/results_test.paired_end.sorted/Runtime_log.txt
-    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_correct_prob.csv
-    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_hist.pdf
-    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_iter.csv
-    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_iter_summ_stat.csv
-    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_post_pred.pdf
-    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_trace.pdf
-    - path: output/mapdamage2/results_test.paired_end.sorted/dnacomp.txt
-      md5sum: 4244d9fa554bbfeebbcea8eba3ad6466
-    - path: output/mapdamage2/results_test.paired_end.sorted/dnacomp_genome.csv
-      md5sum: ea91a3d205717d3c6b3e0b77bb840945
-    - path: output/mapdamage2/results_test.paired_end.sorted/lgdistribution.txt
-      md5sum: f86dfc04b1fff4337cc91add6356e3a0
-    - path: output/mapdamage2/results_test.paired_end.sorted/misincorporation.txt
-      md5sum: 1c89b4c96d1f8996c3d0879cad5129a5
diff --git a/tests/modules/mash/dist/main.nf b/tests/modules/mash/dist/main.nf
deleted file mode 100644
index 10c9c9fa3c3..00000000000
--- a/tests/modules/mash/dist/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MASH_DIST } from '../../../../modules/mash/dist/main.nf'
-
-workflow test_mash_dist {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
-    ]
-
-    reference =  file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    MASH_DIST ( input, reference )
-}
diff --git a/tests/modules/mash/dist/test.yml b/tests/modules/mash/dist/test.yml
deleted file mode 100644
index 2602f87de07..00000000000
--- a/tests/modules/mash/dist/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: mash dist test_mash_dist
-  command: nextflow run tests/modules/mash/dist -entry test_mash_dist -c tests/config/nextflow.config
-  tags:
-    - mash
-    - mash/dist
-  files:
-    - path: output/mash/test.txt
-      md5sum: 1dfd5b53e1996f9fdb9d260b3e81c4d6
-    - path: output/mash/versions.yml
-      md5sum: f786d48a9af59e823d19c171969d0d50
diff --git a/tests/modules/mash/screen/main.nf b/tests/modules/mash/screen/main.nf
deleted file mode 100644
index 5338d932ee8..00000000000
--- a/tests/modules/mash/screen/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MASH_SKETCH } from '../../../../modules/mash/sketch/main.nf'
-include { MASH_SCREEN } from '../../../../modules/mash/screen/main.nf'
-
-workflow test_mash_screen {
-
-    input = [
-        [ id:'test', single_end:false], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    sars_db = [
-        [ id: 'sars_db' ],
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    MASH_SKETCH ( sars_db )
-    MASH_SCREEN ( input, MASH_SKETCH.out.mash.map { meta, sketch -> sketch } )
-}
diff --git a/tests/modules/mash/screen/test.yml b/tests/modules/mash/screen/test.yml
deleted file mode 100644
index e4907ce989b..00000000000
--- a/tests/modules/mash/screen/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: mash screen test_mash_screen
-  command: nextflow run ./tests/modules/mash/screen -entry test_mash_screen -c ./tests/config/nextflow.config  -c ./tests/modules/mash/screen/nextflow.config
-  tags:
-    - mash
-    - mash/screen
-  files:
-    - path: output/mash/sars_db.mash_stats
-      md5sum: 1dafbd23e36e18bf4c87a007d0fc98f7
-    - path: output/mash/sars_db.msh
-      md5sum: 24289e4a13526e88eeb2abfca4a0f0a8
-    - path: output/mash/test.screen
-      md5sum: ac8701e1aab651b2f36c6380b1351b11
diff --git a/tests/modules/mash/sketch/main.nf b/tests/modules/mash/sketch/main.nf
deleted file mode 100644
index cec2035b704..00000000000
--- a/tests/modules/mash/sketch/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MASH_SKETCH } from '../../../../modules/mash/sketch/main.nf'
-
-workflow test_mash_sketch {
-    
-    input = [ [ id:'test', single_end:false], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-              ]
-            ]
-
-    MASH_SKETCH ( input )
-}
diff --git a/tests/modules/mash/sketch/test.yml b/tests/modules/mash/sketch/test.yml
deleted file mode 100644
index d5039956d6c..00000000000
--- a/tests/modules/mash/sketch/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: mash sketch
-  command: nextflow run ./tests/modules/mash/sketch -entry test_mash_sketch -c ./tests/config/nextflow.config -c ./tests/modules/mash/sketch/nextflow.config
-  tags:
-    - mash/sketch
-  files:
-    - path: output/mash/test.msh
-      md5sum: d747145a43dad5f82342036f8f5d9133
-    - path: output/mash/test.mash_stats
-      md5sum: 2a6f297d8e69a5e4160243bc6c89129c
diff --git a/tests/modules/mashtree/main.nf b/tests/modules/mashtree/main.nf
deleted file mode 100644
index 07f5e561f1e..00000000000
--- a/tests/modules/mashtree/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MASHTREE } from '../../../modules/mashtree/main.nf'
-
-workflow test_mashtree {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    MASHTREE ( input )
-}
diff --git a/tests/modules/mashtree/test.yml b/tests/modules/mashtree/test.yml
deleted file mode 100644
index bea9638c2b3..00000000000
--- a/tests/modules/mashtree/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: mashtree test_mashtree
-  command: nextflow run ./tests/modules/mashtree -entry test_mashtree -c ./tests/config/nextflow.config -c ./tests/modules/mashtree/nextflow.config
-  tags:
-    - mashtree
-  files:
-    - path: output/mashtree/test.dnd
-      md5sum: 007b3949a9f0c991624791d2fb076824
-    - path: output/mashtree/test.tsv
diff --git a/tests/modules/maxbin2/main.nf b/tests/modules/maxbin2/main.nf
deleted file mode 100644
index 3df417be3de..00000000000
--- a/tests/modules/maxbin2/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MAXBIN2 } from '../../../modules/maxbin2/main.nf'
-
-workflow test_maxbin2 {
-
-    input = [ 
-        [ id:'test1', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true),
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-        []
-    ]
-
-    MAXBIN2 ( input )
-}
diff --git a/tests/modules/maxbin2/test.yml b/tests/modules/maxbin2/test.yml
deleted file mode 100644
index a8ba98f955b..00000000000
--- a/tests/modules/maxbin2/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: maxbin2
-  command: nextflow run ./tests/modules/maxbin2 -entry test_maxbin2 -c ./tests/config/nextflow.config -c ./tests/modules/maxbin2/nextflow.config
-  tags:
-    - maxbin2
-  files:
-    - path: output/maxbin2/test1.001.fasta.gz
-    - path: output/maxbin2/test1.002.fasta.gz
-    - path: output/maxbin2/test1.log.gz
-    - path: output/maxbin2/test1.marker.gz
-    - path: output/maxbin2/test1.marker_of_each_bin.tar.gz
-    - path: output/maxbin2/test1.noclass.gz
-    - path: output/maxbin2/test1.summary
-      contains:
-        - "Bin name\tAbundance\tCompleteness\tGenome size\tGC content"
-    - path: output/maxbin2/test1.tooshort.gz
diff --git a/tests/modules/maxquant/lfq/main.nf b/tests/modules/maxquant/lfq/main.nf
deleted file mode 100644
index bb9b7976a59..00000000000
--- a/tests/modules/maxquant/lfq/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MAXQUANT_LFQ } from '../../../../modules/maxquant/lfq/main.nf' addParams( options: [:] )
-
-workflow test_maxquant_lfq {
-        
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['proteomics']['database']['yeast_ups'], checkIfExists: true), file(params.test_data['proteomics']['parameter']['maxquant'] , checkIfExists: true)
-            ]
-
-
-    rawfiles = [file(params.test_data['proteomics']['msspectra']['ups_file1']) , file(params.test_data['proteomics']['msspectra']['ups_file2'])]
-
-    MAXQUANT_LFQ ( input, rawfiles.collect() )
-}
diff --git a/tests/modules/maxquant/lfq/test.yml b/tests/modules/maxquant/lfq/test.yml
deleted file mode 100644
index 2b6a2c146b2..00000000000
--- a/tests/modules/maxquant/lfq/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: maxquant lfq
-  command: nextflow run ./tests/modules/maxquant/lfq -entry test_maxquant_lfq  -c tests/config/nextflow.config
-  tags:
-    - maxquant
-    - maxquant/lfq
-  files:
-    - path: output/maxquant/proteinGroups.txt
-      md5sum: 0d0f6aab54fe6dc717d1307bbc207324
diff --git a/tests/modules/mcroni/main.nf b/tests/modules/mcroni/main.nf
deleted file mode 100644
index 6ef0dd49c60..00000000000
--- a/tests/modules/mcroni/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MCRONI } from '../../../modules/mcroni/main.nf'
-
-workflow test_mcroni {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    MCRONI ( input )
-}
diff --git a/tests/modules/mcroni/test.yml b/tests/modules/mcroni/test.yml
deleted file mode 100644
index 3750d5c67ba..00000000000
--- a/tests/modules/mcroni/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: mcroni test_mcroni
-  command: nextflow run ./tests/modules/mcroni -entry test_mcroni -c ./tests/config/nextflow.config  -c ./tests/modules/mcroni/nextflow.config
-  tags:
-    - mcroni
-  files:
-    - path: output/mcroni/test_table.tsv
-      md5sum: 64f8438dcc476e8b4d762fedc2e3f69e
diff --git a/tests/modules/md5sum/main.nf b/tests/modules/md5sum/main.nf
deleted file mode 100644
index f90642b6e4c..00000000000
--- a/tests/modules/md5sum/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MD5SUM } from '../../../modules/md5sum/main.nf'
-
-workflow test_md5sum {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    MD5SUM ( input )
-}
diff --git a/tests/modules/md5sum/test.yml b/tests/modules/md5sum/test.yml
deleted file mode 100644
index 1e6517a76cc..00000000000
--- a/tests/modules/md5sum/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: md5sum test_md5sum
-  command: nextflow run tests/modules/md5sum -entry test_md5sum -c tests/config/nextflow.config
-  tags:
-    - md5sum
-  files:
-    - path: output/md5sum/test.paired_end.bam.md5
-      md5sum: 1163095be8fdfb2acb3cc6c027389c4b
-    - path: output/md5sum/versions.yml
diff --git a/tests/modules/medaka/main.nf b/tests/modules/medaka/main.nf
deleted file mode 100644
index 75fc135b422..00000000000
--- a/tests/modules/medaka/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MEDAKA } from '../../../modules/medaka/main.nf'
-
-workflow test_medaka {
-    
-    input = [ 
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-    
-    MEDAKA ( input )
-}
diff --git a/tests/modules/medaka/test.yml b/tests/modules/medaka/test.yml
deleted file mode 100644
index 02bd8927ded..00000000000
--- a/tests/modules/medaka/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: medaka test_medaka
-  command: nextflow run ./tests/modules/medaka -entry test_medaka -c ./tests/config/nextflow.config -c ./tests/modules/medaka/nextflow.config
-  tags:
-    - medaka
-  files:
-    - path: output/medaka/test.polished.genome.fa.gz
-      md5sum: f42303f1d6c2c79175faeb00e10b9a6e
diff --git a/tests/modules/megahit/main.nf b/tests/modules/megahit/main.nf
deleted file mode 100644
index 88acf3e3706..00000000000
--- a/tests/modules/megahit/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MEGAHIT } from '../../../modules/megahit/main.nf'
-
-workflow test_megahit {
-
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ] 
-    ]
-
-    MEGAHIT ( input )
-}
-
-workflow test_megahit_single {
-
-    input = [ 
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    MEGAHIT ( input )
-}
diff --git a/tests/modules/megahit/test.yml b/tests/modules/megahit/test.yml
deleted file mode 100644
index 2072ac12637..00000000000
--- a/tests/modules/megahit/test.yml
+++ /dev/null
@@ -1,71 +0,0 @@
-- name: megahit
-  command: nextflow run ./tests/modules/megahit -entry test_megahit -c ./tests/config/nextflow.config -process.cpus 1 -c ./tests/modules/megahit/nextflow.config
-  tags:
-    - megahit
-  files:
-    - path: output/megahit/megahit_out/test.contigs.fa.gz
-      md5sum: 8ed114f22130e16df3532d3f6b03e116
-    - path: output/megahit/megahit_out/intermediate_contigs/k21.addi.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k21.contigs.fa.gz
-      md5sum: 4221d45f238045bbdb1eea04e4ce4261
-    - path: output/megahit/megahit_out/intermediate_contigs/k21.final.contigs.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k21.local.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k29.addi.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k29.contigs.fa.gz
-      md5sum: c72aeb242788542af0260098b4d61204
-    - path: output/megahit/megahit_out/intermediate_contigs/k29.final.contigs.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k29.local.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k39.addi.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k39.contigs.fa.gz
-      md5sum: aa188f4c92e69c1a4b396e8f2991236f
-    - path: output/megahit/megahit_out/intermediate_contigs/k39.final.contigs.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k39.local.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-
-- name: megahit_single
-  command: nextflow run ./tests/modules/megahit -entry test_megahit_single -c ./tests/config/nextflow.config -process.cpus 1 -c ./tests/modules/megahit/nextflow.config
-  tags:
-    - megahit
-  files:
-    - path: output/megahit/megahit_out/test.contigs.fa.gz
-      md5sum: f50352838b778cc67824f631197a8346
-    - path: output/megahit/megahit_out/intermediate_contigs/k21.addi.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k21.contigs.fa.gz
-      md5sum: 61554dc60ba8e95d9c1d9dca8d465bef
-    - path: output/megahit/megahit_out/intermediate_contigs/k21.final.contigs.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k21.local.fa.gz
-      md5sum: b916fc620fdf0d23ef33485352c168b3
-    - path: output/megahit/megahit_out/intermediate_contigs/k29.addi.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k29.contigs.fa.gz
-      md5sum: d916bc564854aa0fabaa5234035aa47b
-    - path: output/megahit/megahit_out/intermediate_contigs/k29.final.contigs.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k29.local.fa.gz
-      md5sum: cccf44441e65913b02fb64eb0835dcc1
-    - path: output/megahit/megahit_out/intermediate_contigs/k39.addi.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k39.contigs.fa.gz
-      md5sum: 4416a9e846ccbeb06b880ac2fdc02925
-    - path: output/megahit/megahit_out/intermediate_contigs/k39.final.contigs.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k39.local.fa.gz
-      md5sum: 590d0a08285226d24f7f984f7b3b4f65
-    - path: output/megahit/megahit_out/intermediate_contigs/k59.addi.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k59.contigs.fa.gz
-      md5sum: 51ef726b87a53b0cbdde762d7973a8a7
-    - path: output/megahit/megahit_out/intermediate_contigs/k59.final.contigs.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
-    - path: output/megahit/megahit_out/intermediate_contigs/k59.local.fa.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
diff --git a/tests/modules/megan/daa2info/main.nf b/tests/modules/megan/daa2info/main.nf
deleted file mode 100644
index 840a14a26b2..00000000000
--- a/tests/modules/megan/daa2info/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
-include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf'
-include { MEGAN_DAA2INFO } from '../../../../modules/megan/daa2info/main.nf'
-
-workflow test_megan_daa2info {
-
-    db = [ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true) ]
-    fasta = [ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true) ]
-    out_ext = 'daa'
-    blast_columns = []
-    megan_summary = true
-
-    DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
-    MEGAN_DAA2INFO ( DIAMOND_BLASTX.out.daa, megan_summary )
-}
diff --git a/tests/modules/megan/daa2info/test.yml b/tests/modules/megan/daa2info/test.yml
deleted file mode 100644
index 1dbdc3c920e..00000000000
--- a/tests/modules/megan/daa2info/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: megan daa2info test_megan_daa2info
-  command: nextflow run ./tests/modules/megan/daa2info -entry test_megan_daa2info -c ./tests/config/nextflow.config  -c ./tests/modules/megan/daa2info/nextflow.config
-  tags:
-    - megan/daa2info
-    - megan
-  files:
-    - path: output/megan/test.megan
-      contains: ["@Creator"]
-    - path: output/megan/test.txt.gz
-      contains: ["# Number of reads: 1"]
diff --git a/tests/modules/megan/rma2info/main.nf b/tests/modules/megan/rma2info/main.nf
deleted file mode 100644
index edbe9a4909b..00000000000
--- a/tests/modules/megan/rma2info/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MEGAN_RMA2INFO } from '../../../../modules/megan/rma2info/main.nf'
-
-workflow test_megan_rma2info {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file('https://github.com/nf-core/test-datasets/raw/a7e61654553887475a2f7178108587ecd9b54608/data/delete_me/malt/test.rma6', checkIfExists: true)
-    ]
-    megan_summary = true
-
-    MEGAN_RMA2INFO ( input, megan_summary )
-}
diff --git a/tests/modules/megan/rma2info/test.yml b/tests/modules/megan/rma2info/test.yml
deleted file mode 100644
index dc845bead5d..00000000000
--- a/tests/modules/megan/rma2info/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: megan rma2info test_megan_rma2info
-  command: nextflow run tests/modules/megan/rma2info -entry test_megan_rma2info -c tests/config/nextflow.config
-  tags:
-    - megan
-    - megan/rma2info
-  files:
-    - path: output/megan/test.megan
-      contains:
-        - "@Creator"
-    - path: output/megan/test.txt.gz
-      md5sum: 5c3b876aa0abef12158bcd7c3702740f
-    - path: output/megan/versions.yml
diff --git a/tests/modules/meningotype/main.nf b/tests/modules/meningotype/main.nf
deleted file mode 100644
index a2d0ff10f46..00000000000
--- a/tests/modules/meningotype/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MENINGOTYPE } from '../../../modules/meningotype/main.nf'
-
-workflow test_meningotype {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    MENINGOTYPE ( input )
-}
diff --git a/tests/modules/meningotype/test.yml b/tests/modules/meningotype/test.yml
deleted file mode 100644
index 02ec8e1f629..00000000000
--- a/tests/modules/meningotype/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: meningotype test_meningotype
-  command: nextflow run ./tests/modules/meningotype -entry test_meningotype -c ./tests/config/nextflow.config -c ./tests/modules/meningotype/nextflow.config
-  tags:
-    - meningotype
-  files:
-    - path: output/meningotype/test.tsv
-      md5sum: 25651bccb3d1c64cefcb7946fda30a6c
diff --git a/tests/modules/merqury/main.nf b/tests/modules/merqury/main.nf
deleted file mode 100644
index 9a12294bb7c..00000000000
--- a/tests/modules/merqury/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MERYL_COUNT    } from '../../../modules/meryl/count/main.nf'
-include { MERYL_UNIONSUM } from '../../../modules/meryl/unionsum/main.nf'
-include { MERQURY        } from '../../../modules/merqury/main.nf'
-
-workflow test_merqury {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    assembly = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    MERYL_COUNT ( input )
-    MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db )
-    MERQURY ( MERYL_UNIONSUM.out.meryl_db.join( Channel.value( assembly ) ) )
-}
diff --git a/tests/modules/merqury/test.yml b/tests/modules/merqury/test.yml
deleted file mode 100644
index ca73d7fbc9c..00000000000
--- a/tests/modules/merqury/test.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-- name: merqury test_merqury
-  command: nextflow run ./tests/modules/merqury -entry test_merqury -c ./tests/config/nextflow.config  -c ./tests/modules/merqury/nextflow.config
-  tags:
-    - merqury
-  files:
-    - path: output/merqury/genome_only.bed
-      md5sum: b611f22cde0e410a2ca07c1eefd042d3
-    - path: output/merqury/genome_only.wig
-      md5sum: 19cf44989af72af597ef80d3489b4882
-    - path: output/merqury/test.completeness.stats
-    - path: output/merqury/test.dist_only.hist
-      md5sum: e2e6b54b0febef1f0fcf24cd2afd0b7a
-    - path: output/merqury/test.genome.qv
-      md5sum: c554315aabcc4207c367805cf3090da3
-    - path: output/merqury/test.genome.spectra-cn.fl.png
-      md5sum: 3265701cbb1ddaed6d5cb6b4560564fd
-    - path: output/merqury/test.genome.spectra-cn.hist
-      md5sum: 6140a138ba47cb2b97814c93f80b2575
-    - path: output/merqury/test.genome.spectra-cn.ln.png
-      md5sum: 6386b604a8f0fbc43a1e3473ad9a779e
-    - path: output/merqury/test.genome.spectra-cn.st.png
-      md5sum: d5af80c91d23b182589b0ec131047f00
-    - path: output/merqury/test.qv
-      md5sum: 6e04952bc182221c8b9e242dc3298808
-    - path: output/merqury/test.spectra-asm.fl.png
-      md5sum: 60920481d988018a4f36a9be5b10c4ec
-    - path: output/merqury/test.spectra-asm.hist
-      md5sum: 541c9d1f87ab5c44df5e9e0acc440f8d
-    - path: output/merqury/test.spectra-asm.ln.png
-      md5sum: 54790dd54b5d8948d3676d32da1972df
-    - path: output/merqury/test.spectra-asm.st.png
-      md5sum: 010e013b5411ab2790e9a93ee70a574a
-    - path: output/merqury/test.unionsumdb.hist.ploidy
-      md5sum: f6904468b41a495c7ce255a7a5f3a302
diff --git a/tests/modules/merquryfk/katcomp/main.nf b/tests/modules/merquryfk/katcomp/main.nf
deleted file mode 100644
index 74d9a3ea2c9..00000000000
--- a/tests/modules/merquryfk/katcomp/main.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTK_FASTK as FASTK1 } from '../../../../modules/fastk/fastk/main.nf'
-include { FASTK_FASTK as FASTK2 } from '../../../../modules/fastk/fastk/main.nf'
-include { MERQURYFK_KATCOMP } from '../../../../modules/merquryfk/katcomp/main.nf'
-
-workflow test_merquryfk_katcomp_png {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK1 ( input )
-    FASTK2 ( input )
-    MERQURYFK_KATCOMP (
-        FASTK1.out.hist
-            .join( FASTK1.out.ktab )
-            .join( FASTK2.out.hist )
-            .join( FASTK2.out.ktab )
-    )
-}
-
-workflow test_merquryfk_katcomp_pdf {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK1 ( input )
-    FASTK2 ( input )
-    MERQURYFK_KATCOMP (
-        FASTK1.out.hist
-            .join( FASTK1.out.ktab )
-            .join( FASTK2.out.hist )
-            .join( FASTK2.out.ktab )
-    )
-}
diff --git a/tests/modules/merquryfk/katcomp/test.yml b/tests/modules/merquryfk/katcomp/test.yml
deleted file mode 100644
index 18a35462567..00000000000
--- a/tests/modules/merquryfk/katcomp/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: merquryfk katcomp test_merquryfk_katcomp_png
-  command: nextflow run ./tests/modules/merquryfk/katcomp -entry test_merquryfk_katcomp_png -c ./tests/config/nextflow.config  -c ./tests/modules/merquryfk/katcomp/nextflow.config
-  tags:
-    - merquryfk
-    - merquryfk/katcomp
-  files:
-    - path: output/merquryfk/test.fi.png
-      md5sum: 83b30d2f6103190887e66d3690c63d55
-    - path: output/merquryfk/test.ln.png
-      md5sum: 6d223a9b91937b1f984e3415fd1580bb
-    - path: output/merquryfk/test.st.png
-      md5sum: 00a851c8f1c7f2f5b8bb57c6f07b161c
-
-- name: merquryfk katcomp test_merquryfk_katcomp_pdf
-  command: nextflow run ./tests/modules/merquryfk/katcomp -entry test_merquryfk_katcomp_pdf -c ./tests/config/nextflow.config  -c ./tests/modules/merquryfk/katcomp/nextflow.config
-  tags:
-    - merquryfk
-    - merquryfk/katcomp
-  files:
-    - path: output/merquryfk/test.fi.pdf
-    - path: output/merquryfk/test.ln.pdf
-    - path: output/merquryfk/test.st.pdf
diff --git a/tests/modules/merquryfk/katgc/main.nf b/tests/modules/merquryfk/katgc/main.nf
deleted file mode 100644
index 4dbefab4568..00000000000
--- a/tests/modules/merquryfk/katgc/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTK_FASTK     } from '../../../../modules/fastk/fastk/main.nf'
-include { MERQURYFK_KATGC } from '../../../../modules/merquryfk/katgc/main.nf'
-
-workflow test_merquryfk_katgc_png {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-    MERQURYFK_KATGC ( FASTK_FASTK.out.hist
-        .join( FASTK_FASTK.out.ktab )
-    )
-}
-
-workflow test_merquryfk_katgc_pdf {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-    MERQURYFK_KATGC ( FASTK_FASTK.out.hist
-        .join( FASTK_FASTK.out.ktab )
-    )
-}
diff --git a/tests/modules/merquryfk/katgc/test.yml b/tests/modules/merquryfk/katgc/test.yml
deleted file mode 100644
index eb62940efa5..00000000000
--- a/tests/modules/merquryfk/katgc/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: merquryfk katgc test_merquryfk_katgc_png
-  command: nextflow run ./tests/modules/merquryfk/katgc -entry test_merquryfk_katgc_png -c ./tests/config/nextflow.config  -c ./tests/modules/merquryfk/katgc/nextflow.config
-  tags:
-    - merquryfk
-    - merquryfk/katgc
-  files:
-    - path: output/merquryfk/test.fi.png
-      md5sum: bd4cf549d5c8eaaba82f78010f652dac
-    - path: output/merquryfk/test.ln.png
-      md5sum: 3f55f27a486c9be6187d71e3a570beb5
-    - path: output/merquryfk/test.st.png
-      md5sum: 636339e17af69c4b64f27f36d66edcd8
-
-- name: merquryfk katgc test_merquryfk_katgc_pdf
-  command: nextflow run ./tests/modules/merquryfk/katgc -entry test_merquryfk_katgc_pdf -c ./tests/config/nextflow.config  -c ./tests/modules/merquryfk/katgc/nextflow.config
-  tags:
-    - merquryfk
-    - merquryfk/katgc
-  files:
-    - path: output/merquryfk/test.fi.pdf
-    - path: output/merquryfk/test.ln.pdf
-    - path: output/merquryfk/test.st.pdf
diff --git a/tests/modules/merquryfk/merquryfk/main.nf b/tests/modules/merquryfk/merquryfk/main.nf
deleted file mode 100644
index 99280374911..00000000000
--- a/tests/modules/merquryfk/merquryfk/main.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTK_FASTK         } from '../../../../modules/fastk/fastk/main.nf'
-include { MERQURYFK_MERQURYFK } from '../../../../modules/merquryfk/merquryfk/main.nf'
-
-workflow test_merquryfk_merquryfk_png {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    assembly = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-    MERQURYFK_MERQURYFK ( FASTK_FASTK.out.hist
-        .join( FASTK_FASTK.out.ktab )
-        .join( Channel.value( assembly ) )
-    )
-}
-
-workflow test_merquryfk_merquryfk_pdf {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    assembly = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-    MERQURYFK_MERQURYFK ( FASTK_FASTK.out.hist
-        .join( FASTK_FASTK.out.ktab )
-        .join( Channel.value( assembly ) )
-    )
-}
diff --git a/tests/modules/merquryfk/merquryfk/test.yml b/tests/modules/merquryfk/merquryfk/test.yml
deleted file mode 100644
index c52a302dbce..00000000000
--- a/tests/modules/merquryfk/merquryfk/test.yml
+++ /dev/null
@@ -1,47 +0,0 @@
-- name: merquryfk merquryfk test_merquryfk_merquryfk_png
-  command: nextflow run ./tests/modules/merquryfk/merquryfk -entry test_merquryfk_merquryfk_png -c ./tests/config/nextflow.config  -c ./tests/modules/merquryfk/merquryfk/nextflow.config
-  tags:
-    - merquryfk/merquryfk
-    - merquryfk
-  files:
-    - path: output/merquryfk/test.completeness.stats
-      md5sum: 797224fa75606bbda7f62caae7c9151c
-    - path: output/merquryfk/test.genome.qv
-      md5sum: 1e11be8abfa2230024042832f58f96f9
-    - path: output/merquryfk/test.genome.spectra-cn.fl.png
-      md5sum: 50bad6b85b8f80b8411b50e4119bc959
-    - path: output/merquryfk/test.genome.spectra-cn.ln.png
-      md5sum: 50bad6b85b8f80b8411b50e4119bc959
-    - path: output/merquryfk/test.genome.spectra-cn.st.png
-      md5sum: 50bad6b85b8f80b8411b50e4119bc959
-    - path: output/merquryfk/test.genome_only.bed
-      md5sum: 662d73e8a0019708feb538ec53c220f7
-    - path: output/merquryfk/test.qv
-      md5sum: 02b4d5c639ca706ff707bad89e29d90e
-    - path: output/merquryfk/test.spectra-asm.fl.png
-      md5sum: bb9ac38fe8991fbacbe791e562626d89
-    - path: output/merquryfk/test.spectra-asm.ln.png
-      md5sum: 48534a9d5e2ce9365eb1f0397c76f337
-    - path: output/merquryfk/test.spectra-asm.st.png
-      md5sum: 5e031a8b9ba2800e291721a11f4d9c00
-
-- name: merquryfk merquryfk test_merquryfk_merquryfk_pdf
-  command: nextflow run ./tests/modules/merquryfk/merquryfk -entry test_merquryfk_merquryfk_pdf -c ./tests/config/nextflow.config  -c ./tests/modules/merquryfk/merquryfk/nextflow.config
-  tags:
-    - merquryfk/merquryfk
-    - merquryfk
-  files:
-    - path: output/merquryfk/test.completeness.stats
-      md5sum: 797224fa75606bbda7f62caae7c9151c
-    - path: output/merquryfk/test.genome.qv
-      md5sum: 1e11be8abfa2230024042832f58f96f9
-    - path: output/merquryfk/test.genome.spectra-cn.fl.pdf
-    - path: output/merquryfk/test.genome.spectra-cn.ln.pdf
-    - path: output/merquryfk/test.genome.spectra-cn.st.pdf
-    - path: output/merquryfk/test.genome_only.bed
-      md5sum: 662d73e8a0019708feb538ec53c220f7
-    - path: output/merquryfk/test.qv
-      md5sum: 02b4d5c639ca706ff707bad89e29d90e
-    - path: output/merquryfk/test.spectra-asm.fl.pdf
-    - path: output/merquryfk/test.spectra-asm.ln.pdf
-    - path: output/merquryfk/test.spectra-asm.st.pdf
diff --git a/tests/modules/merquryfk/ploidyplot/main.nf b/tests/modules/merquryfk/ploidyplot/main.nf
deleted file mode 100644
index df582b98841..00000000000
--- a/tests/modules/merquryfk/ploidyplot/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTK_FASTK          } from '../../../../modules/fastk/fastk/main.nf'
-include { MERQURYFK_PLOIDYPLOT } from '../../../../modules/merquryfk/ploidyplot/main.nf'
-
-workflow test_merquryfk_ploidyplot_png {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-    MERQURYFK_PLOIDYPLOT ( FASTK_FASTK.out.hist
-        .join( FASTK_FASTK.out.ktab )
-    )
-}
-
-workflow test_merquryfk_ploidyplot_pdf {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    FASTK_FASTK ( input )
-    MERQURYFK_PLOIDYPLOT (
-        FASTK_FASTK.out.hist
-            .join( FASTK_FASTK.out.ktab )
-    )
-}
diff --git a/tests/modules/merquryfk/ploidyplot/test.yml b/tests/modules/merquryfk/ploidyplot/test.yml
deleted file mode 100644
index 5189f53dc3f..00000000000
--- a/tests/modules/merquryfk/ploidyplot/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: merquryfk ploidyplot test_merquryfk_ploidyplot_png
-  command: nextflow run ./tests/modules/merquryfk/ploidyplot -entry test_merquryfk_ploidyplot_png -c ./tests/config/nextflow.config  -c ./tests/modules/merquryfk/ploidyplot/nextflow.config
-  tags:
-    - merquryfk
-    - merquryfk/ploidyplot
-  files:
-    - path: output/merquryfk/test.fi.png
-      md5sum: c6f883f3d57ad64727219052e97d39b3
-    - path: output/merquryfk/test.ln.png
-      md5sum: bd299e2eceb258328d1a41c024d7fbf4
-    - path: output/merquryfk/test.st.png
-      md5sum: 4f858ed9712196606859675c3f3ba7a9
-
-- name: merquryfk ploidyplot test_merquryfk_ploidyplot_pdf
-  command: nextflow run ./tests/modules/merquryfk/ploidyplot -entry test_merquryfk_ploidyplot_pdf -c ./tests/config/nextflow.config  -c ./tests/modules/merquryfk/ploidyplot/nextflow.config
-  tags:
-    - merquryfk
-    - merquryfk/ploidyplot
-  files:
-    - path: output/merquryfk/test.fi.pdf
-    - path: output/merquryfk/test.ln.pdf
-    - path: output/merquryfk/test.st.pdf
diff --git a/tests/modules/meryl/count/main.nf b/tests/modules/meryl/count/main.nf
deleted file mode 100644
index 3c9a64c7ede..00000000000
--- a/tests/modules/meryl/count/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MERYL_COUNT } from '../../../../modules/meryl/count/main.nf'
-
-workflow test_meryl_count_single_end {
-
-    input = [
-        [ id:'test' , single_end: true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    MERYL_COUNT ( input )
-}
-
-workflow test_meryl_count_paired_end {
-
-    input = [
-        [ id:'test' , single_end: false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    MERYL_COUNT ( input )
-}
diff --git a/tests/modules/meryl/count/test.yml b/tests/modules/meryl/count/test.yml
deleted file mode 100644
index 6291a62f1ec..00000000000
--- a/tests/modules/meryl/count/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: meryl count test_meryl_count_single_end
-  command: nextflow run tests/modules/meryl/count -entry test_meryl_count_single_end -c tests/config/nextflow.config
-  tags:
-    - meryl/count
-    - meryl
-  files:
-    - path: output/meryl/versions.yml
-      md5sum: 5fe537d873925ccbcc4edf0983e9eda0
-
-- name: meryl count test_meryl_count_paired_end
-  command: nextflow run tests/modules/meryl/count -entry test_meryl_count_paired_end -c tests/config/nextflow.config
-  tags:
-    - meryl/count
-    - meryl
-  files:
-    - path: output/meryl/versions.yml
-      md5sum: 4961f13cfb60ba8764ed666e70dbf12c
diff --git a/tests/modules/meryl/histogram/main.nf b/tests/modules/meryl/histogram/main.nf
deleted file mode 100644
index 697a12efe1c..00000000000
--- a/tests/modules/meryl/histogram/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MERYL_COUNT     } from '../../../../modules/meryl/count/main.nf'
-include { MERYL_HISTOGRAM } from '../../../../modules/meryl/histogram/main.nf'
-
-workflow test_meryl_histogram {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    MERYL_COUNT ( input )
-    MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
-}
diff --git a/tests/modules/meryl/histogram/test.yml b/tests/modules/meryl/histogram/test.yml
deleted file mode 100644
index dce26b65d48..00000000000
--- a/tests/modules/meryl/histogram/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: meryl histogram test_meryl_histogram
-  command: nextflow run tests/modules/meryl/histogram -entry test_meryl_histogram -c tests/config/nextflow.config
-  tags:
-    - meryl/histogram
-    - meryl
-  files:
-    - path: output/meryl/test.hist
-      md5sum: 4bfdc8b287ee0cfd9922bbfa8cd64650
-    - path: output/meryl/versions.yml
-      md5sum: 050038f1b1df79977a393cce1b4b2ddb
diff --git a/tests/modules/meryl/unionsum/main.nf b/tests/modules/meryl/unionsum/main.nf
deleted file mode 100644
index 6dd40c82317..00000000000
--- a/tests/modules/meryl/unionsum/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MERYL_COUNT    } from '../../../../modules/meryl/count/main.nf'
-include { MERYL_UNIONSUM } from '../../../../modules/meryl/unionsum/main.nf'
-
-workflow test_meryl_unionsum_single_end {
-
-    input = [
-        [ id:'test', single_end: true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    MERYL_COUNT ( input )
-    MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db )
-}
-
-workflow test_meryl_unionsum_paired_end {
-
-    input = [
-        [ id:'test', single_end: false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    MERYL_COUNT ( input )
-    MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db )
-}
diff --git a/tests/modules/meryl/unionsum/test.yml b/tests/modules/meryl/unionsum/test.yml
deleted file mode 100644
index 10a1a155e4b..00000000000
--- a/tests/modules/meryl/unionsum/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: meryl unionsum test_meryl_unionsum_single_end
-  command: nextflow run tests/modules/meryl/unionsum -entry test_meryl_unionsum_single_end -c tests/config/nextflow.config
-  tags:
-    - meryl
-    - meryl/unionsum
-  files:
-    - path: output/meryl/versions.yml
-      md5sum: 7de859c6d3a29d72f6c9c976609d0913
-
-- name: meryl unionsum test_meryl_unionsum_paired_end
-  command: nextflow run tests/modules/meryl/unionsum -entry test_meryl_unionsum_paired_end -c tests/config/nextflow.config
-  tags:
-    - meryl
-    - meryl/unionsum
-  files:
-    - path: output/meryl/versions.yml
-      md5sum: a16decdec014ccb9bdab69a4a1d30818
diff --git a/tests/modules/metabat2/jgisummarizebamcontigdepths/main.nf b/tests/modules/metabat2/jgisummarizebamcontigdepths/main.nf
deleted file mode 100644
index 00309402134..00000000000
--- a/tests/modules/metabat2/jgisummarizebamcontigdepths/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
-
-workflow test_metabat2_jgisummarizebamcontigdepths {
-    
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input )
-}
diff --git a/tests/modules/metabat2/jgisummarizebamcontigdepths/test.yml b/tests/modules/metabat2/jgisummarizebamcontigdepths/test.yml
deleted file mode 100644
index 86c49d26f78..00000000000
--- a/tests/modules/metabat2/jgisummarizebamcontigdepths/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: metabat2 jgisummarizebamcontigdepths test_metabat2_jgisummarizebamcontigdepths
-  command: nextflow run ./tests/modules/metabat2/jgisummarizebamcontigdepths -entry test_metabat2_jgisummarizebamcontigdepths -c ./tests/config/nextflow.config -c ./tests/modules/metabat2/jgisummarizebamcontigdepths/nextflow.config
-  tags:
-    - metabat2/jgisummarizebamcontigdepths
-    - metabat2
-  files:
-    - path: output/metabat2/test.txt.gz
-      md5sum: 8f735aa408d6c90e5a0310e06ace7a9a
diff --git a/tests/modules/metabat2/metabat2/main.nf b/tests/modules/metabat2/metabat2/main.nf
deleted file mode 100644
index 0179e4c37ab..00000000000
--- a/tests/modules/metabat2/metabat2/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
-
-workflow test_metabat2_no_depth {
-
-    input_depth = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-    Channel.fromPath(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-        .map { it -> [[ id:'test', single_end:false ], it, []] }
-        .set { input_metabat2 }
-    
-    METABAT2_METABAT2 ( input_metabat2 )
-}
-
-workflow test_metabat2_depth {
-
-    input_depth = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
-
-    Channel.fromPath(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-        .map { it -> [[ id:'test', single_end:false ], it] }
-        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
-        .set { input_metabat2 }
-
-        METABAT2_METABAT2 ( input_metabat2 )
-}
diff --git a/tests/modules/metabat2/metabat2/test.yml b/tests/modules/metabat2/metabat2/test.yml
deleted file mode 100644
index 9389295ee21..00000000000
--- a/tests/modules/metabat2/metabat2/test.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-- name: metabat2 metabat2 test_metabat2_no_depth
-  command: nextflow run tests/modules/metabat2/metabat2 -entry test_metabat2_no_depth -c tests/config/nextflow.config
-  tags:
-    - metabat2
-    - metabat2/metabat2
-  files:
-    - path: output/metabat2/bins/test.1.fa.gz
-      md5sum: 0e9bce5b5a0033fd4411a21dec881170
-    - path: output/metabat2/test.tsv.gz
-    - path: output/metabat2/versions.yml
-      md5sum: 5742a71af36c3a748fd5726d76924ba8
-
-- name: metabat2 metabat2 test_metabat2_depth
-  command: nextflow run tests/modules/metabat2/metabat2 -entry test_metabat2_depth -c tests/config/nextflow.config
-  tags:
-    - metabat2
-    - metabat2/metabat2
-  files:
-    - path: output/metabat2/bins/test.1.fa.gz
-      md5sum: 0e9bce5b5a0033fd4411a21dec881170
-    - path: output/metabat2/test.tsv.gz
-    - path: output/metabat2/test.txt.gz
-    - path: output/metabat2/versions.yml
-      md5sum: 538c56b2df7d90580f05097218b5d5b1
diff --git a/tests/modules/metaphlan3/mergemetaphlantables/main.nf b/tests/modules/metaphlan3/mergemetaphlantables/main.nf
deleted file mode 100644
index 6a158d6ae2f..00000000000
--- a/tests/modules/metaphlan3/mergemetaphlantables/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR                           } from '../../../../modules/untar/main.nf'
-include { METAPHLAN3                      } from '../../../../modules/metaphlan3/metaphlan3/main.nf'
-include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../../../modules/metaphlan3/mergemetaphlantables/main.nf'
-
-workflow test_metaphlan3_mergemetaphlantables {
-
-    input = Channel.of(
-        [[ id:'test', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]],
-        [[ id:'test2', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]]
-    )
-
-    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
-
-    UNTAR ( db )
-    METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
-    METAPHLAN3_MERGEMETAPHLANTABLES ( METAPHLAN3.out.profile.map{ [[id:"test"], it[1]] }.groupTuple() )
-
-}
diff --git a/tests/modules/metaphlan3/mergemetaphlantables/test.yml b/tests/modules/metaphlan3/mergemetaphlantables/test.yml
deleted file mode 100644
index 57b69aa551a..00000000000
--- a/tests/modules/metaphlan3/mergemetaphlantables/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: metaphlan3 mergemetaphlantables test_metaphlan3_mergemetaphlantables
-  command: nextflow run ./tests/modules/metaphlan3/mergemetaphlantables -entry test_metaphlan3_mergemetaphlantables -c ./tests/config/nextflow.config  -c ./tests/modules/metaphlan3/mergemetaphlantables/nextflow.config
-  tags:
-    - metaphlan3/mergemetaphlantables
-    - metaphlan3
-  files:
-    - path: output/metaphlan3/test.txt
-      contains: ["clade_name	NCBI_tax_id"]
diff --git a/tests/modules/metaphlan3/metaphlan3/main.nf b/tests/modules/metaphlan3/metaphlan3/main.nf
deleted file mode 100644
index 524936ae9d5..00000000000
--- a/tests/modules/metaphlan3/metaphlan3/main.nf
+++ /dev/null
@@ -1,66 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR                 } from '../../../../modules/untar/main.nf'
-include { METAPHLAN3_METAPHLAN3 } from '../../../../modules/metaphlan3/metaphlan3/main.nf'
-
-workflow test_metaphlan3_single_end {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
-
-    UNTAR ( db )
-    METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
-}
-
-workflow test_metaphlan3_single_end_nodb {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    UNTAR ( db )
-    METAPHLAN3_METAPHLAN3 ( input, [] )
-}
-
-workflow test_metaphlan3_paired_end {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
-
-    UNTAR ( db )
-    METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
-}
-
-workflow test_metaphlan3_sam {
-
-    input = [ [ id:'test'], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
-            ]
-
-    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
-
-    UNTAR ( db )
-    SAMTOOLS_VIEW ( input, [] )
-    METAPHLAN3_METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar.map{ it[1] } )
-}
-
-workflow test_metaphlan3_fasta {
-
-    input = [ [ id:'test', single_end:true], // meta map
-              [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-            ]
-
-    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
-
-    UNTAR ( db )
-    METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
-}
diff --git a/tests/modules/metaphlan3/metaphlan3/test.yml b/tests/modules/metaphlan3/metaphlan3/test.yml
deleted file mode 100644
index 7d7039d7cdd..00000000000
--- a/tests/modules/metaphlan3/metaphlan3/test.yml
+++ /dev/null
@@ -1,123 +0,0 @@
-- name: metaphlan3 test_metaphlan3_single_end
-  command: nextflow run ./tests/modules/metaphlan3/metaphlan3 -entry test_metaphlan3_single_end -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/metaphlan3/nextflow.config
-  tags:
-    - metaphlan3
-  files:
-    - path: output/metaphlan3/test.biom
-      contains:
-        - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"'
-    - path: output/metaphlan3/test.bowtie2out.txt
-      md5sum: ef46a9c6a8ce9cae26fbfd5527116fd5
-    - path: output/metaphlan3/test_profile.txt
-      md5sum: 72d40ee2304c162f3c165e1e578ed152
-    - path: output/untar/metaphlan_database/mpa_latest
-      md5sum: b1337362f607000384563a56a6ff4790
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.1.bt2
-      md5sum: d52a98fe273742ade7c744b819a7c5c1
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.2.bt2
-      md5sum: b14cc7faf3a4fae792160c917aebfe03
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.3.bt2
-      md5sum: 1bca5df879f2c6fad0c54984d0651bfb
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.4.bt2
-      md5sum: 249ee1c672d52d50cee41cb94b6adc42
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.fasta
-      md5sum: d3efe201c9eb449e877ead36656abf5f
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.pkl
-      md5sum: b208bb15eaef50d91cc7d5e35a1518ee
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
-      md5sum: ed05be063280e8629193e52903b07591
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
-      md5sum: 1ca16b905abf657b88ca2bc12e7ad404
-
-- name: metaphlan3 test_metaphlan3_paired_end
-  command: nextflow run ./tests/modules/metaphlan3/metaphlan3 -entry test_metaphlan3_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/metaphlan3/nextflow.config
-  tags:
-    - metaphlan3
-  files:
-    - path: output/metaphlan3/test.biom
-      contains:
-        - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"'
-    - path: output/metaphlan3/test.bowtie2out.txt
-      md5sum: ce11486fcc0e68fe7152867a3634e09a
-    - path: output/metaphlan3/test_profile.txt
-      md5sum: fcf99fec08ee00db6ef2c12fb93bc14b
-    - path: output/untar/metaphlan_database/mpa_latest
-      md5sum: b1337362f607000384563a56a6ff4790
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.1.bt2
-      md5sum: d52a98fe273742ade7c744b819a7c5c1
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.2.bt2
-      md5sum: b14cc7faf3a4fae792160c917aebfe03
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.3.bt2
-      md5sum: 1bca5df879f2c6fad0c54984d0651bfb
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.4.bt2
-      md5sum: 249ee1c672d52d50cee41cb94b6adc42
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.fasta
-      md5sum: d3efe201c9eb449e877ead36656abf5f
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.pkl
-      md5sum: b208bb15eaef50d91cc7d5e35a1518ee
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
-      md5sum: ed05be063280e8629193e52903b07591
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
-      md5sum: 1ca16b905abf657b88ca2bc12e7ad404
-
-- name: metaphlan3 test_metaphlan3_sam
-  command: nextflow run ./tests/modules/metaphlan3/metaphlan3 -entry test_metaphlan3_sam -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/metaphlan3/nextflow.config
-  tags:
-    - metaphlan3
-  files:
-    - path: output/metaphlan3/test.biom
-      contains:
-        - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"'
-    - path: output/metaphlan3/test_profile.txt
-      md5sum: e050d49f7df8a23617880ef9ed7745a0
-    - path: output/samtools/test.sam.bam
-      md5sum: 1d5be3c91979ead358e3980e3e7c9acf
-    - path: output/untar/metaphlan_database/mpa_latest
-      md5sum: b1337362f607000384563a56a6ff4790
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.1.bt2
-      md5sum: d52a98fe273742ade7c744b819a7c5c1
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.2.bt2
-      md5sum: b14cc7faf3a4fae792160c917aebfe03
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.3.bt2
-      md5sum: 1bca5df879f2c6fad0c54984d0651bfb
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.4.bt2
-      md5sum: 249ee1c672d52d50cee41cb94b6adc42
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.fasta
-      md5sum: d3efe201c9eb449e877ead36656abf5f
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.pkl
-      md5sum: b208bb15eaef50d91cc7d5e35a1518ee
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
-      md5sum: ed05be063280e8629193e52903b07591
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
-      md5sum: 1ca16b905abf657b88ca2bc12e7ad404
-
-- name: metaphlan3 test_metaphlan3_fasta
-  command: nextflow run ./tests/modules/metaphlan3/metaphlan3 -entry test_metaphlan3_fasta -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/metaphlan3/nextflow.config
-  tags:
-    - metaphlan3
-  files:
-    - path: output/metaphlan3/test.biom
-      contains:
-        - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"'
-    - path: output/metaphlan3/test.bowtie2out.txt
-      md5sum: fece494a410b8328608a11de10af6396
-    - path: output/metaphlan3/test_profile.txt
-      md5sum: d148c4203e5a9d59f5eea57207e40769
-    - path: output/untar/metaphlan_database/mpa_latest
-      md5sum: b1337362f607000384563a56a6ff4790
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.1.bt2
-      md5sum: d52a98fe273742ade7c744b819a7c5c1
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.2.bt2
-      md5sum: b14cc7faf3a4fae792160c917aebfe03
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.3.bt2
-      md5sum: 1bca5df879f2c6fad0c54984d0651bfb
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.4.bt2
-      md5sum: 249ee1c672d52d50cee41cb94b6adc42
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.fasta
-      md5sum: d3efe201c9eb449e877ead36656abf5f
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.pkl
-      md5sum: b208bb15eaef50d91cc7d5e35a1518ee
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
-      md5sum: ed05be063280e8629193e52903b07591
-    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
-      md5sum: 1ca16b905abf657b88ca2bc12e7ad404
diff --git a/tests/modules/methyldackel/extract/main.nf b/tests/modules/methyldackel/extract/main.nf
deleted file mode 100644
index 92f923087d9..00000000000
--- a/tests/modules/methyldackel/extract/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { METHYLDACKEL_EXTRACT } from '../../../../modules/methyldackel/extract/main.nf'
-
-workflow test_methyldackel_extract {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true) ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    METHYLDACKEL_EXTRACT ( input, fasta, fai )
-}
diff --git a/tests/modules/methyldackel/extract/test.yml b/tests/modules/methyldackel/extract/test.yml
deleted file mode 100644
index 28f969f33b8..00000000000
--- a/tests/modules/methyldackel/extract/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: methyldackel extract
-  command: nextflow run ./tests/modules/methyldackel/extract -entry test_methyldackel_extract -c ./tests/config/nextflow.config -c ./tests/modules/methyldackel/extract/nextflow.config
-  tags:
-    - methyldackel
-    - methyldackel/extract
-  files:
-    - path: output/methyldackel/test.paired_end.methylated.sorted_CpG.bedGraph
-      md5sum: abcc9d1db6e48d5aced567c337b563d4
diff --git a/tests/modules/methyldackel/mbias/main.nf b/tests/modules/methyldackel/mbias/main.nf
deleted file mode 100644
index f304e22fb08..00000000000
--- a/tests/modules/methyldackel/mbias/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { METHYLDACKEL_MBIAS } from '../../../../modules/methyldackel/mbias/main.nf'
-
-workflow test_methyldackel_mbias {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true) ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    METHYLDACKEL_MBIAS ( input, fasta, fai )
-}
diff --git a/tests/modules/methyldackel/mbias/test.yml b/tests/modules/methyldackel/mbias/test.yml
deleted file mode 100644
index 8bb23f24e63..00000000000
--- a/tests/modules/methyldackel/mbias/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: methyldackel mbias
-  command: nextflow run ./tests/modules/methyldackel/mbias -entry test_methyldackel_mbias -c ./tests/config/nextflow.config -c ./tests/modules/methyldackel/mbias/nextflow.config
-  tags:
-    - methyldackel
-    - methyldackel/mbias
-  files:
-    - path: output/methyldackel/test.mbias.txt
-      md5sum: 357bb944dc2cdffcc47fa0d34376e016
diff --git a/tests/modules/minia/main.nf b/tests/modules/minia/main.nf
deleted file mode 100644
index 5be4d17f129..00000000000
--- a/tests/modules/minia/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MINIA } from '../../../modules/minia/main.nf'
-
-workflow test_minia {
-    input = [ [ id:'test' ], // meta map
-              [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
-            ]
-
-    MINIA ( input )
-}
diff --git a/tests/modules/minia/test.yml b/tests/modules/minia/test.yml
deleted file mode 100644
index 78b84f37571..00000000000
--- a/tests/modules/minia/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: minia
-  command: nextflow run ./tests/modules/minia -entry test_minia -c ./tests/config/nextflow.config -c ./tests/modules/minia/nextflow.config
-  tags:
-    - minia
-  files:
-    - path: output/minia/test.h5
-    - path: output/minia/test.contigs.fa
-    - path: output/minia/test.unitigs.fa
diff --git a/tests/modules/miniasm/main.nf b/tests/modules/miniasm/main.nf
deleted file mode 100644
index 949660acb9d..00000000000
--- a/tests/modules/miniasm/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MINIASM } from '../../../modules/miniasm/main.nf'
-
-workflow test_miniasm {
-    
-    input = [ [ id:'test', single_end:true ], // meta map
-             file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true),
-             file(params.test_data['bacteroides_fragilis']['nanopore']['overlap_paf'], checkIfExists: true)
-            ]
-    
-    MINIASM ( input )
-}
diff --git a/tests/modules/miniasm/test.yml b/tests/modules/miniasm/test.yml
deleted file mode 100644
index 0bdc350af8a..00000000000
--- a/tests/modules/miniasm/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: miniasm test_miniasm
-  command: nextflow run ./tests/modules/miniasm -entry test_miniasm -c ./tests/config/nextflow.config -c ./tests/modules/miniasm/nextflow.config
-  tags:
-    - miniasm
-  files:
-    - path: output/miniasm/test.assembly.gfa.gz
-      md5sum: c68e4c2b64338d1c0f5b79b32934da14
-    - path: output/miniasm/test.assembly.fasta.gz
-      md5sum: d2f78ae618c02744e7a57bf4706ab8b4
diff --git a/tests/modules/minimap2/align/main.nf b/tests/modules/minimap2/align/main.nf
deleted file mode 100644
index ee6c083885c..00000000000
--- a/tests/modules/minimap2/align/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MINIMAP2_ALIGN } from '../../../../modules/minimap2/align/main.nf'
-
-workflow test_minimap2_align_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    bam_format = true
-    cigar_paf_format = false
-    cigar_bam = false
-
-    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam)
-}
-
-workflow test_minimap2_align_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    bam_format  = true
-    cigar_paf_format = false
-    cigar_bam = false
-
-    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam )
-}
diff --git a/tests/modules/minimap2/align/test.yml b/tests/modules/minimap2/align/test.yml
deleted file mode 100644
index c392e3132a6..00000000000
--- a/tests/modules/minimap2/align/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: minimap2 align test_minimap2_align_single_end
-  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
-  tags:
-    - minimap2
-    - minimap2/align
-  files:
-    - path: output/minimap2/test.bam
-    - path: output/minimap2/versions.yml
-
-- name: minimap2 align test_minimap2_align_paired_end
-  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
-  tags:
-    - minimap2
-    - minimap2/align
-  files:
-    - path: output/minimap2/test.bam
-    - path: output/minimap2/versions.yml
diff --git a/tests/modules/minimap2/index/main.nf b/tests/modules/minimap2/index/main.nf
deleted file mode 100644
index 8eb515696d5..00000000000
--- a/tests/modules/minimap2/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MINIMAP2_INDEX } from '../../../../modules/minimap2/index/main.nf'
-
-workflow test_minimap2_index {
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    MINIMAP2_INDEX ( [ [id:'test'], fasta ] )
-}
diff --git a/tests/modules/minimap2/index/test.yml b/tests/modules/minimap2/index/test.yml
deleted file mode 100644
index 9570045276b..00000000000
--- a/tests/modules/minimap2/index/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: minimap2 index
-  command: nextflow run ./tests/modules/minimap2/index -entry test_minimap2_index -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/index/nextflow.config
-  tags:
-    - minimap2
-    - minimap2/index
-  files:
-    - path: ./output/minimap2/genome.mmi
-      md5sum: 72e450f12dc691e763c697463bdb1571
diff --git a/tests/modules/mlst/main.nf b/tests/modules/mlst/main.nf
deleted file mode 100644
index f84ec622dee..00000000000
--- a/tests/modules/mlst/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MLST } from '../../../modules/mlst/main.nf'
-
-workflow test_mlst {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("https://raw.githubusercontent.com/nf-core/test-datasets/bactmap/genome/NCTC13799.fna", checkIfExists: true) ]
-
-    MLST ( input )
-}
diff --git a/tests/modules/mlst/test.yml b/tests/modules/mlst/test.yml
deleted file mode 100644
index 53eacc5a957..00000000000
--- a/tests/modules/mlst/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: mlst test_mlst
-  command: nextflow run ./tests/modules/mlst -entry test_mlst -c ./tests/config/nextflow.config -c ./tests/modules/mlst/nextflow.config
-  tags:
-    - mlst
-  files:
-    - path: output/mlst/test.tsv
-      md5sum: b52df6178834a156c9402012718eb65e
diff --git a/tests/modules/mobsuite/recon/main.nf b/tests/modules/mobsuite/recon/main.nf
deleted file mode 100644
index 0d18ef9cd51..00000000000
--- a/tests/modules/mobsuite/recon/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MOBSUITE_RECON } from '../../../../modules/mobsuite/recon/main.nf'
-
-workflow test_mobsuite_recon {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    MOBSUITE_RECON ( input )
-}
diff --git a/tests/modules/mobsuite/recon/test.yml b/tests/modules/mobsuite/recon/test.yml
deleted file mode 100644
index dfff835b94c..00000000000
--- a/tests/modules/mobsuite/recon/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: mobsuite recon test_mobsuite_recon
-  command: nextflow run tests/modules/mobsuite/recon -entry test_mobsuite_recon -c tests/config/nextflow.config
-  tags:
-    - mobsuite/recon
-    - mobsuite
-  files:
-    - path: output/mobsuite/results/chromosome.fasta
-      md5sum: 33b2a0fa321c73c6ba8d8272dd53c6d4
-    - path: output/mobsuite/results/contig_report.txt
-      md5sum: a0ae364a9f2b475f77588d0b3c24b857
-    - path: output/mobsuite/versions.yml
-      md5sum: 7f7a0f8957394b0e526233a0edb8e20a
diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/mosdepth/main.nf
deleted file mode 100644
index 1bb8e8ff5cf..00000000000
--- a/tests/modules/mosdepth/main.nf
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MOSDEPTH                       } from '../../../modules/mosdepth/main.nf'
-include { MOSDEPTH as MOSDEPTH_FAIL      } from '../../../modules/mosdepth/main.nf'
-include { MOSDEPTH as MOSDEPTH_WINDOW    } from '../../../modules/mosdepth/main.nf'
-include { MOSDEPTH as MOSDEPTH_THRESHOLD } from '../../../modules/mosdepth/main.nf'
-include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../modules/mosdepth/main.nf'
-
-workflow test_mosdepth {
-    input = [
-        [ id:'test', single_end:true ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-
-    MOSDEPTH ( input, [], [] )
-}
-
-workflow test_mosdepth_bed {
-    input = [
-        [ id:'test', single_end:true ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-
-    MOSDEPTH ( input, bed, [] )
-}
-
-workflow test_mosdepth_cram {
-    input = [
-        [ id:'test', single_end:true ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    MOSDEPTH ( input, [], fasta )
-}
-
-workflow test_mosdepth_cram_bed {
-    input  = [
-        [ id:'test', single_end:true ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
-    ]
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    MOSDEPTH ( input, bed, fasta )
-}
-
-workflow test_mosdepth_window {
-    input = [
-        [ id:'test', single_end:true ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-
-    MOSDEPTH_WINDOW ( input, [], [] )
-}
-
-workflow test_mosdepth_quantized {
-    input = [
-        [ id:'test', single_end:true ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-
-    MOSDEPTH_QUANTIZED ( input, [], [] )
-}
-
-workflow test_mosdepth_thresholds {
-    input = [
-        [ id:'test', single_end:true ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-
-    MOSDEPTH_THRESHOLD ( input, bed, [] )
-}
-
-workflow test_mosdepth_fail {
-    input = [
-        [ id:'test', single_end:true ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-
-    MOSDEPTH_FAIL ( input, bed, [] )
-}
diff --git a/tests/modules/mosdepth/test.yml b/tests/modules/mosdepth/test.yml
deleted file mode 100644
index 8efadb9d056..00000000000
--- a/tests/modules/mosdepth/test.yml
+++ /dev/null
@@ -1,135 +0,0 @@
-- name: mosdepth test_mosdepth
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
-  tags:
-    - mosdepth
-  files:
-    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 4f0d231060cbde4efdd673863bd2fb59
-    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
-
-- name: mosdepth test_mosdepth_bed
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
-  tags:
-    - mosdepth
-  files:
-    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.region.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 96c037f769974b904beb53edc4f56d82
-    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
-    - path: output/mosdepth/test.regions.bed.gz
-      md5sum: 5d398caf7171ec4406278e2add3009ae
-    - path: output/mosdepth/test.regions.bed.gz.csi
-      md5sum: 47669cfe41f3e222e74d81e1b1be191f
-
-- name: mosdepth test_mosdepth_cram
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_cram -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
-  tags:
-    - mosdepth
-  files:
-    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 4f0d231060cbde4efdd673863bd2fb59
-    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
-
-- name: mosdepth test_mosdepth_cram_bed
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_cram_bed -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
-  tags:
-    - mosdepth
-  files:
-    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.region.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 96c037f769974b904beb53edc4f56d82
-    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
-    - path: output/mosdepth/test.regions.bed.gz
-      md5sum: 5d398caf7171ec4406278e2add3009ae
-    - path: output/mosdepth/test.regions.bed.gz.csi
-      md5sum: 47669cfe41f3e222e74d81e1b1be191f
-
-- name: mosdepth test_mosdepth_window
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
-  tags:
-    - mosdepth
-  files:
-    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.region.dist.txt
-      md5sum: 39e0e707ec32feb5176fd20a95f1f468
-    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 96c037f769974b904beb53edc4f56d82
-    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
-    - path: output/mosdepth/test.regions.bed.gz
-      md5sum: f02e2cb49cc050e13d76942d6960827a
-    - path: output/mosdepth/test.regions.bed.gz.csi
-      md5sum: 257d67678136963d9dd904330079609d
-
-- name: mosdepth test_mosdepth_quantized
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_quantized -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
-  tags:
-    - mosdepth
-  files:
-    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 4f0d231060cbde4efdd673863bd2fb59
-    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
-    - path: output/mosdepth/test.quantized.bed.gz
-      md5sum: 3e434a8bafcf59a67841ae3d4d752838
-    - path: output/mosdepth/test.quantized.bed.gz.csi
-      md5sum: be9617f551f19a33923f1e886eaefb93
-
-- name: mosdepth test_mosdepth_thresholds
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_thresholds -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
-  tags:
-    - mosdepth
-  files:
-    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.region.dist.txt
-      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 96c037f769974b904beb53edc4f56d82
-    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
-    - path: output/mosdepth/test.regions.bed.gz
-      md5sum: 5d398caf7171ec4406278e2add3009ae
-    - path: output/mosdepth/test.regions.bed.gz.csi
-      md5sum: 47669cfe41f3e222e74d81e1b1be191f
-    - path: output/mosdepth/test.thresholds.bed.gz
-      md5sum: 13101e326eea3cbfa1d569b69f494f4c
-    - path: output/mosdepth/test.thresholds.bed.gz.csi
-      md5sum: 912055ee9452229439df6fae95644196
-
-- name: mosdepth test_mosdepth_fail
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_fail -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
-  tags:
-    - mosdepth
-  exit_code: 1
diff --git a/tests/modules/motus/downloaddb/main.nf b/tests/modules/motus/downloaddb/main.nf
deleted file mode 100644
index f7680ca953f..00000000000
--- a/tests/modules/motus/downloaddb/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf'
-
-workflow test_motus_downloaddb {
-
-    input = file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py')
-
-    MOTUS_DOWNLOADDB ( input )
-}
diff --git a/tests/modules/motus/downloaddb/test.yml b/tests/modules/motus/downloaddb/test.yml
deleted file mode 100644
index e61f937f045..00000000000
--- a/tests/modules/motus/downloaddb/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: motus downloaddb test_motus_downloaddb
-  command: nextflow run tests/modules/motus/downloaddb -entry test_motus_downloaddb -c tests/config/nextflow.config
-  tags:
-    - motus
-    - motus/downloaddb
-  files:
-    - path: output/motus/db_mOTU/db_mOTU_versions
diff --git a/tests/modules/motus/merge/main.nf b/tests/modules/motus/merge/main.nf
deleted file mode 100644
index bb1b71500e7..00000000000
--- a/tests/modules/motus/merge/main.nf
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MOTUS_DOWNLOADDB                } from '../../../../modules/motus/downloaddb/main.nf'
-include { MOTUS_PROFILE                   } from '../../../../modules/motus/profile/main.nf'
-include { MOTUS_MERGE                     } from '../../../../modules/motus/merge/main.nf'
-include { MOTUS_MERGE as MOTUS_MERGE_BIOM } from '../../../../modules/motus/merge/main.nf'
-
-workflow test_motus_merge {
-
-    input = Channel.fromList(
-        [
-            [
-                [ id:'test', single_end:true ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ],
-            [
-                [ id:'test2', single_end:true ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ]
-        ]
-    )
-
-    MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') )
-    MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db )
-    MOTUS_MERGE ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first() )
-
-}
-
-workflow test_motus_merge_biom {
-
-    input = Channel.fromList(
-        [
-            [
-                [ id:'test', single_end:true ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ],
-            [
-                [ id:'test2', single_end:true ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ]
-        ]
-    )
-
-    MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') )
-    MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db )
-    MOTUS_MERGE_BIOM ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first() )
-
-}
-
diff --git a/tests/modules/motus/merge/test.yml b/tests/modules/motus/merge/test.yml
deleted file mode 100644
index 5c8845020ef..00000000000
--- a/tests/modules/motus/merge/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: motus merge test_motus_merge
-  command: nextflow run ./tests/modules/motus/merge -entry test_motus_merge -c ./tests/config/nextflow.config  -c ./tests/modules/motus/merge/nextflow.config
-  tags:
-    - motus
-    - motus/merge
-  files:
-    - path: output/motus/test.txt
-      contains:
-        - "consensus_taxonomy"
-
-- name: motus merge test_motus_merge_biom
-  command: nextflow run ./tests/modules/motus/merge -entry test_motus_merge_biom -c ./tests/config/nextflow.config  -c ./tests/modules/motus/merge/nextflow.config
-  tags:
-    - motus
-    - motus/merge
-  files:
-    - path: output/motus/test.biom
-      contains:
-        - "Biological Observation Matrix 1.0.0"
diff --git a/tests/modules/motus/profile/main.nf b/tests/modules/motus/profile/main.nf
deleted file mode 100644
index 068ef6cfde1..00000000000
--- a/tests/modules/motus/profile/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf'
-include { MOTUS_PROFILE    } from '../../../../modules/motus/profile/main.nf'
-
-workflow test_motus_profile_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
-
-    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db )
-}
-
diff --git a/tests/modules/motus/profile/test.yml b/tests/modules/motus/profile/test.yml
deleted file mode 100644
index f5ce5bf7735..00000000000
--- a/tests/modules/motus/profile/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: motus profile test_motus_profile_single_end
-  command: nextflow run tests/modules/motus/profile -entry test_motus_profile_single_end -c tests/config/nextflow.config
-  tags:
-    - motus
-    - motus/profile
-  files:
-    - path: output/motus/test.out
-      contains: ["#consensus_taxonomy\ttest"]
-    - path: output/motus/test.log
-      contains: ["Finished computation"]
diff --git a/tests/modules/msisensor/msi/main.nf b/tests/modules/msisensor/msi/main.nf
deleted file mode 100644
index 259ec8870fb..00000000000
--- a/tests/modules/msisensor/msi/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MSISENSOR_SCAN } from '../../../../modules/msisensor/scan/main.nf'
-include { MSISENSOR_MSI } from '../../../../modules/msisensor/msi/main.nf'
-
-workflow test_msisensor_msi {
-
-    def scaninput  = []
-    scaninput = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-    scan = MSISENSOR_SCAN ( scaninput )
-
-    // IMPERFECT TEST:
-    // USING SARS-COV2 DATA AS NORMAL:TUMOR PAIR THIS WILL SUFFICE TO
-    // TEST MODULE EXECUTION, BUT NOT FUNCTIONALITY.
-    // FUNCTIONALITY HAS BEEN TESTED MANUALY USING AUTHOR-PROVIDED TEST
-    // DATA (https://github.com/ding-lab/msisensor/tree/master/test)
-    def input      = []
-
-    input = Channel.from([ [ id:'test', single_end:false ], // meta map
-               file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'],     checkIfExists: true),
-               file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
-               file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'],         checkIfExists: true),
-               file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'],     checkIfExists: true) ])
-    //scan.txt.view()
-    input.concat(scan.txt).collect().view()
-    // BIT CLUMSY:
-    MSISENSOR_MSI ( input.concat(scan.txt).collect() )
-}
diff --git a/tests/modules/msisensor/msi/test.yml b/tests/modules/msisensor/msi/test.yml
deleted file mode 100644
index 0d0da1ee002..00000000000
--- a/tests/modules/msisensor/msi/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: msisensor msi
-  command: nextflow run ./tests/modules/msisensor/msi -entry test_msisensor_msi -c ./tests/config/nextflow.config -c ./tests/modules/msisensor/msi/nextflow.config
-  tags:
-    - msisensor
-    - msisensor/msi
-  files:
-    - path: output/msisensor/test
-      md5sum: a3290f7539dbbf83777e8590156c0e28
-    - path: output/msisensor/test_dis
-      md5sum: 060a3fc3701f3b10f6b19da9b21a32b7
-    - path: output/msisensor/test_germline
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/msisensor/test_somatic
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/msisensor/scan/main.nf b/tests/modules/msisensor/scan/main.nf
deleted file mode 100644
index de46dd9b524..00000000000
--- a/tests/modules/msisensor/scan/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MSISENSOR_SCAN } from '../../../../modules/msisensor/scan/main.nf'
-
-workflow test_msisensor_scan {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
-
-    MSISENSOR_SCAN ( input )
-}
diff --git a/tests/modules/msisensor/scan/test.yml b/tests/modules/msisensor/scan/test.yml
deleted file mode 100644
index 9e697a590c4..00000000000
--- a/tests/modules/msisensor/scan/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: msisensor scan
-  command: nextflow run ./tests/modules/msisensor/scan -entry test_msisensor_scan -c ./tests/config/nextflow.config -c ./tests/modules/msisensor/scan/nextflow.config
-  tags:
-    - msisensor
-    - msisensor/scan
-  files:
-    - path: output/msisensor/test.msisensor_scan.tab
-      md5sum: b7ae85acdcfc1a51e867ab3446d6fb59
diff --git a/tests/modules/msisensor2/msi/main.nf b/tests/modules/msisensor2/msi/main.nf
deleted file mode 100644
index 6105af62bbd..00000000000
--- a/tests/modules/msisensor2/msi/main.nf
+++ /dev/null
@@ -1,84 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MSISENSOR2_SCAN } from '../../../../modules/msisensor2/scan/main.nf'
-include { MSISENSOR2_MSI } from '../../../../modules/msisensor2/msi/main.nf'
-
-workflow test_msisensor2_msi_tumor_only {
-
-    reference = [
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    MSISENSOR2_SCAN ( reference, "outputfile" )
-
-    input = [
-        [ id:'test' ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        [],
-        [],
-        [],
-    ]
-
-    MSISENSOR2_MSI ( input, MSISENSOR2_SCAN.out.scan, [] )
-}
-
-
-workflow test_msisensor2_msi_tumor_normal {
-
-    reference = [
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    MSISENSOR2_SCAN ( reference, "outputfile" )
-
-    input = [
-        [ id:'test' ],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
-        [],
-    ]
-
-    MSISENSOR2_MSI ( input, MSISENSOR2_SCAN.out.scan, [] )
-}
-
-workflow test_msisensor2_msi_tumor_only_ml {
-
-    input = [
-        [ id:'test' ],
-        file('https://github.com/niu-lab/msisensor2/raw/master/test/example.tumor.only.hg19.bam', checkIfExists: true),
-        file('https://github.com/niu-lab/msisensor2/raw/master/test/example.tumor.only.hg19.bam.bai', checkIfExists: true),
-        [],
-        [],
-        [],
-    ]
-
-    models = Channel.fromPath(
-        [
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/016a16e12aca2bdba3713a3be76f72cd",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/02d42c2bda19aac304d6e86390c7f328",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/1030c0aa35ca5c263daeae866ad18632",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/15c3f5ec1c020d8f44283e40a2d9b6bb",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/15d6012f9a234b7adbbeecec524aea7d",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/2cf9a58f57e78b88acd86d792fe6a7b3",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/3ba04410c7ccbfc33e8b1b11d8132ae9",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/4431c9dc08be932c460a9e67192e7c57",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/4f5fa7bed97b48093375222d242fc982",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/71e6c0d59ea09d2a7acc566560841e34",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/8144b15900bba7086e86b31a0e1f8cfd",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/9bf6f7a544f369c3262a3a6f72cfdd7b",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/b8a36f2274b33cb0ed932e85cd1ddd5a",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/c08f164ded323a8c2606c408c555d73d",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/ceaa36ddbb76dc6eb6199ed946945788",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/e05d5da7208a924762311eddc4ec96c0",
-            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/f8a20acf51ccb2b0ce6af42f24a8b5ef",
-        ],
-        checkIfExists: true
-    )
-
-    MSISENSOR2_MSI ( input, [], models.collect() )
-}
diff --git a/tests/modules/msisensor2/msi/test.yml b/tests/modules/msisensor2/msi/test.yml
deleted file mode 100644
index c59128b38bf..00000000000
--- a/tests/modules/msisensor2/msi/test.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-- name: msisensor2 msi test_msisensor2_msi_tumor_only
-  command: nextflow run ./tests/modules/msisensor2/msi -entry test_msisensor2_msi_tumor_only -c ./tests/config/nextflow.config  -c ./tests/modules/msisensor2/msi/nextflow.config
-  tags:
-    - msisensor2
-    - msisensor2/msi
-  files:
-    - path: output/msisensor2/outputfile
-      md5sum: b1fa373ada56fd5027b705d5e2faa374
-    - path: output/msisensor2/test
-      md5sum: a3290f7539dbbf83777e8590156c0e28
-    - path: output/msisensor2/test_dis
-      md5sum: 236e814ddeb95e21a17b48250f92250d
-    - path: output/msisensor2/test_somatic
-
-- name: msisensor2 msi test_msisensor2_msi_tumor_normal
-  command: nextflow run ./tests/modules/msisensor2/msi -entry test_msisensor2_msi_tumor_normal -c ./tests/config/nextflow.config  -c ./tests/modules/msisensor2/msi/nextflow.config
-  tags:
-    - msisensor2
-    - msisensor2/msi
-  files:
-    - path: output/msisensor2/outputfile
-      md5sum: b1fa373ada56fd5027b705d5e2faa374
-    - path: output/msisensor2/test
-      md5sum: a3290f7539dbbf83777e8590156c0e28
-    - path: output/msisensor2/test_dis
-      md5sum: d47b22c13092707ed64645f118e82cc1
-    - path: output/msisensor2/test_somatic
-
-- name: msisensor2 msi test_msisensor2_msi_tumor_only_ml
-  command: nextflow run ./tests/modules/msisensor2/msi -entry test_msisensor2_msi_tumor_only_ml -c ./tests/config/nextflow.config  -c ./tests/modules/msisensor2/msi/nextflow.config
-  tags:
-    - msisensor2
-    - msisensor2/msi
-  files:
-    - path: output/msisensor2/test
-      md5sum: a3290f7539dbbf83777e8590156c0e28
-    - path: output/msisensor2/test_dis
-      md5sum: 85205504ea8652ebdee46ac07ee1a8f6
-    - path: output/msisensor2/test_somatic
diff --git a/tests/modules/msisensor2/scan/main.nf b/tests/modules/msisensor2/scan/main.nf
deleted file mode 100644
index 52a600bd5fc..00000000000
--- a/tests/modules/msisensor2/scan/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MSISENSOR2_SCAN } from '../../../../modules/msisensor2/scan/main.nf'
-
-workflow test_msisensor2_scan {
-
-    input = [
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true)
-    ]
-
-    MSISENSOR2_SCAN ( input, "outputfile" )
-}
diff --git a/tests/modules/msisensor2/scan/test.yml b/tests/modules/msisensor2/scan/test.yml
deleted file mode 100644
index c4eb53674a9..00000000000
--- a/tests/modules/msisensor2/scan/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: msisensor2 scan test_msisensor2_scan
-  command: nextflow run ./tests/modules/msisensor2/scan -entry test_msisensor2_scan -c ./tests/config/nextflow.config  -c ./tests/modules/msisensor2/scan/nextflow.config
-  tags:
-    - msisensor2/scan
-    - msisensor2
-  files:
-    - path: output/msisensor2/outputfile
-      md5sum: bdc0a576f37bd95a59692f387d083092
diff --git a/tests/modules/msisensorpro/msi_somatic/main.nf b/tests/modules/msisensorpro/msi_somatic/main.nf
deleted file mode 100644
index 4516ada583f..00000000000
--- a/tests/modules/msisensorpro/msi_somatic/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MSISENSORPRO_MSI_SOMATIC } from '../../../../modules/msisensorpro/msi_somatic/main.nf'
-include { MSISENSORPRO_SCAN } from '../../../../modules/msisensorpro/scan/main.nf'
-
-workflow test_msisensorpro_msi {
-
-    scan_in = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    ]
-
-    println scan_in
-
-    MSISENSORPRO_SCAN ( scan_in )
-
-    input = [// meta map
-        [ id:'test'],
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        []
-    ]
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-
-    MSISENSORPRO_SCAN.out.list.map{meta, list -> [list]}.set{list}
-    MSISENSORPRO_MSI_SOMATIC(input, fasta, list)
-
-
-}
diff --git a/tests/modules/msisensorpro/msi_somatic/test.yml b/tests/modules/msisensorpro/msi_somatic/test.yml
deleted file mode 100644
index 22e7e86420e..00000000000
--- a/tests/modules/msisensorpro/msi_somatic/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: msisensorpro msi_somatic test_msisensorpro_msi
-  command: nextflow run tests/modules/msisensorpro/msi_somatic -entry test_msisensorpro_msi -c tests/config/nextflow.config
-  tags:
-    - msisensorpro/msi_somatic
-    - msisensorpro
-  files:
-    - path: output/msisensorpro/test
-      md5sum: db7f2cc99ea79f79b0ba011c4bcbb43d
-    - path: output/msisensorpro/test.msisensor_scan.list
-      md5sum: 309d41b136993db24a9f3dade877753b
-    - path: output/msisensorpro/test_dis
-      md5sum: fc3e205b7ca50c9ecf3f70c87781e96f
-    - path: output/msisensorpro/test_germline
-      md5sum: ba585b355c08877b8bca4901f49d9311
-    - path: output/msisensorpro/test_somatic
-      md5sum: 836e617ddded07ec1e39089fd595c3d8
-    - path: output/msisensorpro/versions.yml
-      md5sum: b57279502ca6863c5406ed46e6b42994
diff --git a/tests/modules/msisensorpro/scan/main.nf b/tests/modules/msisensorpro/scan/main.nf
deleted file mode 100644
index cf57b820f8e..00000000000
--- a/tests/modules/msisensorpro/scan/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MSISENSORPRO_SCAN } from '../../../../modules/msisensorpro/scan/main.nf'
-
-workflow test_msisensorpro_scan {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    ]
-
-    MSISENSORPRO_SCAN ( input )
-}
diff --git a/tests/modules/msisensorpro/scan/test.yml b/tests/modules/msisensorpro/scan/test.yml
deleted file mode 100644
index be5100e2399..00000000000
--- a/tests/modules/msisensorpro/scan/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: msisensorpro scan test_msisensorpro_scan
-  command: nextflow run tests/modules/msisensorpro/scan -entry test_msisensorpro_scan -c tests/config/nextflow.config
-  tags:
-    - msisensorpro
-    - msisensorpro/scan
-  files:
-    - path: output/msisensorpro/test.msisensor_scan.list
-      md5sum: 309d41b136993db24a9f3dade877753b
-    - path: output/msisensorpro/versions.yml
-      md5sum: ed713232c854bce5c74d10097101ed06
diff --git a/tests/modules/mtnucratio/main.nf b/tests/modules/mtnucratio/main.nf
deleted file mode 100644
index 6d6f5e1d1ef..00000000000
--- a/tests/modules/mtnucratio/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MTNUCRATIO } from '../../../modules/mtnucratio/main.nf'
-
-workflow test_mtnucratio {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)]
-    mt_id = 'mt_id'
-
-    MTNUCRATIO ( input, mt_id )
-}
diff --git a/tests/modules/mtnucratio/test.yml b/tests/modules/mtnucratio/test.yml
deleted file mode 100644
index 24dc3d1691f..00000000000
--- a/tests/modules/mtnucratio/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: mtnucratio
-  command: nextflow run ./tests/modules/mtnucratio -entry test_mtnucratio -c ./tests/config/nextflow.config -c ./tests/modules/mtnucratio/nextflow.config
-  tags:
-    - mtnucratio
-  files:
-    - path: output/mtnucratio/test.single_end.sorted.bam.mtnucratio
-      md5sum: 19e96849802c70aa0694785f716274b7
-    - path: output/mtnucratio/test.single_end.sorted.bam.mtnucratiomtnuc.json
-      md5sum: 14d24be6272854d6762f0dfad5918ef6
diff --git a/tests/modules/multiqc/main.nf b/tests/modules/multiqc/main.nf
deleted file mode 100644
index ee0edabc060..00000000000
--- a/tests/modules/multiqc/main.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FASTQC            } from '../../../modules/fastqc/main.nf'
-include { FASTQC as FASTQC2 } from '../../../modules/fastqc/main.nf'
-include { MULTIQC           } from '../../../modules/multiqc/main.nf'
-
-workflow test_multiqc {
-    input = [
-        [ id: 'test', single_end: false ],
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-    ]
-
-    FASTQC  ( input )
-    MULTIQC ( FASTQC.out.zip.collect { it[1] }, [], [], [] )
-}
-
-workflow test_multiqc_fn_collision {
-    fqc_input = [
-        [ id: 'test', single_end: false ],
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-    ]
-    mqc_input = Channel.empty()
-
-    FASTQC  ( fqc_input  )
-    mqc_input = mqc_input.mix(FASTQC.out.zip.collect { it[1] })
-
-    FASTQC2  ( fqc_input )
-    mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] })
-
-    MULTIQC ( mqc_input, [], [], [] )
-}
-
-workflow test_multiqc_config {
-    input = [
-        [ id: 'test', single_end: false ],
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-    ]
-    mqc_config = file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)
-    mqc_input = Channel.empty()
-
-    FASTQC  ( input )
-    MULTIQC ( FASTQC.out.zip.collect { it[1] }, mqc_config, [], [] )
-}
diff --git a/tests/modules/multiqc/test.yml b/tests/modules/multiqc/test.yml
deleted file mode 100644
index 0174630bd9a..00000000000
--- a/tests/modules/multiqc/test.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-- name: multiqc test_multiqc
-  command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config  -c ./tests/modules/multiqc/nextflow.config
-  tags:
-    - multiqc
-  files:
-    - path: output/multiqc/multiqc_data/multiqc.log
-      contains: ["MultiQC complete"]
-    - path: output/multiqc/multiqc_data/multiqc_citations.txt
-      contains: ["10.1093/bioinformatics/btw354"]
-    - path: output/multiqc/multiqc_data/multiqc_data.json
-      contains: ["report_data_sources"]
-    - path: output/multiqc/multiqc_report.html
-      contains: ["Abandon hope all ye who enter here.."]
-
-- name: multiqc test_multiqc_fn_collision
-  command: nextflow run ./tests/modules/multiqc -entry test_multiqc_fn_collision -c ./tests/config/nextflow.config  -c ./tests/modules/multiqc/nextflow.config
-  tags:
-    - multiqc
-  files:
-    - path: output/multiqc/multiqc_data/multiqc.log
-      contains: ["MultiQC complete"]
-    - path: output/multiqc/multiqc_data/multiqc_citations.txt
-      contains: ["10.1093/bioinformatics/btw354"]
-    - path: output/multiqc/multiqc_data/multiqc_data.json
-      contains: ["report_data_sources"]
-    - path: output/multiqc/multiqc_report.html
-      contains: ["Abandon hope all ye who enter here.."]
-
-- name: multiqc test_multiqc_config
-  command: nextflow run ./tests/modules/multiqc -entry test_multiqc_config -c ./tests/config/nextflow.config  -c ./tests/modules/multiqc/nextflow.config
-  tags:
-    - multiqc
-  files:
-    - path: output/multiqc/multiqc_data/multiqc.log
-      contains: ["MultiQC complete"]
-    - path: output/multiqc/multiqc_data/multiqc_citations.txt
-      contains: ["10.1093/bioinformatics/btw354"]
-    - path: output/multiqc/multiqc_data/multiqc_data.json
-      contains: ["report_data_sources"]
-    - path: output/multiqc/multiqc_report.html
-      contains: ["Abandon hope all ye who enter here.."]
diff --git a/tests/modules/multivcfanalyzer/main.nf b/tests/modules/multivcfanalyzer/main.nf
deleted file mode 100644
index 07e6831bf13..00000000000
--- a/tests/modules/multivcfanalyzer/main.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK_UNIFIEDGENOTYPER } from '../../../modules/gatk/unifiedgenotyper/main.nf'
-include { GUNZIP                } from '../../../modules/gunzip/main.nf'
-include { MULTIVCFANALYZER      } from '../../../modules/multivcfanalyzer/main.nf'
-
-workflow test_multivcfanalyzer {
-
-    input     = Channel.of([ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                ],
-                [ [ id:'test2' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-                  file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true),
-                ],
-                )
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [], [], [], [])
-
-    mva_vcf = GUNZIP ( GATK_UNIFIEDGENOTYPER.out.vcf ).gunzip
-        .map{it[1]}
-        .collect()
-        .dump()
-
-    snpeff_results          = []
-    gff                     = []
-    allele_freqs            = true
-    genotype_quality        = 30
-    coverage                = 5
-    homozygous_freq         = 0.8
-    heterozygous_freq       = 0.2
-    gff_exclude             = []
-
-    MULTIVCFANALYZER ( mva_vcf, fasta, snpeff_results, gff, allele_freqs, genotype_quality, coverage, homozygous_freq, heterozygous_freq, gff_exclude )
-}
diff --git a/tests/modules/multivcfanalyzer/test.yml b/tests/modules/multivcfanalyzer/test.yml
deleted file mode 100644
index 8db0136face..00000000000
--- a/tests/modules/multivcfanalyzer/test.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- name: multivcfanalyzer test_multivcfanalyzer
-  command: nextflow run ./tests/modules/multivcfanalyzer -entry test_multivcfanalyzer -c ./tests/config/nextflow.config  -c ./tests/modules/multivcfanalyzer/nextflow.config
-  tags:
-    - multivcfanalyzer
-  files:
-    - path: output/multivcfanalyzer/MultiVCFAnalyzer.json
-      md5sum: c841c9f04c6114911f308ea09a08980e
-    - path: output/multivcfanalyzer/fullAlignment.fasta.gz
-      contains:
-        - ">Reference_MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome"
-    - path: output/multivcfanalyzer/info.txt
-      contains:
-        - "Run finished"
-    - path: output/multivcfanalyzer/snpAlignment.fasta.gz
-      contains:
-        - "test.vcf"
-    - path: output/multivcfanalyzer/snpAlignmentIncludingRefGenome.fasta.gz
-      contains:
-        - ">Reference_MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome"
-    - path: output/multivcfanalyzer/snpStatistics.tsv
-      contains: ["statistics", "test.vcf", "test2.vcf"]
-    - path: output/multivcfanalyzer/snpTable.tsv
-      contains: ["Position", "test.vcf", "test2.vcf"]
-    - path: output/multivcfanalyzer/snpTableForSnpEff.tsv
-      md5sum: 8d7ab4ec98a89d290e301d6feae461aa
-    - path: output/multivcfanalyzer/snpTableWithUncertaintyCalls.tsv
-      contains: ["Position", "test.vcf", "test2.vcf"]
-    - path: output/multivcfanalyzer/structureGenotypes.tsv
-      contains: ["test.vcf", "test2.vcf"]
-    - path: output/multivcfanalyzer/structureGenotypes_noMissingData-Columns.tsv
-      contains: ["test.vcf", "test2.vcf"]
diff --git a/tests/modules/mummer/main.nf b/tests/modules/mummer/main.nf
deleted file mode 100644
index 30c8c4b82a8..00000000000
--- a/tests/modules/mummer/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MUMMER } from '../../../modules/mummer/main.nf'
-
-workflow test_mummer {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-
-    MUMMER ( input )
-}
diff --git a/tests/modules/mummer/test.yml b/tests/modules/mummer/test.yml
deleted file mode 100644
index 359fd4adcfb..00000000000
--- a/tests/modules/mummer/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: mummer test_mummer
-  command: nextflow run ./tests/modules/mummer -entry test_mummer -c ./tests/config/nextflow.config -c ./tests/modules/mummer/nextflow.config
-  tags:
-    - mummer
-  files:
-    - path: output/mummer/test.coords
-      md5sum: 6084fe43c7cb2eca8b96d674560bdefc
diff --git a/tests/modules/muscle/main.nf b/tests/modules/muscle/main.nf
deleted file mode 100644
index a62945198e2..00000000000
--- a/tests/modules/muscle/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MUSCLE } from '../../../modules/muscle/main.nf'
-include { MUSCLE as MUSCLE_TREE } from '../../../modules/muscle/main.nf'
-
-workflow test_muscle {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
-
-    MUSCLE ( input )
-    MUSCLE_TREE ( MUSCLE.out.aligned_fasta )
-}
diff --git a/tests/modules/muscle/test.yml b/tests/modules/muscle/test.yml
deleted file mode 100644
index 6995d71d299..00000000000
--- a/tests/modules/muscle/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: muscle test_muscle
-  command: nextflow run ./tests/modules/muscle -entry test_muscle -c ./tests/config/nextflow.config -c ./tests/modules/muscle/nextflow.config
-  tags:
-    - muscle
-  files:
-    - path: output/muscle/muscle_msa.log
-    - path: output/muscle/test_muscle_msa.afa
-      md5sum: 93732f6876054d82b0cd252d702c143f
-    - path: output/muscle/test_muscle_msa.phyi
-      md5sum: 1f2a246dcca53125456149770763d5d1
-    - path: output/muscle/test_muscle_msa.phys
-      md5sum: 12f9dd45672a3d92ba1205fcc8010490
-    - path: output/muscle/test_muscle_msa.tree
-      md5sum: 6bf1080bca2440f08ffa2675f74f732a
diff --git a/tests/modules/mykrobe/predict/main.nf b/tests/modules/mykrobe/predict/main.nf
deleted file mode 100644
index 384add1e3e3..00000000000
--- a/tests/modules/mykrobe/predict/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MYKROBE_PREDICT } from '../../../../modules/mykrobe/predict/main.nf'
-
-workflow test_mykrobe_predict {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    MYKROBE_PREDICT ( input, "typhi" )
-}
diff --git a/tests/modules/mykrobe/predict/test.yml b/tests/modules/mykrobe/predict/test.yml
deleted file mode 100644
index 9116bde4383..00000000000
--- a/tests/modules/mykrobe/predict/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: mykrobe predict test_mykrobe_predict
-  command: nextflow run ./tests/modules/mykrobe/predict -entry test_mykrobe_predict -c ./tests/config/nextflow.config  -c ./tests/modules/mykrobe/predict/nextflow.config
-  tags:
-    - mykrobe/predict
-    - mykrobe
-  files:
-    - path: output/mykrobe/test.csv
-      contains: ["susceptibility", "genotype_model", "variants", "test.paired_end.bam"]
-    - path: output/mykrobe/test.json
-      contains: ["susceptibility", "kmer_count", "files", "test.paired_end.bam"]
diff --git a/tests/modules/nanolyse/main.nf b/tests/modules/nanolyse/main.nf
deleted file mode 100644
index 91013cd00fe..00000000000
--- a/tests/modules/nanolyse/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NANOLYSE } from '../../../modules/nanolyse/main.nf'
-
-workflow test_nanolyse {
-    input = [ 
-        [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)]
-    ]
-
-    fasta = file("https://github.com/wdecoster/nanolyse/raw/master/reference/lambda.fasta.gz", checkIfExists: true)
-
-    NANOLYSE ( input, fasta )
-}
diff --git a/tests/modules/nanolyse/test.yml b/tests/modules/nanolyse/test.yml
deleted file mode 100644
index 5af2e65e52b..00000000000
--- a/tests/modules/nanolyse/test.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-- name: nanolyse
-  command: nextflow run ./tests/modules/nanolyse -entry test_nanolyse -c ./tests/config/nextflow.config -c ./tests/modules/nanolyse/nextflow.config
-  tags:
-    - nanolyse
-  files:
-    - path: ./output/nanolyse/test.clean.fastq.gz
diff --git a/tests/modules/nanoplot/main.nf b/tests/modules/nanoplot/main.nf
deleted file mode 100644
index 04c923c2961..00000000000
--- a/tests/modules/nanoplot/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NANOPLOT  } from '../../../modules/nanoplot/main.nf'
-
-workflow test_nanoplot_summary {
-    def input = []
-    input = [ [ id:'test' ], // meta map
-            [ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ] ]
-              
-    NANOPLOT ( input )
-}
-
-workflow test_nanoplot_fastq {
-    def input = []
-    input = [ [ id:'test' ], // meta map
-            [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ] ]
-
-    NANOPLOT ( input )
-}
diff --git a/tests/modules/nanoplot/test.yml b/tests/modules/nanoplot/test.yml
deleted file mode 100644
index fc100a12577..00000000000
--- a/tests/modules/nanoplot/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: nanoplot_summary
-  command: nextflow run ./tests/modules/nanoplot -entry test_nanoplot_summary -c ./tests/config/nextflow.config -c ./tests/modules/nanoplot/nextflow.config
-  tags:
-    - nanoplot
-  files:
-    - path: ./output/nanoplot/NanoPlot-report.html
-      contains:
-        - "report"
-- name: nanoplot_fastq
-  command: nextflow run ./tests/modules/nanoplot -entry test_nanoplot_fastq -c ./tests/config/nextflow.config -c ./tests/modules/nanoplot/nextflow.config
-  tags:
-    - nanoplot
-  files:
-    - path: ./output/nanoplot/NanoPlot-report.html
-      contains:
-        - "report"
diff --git a/tests/modules/ncbigenomedownload/main.nf b/tests/modules/ncbigenomedownload/main.nf
deleted file mode 100644
index 2447b97c7f4..00000000000
--- a/tests/modules/ncbigenomedownload/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NCBIGENOMEDOWNLOAD } from '../../../modules/ncbigenomedownload/main.nf'
-
-workflow test_ncbigenomedownload {
-    
-    input = [ [ id:'test', single_end:false ] ]
-
-    accessions = []
-
-    NCBIGENOMEDOWNLOAD ( input, accessions)
-}
-
-
diff --git a/tests/modules/ncbigenomedownload/test.yml b/tests/modules/ncbigenomedownload/test.yml
deleted file mode 100644
index 8765e04f028..00000000000
--- a/tests/modules/ncbigenomedownload/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: ncbigenomedownload test_ncbigenomedownload
-  command: nextflow run ./tests/modules/ncbigenomedownload -entry test_ncbigenomedownload -c ./tests/config/nextflow.config -c ./tests/modules/ncbigenomedownload/nextflow.config
-  tags:
-    - ncbigenomedownload
-  files:
-    - path: output/ncbigenomedownload/GCF_000013425.1_ASM1342v1_assembly_stats.txt
-      md5sum: f78c6a373130e50fac5472962a5fdf44
-    - path: output/ncbigenomedownload/GCF_000013425.1_ASM1342v1_genomic.fna.gz
-      md5sum: b086eb1020e7df022afa545dc6d93297
-    - path: output/ncbigenomedownload/GCF_000013425.1_ASM1342v1_genomic.gbff.gz
-      md5sum: ae2da70e32c783858e6c60c72e9eeb7a
diff --git a/tests/modules/nextclade/datasetget/main.nf b/tests/modules/nextclade/datasetget/main.nf
deleted file mode 100644
index 8f4fa87b1e1..00000000000
--- a/tests/modules/nextclade/datasetget/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NEXTCLADE_DATASETGET } from '../../../../modules/nextclade/datasetget/main.nf'
-
-workflow test_nextclade_datasetget {
-
-    dataset = 'sars-cov-2'
-    reference = 'MN908947'
-    tag = '2022-01-18T12:00:00Z'
-
-    NEXTCLADE_DATASETGET ( dataset, reference, tag )
-
-}
diff --git a/tests/modules/nextclade/datasetget/test.yml b/tests/modules/nextclade/datasetget/test.yml
deleted file mode 100644
index d610b428904..00000000000
--- a/tests/modules/nextclade/datasetget/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: nextclade datasetget
-  command: nextflow run ./tests/modules/nextclade/datasetget -entry test_nextclade_datasetget -c ./tests/config/nextflow.config -c ./tests/modules/nextclade/datasetget/nextflow.config
-  tags:
-    - nextclade
-    - nextclade/datasetget
-  files:
-    - path: output/nextclade/sars-cov-2/genemap.gff
-      md5sum: 21ebebfd0f416eeb959e55ebffd808e8
-    - path: output/nextclade/sars-cov-2/primers.csv
-      md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
-    - path: output/nextclade/sars-cov-2/qc.json
-      md5sum: c512f51fda0212b21ffff05779180963
-    - path: output/nextclade/sars-cov-2/reference.fasta
-      md5sum: c7ce05f28e4ec0322c96f24e064ef55c
-    - path: output/nextclade/sars-cov-2/sequences.fasta
-      md5sum: 41129d255b99e0e92bdf20e866b99a1b
-    - path: output/nextclade/sars-cov-2/tag.json
-      md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3
-    - path: output/nextclade/sars-cov-2/tree.json
-      md5sum: b8f32f547ff9e2131d6fc66b68fc54b1
-    - path: output/nextclade/sars-cov-2/virus_properties.json
-      md5sum: 5f2de3949e07cb633f3d9e4a7654dc81
diff --git a/tests/modules/nextclade/run/main.nf b/tests/modules/nextclade/run/main.nf
deleted file mode 100644
index ed674a0d42a..00000000000
--- a/tests/modules/nextclade/run/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NEXTCLADE_DATASETGET } from '../../../../modules/nextclade/datasetget/main.nf'
-include { NEXTCLADE_RUN        } from '../../../../modules/nextclade/run/main.nf'
-
-workflow test_nextclade_run {
-
-    dataset = 'sars-cov-2'
-    reference = 'MN908947'
-    tag = '2022-01-18T12:00:00Z'
-
-    NEXTCLADE_DATASETGET ( dataset, reference, tag )
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset )
-}
-
diff --git a/tests/modules/nextclade/run/test.yml b/tests/modules/nextclade/run/test.yml
deleted file mode 100644
index 5cf25e42df2..00000000000
--- a/tests/modules/nextclade/run/test.yml
+++ /dev/null
@@ -1,62 +0,0 @@
-- name: nextclade run test_nextclade_run
-  command: nextflow run ./tests/modules/nextclade/run -entry test_nextclade_run -c ./tests/config/nextflow.config  -c ./tests/modules/nextclade/run/nextflow.config
-  tags:
-    - nextclade/run
-    - nextclade
-  files:
-    - path: output/nextclade/sars-cov-2/genemap.gff
-      md5sum: 21ebebfd0f416eeb959e55ebffd808e8
-    - path: output/nextclade/sars-cov-2/primers.csv
-      md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
-    - path: output/nextclade/sars-cov-2/qc.json
-      md5sum: c512f51fda0212b21ffff05779180963
-    - path: output/nextclade/sars-cov-2/reference.fasta
-      md5sum: c7ce05f28e4ec0322c96f24e064ef55c
-    - path: output/nextclade/sars-cov-2/sequences.fasta
-      md5sum: 41129d255b99e0e92bdf20e866b99a1b
-    - path: output/nextclade/sars-cov-2/tag.json
-      md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3
-    - path: output/nextclade/sars-cov-2/tree.json
-      md5sum: b8f32f547ff9e2131d6fc66b68fc54b1
-    - path: output/nextclade/sars-cov-2/virus_properties.json
-      md5sum: 5f2de3949e07cb633f3d9e4a7654dc81
-    - path: output/nextclade/test.aligned.fasta
-      md5sum: 1bf54662837b0df37f1857c7fa631225
-    - path: output/nextclade/test.auspice.json
-      md5sum: 04d8c32f141435ca45bf430dcb59bcba
-    - path: output/nextclade/test.csv
-      md5sum: 9489bab7f58c07c0b6949182789aa435
-    - path: output/nextclade/test.errors.csv
-      md5sum: 810d1c72e1ed010a9a017afba7ce8063
-    - path: output/nextclade/test.insertions.csv
-      md5sum: c3aa7071d06122ec07ba7c7c4ba6e84a
-    - path: output/nextclade/test.json
-      contains: ["nextcladeAlgoVersion"]
-    - path: output/nextclade/test.ndjson
-      md5sum: 32e3c1e733be19509faa0a45260a3d96
-    - path: output/nextclade/test.tsv
-      md5sum: 7f4bea521bcef4d1bca02c51d11b2fe1
-    - path: output/nextclade/test_gene_E.translation.fasta
-      md5sum: 1a6d93bd7abfeb193476a86950f07202
-    - path: output/nextclade/test_gene_M.translation.fasta
-      md5sum: 6f79ab0742c078fcd9d2a474518c7022
-    - path: output/nextclade/test_gene_N.translation.fasta
-      md5sum: bef9912f101777bfff36225d7e5c3c1f
-    - path: output/nextclade/test_gene_ORF1a.translation.fasta
-      md5sum: 4dc0e2eb1f2a61939ba49500ee3fa41a
-    - path: output/nextclade/test_gene_ORF1b.translation.fasta
-      md5sum: 9c2e83d26161b5c887ff51cd64bd15bb
-    - path: output/nextclade/test_gene_ORF3a.translation.fasta
-      md5sum: adcbede4ebc2cac7af755a9d29d28ea3
-    - path: output/nextclade/test_gene_ORF6.translation.fasta
-      md5sum: 3785b34cce978c95256f83db6ee82af0
-    - path: output/nextclade/test_gene_ORF7a.translation.fasta
-      md5sum: 6ede1acb9e75afc84aa30bbc40551d37
-    - path: output/nextclade/test_gene_ORF7b.translation.fasta
-      md5sum: 460e4cbc5f8c632c2bc9a8aedad5cf43
-    - path: output/nextclade/test_gene_ORF8.translation.fasta
-      md5sum: c733c88e61b29542664368fbf6dd4c76
-    - path: output/nextclade/test_gene_ORF9b.translation.fasta
-      md5sum: 0aa13afc6cbf445fc92caa2e6c0a7548
-    - path: output/nextclade/test_gene_S.translation.fasta
-      md5sum: 77740927a3f00b7e5bfac392fa6d264c
diff --git a/tests/modules/nextgenmap/main.nf b/tests/modules/nextgenmap/main.nf
deleted file mode 100644
index 450551debc9..00000000000
--- a/tests/modules/nextgenmap/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NEXTGENMAP } from '../../../modules/nextgenmap/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_nextgenmap_single {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    NEXTGENMAP ( input, fasta )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_bwamem2_mem_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    NEXTGENMAP ( input, fasta )
-}
diff --git a/tests/modules/nextgenmap/test.yml b/tests/modules/nextgenmap/test.yml
deleted file mode 100644
index 96c51d2c4ad..00000000000
--- a/tests/modules/nextgenmap/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: nextgenmap test_nextgenmap_single
-  command: nextflow run ./tests/modules/nextgenmap -entry test_nextgenmap_single -c ./tests/config/nextflow.config  -c ./tests/modules/nextgenmap/nextflow.config
-  tags:
-    - nextgenmap
-  files:
-    - path: output/nextgenmap/test.bam
-      md5sum: ada069bc5c670ffee23871f3ca525d0a
-
-- name: nextgenmap test_bwamem2_mem_paired_end
-  command: nextflow run ./tests/modules/nextgenmap -entry test_bwamem2_mem_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nextgenmap/nextflow.config
-  tags:
-    - nextgenmap
-  files:
-    - path: output/nextgenmap/test.bam
-      md5sum: fa76167e236cf1aabdafdbb0632253cd
diff --git a/tests/modules/nf-core/abacas/main.nf b/tests/modules/nf-core/abacas/main.nf
new file mode 100644
index 00000000000..ee1a56b22b9
--- /dev/null
+++ b/tests/modules/nf-core/abacas/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ABACAS } from '../../../../modules/nf-core/abacas/main.nf'
+
+workflow test_abacas {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
+            ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    ABACAS ( input, fasta )
+}
diff --git a/tests/modules/abacas/nextflow.config b/tests/modules/nf-core/abacas/nextflow.config
similarity index 100%
rename from tests/modules/abacas/nextflow.config
rename to tests/modules/nf-core/abacas/nextflow.config
diff --git a/tests/modules/nf-core/abacas/test.yml b/tests/modules/nf-core/abacas/test.yml
new file mode 100644
index 00000000000..3856b63a54d
--- /dev/null
+++ b/tests/modules/nf-core/abacas/test.yml
@@ -0,0 +1,24 @@
+- name: abacas
+  command: nextflow run ./tests/modules/nf-core/abacas -entry test_abacas -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/abacas/nextflow.config
+  tags:
+    - abacas
+  files:
+    - path: output/abacas/test.abacas.bin
+    - path: output/abacas/test.abacas.crunch
+      md5sum: 9a95358a9bd8ee97d1f2253d95623a17
+    - path: output/abacas/test.abacas.fasta
+      md5sum: 5e6c403d3850d52f6bde956fa2403b13
+    - path: output/abacas/test.abacas.gaps
+      md5sum: 5361af445b8d18a85c3af6527a97c89a
+    - path: output/abacas/test.abacas.gaps.tab
+      md5sum: 193024ec9e5a553573519b218eb06e29
+    - path: output/abacas/test.abacas.nucmer.delta
+    - path: output/abacas/test.abacas.nucmer.filtered.delta
+    - path: output/abacas/test.abacas.nucmer.tiling
+      md5sum: 0adaa0ce800d92c149a523d447148d95
+    - path: output/abacas/test.abacas.tab
+      md5sum: a5b9b452516f519a4201ff809655ef69
+    - path: output/abacas/test.abacas.unused.contigs.out
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/abacas/test.abacas.MULTIFASTA.fa
+      md5sum: 46c899ad70dcef8d14b5829fd8fbab82
diff --git a/tests/modules/nf-core/abricate/run/main.nf b/tests/modules/nf-core/abricate/run/main.nf
new file mode 100644
index 00000000000..b8c2efa239a
--- /dev/null
+++ b/tests/modules/nf-core/abricate/run/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ABRICATE_RUN } from '../../../../../modules/nf-core/abricate/run/main.nf'
+
+workflow test_abricate_run {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+
+    ABRICATE_RUN ( input )
+}
diff --git a/tests/modules/abricate/run/nextflow.config b/tests/modules/nf-core/abricate/run/nextflow.config
similarity index 100%
rename from tests/modules/abricate/run/nextflow.config
rename to tests/modules/nf-core/abricate/run/nextflow.config
diff --git a/tests/modules/nf-core/abricate/run/test.yml b/tests/modules/nf-core/abricate/run/test.yml
new file mode 100644
index 00000000000..76d8d751ea9
--- /dev/null
+++ b/tests/modules/nf-core/abricate/run/test.yml
@@ -0,0 +1,10 @@
+- name: abricate run
+  command: nextflow run ./tests/modules/nf-core/abricate/run -entry test_abricate_run -c ./tests/config/nextflow.config
+  tags:
+    - abricate
+    - abricate/run
+  files:
+    - path: output/abricate/test.txt
+      md5sum: cd07e2953b127aed8d09bf1b2b903a1f
+    - path: output/abricate/versions.yml
+      md5sum: ae9cafaae96a644bb852e337aa7251f3
diff --git a/tests/modules/nf-core/abricate/summary/main.nf b/tests/modules/nf-core/abricate/summary/main.nf
new file mode 100644
index 00000000000..aa545408287
--- /dev/null
+++ b/tests/modules/nf-core/abricate/summary/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ABRICATE_RUN } from '../../../../../modules/nf-core/abricate/run/main.nf'
+include { ABRICATE_SUMMARY } from '../../../../../modules/nf-core/abricate/summary/main.nf'
+
+workflow test_abricate_summary {
+
+    inputs = [
+        tuple([ id:'test1', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)),
+        tuple([ id:'test2', single_end:false ],
+              file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true))
+    ]
+
+    ABRICATE_RUN ( Channel.fromList(inputs) )
+    ABRICATE_SUMMARY ( 
+        ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
+    )
+}
diff --git a/tests/modules/abricate/summary/nextflow.config b/tests/modules/nf-core/abricate/summary/nextflow.config
similarity index 100%
rename from tests/modules/abricate/summary/nextflow.config
rename to tests/modules/nf-core/abricate/summary/nextflow.config
diff --git a/tests/modules/nf-core/abricate/summary/test.yml b/tests/modules/nf-core/abricate/summary/test.yml
new file mode 100644
index 00000000000..17ef0a7f34e
--- /dev/null
+++ b/tests/modules/nf-core/abricate/summary/test.yml
@@ -0,0 +1,14 @@
+- name: abricate summary
+  command: nextflow run ./tests/modules/nf-core/abricate/summary -entry test_abricate_summary -c ./tests/config/nextflow.config
+  tags:
+    - abricate
+    - abricate/summary
+  files:
+    - path: output/abricate/test1.txt
+      md5sum: cd07e2953b127aed8d09bf1b2b903a1f
+    - path: output/abricate/test2.txt
+      md5sum: 69af3321b0bc808b7ef85f102395736f
+    - path: output/abricate/test_summary.txt
+      md5sum: a4ec7010e75404ce3a1033f0c4b4a7f9
+    - path: output/abricate/versions.yml
+      md5sum: a18f0471c49e5f25ec0b0c4ad5fab08e
diff --git a/tests/modules/nf-core/adapterremoval/main.nf b/tests/modules/nf-core/adapterremoval/main.nf
new file mode 100644
index 00000000000..01be917bec1
--- /dev/null
+++ b/tests/modules/nf-core/adapterremoval/main.nf
@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ADAPTERREMOVAL                            } from '../../../../modules/nf-core/adapterremoval/main.nf'
+include { ADAPTERREMOVAL as ADAPTERREMOVAL_COLLAPSE } from '../../../../modules/nf-core/adapterremoval/main.nf'
+
+
+workflow test_adapterremoval_single_end {
+    input = [ [ id:'test', single_end:true, collapse:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ]
+
+    ADAPTERREMOVAL ( input, [] )
+}
+
+workflow test_adapterremoval_paired_end {
+    input = [ [ id:'test', single_end:false, collapse:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    ADAPTERREMOVAL ( input, [] )
+}
+
+workflow test_adapterremoval_paired_end_collapse {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    ADAPTERREMOVAL_COLLAPSE ( input, [] )
+}
+
diff --git a/tests/modules/adapterremoval/nextflow.config b/tests/modules/nf-core/adapterremoval/nextflow.config
similarity index 100%
rename from tests/modules/adapterremoval/nextflow.config
rename to tests/modules/nf-core/adapterremoval/nextflow.config
diff --git a/tests/modules/nf-core/adapterremoval/test.yml b/tests/modules/nf-core/adapterremoval/test.yml
new file mode 100644
index 00000000000..a17312019ef
--- /dev/null
+++ b/tests/modules/nf-core/adapterremoval/test.yml
@@ -0,0 +1,45 @@
+- name: adapterremoval test_adapterremoval_single_end
+  command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_single_end -c ./tests/config/nextflow.config
+  tags:
+    - adapterremoval
+  files:
+    - path: output/adapterremoval/test.discarded.fastq.gz
+    - path: output/adapterremoval/test.settings
+      md5sum: 2fd3d5d703b63ba33a83021fccf25f77
+    - path: output/adapterremoval/test.truncated.fastq.gz
+      md5sum: 62139afee94defad5b83bdd0b8475a1f
+    - path: output/adapterremoval/versions.yml
+      md5sum: ac5b46719719b7ee62739530b80869fc
+
+- name: adapterremoval test_adapterremoval_paired_end
+  command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - adapterremoval
+  files:
+    - path: output/adapterremoval/test.discarded.fastq.gz
+    - path: output/adapterremoval/test.settings
+      md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
+    - path: output/adapterremoval/test.pair1.truncated.fastq.gz
+      md5sum: 294a6277f0139bd597e57c6fa31f39c7
+    - path: output/adapterremoval/test.pair2.truncated.fastq.gz
+      md5sum: de7b38e2c881bced8671acb1ab452d78
+    - path: output/adapterremoval/versions.yml
+      md5sum: fa621c887897da5a379c719399c17db7
+
+- name: adapterremoval test_adapterremoval_paired_end_collapse
+  command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_paired_end_collapse -c ./tests/config/nextflow.config
+  tags:
+    - adapterremoval
+  files:
+    - path: output/adapterremoval/test.collapsed.fastq.gz
+      md5sum: ff956de3532599a56c3efe5369f0953f
+    - path: output/adapterremoval/test.collapsed.truncated.fastq.gz
+    - path: output/adapterremoval/test.discarded.fastq.gz
+    - path: output/adapterremoval/test.settings
+      md5sum: 7f0b2328152226e46101a535cce718b3
+    - path: output/adapterremoval/test.pair1.truncated.fastq.gz
+      md5sum: 683be19bc1c83008944b6b719bfa34e1
+    - path: output/adapterremoval/test.pair2.truncated.fastq.gz
+      md5sum: e6548fe061f3ef86368b26da930174d0
+    - path: output/adapterremoval/versions.yml
+      md5sum: 78f589bb313c8da0147ca8ce77d7f3bf
diff --git a/tests/modules/nf-core/adapterremovalfixprefix/main.nf b/tests/modules/nf-core/adapterremovalfixprefix/main.nf
new file mode 100644
index 00000000000..153eae37185
--- /dev/null
+++ b/tests/modules/nf-core/adapterremovalfixprefix/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ADAPTERREMOVAL          } from '../../../../modules/nf-core/adapterremoval/main.nf'
+include { ADAPTERREMOVALFIXPREFIX } from '../../../../modules/nf-core/adapterremovalfixprefix/main.nf'
+
+workflow test_adapterremovalfixprefix {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    ADAPTERREMOVAL ( input, [] )
+    ADAPTERREMOVALFIXPREFIX ( ADAPTERREMOVAL.out.collapsed )
+}
diff --git a/tests/modules/adapterremovalfixprefix/nextflow.config b/tests/modules/nf-core/adapterremovalfixprefix/nextflow.config
similarity index 100%
rename from tests/modules/adapterremovalfixprefix/nextflow.config
rename to tests/modules/nf-core/adapterremovalfixprefix/nextflow.config
diff --git a/tests/modules/nf-core/adapterremovalfixprefix/test.yml b/tests/modules/nf-core/adapterremovalfixprefix/test.yml
new file mode 100644
index 00000000000..f1ae13832d6
--- /dev/null
+++ b/tests/modules/nf-core/adapterremovalfixprefix/test.yml
@@ -0,0 +1,7 @@
+- name: adapterremovalfixprefix test_adapterremovalfixprefix
+  command: nextflow run ./tests/modules/nf-core/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c ./tests/config/nextflow.config
+  tags:
+    - adapterremovalfixprefix
+  files:
+    - path: output/adapterremovalfixprefix/test.fq.gz
+      md5sum: ff956de3532599a56c3efe5369f0953f
diff --git a/tests/modules/nf-core/agrvate/main.nf b/tests/modules/nf-core/agrvate/main.nf
new file mode 100644
index 00000000000..d19d110cf04
--- /dev/null
+++ b/tests/modules/nf-core/agrvate/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { AGRVATE } from '../../../../modules/nf-core/agrvate/main.nf'
+
+workflow test_agrvate {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    AGRVATE ( input )
+}
diff --git a/tests/modules/agrvate/nextflow.config b/tests/modules/nf-core/agrvate/nextflow.config
similarity index 100%
rename from tests/modules/agrvate/nextflow.config
rename to tests/modules/nf-core/agrvate/nextflow.config
diff --git a/tests/modules/nf-core/agrvate/test.yml b/tests/modules/nf-core/agrvate/test.yml
new file mode 100644
index 00000000000..04f9fabdafd
--- /dev/null
+++ b/tests/modules/nf-core/agrvate/test.yml
@@ -0,0 +1,7 @@
+- name: agrvate
+  command: nextflow run ./tests/modules/nf-core/agrvate -entry test_agrvate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/agrvate/nextflow.config
+  tags:
+    - agrvate
+  files:
+    - path: output/agrvate/genome-results/genome-summary.tab
+      md5sum: 781a9e5fc6ebc9f90ddfe8753d1633db
diff --git a/tests/modules/nf-core/allelecounter/main.nf b/tests/modules/nf-core/allelecounter/main.nf
new file mode 100644
index 00000000000..4925aa94998
--- /dev/null
+++ b/tests/modules/nf-core/allelecounter/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl = 2
+
+include { ALLELECOUNTER } from '../../../../modules/nf-core/allelecounter/main.nf'
+
+workflow test_allelecounter_bam {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+            ]
+    positions = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+
+    ALLELECOUNTER ( input, positions, [] )
+}
+
+
+workflow test_allelecounter_cram {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+            ]
+    positions = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    ALLELECOUNTER ( input, positions, fasta )
+}
diff --git a/tests/modules/allelecounter/nextflow.config b/tests/modules/nf-core/allelecounter/nextflow.config
similarity index 100%
rename from tests/modules/allelecounter/nextflow.config
rename to tests/modules/nf-core/allelecounter/nextflow.config
diff --git a/tests/modules/nf-core/allelecounter/test.yml b/tests/modules/nf-core/allelecounter/test.yml
new file mode 100644
index 00000000000..048b0d572d1
--- /dev/null
+++ b/tests/modules/nf-core/allelecounter/test.yml
@@ -0,0 +1,15 @@
+- name: allelecounter test_allelecounter_bam
+  command: nextflow run ./tests/modules/nf-core/allelecounter -entry test_allelecounter_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/allelecounter/nextflow.config
+  tags:
+    - allelecounter
+  files:
+    - path: output/allelecounter/test.alleleCount
+      md5sum: 2bbe9d7331b78bdac30fe30dbc5fdaf3
+
+- name: allelecounter test_allelecounter_cram
+  command: nextflow run ./tests/modules/nf-core/allelecounter -entry test_allelecounter_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/allelecounter/nextflow.config
+  tags:
+    - allelecounter
+  files:
+    - path: output/allelecounter/test.alleleCount
+      md5sum: 2f83352a185168c7c98e9e42550b2856
diff --git a/tests/modules/nf-core/ampir/main.nf b/tests/modules/nf-core/ampir/main.nf
new file mode 100644
index 00000000000..0628795cc97
--- /dev/null
+++ b/tests/modules/nf-core/ampir/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { AMPIR } from '../../../../modules/nf-core/ampir/main.nf'
+
+workflow test_ampir {
+
+    fasta = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true),
+    ]
+
+    model = "precursor"
+
+    min_length = []
+
+    min_probability = "0.7"
+
+    AMPIR ( fasta, model, min_length, min_probability )
+}
diff --git a/tests/modules/ampir/nextflow.config b/tests/modules/nf-core/ampir/nextflow.config
similarity index 100%
rename from tests/modules/ampir/nextflow.config
rename to tests/modules/nf-core/ampir/nextflow.config
diff --git a/tests/modules/nf-core/ampir/test.yml b/tests/modules/nf-core/ampir/test.yml
new file mode 100644
index 00000000000..549dad70a43
--- /dev/null
+++ b/tests/modules/nf-core/ampir/test.yml
@@ -0,0 +1,11 @@
+- name: ampir test_ampir
+  command: nextflow run ./tests/modules/nf-core/ampir -entry test_ampir -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ampir/nextflow.config
+  tags:
+    - ampir
+  files:
+    - path: output/ampir/test.tsv
+      contains: ["seq_name\tseq_aa\tprob_AMP", "WP_014895017.1"]
+    - path: output/ampir/test.faa
+      md5sum: 0435609144022c55ac196db053f0df89
+    - path: output/ampir/versions.yml
+      md5sum: 4a11d25b8a904a7ffb34ae88f6826888
diff --git a/tests/modules/nf-core/amplify/predict/main.nf b/tests/modules/nf-core/amplify/predict/main.nf
new file mode 100644
index 00000000000..e8b3b5df525
--- /dev/null
+++ b/tests/modules/nf-core/amplify/predict/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRODIGAL } from '../../../../modules/nf-core/prodigal/main.nf' addParams( options: [:] )
+include { AMPLIFY_PREDICT } from '../../../../../modules/nf-core/amplify/predict/main.nf' addParams( options: [:] )
+
+workflow amplify_predict {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+    ]
+    model_dir = []
+
+    PRODIGAL ( input, "gff" )
+    AMPLIFY_PREDICT ( PRODIGAL.out.amino_acid_fasta, model_dir)
+}
diff --git a/tests/modules/amplify/predict/nextflow.config b/tests/modules/nf-core/amplify/predict/nextflow.config
similarity index 100%
rename from tests/modules/amplify/predict/nextflow.config
rename to tests/modules/nf-core/amplify/predict/nextflow.config
diff --git a/tests/modules/nf-core/amplify/predict/test.yml b/tests/modules/nf-core/amplify/predict/test.yml
new file mode 100644
index 00000000000..ce5c8531a82
--- /dev/null
+++ b/tests/modules/nf-core/amplify/predict/test.yml
@@ -0,0 +1,9 @@
+- name: amplify predict amplify_predict
+  command: nextflow run ./tests/modules/nf-core/amplify/predict -entry amplify_predict -c ./tests/config/nextflow.config
+  tags:
+    - amplify/predict
+    - amplify
+  files:
+    - path: output/amplify/test.tsv
+      md5sum: 1951084ce1d410028be86754997e5852
+    - path: output/amplify/versions.yml
diff --git a/tests/modules/nf-core/amps/main.nf b/tests/modules/nf-core/amps/main.nf
new file mode 100644
index 00000000000..e0615367a86
--- /dev/null
+++ b/tests/modules/nf-core/amps/main.nf
@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNZIP as UNZIP_MALT        } from '../../../../modules/nf-core/unzip/main.nf'
+include { UNZIP as UNZIP_MALTEXTRACT } from '../../../../modules/nf-core/unzip/main.nf'
+include { MALT_BUILD  } from  '../../../../modules/nf-core/malt/build/main.nf'
+include { MALT_RUN    } from '../../../../modules/nf-core/malt/run/main.nf'
+include { MALTEXTRACT } from '../../../../modules/nf-core/maltextract/main.nf'
+include { AMPS        } from '../../../../modules/nf-core/amps/main.nf'
+
+
+workflow test_amps {
+
+    fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gff = []
+    seq_type = "DNA"
+    map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    mode = "BlastN"
+    taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
+    ncbi_dir = [ [], file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true) ]
+
+    UNZIP_MALT ( map_db )
+    UNZIP_MALTEXTRACT ( ncbi_dir )
+    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive.map{ it[1] } )
+    MALT_RUN ( input, mode, MALT_BUILD.out.index )
+    ch_input_to_maltextract = MALT_RUN.out.rma6.map{ it[1] }
+    MALTEXTRACT ( ch_input_to_maltextract, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive.map{ it[1] })
+
+    AMPS ( MALTEXTRACT.out.results, taxon_list, filter )
+}
diff --git a/tests/modules/amps/nextflow.config b/tests/modules/nf-core/amps/nextflow.config
similarity index 100%
rename from tests/modules/amps/nextflow.config
rename to tests/modules/nf-core/amps/nextflow.config
diff --git a/tests/modules/nf-core/amps/test.yml b/tests/modules/nf-core/amps/test.yml
new file mode 100644
index 00000000000..80773184a18
--- /dev/null
+++ b/tests/modules/nf-core/amps/test.yml
@@ -0,0 +1,11 @@
+- name: amps
+  command: nextflow run ./tests/modules/nf-core/amps -entry test_amps -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/amps/nextflow.config
+  tags:
+    - amps
+  files:
+    - path: output/amps/results/heatmap_overview_Wevid.json
+      md5sum: 82f484d02a9e3d0cc3d5bcdcc2965e44
+    - path: output/amps/results/heatmap_overview_Wevid.pdf
+    - path: output/amps/results/heatmap_overview_Wevid.tsv
+      md5sum: 1a7d565a37ef4d6054f7ade63fbadc2f
+    - path: output/amps/results/pdf_candidate_profiles/Severe_acute_respiratory_syndrome_coronavirus_2/stp1_test_1.rma6_Severe_acute_respiratory_syndrome_coronavirus_2_summary.pdf
diff --git a/tests/modules/nf-core/amrfinderplus/run/main.nf b/tests/modules/nf-core/amrfinderplus/run/main.nf
new file mode 100644
index 00000000000..0f887457fc2
--- /dev/null
+++ b/tests/modules/nf-core/amrfinderplus/run/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { AMRFINDERPLUS_UPDATE } from '../../../../../modules/nf-core/amrfinderplus/update/main.nf'
+include { AMRFINDERPLUS_RUN } from '../../../../../modules/nf-core/amrfinderplus/run/main.nf'
+
+workflow test_amrfinderplus_run {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    AMRFINDERPLUS_UPDATE ( )
+    AMRFINDERPLUS_RUN ( input, AMRFINDERPLUS_UPDATE.out.db )
+}
diff --git a/tests/modules/amrfinderplus/run/nextflow.config b/tests/modules/nf-core/amrfinderplus/run/nextflow.config
similarity index 100%
rename from tests/modules/amrfinderplus/run/nextflow.config
rename to tests/modules/nf-core/amrfinderplus/run/nextflow.config
diff --git a/tests/modules/nf-core/amrfinderplus/run/test.yml b/tests/modules/nf-core/amrfinderplus/run/test.yml
new file mode 100644
index 00000000000..09e9d4d69a3
--- /dev/null
+++ b/tests/modules/nf-core/amrfinderplus/run/test.yml
@@ -0,0 +1,8 @@
+- name: amrfinderplus run test_amrfinderplus_run
+  command: nextflow run ./tests/modules/nf-core/amrfinderplus/run -entry test_amrfinderplus_run -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/amrfinderplus/run/nextflow.config
+  tags:
+    - amrfinderplus
+    - amrfinderplus/run
+  files:
+    - path: output/amrfinderplus/test.tsv
+      md5sum: b4d261ace9be7d013c19d1f5c0005bfe
diff --git a/tests/modules/nf-core/amrfinderplus/update/main.nf b/tests/modules/nf-core/amrfinderplus/update/main.nf
new file mode 100644
index 00000000000..4f5c73cfafa
--- /dev/null
+++ b/tests/modules/nf-core/amrfinderplus/update/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { AMRFINDERPLUS_UPDATE } from '../../../../../modules/nf-core/amrfinderplus/update/main.nf'
+
+workflow test_amrfinderplus_update {
+
+    AMRFINDERPLUS_UPDATE ( )
+
+}
diff --git a/tests/modules/amrfinderplus/update/nextflow.config b/tests/modules/nf-core/amrfinderplus/update/nextflow.config
similarity index 100%
rename from tests/modules/amrfinderplus/update/nextflow.config
rename to tests/modules/nf-core/amrfinderplus/update/nextflow.config
diff --git a/tests/modules/nf-core/amrfinderplus/update/test.yml b/tests/modules/nf-core/amrfinderplus/update/test.yml
new file mode 100644
index 00000000000..83c699bc3d4
--- /dev/null
+++ b/tests/modules/nf-core/amrfinderplus/update/test.yml
@@ -0,0 +1,7 @@
+- name: amrfinderplus update test_amrfinderplus_update
+  command: nextflow run ./tests/modules/nf-core/amrfinderplus/update -entry test_amrfinderplus_update -c ./tests/config/nextflow.config
+  tags:
+    - amrfinderplus
+    - amrfinderplus/update
+  files:
+    - path: output/amrfinderplus/amrfinderdb.tar.gz
diff --git a/tests/modules/nf-core/angsd/docounts/main.nf b/tests/modules/nf-core/angsd/docounts/main.nf
new file mode 100644
index 00000000000..2188a097c03
--- /dev/null
+++ b/tests/modules/nf-core/angsd/docounts/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ANGSD_DOCOUNTS } from '../../../../../modules/nf-core/angsd/docounts/main.nf'
+
+workflow test_angsd_docounts {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true),
+        []
+    ]
+
+    ANGSD_DOCOUNTS ( input )
+}
diff --git a/tests/modules/angsd/docounts/nextflow.config b/tests/modules/nf-core/angsd/docounts/nextflow.config
similarity index 100%
rename from tests/modules/angsd/docounts/nextflow.config
rename to tests/modules/nf-core/angsd/docounts/nextflow.config
diff --git a/tests/modules/nf-core/angsd/docounts/test.yml b/tests/modules/nf-core/angsd/docounts/test.yml
new file mode 100644
index 00000000000..eea06d7bcc5
--- /dev/null
+++ b/tests/modules/nf-core/angsd/docounts/test.yml
@@ -0,0 +1,11 @@
+- name: angsd docounts test_angsd_docounts
+  command: nextflow run ./tests/modules/nf-core/angsd/docounts -entry test_angsd_docounts -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/angsd/docounts/nextflow.config
+  tags:
+    - angsd/docounts
+    - angsd
+  files:
+    - path: output/angsd/test.counts.gz
+      contains: ["ind0TotDepth"]
+    - path: output/angsd/test.icnts.gz
+    - path: output/angsd/test.pos.gz
+      contains: ["chr	pos	totDepth"]
diff --git a/tests/modules/nf-core/antismash/antismashlite/main.nf b/tests/modules/nf-core/antismash/antismashlite/main.nf
new file mode 100644
index 00000000000..73c55dc8bcb
--- /dev/null
+++ b/tests/modules/nf-core/antismash/antismashlite/main.nf
@@ -0,0 +1,46 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ANTISMASH_ANTISMASHLITE                  } from '../../../../../modules/nf-core/antismash/antismashlite/main.nf'
+include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf'
+include { GUNZIP as GUNZIP1 } from '../../../../../modules/nf-core/gunzip/main.nf'
+include { GUNZIP as GUNZIP2 } from '../../../../../modules/nf-core/gunzip/main.nf'
+include { UNTAR as UNTAR1 } from '../../../../../modules/nf-core/untar/main.nf'
+include { UNTAR as UNTAR2 } from '../../../../../modules/nf-core/untar/main.nf'
+include { UNTAR as UNTAR3 } from '../../../../../modules/nf-core/untar/main.nf'
+
+workflow test_antismashlite {
+    genome_fna = [
+        [ id:'test' ],
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+
+    genome_gff = [
+        [],
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gff_gz'], checkIfExists: true)
+    ]
+
+    antismash_css = [
+        [],
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
+    ]
+
+    antismash_detection = [
+        [],
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
+    ]
+
+    antismash_modules = [
+        [],
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
+    ]
+
+    GUNZIP1 ( genome_fna )
+    GUNZIP2 ( genome_gff )
+    UNTAR1 ( antismash_css )
+    UNTAR2 ( antismash_detection )
+    UNTAR3 ( antismash_modules )
+    ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
+    ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, GUNZIP2.out.gunzip.map{ it[1] } )
+}
diff --git a/tests/modules/antismash/antismashlite/nextflow.config b/tests/modules/nf-core/antismash/antismashlite/nextflow.config
similarity index 100%
rename from tests/modules/antismash/antismashlite/nextflow.config
rename to tests/modules/nf-core/antismash/antismashlite/nextflow.config
diff --git a/tests/modules/nf-core/antismash/antismashlite/test.yml b/tests/modules/nf-core/antismash/antismashlite/test.yml
new file mode 100644
index 00000000000..63119336a49
--- /dev/null
+++ b/tests/modules/nf-core/antismash/antismashlite/test.yml
@@ -0,0 +1,35 @@
+- name: antismash antismashlite test_antismashlite
+  command: nextflow run ./tests/modules/nf-core/antismash/antismashlite -entry test_antismashlite -c ./tests/config/nextflow.config
+  tags:
+    - antismash/antismashlite
+    - antismash
+  files:
+    - path: output/antismash/test/NZ_CP069563.1.region001.gbk
+      contains: ['/tool="antismash"']
+    - path: output/antismash/test/NZ_CP069563.1.region002.gbk
+      contains: ['/tool="antismash"']
+    - path: output/antismash/test/css/bacteria.css
+      md5sum: 8b3c2f8b143d5245a5f42f55803c532c
+    - path: output/antismash/test/genome.gbk
+      contains: ['/tool="antismash"']
+    - path: output/antismash/test/genome.json
+      contains: ['{"version": "6.0.1", "input_file": "genome.fna", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
+    - path: output/antismash/test/genome.zip
+    - path: output/antismash/test/index.html
+      md5sum: de787e865c3a1eec143a19d2facb4de4
+    - path: output/antismash/test/js/antismash.js
+      md5sum: 58e90c3d783ae014cc3d51849bcb50a2
+    - path: output/antismash/test/js/jquery.js
+      md5sum: 397754ba49e9e0cf4e7c190da78dda05
+    - path: output/antismash/test/js/jquery.tablesorter.min.js
+      md5sum: 5e9e08cef4d1be0eaa538e6eb28809a7
+    - path: output/antismash/test/regions.js
+      contains: ['"seq_id": "NZ_CP069563.1"']
+    - path: output/antismash/test/test.log
+      contains: ["antiSMASH version: 6.0.1"]
+    - path: output/antismash/versions.yml
+      md5sum: 759431a43da33e2ef8e2d0ebd79a439b
+    - path: output/gunzip1/genome.fna
+      md5sum: dafd38f5454b54fbea38245d773062a5
+    - path: output/gunzip2/genome.gff
+      md5sum: 9b9c848b1946d43fa68128f4d6316052
diff --git a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf
new file mode 100644
index 00000000000..9d91eea4d65
--- /dev/null
+++ b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR as UNTAR1 } from '../../../../../modules/nf-core/untar/main.nf'
+include { UNTAR as UNTAR2 } from '../../../../../modules/nf-core/untar/main.nf'
+include { UNTAR as UNTAR3 } from '../../../../../modules/nf-core/untar/main.nf'
+include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../../modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf'
+
+workflow test_antismash_antismashlitedownloaddatabases {
+    input1 = [
+        [],
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
+    ]
+    input2 = [
+        [],
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
+    ]
+    input3 = [
+        [],
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
+    ]
+
+    UNTAR1 ( input1 )
+    UNTAR2 ( input2 )
+    UNTAR3 ( input3 )
+
+    ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
+}
diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/nextflow.config b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/nextflow.config
similarity index 100%
rename from tests/modules/antismash/antismashlitedownloaddatabases/nextflow.config
rename to tests/modules/nf-core/antismash/antismashlitedownloaddatabases/nextflow.config
diff --git a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml
new file mode 100644
index 00000000000..98739d6cc19
--- /dev/null
+++ b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml
@@ -0,0 +1,16 @@
+- name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
+  command: nextflow run ./tests/modules/nf-core/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c ./tests/config/nextflow.config
+  tags:
+    - antismash/antismashlitedownloaddatabases
+    - antismash
+  files:
+    - path: output/antismash/versions.yml
+      md5sum: 24859c67023abab99de295d3675a24b6
+    - path: output/antismash/antismash_db
+    - path: output/antismash/antismash_db/clusterblast
+    - path: output/antismash/antismash_db/clustercompare
+    - path: output/antismash/antismash_db/pfam
+    - path: output/antismash/antismash_db/resfam
+    - path: output/antismash/antismash_db/tigrfam
+    - path: output/antismash/antismash_dir
+    - path: output/antismash/antismash_dir/detection/hmm_detection/data/bgc_seeds.hmm
diff --git a/tests/modules/nf-core/ariba/getref/main.nf b/tests/modules/nf-core/ariba/getref/main.nf
new file mode 100644
index 00000000000..6cbcb251415
--- /dev/null
+++ b/tests/modules/nf-core/ariba/getref/main.nf
@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ARIBA_GETREF } from '../../../../../modules/nf-core/ariba/getref/main.nf'
+
+workflow test_ariba_getref {
+    ARIBA_GETREF ( "card" )
+}
diff --git a/tests/modules/ariba/getref/nextflow.config b/tests/modules/nf-core/ariba/getref/nextflow.config
similarity index 100%
rename from tests/modules/ariba/getref/nextflow.config
rename to tests/modules/nf-core/ariba/getref/nextflow.config
diff --git a/tests/modules/nf-core/ariba/getref/test.yml b/tests/modules/nf-core/ariba/getref/test.yml
new file mode 100644
index 00000000000..7f67b0a8acc
--- /dev/null
+++ b/tests/modules/nf-core/ariba/getref/test.yml
@@ -0,0 +1,7 @@
+- name: ariba getref test_ariba_getref
+  command: nextflow run ./tests/modules/nf-core/ariba/getref -entry test_ariba_getref -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ariba/getref/nextflow.config
+  tags:
+    - ariba
+    - ariba/getref
+  files:
+    - path: output/ariba/card.tar.gz
diff --git a/tests/modules/nf-core/ariba/run/main.nf b/tests/modules/nf-core/ariba/run/main.nf
new file mode 100644
index 00000000000..d99362c4477
--- /dev/null
+++ b/tests/modules/nf-core/ariba/run/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ARIBA_GETREF } from '../../../../../modules/nf-core/ariba/getref/main.nf'
+include { ARIBA_RUN } from '../../../../../modules/nf-core/ariba/run/main.nf'
+
+workflow test_ariba_run {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    ARIBA_GETREF ( "card" )
+    ARIBA_RUN ( input, ARIBA_GETREF.out.db)
+}
diff --git a/tests/modules/ariba/run/nextflow.config b/tests/modules/nf-core/ariba/run/nextflow.config
similarity index 100%
rename from tests/modules/ariba/run/nextflow.config
rename to tests/modules/nf-core/ariba/run/nextflow.config
diff --git a/tests/modules/nf-core/ariba/run/test.yml b/tests/modules/nf-core/ariba/run/test.yml
new file mode 100644
index 00000000000..fb4033fc47f
--- /dev/null
+++ b/tests/modules/nf-core/ariba/run/test.yml
@@ -0,0 +1,15 @@
+- name: ariba run test_ariba_run
+  command: nextflow run ./tests/modules/nf-core/ariba/run -entry test_ariba_run -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ariba/run/nextflow.config
+  tags:
+    - ariba
+    - ariba/run
+  files:
+    - path: output/ariba/test/assembled_genes.fa.gz
+    - path: output/ariba/test/assembled_seqs.fa.gz
+    - path: output/ariba/test/assemblies.fa.gz
+    - path: output/ariba/test/debug.report.tsv
+      contains: ["ariba_ref_name", "reads", "free_text", "known_var_change"]
+    - path: output/ariba/test/report.tsv
+      contains: ["ariba_ref_name", "reads", "free_text", "known_var_change"]
+    - path: output/ariba/test/version_info.txt
+      contains: ["ARIBA", "Python", "OK", "True"]
diff --git a/tests/modules/nf-core/arriba/main.nf b/tests/modules/nf-core/arriba/main.nf
new file mode 100644
index 00000000000..17978f4c129
--- /dev/null
+++ b/tests/modules/nf-core/arriba/main.nf
@@ -0,0 +1,42 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STAR_GENOMEGENERATE   } from '../../../../modules/nf-core/star/genomegenerate/main.nf'
+include { STAR_ALIGN            } from '../../../../modules/nf-core/star/align/main.nf'
+include { ARRIBA                } from '../../../../modules/nf-core/arriba/main.nf'
+
+workflow test_arriba_single_end {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+                [   file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    star_ignore_sjdbgtf = false
+    seq_platform = 'illumina'
+    seq_center = false
+
+    STAR_GENOMEGENERATE ( fasta, gtf )
+    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
+    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf , [], [], [], [], [])
+}
+
+workflow test_arriba_paired_end {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                [   file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    star_ignore_sjdbgtf = false
+    seq_platform = 'illumina'
+    seq_center = false
+
+    STAR_GENOMEGENERATE ( fasta, gtf )
+    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
+    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf, [], [], [], [], [])
+}
diff --git a/tests/modules/arriba/nextflow.config b/tests/modules/nf-core/arriba/nextflow.config
similarity index 100%
rename from tests/modules/arriba/nextflow.config
rename to tests/modules/nf-core/arriba/nextflow.config
diff --git a/tests/modules/nf-core/arriba/test.yml b/tests/modules/nf-core/arriba/test.yml
new file mode 100644
index 00000000000..8110d08483d
--- /dev/null
+++ b/tests/modules/nf-core/arriba/test.yml
@@ -0,0 +1,92 @@
+- name: arriba test_arriba_single_end
+  command: nextflow run ./tests/modules/nf-core/arriba -entry test_arriba_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/arriba/nextflow.config
+  tags:
+    - arriba
+  files:
+    - path: output/arriba/test.fusions.discarded.tsv
+      md5sum: 7602ab4ccbbb0c54fbca12a942877e6d
+    - path: output/arriba/test.fusions.tsv
+      md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
+    - path: output/star/star/Genome
+      md5sum: a654229fbca6071dcb6b01ce7df704da
+    - path: output/star/star/Log.out
+    - path: output/star/star/SA
+      md5sum: 8c3edc46697b72c9e92440d4cf43506c
+    - path: output/star/star/SAindex
+      md5sum: 9f085c626553b1c52f2827421972ac10
+    - path: output/star/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/star/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/star/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/star/star/chrStart.txt
+      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: d04497f69d6ef889efd4d34fe63edcc4
+    - path: output/star/star/exonInfo.tab
+      md5sum: 0d560290fab688b7268d88d5494bf9fe
+    - path: output/star/star/geneInfo.tab
+      md5sum: 8b608537307443ffaee4927d2b428805
+    - path: output/star/star/genomeParameters.txt
+      md5sum: 9e42067b1ec70b773257529230dd7b3a
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: 8760c33e966dad0b39f440301ebbdee4
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
+    - path: output/star/test.Aligned.out.bam
+      md5sum: e6f850505492f1c7d47bb1ad05fddbfd
+    - path: output/star/test.Log.final.out
+    - path: output/star/test.Log.out
+    - path: output/star/test.Log.progress.out
+    - path: output/star/test.SJ.out.tab
+
+- name: arriba test_arriba_paired_end
+  command: nextflow run ./tests/modules/nf-core/arriba -entry test_arriba_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/arriba/nextflow.config
+  tags:
+    - arriba
+  files:
+    - path: output/arriba/test.fusions.discarded.tsv
+      md5sum: 445cb87a27f063e751f93498cf8d10b5
+    - path: output/arriba/test.fusions.tsv
+      md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
+    - path: output/star/star/Genome
+      md5sum: a654229fbca6071dcb6b01ce7df704da
+    - path: output/star/star/Log.out
+    - path: output/star/star/SA
+      md5sum: 8c3edc46697b72c9e92440d4cf43506c
+    - path: output/star/star/SAindex
+      md5sum: 9f085c626553b1c52f2827421972ac10
+    - path: output/star/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/star/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/star/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/star/star/chrStart.txt
+      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: d04497f69d6ef889efd4d34fe63edcc4
+    - path: output/star/star/exonInfo.tab
+      md5sum: 0d560290fab688b7268d88d5494bf9fe
+    - path: output/star/star/geneInfo.tab
+      md5sum: 8b608537307443ffaee4927d2b428805
+    - path: output/star/star/genomeParameters.txt
+      md5sum: 9e42067b1ec70b773257529230dd7b3a
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: 8760c33e966dad0b39f440301ebbdee4
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
+    - path: output/star/test.Aligned.out.bam
+    - path: output/star/test.Log.final.out
+    - path: output/star/test.Log.out
+    - path: output/star/test.Log.progress.out
+    - path: output/star/test.SJ.out.tab
diff --git a/tests/modules/nf-core/artic/guppyplex/main.nf b/tests/modules/nf-core/artic/guppyplex/main.nf
new file mode 100644
index 00000000000..bd60545d1d4
--- /dev/null
+++ b/tests/modules/nf-core/artic/guppyplex/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ARTIC_GUPPYPLEX } from '../../../../../modules/nf-core/artic/guppyplex/main.nf'
+
+process STAGE_FASTQ_DIR {
+    input:
+    tuple val(meta), path(fastq_file)
+
+    output:
+    tuple val(meta), path('fastq'), emit: fastq_dir
+
+    script:
+    """
+    mkdir fastq
+    mv ${fastq_file} fastq
+    """
+}
+
+workflow test_artic_guppyplex {
+
+    input =  [ [ id:'test' ],
+               file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+
+    STAGE_FASTQ_DIR ( input )
+
+    ARTIC_GUPPYPLEX ( STAGE_FASTQ_DIR.out.fastq_dir )
+}
diff --git a/tests/modules/artic/guppyplex/nextflow.config b/tests/modules/nf-core/artic/guppyplex/nextflow.config
similarity index 100%
rename from tests/modules/artic/guppyplex/nextflow.config
rename to tests/modules/nf-core/artic/guppyplex/nextflow.config
diff --git a/tests/modules/nf-core/artic/guppyplex/test.yml b/tests/modules/nf-core/artic/guppyplex/test.yml
new file mode 100644
index 00000000000..81514394350
--- /dev/null
+++ b/tests/modules/nf-core/artic/guppyplex/test.yml
@@ -0,0 +1,7 @@
+- name: artic guppyplex
+  command: nextflow run ./tests/modules/nf-core/artic/guppyplex -entry test_artic_guppyplex -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/artic/guppyplex/nextflow.config
+  tags:
+    - artic
+    - artic/guppyplex
+  files:
+    - path: output/artic/test.fastq.gz
diff --git a/tests/modules/nf-core/artic/minion/main.nf b/tests/modules/nf-core/artic/minion/main.nf
new file mode 100644
index 00000000000..4a47f563655
--- /dev/null
+++ b/tests/modules/nf-core/artic/minion/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR        } from '../../../../../modules/nf-core/untar/main.nf'
+include { ARTIC_MINION } from '../../../../../modules/nf-core/artic/minion/main.nf'
+
+workflow test_artic_minion {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+    ]
+    fast5_tar          = [ [], file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true) ]
+    sequencing_summary = file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true)
+    fasta              = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true)
+    bed                = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true)
+
+    fast5_dir = UNTAR ( fast5_tar ).untar.map{ it[1] }
+
+    ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, [], '', 'nCoV-2019', '3')
+}
diff --git a/tests/modules/artic/minion/nextflow.config b/tests/modules/nf-core/artic/minion/nextflow.config
similarity index 100%
rename from tests/modules/artic/minion/nextflow.config
rename to tests/modules/nf-core/artic/minion/nextflow.config
diff --git a/tests/modules/nf-core/artic/minion/test.yml b/tests/modules/nf-core/artic/minion/test.yml
new file mode 100644
index 00000000000..fcc5fa171c7
--- /dev/null
+++ b/tests/modules/nf-core/artic/minion/test.yml
@@ -0,0 +1,260 @@
+- name: artic minion
+  command: nextflow run ./tests/modules/nf-core/artic/minion -entry test_artic_minion -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/artic/minion/nextflow.config
+  tags:
+    - artic
+    - artic/minion
+  files:
+    - path: output/artic/test.1.vcf
+      md5sum: f0278719cbb853addcad74b73d810a24
+    - path: output/artic/test.2.vcf
+      md5sum: f0278719cbb853addcad74b73d810a24
+    - path: output/artic/test.alignreport.er
+      md5sum: ddfff35c7ebc9837530c78f7a213cea0
+    - path: output/artic/test.alignreport.txt
+      md5sum: 0fcadf1467ac253476b2d43bbfa36616
+    - path: output/artic/test.consensus.fasta
+      md5sum: 60ace9fea33aca4c13f3502e330bff85
+    - path: output/artic/test.coverage_mask.txt
+      md5sum: 7abd414756c444c86766123a60687ed1
+    - path: output/artic/test.coverage_mask.txt.1.depths
+      md5sum: d4170a48491e12f34b0a15a336bdf5e6
+    - path: output/artic/test.coverage_mask.txt.2.depths
+      md5sum: 130f85d80c22fccc3e0bbd9de12d310d
+    - path: output/artic/test.fail.vcf
+      md5sum: e6e184f1fa153868e3acea0eab42e484
+    - path: output/artic/test.fastq.gz.index
+      md5sum: eaa2b34db5a53fb2d410c5b3bf857fd9
+    - path: output/artic/test.fastq.gz.index.fai
+      md5sum: 81d718eeaaaae68cb33003f56194e956
+    - path: output/artic/test.fastq.gz.index.gzi
+      md5sum: 7dea362b3fac8e00956a4952a3d4f474
+    - path: output/artic/test.fastq.gz.index.readdb
+      md5sum: 3c6296842e91578db93688b4021c8947
+    - path: output/artic/test.merged.vcf
+      md5sum: e6e184f1fa153868e3acea0eab42e484
+    - path: output/artic/test.minion.log.txt
+      contains:
+        - "artic_vcf_merge"
+    - path: output/artic/test.muscle.in.fasta
+      md5sum: 40ae4c89de797d1548c642f0da7a86cc
+    - path: output/artic/test.muscle.out.fasta
+      md5sum: 40ae4c89de797d1548c642f0da7a86cc
+    - path: output/artic/test.pass.vcf.gz
+      md5sum: baeafcfc2f738cce771ba895d66e9e01
+    - path: output/artic/test.pass.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/artic/test.preconsensus.fasta
+      md5sum: 12b16397bae7c68d38150571a6ac6185
+    - path: output/artic/test.primers.vcf
+      md5sum: e6e184f1fa153868e3acea0eab42e484
+    - path: output/artic/test.primersitereport.txt
+    - path: output/artic/test.primertrimmed.rg.sorted.bam
+    - path: output/artic/test.primertrimmed.rg.sorted.bam.bai
+      md5sum: 0d76977b2e36046cc176112776c5fa4e
+    - path: output/artic/test.sorted.bam
+      md5sum: 292611ae9885df12575b80853cb5508b
+    - path: output/artic/test.sorted.bam.bai
+      md5sum: 0d76977b2e36046cc176112776c5fa4e
+    - path: output/artic/test.trimmed.rg.sorted.bam
+    - path: output/artic/test.trimmed.rg.sorted.bam.bai
+      md5sum: 0d76977b2e36046cc176112776c5fa4e
+    - path: output/untar/fast5/100read_fast5/00068f7a-51b3-4933-8fc6-7d6e29181ff9.fast5
+      md5sum: b7aeb3cc877d858f97144d45551264bc
+    - path: output/untar/fast5/100read_fast5/001ed67f-906f-4f37-9770-85d40f5ffee6.fast5
+      md5sum: add9b8658095173f7cef6fc23236d913
+    - path: output/untar/fast5/100read_fast5/0043238c-3a78-48f1-a8ec-d492280da6e4.fast5
+      md5sum: 11d83db48d3b284017b919d476e44294
+    - path: output/untar/fast5/100read_fast5/004a65aa-6700-4ad7-9550-dc59f8708908.fast5
+      md5sum: fb9f124a05af59ea3ede371cd48e404c
+    - path: output/untar/fast5/100read_fast5/00c6481f-9022-4173-9b74-f375c34b9a9b.fast5
+      md5sum: c186053a4fee2d509e1d108be8e131e1
+    - path: output/untar/fast5/100read_fast5/00da3999-12fd-449d-bd07-32a879667a3d.fast5
+      md5sum: ec051e5ce357d632ff740a88087a08fd
+    - path: output/untar/fast5/100read_fast5/018c4b52-48fa-4cc8-a7b4-500f41420279.fast5
+      md5sum: 9d5bae9c9df0105b3b329777977d6f34
+    - path: output/untar/fast5/100read_fast5/01faaaa1-eca2-4bcd-8666-b4d69497107e.fast5
+      md5sum: 5855c80a192a242f03a93b74f12dfa46
+    - path: output/untar/fast5/100read_fast5/02085a68-dc6e-4275-bd1e-f112fed3bd83.fast5
+      md5sum: 6b30e06080aab94b6fa8f476e537f3d2
+    - path: output/untar/fast5/100read_fast5/022647b9-0e16-4318-a794-c5749705b67d.fast5
+      md5sum: 6606f2661a5463772f4ee30a3dba520e
+    - path: output/untar/fast5/100read_fast5/022fc908-aa6e-4d29-a5ad-6a30a9da7e3b.fast5
+      md5sum: 53d611cf6465ef914392c11b88339ba0
+    - path: output/untar/fast5/100read_fast5/02445dc2-39ee-49f1-8a42-51ebfea52c33.fast5
+      md5sum: f7c5844165cbc0566ce1569184fc4213
+    - path: output/untar/fast5/100read_fast5/031ff99b-b11f-40dc-9258-273ec97683f8.fast5
+      md5sum: e78faae6230537a20497d3114cffcafd
+    - path: output/untar/fast5/100read_fast5/03e0e732-cb7a-4084-8fc9-303180c83786.fast5
+      md5sum: 27c8ce19a0955d045053a6925e249ae4
+    - path: output/untar/fast5/100read_fast5/0457184e-6e09-4883-baf3-824d11101c43.fast5
+      md5sum: 7a89c45ae6b360bc585c8b14196ab3f7
+    - path: output/untar/fast5/100read_fast5/045f1e6a-9b5d-4840-bad9-c4b738b61267.fast5
+      md5sum: ee0c3e5fa1f6820968482594f45e8948
+    - path: output/untar/fast5/100read_fast5/046258fa-b951-43a1-bbed-66cdbeac8e71.fast5
+      md5sum: 262d3ee396bab6014505b25ba88cea90
+    - path: output/untar/fast5/100read_fast5/048d5d3a-16ed-4f36-aeb9-3311dd9dc593.fast5
+      md5sum: deea9c03b10aa287f873779baea2a649
+    - path: output/untar/fast5/100read_fast5/04a0ee1e-0406-4394-87ba-a67344318a5d.fast5
+      md5sum: 7f43a0e0de0053a63a28e36374ec20b4
+    - path: output/untar/fast5/100read_fast5/04c07133-cd56-48b9-9f16-86e12cacaf92.fast5
+      md5sum: d607992919072ddb025d766d8ba1a465
+    - path: output/untar/fast5/100read_fast5/052036a3-6af0-4650-9f96-e97e34c52bbc.fast5
+      md5sum: 22ccc03bee288edfc589d5f4b11cb70d
+    - path: output/untar/fast5/100read_fast5/0562aebd-b55b-4752-83eb-12323938c242.fast5
+      md5sum: 1668668f2d0658a6e3417b08ea093c43
+    - path: output/untar/fast5/100read_fast5/0565fd27-4849-4d14-83ff-2864dc3e109e.fast5
+      md5sum: 649ff949e10052b877d9ddb7d6a19009
+    - path: output/untar/fast5/100read_fast5/05f48799-d4ca-4f54-90e2-de208c0c1711.fast5
+      md5sum: 5bddb9c020ddd233adc399c806186af6
+    - path: output/untar/fast5/100read_fast5/064b4a28-a036-46cb-b466-62b8486de288.fast5
+      md5sum: 4f0d1d5400caa14c376c5c2ba5cf4e90
+    - path: output/untar/fast5/100read_fast5/064ef037-67eb-49a4-9a72-e2b2e34cfe5c.fast5
+      md5sum: e8420b20501c06a31223204611aacd44
+    - path: output/untar/fast5/100read_fast5/066c72de-139a-4514-aef9-36cc3927a2c6.fast5
+      md5sum: f703f4942aaa470e2d00706687cea430
+    - path: output/untar/fast5/100read_fast5/069ce6e7-41b9-41b2-a6d8-8d39c16dbaa2.fast5
+      md5sum: 4ef4d47bf346c9cca805e991a6f5400b
+    - path: output/untar/fast5/100read_fast5/06f0339b-75b5-4926-b1a7-878818b5fe67.fast5
+      md5sum: 163a97396e5cf91c40fab7432f52d101
+    - path: output/untar/fast5/100read_fast5/074ebef4-edbd-4d2a-af6c-46512693a990.fast5
+      md5sum: da9798ae314dca12f69ef45c10c8a5a7
+    - path: output/untar/fast5/100read_fast5/08239d1b-1710-4187-b96e-da861a0e4624.fast5
+      md5sum: 8ff2a720e61c52a29e2863d68f84c917
+    - path: output/untar/fast5/100read_fast5/084af0ac-0334-4840-a3a5-3ff62464ae71.fast5
+      md5sum: 3c2f27f6c21eefa53eafaa70252f9f49
+    - path: output/untar/fast5/100read_fast5/08db75dc-49a9-459d-afc8-5ed1d8e47901.fast5
+      md5sum: 6f25bb694f859d53b9dfd4047610d97f
+    - path: output/untar/fast5/100read_fast5/091fba78-028e-4ed2-a799-35e9ba64541c.fast5
+      md5sum: 58da6a195dad9cb15fb5ebb76f9ecd19
+    - path: output/untar/fast5/100read_fast5/094a4c34-c97b-4b83-bd02-1f69e6ccadc0.fast5
+      md5sum: adfb65496a10bae743e3f0e144220b43
+    - path: output/untar/fast5/100read_fast5/09b7f97c-fb32-4a4a-84d9-c45dfc2b46d0.fast5
+      md5sum: fcce7b510edcf012eae95662370d663c
+    - path: output/untar/fast5/100read_fast5/0a30e10c-26b5-4c23-a7ee-493e7b3ebffb.fast5
+      md5sum: fd730b0b9e01a9ce3a0a4f7b39ee838e
+    - path: output/untar/fast5/100read_fast5/0a86654b-30ec-4271-9882-b490de473b5e.fast5
+      md5sum: 9114d618e2713681e7db42932d4b5e92
+    - path: output/untar/fast5/100read_fast5/0a92fbf4-99b4-40cd-98e7-93cfbddeb35e.fast5
+      md5sum: 516a3d935f9cef2abf4eb0a781ba8d19
+    - path: output/untar/fast5/100read_fast5/0af92aee-911c-4402-ba14-ecaabdb73548.fast5
+      md5sum: ccbcd71ecb9a46bd2b657f2e2c11354a
+    - path: output/untar/fast5/100read_fast5/0b168ee0-74c4-494d-a593-a4b4b538a9cb.fast5
+      md5sum: 9f8abf45b60ac800d4195e79bad26ea1
+    - path: output/untar/fast5/100read_fast5/0b8b3929-730d-42a6-84e0-5689b7439c71.fast5
+      md5sum: 1d03a26a58ec0668a1c54cc38fb65c3a
+    - path: output/untar/fast5/100read_fast5/0bb9f17c-3b8f-486d-ac03-6550199a0a49.fast5
+      md5sum: b713ea7f1cd45b5f5041a3a97e87106d
+    - path: output/untar/fast5/100read_fast5/0c5e39bf-e1c5-4208-b110-9a00b55132e4.fast5
+      md5sum: 31e32600bbf9b3523233260868468b00
+    - path: output/untar/fast5/100read_fast5/0cc2613c-9ade-4ec9-96c7-07ab2820bbd7.fast5
+      md5sum: f84eb9bf15a0af603b9f656fb469f305
+    - path: output/untar/fast5/100read_fast5/0cc85c6c-ed86-422e-a093-d2b81089cc6b.fast5
+      md5sum: 536ad1a1c1f8e5c17d8183c7950034a0
+    - path: output/untar/fast5/100read_fast5/0d448640-aa67-4e58-9ce8-004ca23b0412.fast5
+      md5sum: c97a3ae4fcb9123ea4ca89e8a6e391af
+    - path: output/untar/fast5/100read_fast5/0dad8e5f-77e3-4fd1-b569-b06f5b87d8c3.fast5
+      md5sum: 1225db8f9879447708aa85f8a096aafb
+    - path: output/untar/fast5/100read_fast5/0dd4696c-a7dd-4e3a-9ce5-37a258b45373.fast5
+      md5sum: 361426f4430ad8edadae17ab4ddfd7cf
+    - path: output/untar/fast5/100read_fast5/0e5018bc-45fc-40d4-8806-e22e07a915d0.fast5
+      md5sum: f21cba587246cf4c9e0db4f4914db634
+    - path: output/untar/fast5/100read_fast5/0e51c070-d577-4293-8389-bd34fdda9eac.fast5
+      md5sum: e426287a64d0fe356878673c7990e457
+    - path: output/untar/fast5/100read_fast5/0e5ff4de-814b-4ee2-bf8f-3291b8bbdaae.fast5
+      md5sum: a2429274097a3762eb8fd9290208e35d
+    - path: output/untar/fast5/100read_fast5/0f06cd06-1136-4b10-b248-cd4324f6de22.fast5
+      md5sum: 4ddea20115ae9875bff711cb0f2cbcd3
+    - path: output/untar/fast5/100read_fast5/0f3ca011-bb96-4fe2-92e2-31b0bac90d97.fast5
+      md5sum: df29e75d7a273d3b6a75e807a814993a
+    - path: output/untar/fast5/100read_fast5/0f7db51f-ff49-45ea-b58a-9fb58daf249d.fast5
+      md5sum: 671423af2189b08850eaab29b42566ca
+    - path: output/untar/fast5/100read_fast5/0fd3ec80-6fb4-4378-bdb6-df4f84951049.fast5
+      md5sum: 7376ee3f340c041afda6bbd2c3df353f
+    - path: output/untar/fast5/100read_fast5/10361e9b-159a-447d-8cf0-1976515f00f4.fast5
+      md5sum: f73c994cb9b6ec891ea936c54aa2f7a2
+    - path: output/untar/fast5/100read_fast5/10508138-2f5e-4405-99f4-46af4452893c.fast5
+      md5sum: c6a0b38fcd5a4be72793b43149ba04be
+    - path: output/untar/fast5/100read_fast5/10ac42d4-2818-48f6-9d67-1c3019fde890.fast5
+      md5sum: 5e5ae354e0aa8f985f5e5e8bd811eb73
+    - path: output/untar/fast5/100read_fast5/10f98781-e47e-43c3-9006-6d73963ee710.fast5
+      md5sum: 93f6e790fc41c1e266b1c4b18f2ab0ee
+    - path: output/untar/fast5/100read_fast5/1147d9c6-c190-47e6-8007-2e0f18d88f2b.fast5
+      md5sum: 15fbf533ac4a98124cb043abef23d0ba
+    - path: output/untar/fast5/100read_fast5/11e4024c-1997-4372-b1d7-4c884cf58047.fast5
+      md5sum: 788bb232b0b3b059a7f39a72c1f8d1e5
+    - path: output/untar/fast5/100read_fast5/11e944d1-a2c9-409c-ac72-9c1563443df7.fast5
+      md5sum: 31975cf5048b6af550f14b1e217a8f5d
+    - path: output/untar/fast5/100read_fast5/123114b2-247c-4abc-be0c-3a94f02043a2.fast5
+      md5sum: 633689761b59db120dcc5d560587416c
+    - path: output/untar/fast5/100read_fast5/1294c94b-1dac-4c4c-9c36-e8e8996e7f09.fast5
+      md5sum: 161fc1cb25ce05775f81e778f5bb8e93
+    - path: output/untar/fast5/100read_fast5/12ac7997-50bc-4183-95c4-e953ad4eaad1.fast5
+      md5sum: 4a3a4966ede5f0251a65c93c99a66eeb
+    - path: output/untar/fast5/100read_fast5/13265c3e-bbb3-4ebe-b4db-9fbb4bdaff01.fast5
+      md5sum: ad799b6a66cb2d8c08acbf232c23bf49
+    - path: output/untar/fast5/100read_fast5/1377f442-7e38-4c3f-aacb-e8049ad884fe.fast5
+      md5sum: f202ebf7b46bf289b9b1d9e82d8e96db
+    - path: output/untar/fast5/100read_fast5/137cae6b-0009-4ee2-8a0e-7a2e88179c16.fast5
+      md5sum: 6afbc7da1554e1d5328f6e47cc086772
+    - path: output/untar/fast5/100read_fast5/139c8fcc-8dcb-4cf7-aa52-632718587fe7.fast5
+      md5sum: 6aade40bab37e9a4fe008d21732c6790
+    - path: output/untar/fast5/100read_fast5/13bc3b77-a88e-44b9-b119-cd56aa972f61.fast5
+      md5sum: 1d668e59bc724ce47d17f2a4850a9b43
+    - path: output/untar/fast5/100read_fast5/13dbd26f-978f-49ad-9ae6-ca909083b6ce.fast5
+      md5sum: 2106344b03e8b834c20fef4406cf2aa6
+    - path: output/untar/fast5/100read_fast5/151bd13c-c12f-41a6-be02-e97e70a57814.fast5
+      md5sum: 8718a5b883496cde586dbbb256f13bb2
+    - path: output/untar/fast5/100read_fast5/16325928-3440-4a49-94c5-a93b4f6da961.fast5
+      md5sum: da871b8be0d502e05ba6b105f9bd4673
+    - path: output/untar/fast5/100read_fast5/16d9892d-bead-4a6f-b6c5-736c6f602fc1.fast5
+      md5sum: b7844e2a38c120fad74dec350dfd8adf
+    - path: output/untar/fast5/100read_fast5/1721053e-98f4-47a1-ab93-f75bc1c03c79.fast5
+      md5sum: 839e7a9335d54c6dd185a1a9486d9b9e
+    - path: output/untar/fast5/100read_fast5/1730fabf-f1ac-4a02-aa2e-21dcd14fed00.fast5
+      md5sum: ee53b732d0c4dd87dd8742cf4346b311
+    - path: output/untar/fast5/100read_fast5/1783d96c-3955-4405-b765-472c6286be46.fast5
+      md5sum: 6bcbda04b219c8bf971253cc2423a527
+    - path: output/untar/fast5/100read_fast5/180da5c9-4574-48ab-8e6a-8f8a73767e30.fast5
+      md5sum: 8ef4d3255d87a6fb0fa24b621b72e75a
+    - path: output/untar/fast5/100read_fast5/1870a88c-439f-4125-a06c-38b1bf4416e4.fast5
+      md5sum: 62db261bbc152a16b0d910680202ba8a
+    - path: output/untar/fast5/100read_fast5/188b5eae-fce2-439c-b490-aff6c4327499.fast5
+      md5sum: c3157f03f56d03820726ff8ff981b8c9
+    - path: output/untar/fast5/100read_fast5/18cef30b-9fe5-40b4-9094-0389bb5aeb8e.fast5
+      md5sum: 9fc63db9ca59ac6ff6fa15cfe55b3106
+    - path: output/untar/fast5/100read_fast5/18ee103f-1cf8-4694-b2e7-ac228fe70ccd.fast5
+      md5sum: 24dc02b54e6712c583f5977bce1d3cd3
+    - path: output/untar/fast5/100read_fast5/190a9ebe-4d5f-43c0-a495-82ff58944d07.fast5
+      md5sum: 489aa874a1c7c0603076f7ef359d6ace
+    - path: output/untar/fast5/100read_fast5/190c4417-c4cf-40fe-a0df-db4b495a3f77.fast5
+      md5sum: 997a74664ddab756907435890465d554
+    - path: output/untar/fast5/100read_fast5/1a0c9927-e355-49c3-877a-e6b95bc1a402.fast5
+      md5sum: fdc9f5f461d0e30ad29cf84e03b6c18d
+    - path: output/untar/fast5/100read_fast5/1a276f1c-5a5b-4ed2-b071-87f59f7c5233.fast5
+      md5sum: 6269d04009267b7e0df724d7ce355346
+    - path: output/untar/fast5/100read_fast5/1a5c9192-aded-4e94-8dcb-9c04a402978e.fast5
+      md5sum: 78ce5c5d770d7905bc1986203d69ed49
+    - path: output/untar/fast5/100read_fast5/1af84d7e-8fc6-4dba-8750-a0d701f36d1d.fast5
+      md5sum: ed5970f92ecdcce95f84dbb1bd275b8e
+    - path: output/untar/fast5/100read_fast5/1b753736-87b1-4753-ab1d-bfd7e2d94e9e.fast5
+      md5sum: 6b5a2fd8b445d4e43eef6d8597932d88
+    - path: output/untar/fast5/100read_fast5/1b760e8d-7b17-47e0-ba96-5755fc4ddd63.fast5
+      md5sum: 43eb9e8276e9d0870a4c74882d42e5a0
+    - path: output/untar/fast5/100read_fast5/1b86544f-8075-46a2-91f4-baac36216ac2.fast5
+      md5sum: d6266147405391c00aa4dc0ad6797532
+    - path: output/untar/fast5/100read_fast5/1bd0dad7-1600-44a2-90b8-d5cd7b7caa6d.fast5
+      md5sum: 863226172b856834a779eb2013c3a765
+    - path: output/untar/fast5/100read_fast5/1d568051-bdd6-4204-ac34-97b5a3f7375c.fast5
+      md5sum: 7d4cdf29110898e5f6a3288a0a2b9342
+    - path: output/untar/fast5/100read_fast5/1d650a9e-4e67-456a-9abe-bd34b238abe4.fast5
+      md5sum: 3fac1d13ed49703e33e92b8aaab3dac6
+    - path: output/untar/fast5/100read_fast5/1d86c2b3-c2c6-43a1-97ed-8c1f0cbf6476.fast5
+      md5sum: 2eed32c760d94aac2dce49c2364f6cd9
+    - path: output/untar/fast5/100read_fast5/20586d1a-2cd0-45aa-abc2-04ac66d8ea46.fast5
+      md5sum: d89ef1d32a52fc5d45a17d7682e4de22
+    - path: output/untar/fast5/100read_fast5/206626c5-ccf2-4927-9987-164f627bdede.fast5
+      md5sum: 045d9fdb48f0b58456c7012b735c8101
+    - path: output/untar/fast5/100read_fast5/2109d790-67ec-4fd1-8931-6c7e61908ff3.fast5
+      md5sum: 623d2e3213f0423e33b7993d803e4ae5
+    - path: output/untar/fast5/100read_fast5/2166cca5-c0ab-49eb-aec1-fec09bdfbd83.fast5
+      md5sum: 54ac4ec12232104381d2dcd619c9b4be
diff --git a/tests/modules/nf-core/ascat/main.nf b/tests/modules/nf-core/ascat/main.nf
new file mode 100644
index 00000000000..cf76c6f0b12
--- /dev/null
+++ b/tests/modules/nf-core/ascat/main.nf
@@ -0,0 +1,113 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ASCAT as ASCAT_SIMPLE }            from '../../../../modules/nf-core/ascat/main.nf'
+include { ASCAT as ASCAT_PLOIDY_AND_PURITY } from '../../../../modules/nf-core/ascat/main.nf'
+include { ASCAT as ASCAT_CRAM }              from '../../../../modules/nf-core/ascat/main.nf'
+include { UNZIP as UNZIP_ALLELES }           from '../../../../modules/nf-core/unzip/main.nf'
+include { UNZIP as UNZIP_LOCI }              from '../../../../modules/nf-core/unzip/main.nf'
+include { UNZIP as UNZIP_GC }                from '../../../../modules/nf-core/unzip/main.nf'
+include { UNZIP as UNZIP_RT }                from '../../../../modules/nf-core/unzip/main.nf'
+
+
+
+workflow test_ascat {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    ASCAT_SIMPLE ( input , [], [], [], [], [], [])
+}
+
+// extended tests running with 1000 genomes data. Data is downloaded as follows:
+// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
+// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
+// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
+// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
+
+// workflow test_ascat_with_ploidy_and_purity {
+//     input = [ [ id:'test', single_end:false ], // meta map
+//             file("/mnt/volume/ascat/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true),
+//             file("/mnt/volume/ascat/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true),
+//             file("/mnt/volume/ascat/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true),
+//             file("/mnt/volume/ascat/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true)
+//     ]
+
+//     allele_path  = file("/mnt/volume/repos/modules/test_ascat2/G1000_alleles_hg19.zip", checkIfExists: true)
+//     allele_files = [[ id: allele_path.BaseName ], allele_path  ]
+
+//     loci_path    = file("/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip", checkIfExists: true)
+//     loci_files   = [[ id: loci_path.BaseName ], loci_path  ]
+
+//     gc_path      = file("/mnt/volume/repos/modules/test_ascat2/GC_G1000_hg19.zip", checkIfExists: true)
+//     gc_file      = [[ id: gc_path.BaseName ], gc_path  ]
+
+//     rt_path     = file("/mnt/volume/repos/modules/test_ascat2/RT_G1000_hg19.zip", checkIfExists: true)
+//     rt_file     = [[ id: rt_path.BaseName ], rt_path  ]
+
+//     UNZIP_ALLELES(allele_files)
+//     UNZIP_LOCI(loci_files)
+//     UNZIP_GC(gc_file)
+
+//     ASCAT_PLOIDY_AND_PURITY ( input ,
+//                                 UNZIP_ALLELES.out.unzipped_archive.map{ it[1] },
+//                                 UNZIP_LOCI.out.unzipped_archive.map{ it[1] },
+//                                 [],                                             // optional bed_file for WES
+//                                 [],                                             // optional fasta
+//                                 UNZIP_GC.out.unzipped_archive.map{ it[1] },     // optional GC_correction
+//                                 [])     // optional RT_correction
+
+//
+
+// }
+
+// extended tests running with 1000 genomes data. Data is downloaded as follows:
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
+// workflow test_ascat_with_crams {
+//     input = [
+//        [ id:'test', single_end:false ], // meta map
+//         file("/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true),
+//         file("/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true),
+//         file("/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true),
+//         file("/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true)
+//     ]
+
+//     allele_path  = file("/mnt/volume/repos/modules/test_ascat2/G1000_alleles_hg19.zip", checkIfExists: true)
+//     allele_files = [[ id: allele_path.BaseName ], allele_path  ]
+
+//     loci_path    = file("/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip", checkIfExists: true)
+//     loci_files   = [[ id: loci_path.BaseName ], loci_path  ]
+
+//     gc_path      = file("/mnt/volume/repos/modules/test_ascat2/GC_G1000_hg19.zip", checkIfExists: true)
+//     gc_file      = [[ id: gc_path.BaseName ], gc_path  ]
+
+//     rt_path     = file("/mnt/volume/repos/modules/test_ascat2/RT_G1000_hg19.zip", checkIfExists: true)
+//     rt_file     = [[ id: rt_path.BaseName ], rt_path  ]
+
+//     fasta   = file("/mnt/volume/ascat/human_g1k_v37.fasta", checkIfExists: true)
+
+//     UNZIP_ALLELES(allele_files)
+//     UNZIP_LOCI(loci_files)
+//     UNZIP_GC(gc_file)
+//     UNZIP_RT(rt_file)
+
+//     ASCAT_CRAM ( input ,
+//                 UNZIP_ALLELES.out.unzipped_archive.map{ it[1] },
+//                 UNZIP_LOCI.out.unzipped_archive.map{ it[1] },
+//                 [],
+//                 fasta,
+//                 UNZIP_GC.out.unzipped_archive.map{ it[1] },
+//                 UNZIP_RT.out.unzipped_archive.map{ it[1] })
+
+// }
+
+
+
diff --git a/tests/modules/ascat/nextflow.config b/tests/modules/nf-core/ascat/nextflow.config
similarity index 100%
rename from tests/modules/ascat/nextflow.config
rename to tests/modules/nf-core/ascat/nextflow.config
diff --git a/tests/modules/nf-core/ascat/test.yml b/tests/modules/nf-core/ascat/test.yml
new file mode 100644
index 00000000000..760f4b0e8b4
--- /dev/null
+++ b/tests/modules/nf-core/ascat/test.yml
@@ -0,0 +1,23 @@
+- name: ascat test_ascat
+  command: nextflow run ./tests/modules/nf-core/ascat -entry test_ascat -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - ascat
+  files:
+    - path: output/ascat/test.after_correction.gc_rt.test.tumour.germline.png
+    - path: output/ascat/test.after_correction.gc_rt.test.tumour.tumour.png
+    - path: output/ascat/test.before_correction.test.tumour.germline.png
+    - path: output/ascat/test.before_correction.test.tumour.tumour.png
+    - path: output/ascat/test.cnvs.txt
+    - path: output/ascat/test.metrics.txt
+    - path: output/ascat/test.normal_alleleFrequencies_chr21.txt
+    - path: output/ascat/test.normal_alleleFrequencies_chr22.txt
+    - path: output/ascat/test.purityploidy.txt
+    - path: output/ascat/test.segments.txt
+    - path: output/ascat/test.tumour.ASPCF.png
+    - path: output/ascat/test.tumour.sunrise.png
+    - path: output/ascat/test.tumour_alleleFrequencies_chr21.txt
+    - path: output/ascat/test.tumour_alleleFrequencies_chr22.txt
+    - path: output/ascat/test.tumour_normalBAF.txt
+    - path: output/ascat/test.tumour_normalLogR.txt
+    - path: output/ascat/test.tumour_tumourBAF.txt
+    - path: output/ascat/test.tumour_tumourLogR.txt
diff --git a/tests/modules/nf-core/assemblyscan/main.nf b/tests/modules/nf-core/assemblyscan/main.nf
new file mode 100644
index 00000000000..7ad80531fd3
--- /dev/null
+++ b/tests/modules/nf-core/assemblyscan/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ASSEMBLYSCAN } from '../../../../modules/nf-core/assemblyscan/main.nf'
+
+workflow test_assemblyscan {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    ASSEMBLYSCAN ( input )
+}
diff --git a/tests/modules/assemblyscan/nextflow.config b/tests/modules/nf-core/assemblyscan/nextflow.config
similarity index 100%
rename from tests/modules/assemblyscan/nextflow.config
rename to tests/modules/nf-core/assemblyscan/nextflow.config
diff --git a/tests/modules/nf-core/assemblyscan/test.yml b/tests/modules/nf-core/assemblyscan/test.yml
new file mode 100644
index 00000000000..c1162f1f76a
--- /dev/null
+++ b/tests/modules/nf-core/assemblyscan/test.yml
@@ -0,0 +1,7 @@
+- name: assemblyscan test_assemblyscan
+  command: nextflow run ./tests/modules/nf-core/assemblyscan -entry test_assemblyscan -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/assemblyscan/nextflow.config
+  tags:
+    - assemblyscan
+  files:
+    - path: output/assemblyscan/test.json
+      md5sum: 9140e3d43f2d676f62e1325ace5dd8bd
diff --git a/tests/modules/nf-core/ataqv/ataqv/main.nf b/tests/modules/nf-core/ataqv/ataqv/main.nf
new file mode 100644
index 00000000000..9680d68d47a
--- /dev/null
+++ b/tests/modules/nf-core/ataqv/ataqv/main.nf
@@ -0,0 +1,69 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ATAQV_ATAQV } from '../../../../../modules/nf-core/ataqv/ataqv/main.nf'
+include { ATAQV_ATAQV as ATAQV_ATAQV_PROBLEM_READS} from '../../../../../modules/nf-core/ataqv/ataqv/main.nf'
+
+workflow test_ataqv_ataqv {
+    
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+        [],
+        []
+    ]
+    
+    ATAQV_ATAQV ( input, 'human', [], [], [] )
+}
+
+workflow test_ataqv_ataqv_problem_reads {
+    
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+        [],
+        []
+    ]
+    
+    ATAQV_ATAQV_PROBLEM_READS ( input, 'human', [], [], [] )
+}
+
+workflow test_ataqv_ataqv_peak {
+    
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        [],
+        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    ]
+    
+    ATAQV_ATAQV ( input, 'human', [], [], [] )
+}
+
+workflow test_ataqv_ataqv_tss {
+    
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        []
+    ] 
+    tss_file = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+   
+    ATAQV_ATAQV ( input, 'human', tss_file, [], [] )
+}
+
+workflow test_ataqv_ataqv_excluded_regs {
+    
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        []
+    ] 
+    tss_file = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    excl_regs_file = file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
+   
+    ATAQV_ATAQV ( input, 'human', tss_file, excl_regs_file, [] )
+}
diff --git a/tests/modules/ataqv/ataqv/nextflow.config b/tests/modules/nf-core/ataqv/ataqv/nextflow.config
similarity index 100%
rename from tests/modules/ataqv/ataqv/nextflow.config
rename to tests/modules/nf-core/ataqv/ataqv/nextflow.config
diff --git a/tests/modules/nf-core/ataqv/ataqv/test.yml b/tests/modules/nf-core/ataqv/ataqv/test.yml
new file mode 100644
index 00000000000..921c3ec636c
--- /dev/null
+++ b/tests/modules/nf-core/ataqv/ataqv/test.yml
@@ -0,0 +1,50 @@
+- name: ataqv ataqv test_ataqv_ataqv
+  command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config
+  tags:
+    - ataqv
+    - ataqv/ataqv
+  files:
+    - path: output/ataqv/test.ataqv.json
+      contains:
+        - '"forward_mate_reads": 101'
+
+- name: ataqv ataqv test_ataqv_ataqv_problem_reads
+  command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv_problem_reads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config
+  tags:
+    - ataqv
+    - ataqv/ataqv
+  files:
+    - path: output/ataqv/1.problems
+    - path: output/ataqv/test.ataqv.json
+      contains:
+        - '"forward_mate_reads": 101'
+
+- name: ataqv ataqv test_ataqv_ataqv_peak
+  command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv_peak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config
+  tags:
+    - ataqv
+    - ataqv/ataqv
+  files:
+    - path: output/ataqv/test.ataqv.json
+      contains:
+        - '"forward_mate_reads": 101'
+
+- name: ataqv ataqv test_ataqv_ataqv_tss
+  command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv_tss -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config
+  tags:
+    - ataqv
+    - ataqv/ataqv
+  files:
+    - path: output/ataqv/test.ataqv.json
+      contains:
+        - '"forward_mate_reads": 101'
+
+- name: ataqv ataqv test_ataqv_ataqv_excluded_regs
+  command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv_excluded_regs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config
+  tags:
+    - ataqv
+    - ataqv/ataqv
+  files:
+    - path: output/ataqv/test.ataqv.json
+      contains:
+        - '"forward_mate_reads": 101'
diff --git a/tests/modules/nf-core/ataqv/mkarv/main.nf b/tests/modules/nf-core/ataqv/mkarv/main.nf
new file mode 100644
index 00000000000..f6b05248122
--- /dev/null
+++ b/tests/modules/nf-core/ataqv/mkarv/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ATAQV_ATAQV } from '../../../../../modules/nf-core/ataqv/ataqv/main.nf'
+include { ATAQV_MKARV } from '../../../../../modules/nf-core/ataqv/mkarv/main.nf'
+
+workflow test_ataqv_mkarv {
+
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+        [],
+        []
+    ]
+
+    ATAQV_ATAQV ( input, 'human', [], [], [] )
+    ATAQV_MKARV ( ATAQV_ATAQV.out.json.collect{ it[1]} )
+}
diff --git a/tests/modules/ataqv/mkarv/nextflow.config b/tests/modules/nf-core/ataqv/mkarv/nextflow.config
similarity index 100%
rename from tests/modules/ataqv/mkarv/nextflow.config
rename to tests/modules/nf-core/ataqv/mkarv/nextflow.config
diff --git a/tests/modules/nf-core/ataqv/mkarv/test.yml b/tests/modules/nf-core/ataqv/mkarv/test.yml
new file mode 100644
index 00000000000..184fac699e6
--- /dev/null
+++ b/tests/modules/nf-core/ataqv/mkarv/test.yml
@@ -0,0 +1,55 @@
+- name: ataqv mkarv test_ataqv_mkarv
+  command: nextflow run ./tests/modules/nf-core/ataqv/mkarv -entry test_ataqv_mkarv -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ataqv/mkarv/nextflow.config
+  tags:
+    - ataqv/mkarv
+    - ataqv
+
+  files:
+    - path: output/ataqv/html/css/ataqv.css
+      md5sum: 7bb9e18974018dd29bdc12a46a6d6d65
+    - path: output/ataqv/html/css/datatables.buttons.min.css
+      md5sum: 675306abc9d3239314f2c66c0e22ef7a
+    - path: output/ataqv/html/css/datatables.fontawesome.css
+      md5sum: 716d7a3edd2c75e712b1ffe26f12a861
+    - path: output/ataqv/html/css/datatables.min.css
+      md5sum: 00ef3e39d9302618395ab189ec8bcd9f
+    - path: output/ataqv/html/css/font-awesome.min.css
+      md5sum: 89916fa773ce96569604016ef25cab50
+    - path: output/ataqv/html/css/normalize.css
+      md5sum: 40d20cc85100840580df4346bb99d7ed
+    - path: output/ataqv/html/data/1.json.gz
+    - path: output/ataqv/html/fonts/FontAwesome.otf
+      md5sum: 9ccfa32dd4cd1b8e83f68899d85bd5e6
+    - path: output/ataqv/html/fonts/fontawesome-webfont.eot
+      md5sum: 404a525502f8e5ba7e93b9f02d9e83a9
+    - path: output/ataqv/html/fonts/fontawesome-webfont.svg
+      md5sum: bae4a87c1e5dff40baa3f49d52f5347a
+    - path: output/ataqv/html/fonts/fontawesome-webfont.ttf
+      md5sum: fb650aaf10736ffb9c4173079616bf01
+    - path: output/ataqv/html/fonts/fontawesome-webfont.woff
+      md5sum: 891e3f340c1126b4c7c142e5f6e86816
+    - path: output/ataqv/html/fonts/fontawesome-webfont.woff2
+      md5sum: 926c93d201fe51c8f351e858468980c3
+    - path: output/ataqv/html/fonts/sourcesanspro-regular.woff
+      md5sum: f7bd788f18b8c4bb93dd37d140348e1e
+    - path: output/ataqv/html/fonts/sourcesanspro-regularit.woff
+      md5sum: c3638b17f4fd76dae12fe2ae14571e57
+    - path: output/ataqv/html/fonts/sourcesanspro-semibold.woff
+      md5sum: e7fc8925d9364e9d177d9e1d08bb1855
+    - path: output/ataqv/html/fonts/sourcesanspro-semiboldit.woff
+      md5sum: f1d255aa459786dfc6aa2e488ac01245
+    - path: output/ataqv/html/index.html
+      md5sum: bf7747be761e56ad7c54c842ac88461a
+    - path: output/ataqv/html/js/ataqv.js
+      md5sum: feb291b7839e9e43ed304565e3a605d9
+    - path: output/ataqv/html/js/configuration.js
+      md5sum: 073bc07f1371e28a97098f8b10469ae4
+    - path: output/ataqv/html/js/d3.min.js
+      md5sum: db69fb2626a71a286ee772d673138aca
+    - path: output/ataqv/html/js/datatables.min.js
+      md5sum: e369b872620dadb05e4eb555b81f9112
+    - path: output/ataqv/html/js/jszip.min.js
+      md5sum: 09e492cb492ffa75484bbe10f1f721d1
+    - path: output/ataqv/test.ataqv.json
+      contains:
+        - '"properly_paired_and_mapped_reads": 192,'
diff --git a/tests/modules/nf-core/atlas/call/main.nf b/tests/modules/nf-core/atlas/call/main.nf
new file mode 100644
index 00000000000..02c3aaa156a
--- /dev/null
+++ b/tests/modules/nf-core/atlas/call/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ATLAS_CALL } from '../../../../../modules/nf-core/atlas/call/main.nf'
+
+workflow test_atlas_call {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+    fasta         = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai           = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    recal         = []
+    pmd           = []
+    known_alleles = []
+    method        = 'randomBase'
+
+    ATLAS_CALL ( input, fasta, fai, recal, pmd, known_alleles, method )
+}
diff --git a/tests/modules/atlas/call/nextflow.config b/tests/modules/nf-core/atlas/call/nextflow.config
similarity index 100%
rename from tests/modules/atlas/call/nextflow.config
rename to tests/modules/nf-core/atlas/call/nextflow.config
diff --git a/tests/modules/nf-core/atlas/call/test.yml b/tests/modules/nf-core/atlas/call/test.yml
new file mode 100644
index 00000000000..78549fa3feb
--- /dev/null
+++ b/tests/modules/nf-core/atlas/call/test.yml
@@ -0,0 +1,9 @@
+- name: atlas call test_atlas_call
+  command: nextflow run ./tests/modules/nf-core/atlas/call -entry test_atlas_call -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/atlas/call/nextflow.config
+  tags:
+    - atlas
+    - atlas/call
+  files:
+    - path: output/atlas/test.paired_end.sorted_randomBase.vcf.gz
+      contains:
+        - "##source=atlas"
diff --git a/tests/modules/nf-core/atlas/pmd/main.nf b/tests/modules/nf-core/atlas/pmd/main.nf
new file mode 100644
index 00000000000..bcba7dc3f4f
--- /dev/null
+++ b/tests/modules/nf-core/atlas/pmd/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ATLAS_PMD } from '../../../../../modules/nf-core/atlas/pmd/main.nf'
+
+workflow test_atlas_pmd {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        []
+    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    ATLAS_PMD ( input, fasta, fai )
+}
diff --git a/tests/modules/atlas/pmd/nextflow.config b/tests/modules/nf-core/atlas/pmd/nextflow.config
similarity index 100%
rename from tests/modules/atlas/pmd/nextflow.config
rename to tests/modules/nf-core/atlas/pmd/nextflow.config
diff --git a/tests/modules/nf-core/atlas/pmd/test.yml b/tests/modules/nf-core/atlas/pmd/test.yml
new file mode 100644
index 00000000000..bb2c3f973ac
--- /dev/null
+++ b/tests/modules/nf-core/atlas/pmd/test.yml
@@ -0,0 +1,14 @@
+- name: atlas pmd test_atlas_pmd
+  command: nextflow run ./tests/modules/nf-core/atlas/pmd -entry test_atlas_pmd -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/atlas/pmd/nextflow.config
+  tags:
+    - atlas/pmd
+    - atlas
+  files:
+    - path: output/atlas/test.paired_end.sorted_PMD_Table.txt
+      md5sum: b28a9f4784f30a711046708eb7d94642
+    - path: output/atlas/test.paired_end.sorted_PMD_Table_counts.txt
+      md5sum: 1aabfb83cfff6e0413f52d016c943e3e
+    - path: output/atlas/test.paired_end.sorted_PMD_input_Empiric.txt
+      md5sum: 8ff876f50ce05dc9aac0646a31682df0
+    - path: output/atlas/test.paired_end.sorted_PMD_input_Exponential.txt
+      md5sum: 2421450ef643316f4eacf5cb811e4df7
diff --git a/tests/modules/nf-core/atlas/recal/main.nf b/tests/modules/nf-core/atlas/recal/main.nf
new file mode 100644
index 00000000000..fadda2019e6
--- /dev/null
+++ b/tests/modules/nf-core/atlas/recal/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ATLAS_RECAL } from '../../../../../modules/nf-core/atlas/recal/main.nf'
+
+workflow test_atlas_recal {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        [],
+        []
+    ]
+    alleles = []
+    invariant_sites = []
+
+    ATLAS_RECAL ( input, alleles, invariant_sites )
+}
+
+
diff --git a/tests/modules/atlas/recal/nextflow.config b/tests/modules/nf-core/atlas/recal/nextflow.config
similarity index 100%
rename from tests/modules/atlas/recal/nextflow.config
rename to tests/modules/nf-core/atlas/recal/nextflow.config
diff --git a/tests/modules/nf-core/atlas/recal/test.yml b/tests/modules/nf-core/atlas/recal/test.yml
new file mode 100644
index 00000000000..a18b22c01dc
--- /dev/null
+++ b/tests/modules/nf-core/atlas/recal/test.yml
@@ -0,0 +1,8 @@
+- name: atlas recal test_atlas_recal
+  command: nextflow run ./tests/modules/nf-core/atlas/recal -entry test_atlas_recal -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/atlas/recal/nextflow.config
+  tags:
+    - atlas/recal
+    - atlas
+  files:
+    - path: output/atlas/test_recalibrationEM.txt
+      contains: ["readGroup"]
diff --git a/tests/modules/nf-core/atlas/splitmerge/main.nf b/tests/modules/nf-core/atlas/splitmerge/main.nf
new file mode 100644
index 00000000000..bde3c197329
--- /dev/null
+++ b/tests/modules/nf-core/atlas/splitmerge/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ATLAS_SPLITMERGE } from '../../../../../modules/nf-core/atlas/splitmerge/main.nf'
+
+//MAIN
+workflow test_atlas_splitmerge {
+    meta = [ id:'test', single_end:false ]
+    bam = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    bai = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    settings = file(params.test_data['homo_sapiens']['illumina']['read_group_settings_txt'], checkIfExists: true)
+
+    ATLAS_SPLITMERGE ( [meta, bam, bai, settings, []] )
+}
diff --git a/tests/modules/atlas/splitmerge/nextflow.config b/tests/modules/nf-core/atlas/splitmerge/nextflow.config
similarity index 100%
rename from tests/modules/atlas/splitmerge/nextflow.config
rename to tests/modules/nf-core/atlas/splitmerge/nextflow.config
diff --git a/tests/modules/nf-core/atlas/splitmerge/test.yml b/tests/modules/nf-core/atlas/splitmerge/test.yml
new file mode 100644
index 00000000000..c41c8e06a69
--- /dev/null
+++ b/tests/modules/nf-core/atlas/splitmerge/test.yml
@@ -0,0 +1,11 @@
+- name: atlas splitmerge test_atlas_splitmerge
+  command: nextflow run ./tests/modules/nf-core/atlas/splitmerge -entry test_atlas_splitmerge -c ./tests/config/nextflow.config
+  tags:
+    - atlas
+    - atlas/splitmerge
+  files:
+    - path: output/atlas/test.paired_end.sorted_ignoredReads.txt.gz
+      md5sum: 9b64c47313d2de89c26790f713707ee6
+    - path: output/atlas/test.paired_end.sorted_mergedReads.bam
+    - path: output/atlas/versions.yml
+      md5sum: 11735bec9c2f4b395b987fd00d4e4294
diff --git a/tests/modules/nf-core/bakta/main.nf b/tests/modules/nf-core/bakta/main.nf
new file mode 100644
index 00000000000..659d235705c
--- /dev/null
+++ b/tests/modules/nf-core/bakta/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAKTA } from '../../../../modules/nf-core/bakta/main.nf'
+
+workflow test_bakta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BAKTA ( input, [], [], [] )
+}
diff --git a/tests/modules/bakta/nextflow.config b/tests/modules/nf-core/bakta/nextflow.config
similarity index 100%
rename from tests/modules/bakta/nextflow.config
rename to tests/modules/nf-core/bakta/nextflow.config
diff --git a/tests/modules/nf-core/bakta/test.yml b/tests/modules/nf-core/bakta/test.yml
new file mode 100644
index 00000000000..1b046eec01b
--- /dev/null
+++ b/tests/modules/nf-core/bakta/test.yml
@@ -0,0 +1,14 @@
+- name: bakta
+  command: nextflow run ./tests/modules/nf-core/bakta -entry test_bakta -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - bakta
+  files:
+    - path: output/bakta/test.embl
+    - path: output/bakta/test.faa
+    - path: output/bakta/test.ffn
+    - path: output/bakta/test.fna
+    - path: output/bakta/test.gbff
+    - path: output/bakta/test.gff3
+    - path: output/bakta/test.hypotheticals.tsv
+    - path: output/bakta/test.hypotheticals.faa
+    - path: output/bakta/test.tsv
diff --git a/tests/modules/nf-core/bamaligncleaner/main.nf b/tests/modules/nf-core/bamaligncleaner/main.nf
new file mode 100644
index 00000000000..a84d410a476
--- /dev/null
+++ b/tests/modules/nf-core/bamaligncleaner/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAMALIGNCLEANER } from '../../../../modules/nf-core/bamaligncleaner/main.nf'
+
+workflow test_bamaligncleaner {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) ]
+
+    BAMALIGNCLEANER ( input )
+}
diff --git a/tests/modules/bamaligncleaner/nextflow.config b/tests/modules/nf-core/bamaligncleaner/nextflow.config
similarity index 100%
rename from tests/modules/bamaligncleaner/nextflow.config
rename to tests/modules/nf-core/bamaligncleaner/nextflow.config
diff --git a/tests/modules/nf-core/bamaligncleaner/test.yml b/tests/modules/nf-core/bamaligncleaner/test.yml
new file mode 100644
index 00000000000..a077d6124cb
--- /dev/null
+++ b/tests/modules/nf-core/bamaligncleaner/test.yml
@@ -0,0 +1,7 @@
+- name: bamaligncleaner
+  command: nextflow run ./tests/modules/nf-core/bamaligncleaner -entry test_bamaligncleaner -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamaligncleaner/nextflow.config
+  tags:
+    - bamaligncleaner
+  files:
+    - path: output/bamaligncleaner/test.bam
+      md5sum: 173cdb4c2713b77c528cac36ca2610fb
diff --git a/tests/modules/nf-core/bamcmp/main.nf b/tests/modules/nf-core/bamcmp/main.nf
new file mode 100644
index 00000000000..85d0dc5ad3c
--- /dev/null
+++ b/tests/modules/nf-core/bamcmp/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf'
+include { BWA_MEM   } from '../../../../modules/nf-core/bwa/mem/main.nf'
+include { BWA_INDEX as BWA_INDEX_COV2 } from '../../../../modules/nf-core/bwa/index/main.nf'
+include { BWA_MEM as BWA_MEM_COV2   } from '../../../../modules/nf-core/bwa/mem/main.nf'
+
+include { SAMTOOLS_SORT } from '../../../../modules/nf-core/samtools/sort/main.nf'
+include { SAMTOOLS_SORT as SAMTOOLS_SORT_COV2   } from '../../../../modules/nf-core/samtools/sort/main.nf'
+
+include { BAMCMP } from '../../../../modules/nf-core/bamcmp/main.nf'
+
+workflow test_bamcmp {
+
+    input = [
+        [ id:'test'], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    fasta1 = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta2 = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta1 )
+    BWA_MEM ( input, BWA_INDEX.out.index, false )
+    SAMTOOLS_SORT (BWA_MEM.out.bam)
+
+
+    BWA_INDEX_COV2 ( fasta2 )
+    BWA_MEM_COV2 ( input, BWA_INDEX_COV2.out.index, false )
+    SAMTOOLS_SORT_COV2 (BWA_MEM_COV2.out.bam)
+
+    BAMCMP (SAMTOOLS_SORT.out.bam.join(SAMTOOLS_SORT_COV2.out.bam, by: [0]))
+
+}
diff --git a/tests/modules/bamcmp/nextflow.config b/tests/modules/nf-core/bamcmp/nextflow.config
similarity index 100%
rename from tests/modules/bamcmp/nextflow.config
rename to tests/modules/nf-core/bamcmp/nextflow.config
diff --git a/tests/modules/nf-core/bamcmp/test.yml b/tests/modules/nf-core/bamcmp/test.yml
new file mode 100644
index 00000000000..a7b65bae1f5
--- /dev/null
+++ b/tests/modules/nf-core/bamcmp/test.yml
@@ -0,0 +1,11 @@
+- name: bamcmp test_bamcmp
+  command: nextflow run ./tests/modules/nf-core/bamcmp -entry test_bamcmp -c ./tests/config/nextflow.config
+  tags:
+    - bamcmp
+  files:
+    - path: output/bamcmp/test_contamination.bam
+      md5sum: 1fe730936d489c637479c1e51dd8ca55
+    - path: output/bamcmp/test_primary.bam
+      md5sum: 80b9abd8ef83e63548a9b8b82be2a034
+    - path: output/bamcmp/versions.yml
+      md5sum: 34d569665ff0459e84114e966dd3483b
diff --git a/tests/modules/nf-core/bamtools/convert/main.nf b/tests/modules/nf-core/bamtools/convert/main.nf
new file mode 100644
index 00000000000..e4bbfb61b8b
--- /dev/null
+++ b/tests/modules/nf-core/bamtools/convert/main.nf
@@ -0,0 +1,104 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR }   from '../../../../../modules/nf-core/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../../modules/nf-core/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED }         from '../../../../../modules/nf-core/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA }       from '../../../../../modules/nf-core/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ }       from '../../../../../modules/nf-core/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON }        from '../../../../../modules/nf-core/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP }      from '../../../../../modules/nf-core/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM }         from '../../../../../modules/nf-core/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML }        from '../../../../../modules/nf-core/bamtools/convert/main.nf'
+
+workflow test_bamtools_convert_ext_error {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_EXT_ERROR ( input )
+}
+
+workflow test_bamtools_convert_noext_error {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_NOEXT_ERROR ( input )
+}
+
+workflow test_bamtools_convert_bed {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_BED ( input )
+}
+
+workflow test_bamtools_convert_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_FASTA ( input )
+}
+
+workflow test_bamtools_convert_fastq {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_FASTQ ( input )
+}
+
+workflow test_bamtools_convert_json {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_JSON ( input )
+}
+
+workflow test_bamtools_convert_pileup {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_PILEUP ( input )
+}
+
+workflow test_bamtools_convert_sam {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_SAM ( input )
+}
+
+workflow test_bamtools_convert_yaml {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_YAML ( input )
+}
+
diff --git a/tests/modules/bamtools/convert/nextflow.config b/tests/modules/nf-core/bamtools/convert/nextflow.config
similarity index 100%
rename from tests/modules/bamtools/convert/nextflow.config
rename to tests/modules/nf-core/bamtools/convert/nextflow.config
diff --git a/tests/modules/nf-core/bamtools/convert/test.yml b/tests/modules/nf-core/bamtools/convert/test.yml
new file mode 100644
index 00000000000..f930f0d5846
--- /dev/null
+++ b/tests/modules/nf-core/bamtools/convert/test.yml
@@ -0,0 +1,90 @@
+- name: bamtools convert test_bamtools_convert_ext_error
+  command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_ext_error -c ./tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  exit_code: 1
+
+- name: bamtools convert test_bamtools_convert_noext_error
+  command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_noext_error -c ./tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  exit_code: 1
+
+- name: bamtools convert test_bamtools_convert_bed
+  command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_bed -c ./tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.bed
+      md5sum: 4e34cc15bf31e700f5f3a9f8fffb6c81
+    - path: output/bamtools/versions.yml
+      md5sum: eb7a144b8a97965d3482f6f96b8a8243
+
+- name: bamtools convert test_bamtools_convert_fasta
+  command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_fasta -c ./tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.fasta
+      md5sum: 52aeacf78571862b7e97c7d44ac8f827
+    - path: output/bamtools/versions.yml
+      md5sum: 42d19a2b2b07f05edb82b34369dfd754
+
+- name: bamtools convert test_bamtools_convert_fastq
+  command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_fastq -c ./tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.fastq
+      md5sum: e591c48daad2c56638e5d6f21f1f71c5
+    - path: output/bamtools/versions.yml
+      md5sum: 13f0bf8a3e1f8f527f96dabaa5c8051e
+
+- name: bamtools convert test_bamtools_convert_json
+  command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_json -c ./tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.json
+      md5sum: 04afed696f9f14da85a460353645d1f5
+    - path: output/bamtools/versions.yml
+      md5sum: 33d633dbd6209cb93c9b071f8c0ed3b3
+
+- name: bamtools convert test_bamtools_convert_pileup
+  command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_pileup -c ./tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.pileup
+      md5sum: e5a3cb4a3e1bf980a575fafce6a2826f
+    - path: output/bamtools/versions.yml
+      md5sum: fd3ad0edd1e085b1a002e0593d1d5814
+
+- name: bamtools convert test_bamtools_convert_sam
+  command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_sam -c ./tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.sam
+      md5sum: 61ab3d0de16a9da8b651f9c692e19d5e
+    - path: output/bamtools/versions.yml
+      md5sum: 4be470ce3cc0143ae5ae415b612a4965
+
+- name: bamtools convert test_bamtools_convert_yaml
+  command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_yaml -c ./tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.yaml
+      md5sum: 68b56f198da036fef33e150eb773dc3b
+    - path: output/bamtools/versions.yml
+      md5sum: 1116abc088c5edf11bee393961c18b3e
diff --git a/tests/modules/nf-core/bamtools/split/main.nf b/tests/modules/nf-core/bamtools/split/main.nf
new file mode 100644
index 00000000000..504ecef4bbd
--- /dev/null
+++ b/tests/modules/nf-core/bamtools/split/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE   } from '../../../../../modules/nf-core/bamtools/split/main.nf'
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../../modules/nf-core/bamtools/split/main.nf'
+
+workflow test_bamtools_split_single_input {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_SPLIT_SINGLE ( input )
+}
+
+workflow test_bamtools_split_multiple {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+        ]
+    ]
+
+    BAMTOOLS_SPLIT_MULTIPLE ( input )
+}
+
diff --git a/tests/modules/bamtools/split/nextflow.config b/tests/modules/nf-core/bamtools/split/nextflow.config
similarity index 100%
rename from tests/modules/bamtools/split/nextflow.config
rename to tests/modules/nf-core/bamtools/split/nextflow.config
diff --git a/tests/modules/nf-core/bamtools/split/test.yml b/tests/modules/nf-core/bamtools/split/test.yml
new file mode 100644
index 00000000000..5decdc06e6f
--- /dev/null
+++ b/tests/modules/nf-core/bamtools/split/test.yml
@@ -0,0 +1,23 @@
+- name: bamtools split test_bamtools_split_single_input
+  command: nextflow run ./tests/modules/nf-core/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamtools/split/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/split
+  files:
+    - path: output/bamtools/test.REF_chr22.bam
+      md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
+    - path: output/bamtools/test.REF_unmapped.bam
+      md5sum: e0754bf72c51543b2d745d96537035fb
+    - path: output/bamtools/versions.yml
+
+- name: bamtools split test_bamtools_split_multiple
+  command: nextflow run ./tests/modules/nf-core/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamtools/split/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/split
+  files:
+    - path: output/bamtools/test.REF_chr22.bam
+      md5sum: 585675bea34c48ebe9db06a561d4b4fa
+    - path: output/bamtools/test.REF_unmapped.bam
+      md5sum: 16ad644c87b9471f3026bc87c98b4963
+    - path: output/bamtools/versions.yml
diff --git a/tests/modules/nf-core/bamtools/stats/main.nf b/tests/modules/nf-core/bamtools/stats/main.nf
new file mode 100644
index 00000000000..6adbb060bea
--- /dev/null
+++ b/tests/modules/nf-core/bamtools/stats/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAMTOOLS_STATS } from '../../../../../modules/nf-core/bamtools/stats/main.nf'
+
+workflow test_bamtools_stats {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_STATS ( input )
+}
diff --git a/tests/modules/bamtools/stats/nextflow.config b/tests/modules/nf-core/bamtools/stats/nextflow.config
similarity index 100%
rename from tests/modules/bamtools/stats/nextflow.config
rename to tests/modules/nf-core/bamtools/stats/nextflow.config
diff --git a/tests/modules/nf-core/bamtools/stats/test.yml b/tests/modules/nf-core/bamtools/stats/test.yml
new file mode 100644
index 00000000000..938a2c7c9ef
--- /dev/null
+++ b/tests/modules/nf-core/bamtools/stats/test.yml
@@ -0,0 +1,8 @@
+- name: bamtools stats test_bamtools_stats
+  command: nextflow run ./tests/modules/nf-core/bamtools/stats -entry test_bamtools_stats -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bamtools/stats/nextflow.config
+  tags:
+    - bamtools/stats
+    - bamtools
+  files:
+    - path: output/bamtools/test.bam.stats
+      md5sum: b7c3f01682673a652d664a2889b15b66
diff --git a/tests/modules/nf-core/bamutil/trimbam/main.nf b/tests/modules/nf-core/bamutil/trimbam/main.nf
new file mode 100644
index 00000000000..b2359338d88
--- /dev/null
+++ b/tests/modules/nf-core/bamutil/trimbam/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAMUTIL_TRIMBAM } from '../../../../../modules/nf-core/bamutil/trimbam/main.nf'
+
+workflow test_bamutil_trimbam {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+              2,
+              2 ]
+
+    BAMUTIL_TRIMBAM ( input )
+}
diff --git a/tests/modules/bamutil/trimbam/nextflow.config b/tests/modules/nf-core/bamutil/trimbam/nextflow.config
similarity index 100%
rename from tests/modules/bamutil/trimbam/nextflow.config
rename to tests/modules/nf-core/bamutil/trimbam/nextflow.config
diff --git a/tests/modules/nf-core/bamutil/trimbam/test.yml b/tests/modules/nf-core/bamutil/trimbam/test.yml
new file mode 100644
index 00000000000..ec9371afd74
--- /dev/null
+++ b/tests/modules/nf-core/bamutil/trimbam/test.yml
@@ -0,0 +1,8 @@
+- name: bamutil trimbam test_bamutil_trimbam
+  command: nextflow run ./tests/modules/nf-core/bamutil/trimbam -entry test_bamutil_trimbam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamutil/trimbam/nextflow.config
+  tags:
+    - bamutil/trimbam
+    - bamutil
+  files:
+    - path: output/bamutil/test.bam
+      md5sum: 9ddd0ecca82f7f3433383f3d1308970e
diff --git a/tests/modules/nf-core/bandage/image/main.nf b/tests/modules/nf-core/bandage/image/main.nf
new file mode 100644
index 00000000000..3da08d40bc0
--- /dev/null
+++ b/tests/modules/nf-core/bandage/image/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BANDAGE_IMAGE } from '../../../../../modules/nf-core/bandage/image/main.nf'
+
+workflow test_bandage_image {
+    input = [
+        [ id:'B-3106' ], // meta map
+        file( params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)
+    ]
+
+    BANDAGE_IMAGE ( input )
+}
diff --git a/tests/modules/bandage/image/nextflow.config b/tests/modules/nf-core/bandage/image/nextflow.config
similarity index 100%
rename from tests/modules/bandage/image/nextflow.config
rename to tests/modules/nf-core/bandage/image/nextflow.config
diff --git a/tests/modules/nf-core/bandage/image/test.yml b/tests/modules/nf-core/bandage/image/test.yml
new file mode 100644
index 00000000000..07949fcd17c
--- /dev/null
+++ b/tests/modules/nf-core/bandage/image/test.yml
@@ -0,0 +1,8 @@
+- name: bandage image
+  command: nextflow run ./tests/modules/nf-core/bandage/image -entry test_bandage_image -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bandage/image/nextflow.config
+  tags:
+    - bandage
+    - bandage/image
+  files:
+    - path: output/bandage/B-3106.png
+    - path: output/bandage/B-3106.svg
diff --git a/tests/modules/nf-core/bases2fastq/main.nf b/tests/modules/nf-core/bases2fastq/main.nf
new file mode 100644
index 00000000000..d9fdac02715
--- /dev/null
+++ b/tests/modules/nf-core/bases2fastq/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BASES2FASTQ } from '../../../../modules/nf-core/bases2fastq/main.nf'
+include { UNTAR      } from '../../../../modules/nf-core/untar/main.nf'
+
+workflow test_bases2fastq {
+    
+    input = Channel.value([
+        [ id:'sim-data' ], // meta map
+        file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv", checkIfExists: true),
+    ])
+
+    ch_input = input.join(
+        UNTAR ( [
+            [ id:'sim-data' ],
+            file("https://github.com/nf-core/test-datasets/raw/demultiplex/testdata/sim-data/sim-data.tar.gz", checkIfExists: true)
+        ]).untar
+    )
+
+    BASES2FASTQ ( ch_input )
+}
diff --git a/tests/modules/bases2fastq/nextflow.config b/tests/modules/nf-core/bases2fastq/nextflow.config
similarity index 100%
rename from tests/modules/bases2fastq/nextflow.config
rename to tests/modules/nf-core/bases2fastq/nextflow.config
diff --git a/tests/modules/nf-core/bases2fastq/test.yml b/tests/modules/nf-core/bases2fastq/test.yml
new file mode 100644
index 00000000000..88fe9c238da
--- /dev/null
+++ b/tests/modules/nf-core/bases2fastq/test.yml
@@ -0,0 +1,18 @@
+- name: "bases2fastq"
+  command: nextflow run ./tests/modules/nf-core/bases2fastq -entry test_bases2fastq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bases2fastq/nextflow.config
+  tags:
+    - "bases2fastq"
+  files:
+    - path: output/bases2fastq/output/Bases2Fastq-Sim_QC.html
+    - path: output/bases2fastq/output/Metrics.csv
+      md5sum: 0ec6da2b82e191098283474356024abf
+    - path: output/bases2fastq/output/RunManifest.json
+      md5sum: a07dce8ee25c2a6f9355b677c26b53e2
+    - path: output/bases2fastq/output/RunStats.json
+    - path: output/bases2fastq/output/UnassignedSequences.csv
+      md5sum: 11c1693830ce941b8cfb8d2431a59097
+    - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R1.fastq.gz
+      md5sum: 218abc70f61e8e8199a68f83ae836184
+    - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R2.fastq.gz
+      md5sum: b95109bfb204daa150b61239d3368ee2
+    - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_stats.json
diff --git a/tests/modules/nf-core/bbmap/align/main.nf b/tests/modules/nf-core/bbmap/align/main.nf
new file mode 100644
index 00000000000..f2bfcd9069c
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/align/main.nf
@@ -0,0 +1,59 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BBMAP_INDEX } from '../../../../../modules/nf-core/bbmap/index/main.nf'
+include { BBMAP_ALIGN } from '../../../../../modules/nf-core/bbmap/align/main.nf'
+include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../../modules/nf-core/bbmap/align/main.nf'
+
+workflow test_bbmap_align_paired_end_fasta_ref {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                [
+                    file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                    file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BBMAP_ALIGN ( input, fasta )
+}
+
+workflow test_bbmap_align_paired_end_index_ref {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                [
+                    file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                    file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BBMAP_INDEX ( fasta )
+    BBMAP_ALIGN ( input, BBMAP_INDEX.out.index )
+}
+
+workflow test_bbmap_align_single_end_index_ref {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+                file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BBMAP_INDEX ( fasta )
+    BBMAP_ALIGN ( input, BBMAP_INDEX.out.index )
+}
+
+workflow test_bbmap_align_paired_end_index_ref_pigz {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                [
+                    file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                    file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BBMAP_INDEX ( fasta )
+    BBMAP_ALIGN_PIGZ ( input, BBMAP_INDEX.out.index )
+}
diff --git a/tests/modules/bbmap/align/nextflow.config b/tests/modules/nf-core/bbmap/align/nextflow.config
similarity index 100%
rename from tests/modules/bbmap/align/nextflow.config
rename to tests/modules/nf-core/bbmap/align/nextflow.config
diff --git a/tests/modules/nf-core/bbmap/align/test.yml b/tests/modules/nf-core/bbmap/align/test.yml
new file mode 100644
index 00000000000..cc3c7f76d3a
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/align/test.yml
@@ -0,0 +1,39 @@
+- name: bbmap align paired end fasta ref
+  command: nextflow run ./tests/modules/nf-core/bbmap/align -entry test_bbmap_align_paired_end_fasta_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/align/nextflow.config
+  tags:
+    - bbmap
+    - bbmap/align
+  files:
+    - path: output/bbmap/test.bam
+      md5sum: 8549040067d23949bddb6fe2ad211c92
+    - path: output/bbmap/test.bbmap.log
+
+- name: bbmap align paired end index ref
+  command: nextflow run ./tests/modules/nf-core/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/align/nextflow.config
+  tags:
+    - bbmap
+    - bbmap/align
+  files:
+    - path: output/bbmap/test.bam
+      md5sum: aeb842491ca6c7806aa7103b5223620f
+    - path: output/bbmap/test.bbmap.log
+
+- name: bbmap align single end index ref
+  command: nextflow run ./tests/modules/nf-core/bbmap/align -entry test_bbmap_align_single_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/align/nextflow.config
+  tags:
+    - bbmap
+    - bbmap/align
+  files:
+    - path: output/bbmap/test.bam
+      md5sum: b6a41cb344a343d46244d8f94eb66ec0
+    - path: output/bbmap/test.bbmap.log
+
+- name: bbmap align paired end index ref pigz
+  command: nextflow run ./tests/modules/nf-core/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/align/nextflow.config
+  tags:
+    - bbmap
+    - bbmap/align
+  files:
+    - path: output/bbmap/test.bam
+      md5sum: 74944e24acccb8c5abc316dcdd623c84
+    - path: output/bbmap/test.bbmap.log
diff --git a/tests/modules/nf-core/bbmap/bbduk/main.nf b/tests/modules/nf-core/bbmap/bbduk/main.nf
new file mode 100644
index 00000000000..a0e8c57d9c8
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/bbduk/main.nf
@@ -0,0 +1,45 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BBMAP_BBDUK } from '../../../../../modules/nf-core/bbmap/bbduk/main.nf'
+
+workflow test_bbmap_bbduk_single_end {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    BBMAP_BBDUK ( input, [] )
+}
+
+workflow test_bbmap_bbduk_paired_end {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    BBMAP_BBDUK ( input, [] )
+}
+
+workflow test_bbmap_bbduk_se_ref {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    contaminants = [file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] // transciptome file - remove contaminants (*trim.fastq files empty)
+
+    BBMAP_BBDUK ( input, contaminants )
+}
+
+workflow test_bbmap_bbduk_pe_ref {
+
+    input =  [  [ id:'test', single_end:false ], // meta map
+                [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+             ]
+    contaminants = [file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+
+    BBMAP_BBDUK ( input, contaminants )
+}
diff --git a/tests/modules/bbmap/bbduk/nextflow.config b/tests/modules/nf-core/bbmap/bbduk/nextflow.config
similarity index 100%
rename from tests/modules/bbmap/bbduk/nextflow.config
rename to tests/modules/nf-core/bbmap/bbduk/nextflow.config
diff --git a/tests/modules/nf-core/bbmap/bbduk/test.yml b/tests/modules/nf-core/bbmap/bbduk/test.yml
new file mode 100644
index 00000000000..61543e0042f
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/bbduk/test.yml
@@ -0,0 +1,47 @@
+- name: bbmap bbduk test_bbmap_bbduk_single_end
+  command: nextflow run ./tests/modules/nf-core/bbmap/bbduk -entry test_bbmap_bbduk_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbduk/nextflow.config
+  tags:
+    - bbmap/bbduk
+  files:
+    - path: output/bbmap/test.trim.bbduk.log
+      contains:
+        - "Input is being processed as unpaired"
+    - path: output/bbmap/test.trim.fastq.gz
+      md5sum: a87d0cbd5ced7df8bf1751e4cb407482
+
+- name: bbmap bbduk test_bbmap_bbduk_paired_end
+  command: nextflow run ./tests/modules/nf-core/bbmap/bbduk -entry test_bbmap_bbduk_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbduk/nextflow.config
+  tags:
+    - bbmap/bbduk
+  files:
+    - path: output/bbmap/test.trim.bbduk.log
+      contains:
+        - "Input is being processed as paired"
+    - path: output/bbmap/test.trim_1.fastq.gz
+      md5sum: a87d0cbd5ced7df8bf1751e4cb407482
+    - path: output/bbmap/test.trim_2.fastq.gz
+      md5sum: 406e068fbe198f02b48e7e210cc0c69f
+
+- name: bbmap bbduk test_bbmap_bbduk_se_ref
+  command: nextflow run ./tests/modules/nf-core/bbmap/bbduk -entry test_bbmap_bbduk_se_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbduk/nextflow.config
+  tags:
+    - bbmap/bbduk
+  files:
+    - path: output/bbmap/test.trim.bbduk.log
+      contains:
+        - "Input is being processed as unpaired"
+    - path: output/bbmap/test.trim.fastq.gz
+      md5sum: 3970e82605c7d109bb348fc94e9eecc0
+
+- name: bbmap bbduk test_bbmap_bbduk_pe_ref
+  command: nextflow run ./tests/modules/nf-core/bbmap/bbduk -entry test_bbmap_bbduk_pe_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbduk/nextflow.config
+  tags:
+    - bbmap/bbduk
+  files:
+    - path: output/bbmap/test.trim.bbduk.log
+      contains:
+        - "Input is being processed as paired"
+    - path: output/bbmap/test.trim_1.fastq.gz
+      md5sum: 3970e82605c7d109bb348fc94e9eecc0
+    - path: output/bbmap/test.trim_2.fastq.gz
+      md5sum: 3970e82605c7d109bb348fc94e9eecc0
diff --git a/tests/modules/nf-core/bbmap/bbsplit/main.nf b/tests/modules/nf-core/bbmap/bbsplit/main.nf
new file mode 100644
index 00000000000..ede4b7d0bef
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/bbsplit/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../../modules/nf-core/bbmap/bbsplit/main.nf'
+include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../../modules/nf-core/bbmap/bbsplit/main.nf'
+
+workflow test_bbmap_bbsplit {
+
+    input = [ 
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    bbsplit_fasta_list = [ 
+        ['human'],
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/chr22_23800000-23980000.fa', checkIfExists: true) 
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+	
+    BBMAP_BBSPLIT_INDEX ( [ [:], [] ], [], fasta, bbsplit_fasta_list, true )
+    BBMAP_BBSPLIT_SPLIT ( input, BBMAP_BBSPLIT_INDEX.out.index, fasta, bbsplit_fasta_list, true )
+}
diff --git a/tests/modules/bbmap/bbsplit/nextflow.config b/tests/modules/nf-core/bbmap/bbsplit/nextflow.config
similarity index 100%
rename from tests/modules/bbmap/bbsplit/nextflow.config
rename to tests/modules/nf-core/bbmap/bbsplit/nextflow.config
diff --git a/tests/modules/nf-core/bbmap/bbsplit/test.yml b/tests/modules/nf-core/bbmap/bbsplit/test.yml
new file mode 100644
index 00000000000..7c6e4f37d18
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/bbsplit/test.yml
@@ -0,0 +1,24 @@
+- name: bbmap bbsplit test_bbmap_bbsplit
+  command: nextflow run ./tests/modules/nf-core/bbmap/bbsplit -entry test_bbmap_bbsplit -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbsplit/nextflow.config
+  tags:
+    - bbmap/bbsplit
+    - bbmap
+  files:
+    - path: output/bbmap/bbsplit/ref/genome/1/chr1.chrom.gz
+    - path: output/bbmap/bbsplit/ref/genome/1/info.txt
+      contains:
+        - "Chromosome"
+    - path: output/bbmap/bbsplit/ref/genome/1/merged_ref_9222711925172838098.fa.gz
+    - path: output/bbmap/bbsplit/ref/genome/1/namelist.txt
+      md5sum: 45e7a4cdc7a11a39ada56844ca3a1e30
+    - path: output/bbmap/bbsplit/ref/genome/1/reflist.txt
+      contains:
+        - "genome.fasta"
+    - path: output/bbmap/bbsplit/ref/genome/1/scaffolds.txt.gz
+    - path: output/bbmap/bbsplit/ref/genome/1/summary.txt
+      contains:
+        - "scaffolds"
+    - path: output/bbmap/bbsplit/ref/index/1/chr1_index_k13_c13_b1.block
+      md5sum: 385913c1e84b77dc7bf36288ee1c8706
+    - path: output/bbmap/bbsplit/ref/index/1/chr1_index_k13_c13_b1.block2.gz
+      md5sum: 9de572b603abe5b6540056db8dee05a5
diff --git a/tests/modules/nf-core/bbmap/clumpify/main.nf b/tests/modules/nf-core/bbmap/clumpify/main.nf
new file mode 100644
index 00000000000..65b49acce8e
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/clumpify/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BBMAP_CLUMPIFY } from '../../../../../modules/nf-core/bbmap/clumpify/main.nf'
+
+workflow test_bbmap_clumpify_single_end {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    BBMAP_CLUMPIFY ( input )
+}
+
+workflow test_bbmap_clumpify_paired_end {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              [  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    BBMAP_CLUMPIFY ( input )
+}
diff --git a/tests/modules/bbmap/clumpify/nextflow.config b/tests/modules/nf-core/bbmap/clumpify/nextflow.config
similarity index 100%
rename from tests/modules/bbmap/clumpify/nextflow.config
rename to tests/modules/nf-core/bbmap/clumpify/nextflow.config
diff --git a/tests/modules/nf-core/bbmap/clumpify/test.yml b/tests/modules/nf-core/bbmap/clumpify/test.yml
new file mode 100644
index 00000000000..65975b4f70d
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/clumpify/test.yml
@@ -0,0 +1,18 @@
+- name: bbmap clumpify test_bbmap_clumpify_single_end
+  command: nextflow run ./tests/modules/nf-core/bbmap/clumpify -entry test_bbmap_clumpify_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bbmap/clumpify/nextflow.config
+  tags:
+    - bbmap/clumpify
+    - bbmap
+  files:
+    - path: output/bbmap/test.clumped.fastq.gz
+    - path: output/bbmap/test.clumpify.log
+
+- name: bbmap clumpify test_bbmap_clumpify_paired_end
+  command: nextflow run ./tests/modules/nf-core/bbmap/clumpify -entry test_bbmap_clumpify_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bbmap/clumpify/nextflow.config
+  tags:
+    - bbmap/clumpify
+    - bbmap
+  files:
+    - path: output/bbmap/test.clumpify.log
+    - path: output/bbmap/test_1.clumped.fastq.gz
+    - path: output/bbmap/test_2.clumped.fastq.gz
diff --git a/tests/modules/nf-core/bbmap/index/main.nf b/tests/modules/nf-core/bbmap/index/main.nf
new file mode 100644
index 00000000000..1c1ad0f422e
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/index/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BBMAP_INDEX } from '../../../../../modules/nf-core/bbmap/index/main.nf'
+
+workflow test_bbmap_index {
+    
+    input = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BBMAP_INDEX ( input )
+}
diff --git a/tests/modules/bbmap/index/nextflow.config b/tests/modules/nf-core/bbmap/index/nextflow.config
similarity index 100%
rename from tests/modules/bbmap/index/nextflow.config
rename to tests/modules/nf-core/bbmap/index/nextflow.config
diff --git a/tests/modules/nf-core/bbmap/index/test.yml b/tests/modules/nf-core/bbmap/index/test.yml
new file mode 100644
index 00000000000..d9956fabca4
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/index/test.yml
@@ -0,0 +1,9 @@
+- name: bbmap index
+  command: nextflow run ./tests/modules/nf-core/bbmap/index -entry test_bbmap_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/index/nextflow.config
+  tags:
+    - bbmap
+    - bbmap/index
+  files:
+    - path: output/bbmap/ref/genome/1/chr1.chrom.gz
+    - path: output/bbmap/ref/index/1/chr1_index_k13_c15_b1.block
+      md5sum: 9f0d9a7413c1d2c16cc24555b2381163
diff --git a/tests/modules/nf-core/bbmap/pileup/main.nf b/tests/modules/nf-core/bbmap/pileup/main.nf
new file mode 100644
index 00000000000..beb482abfce
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/pileup/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BBMAP_PILEUP } from '../../../../../modules/nf-core/bbmap/pileup/main.nf'
+
+workflow test_bbmap_pileup {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BBMAP_PILEUP ( input )
+}
diff --git a/tests/modules/bbmap/pileup/nextflow.config b/tests/modules/nf-core/bbmap/pileup/nextflow.config
similarity index 100%
rename from tests/modules/bbmap/pileup/nextflow.config
rename to tests/modules/nf-core/bbmap/pileup/nextflow.config
diff --git a/tests/modules/nf-core/bbmap/pileup/test.yml b/tests/modules/nf-core/bbmap/pileup/test.yml
new file mode 100644
index 00000000000..ac65b30a914
--- /dev/null
+++ b/tests/modules/nf-core/bbmap/pileup/test.yml
@@ -0,0 +1,12 @@
+- name: "bbmap pileup"
+  command: nextflow run ./tests/modules/nf-core/bbmap/pileup -entry test_bbmap_pileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/pileup/nextflow.config
+  tags:
+    - "bbmap"
+    - "bbmap/pileup"
+  files:
+    - path: "output/bbmap/test.coverage.stats.txt"
+      md5sum: c3fc9d0681589b69e3301ca3cb27b7a4
+    - path: "output/bbmap/test.coverage.hist.txt"
+      md5sum: 96915920ef42ddc9483457dd4585a088
+    - path: output/bbmap/versions.yml
+      md5sum: e2bc51873b24e7fea269b7c1501de060
diff --git a/tests/modules/nf-core/bcftools/annotate/main.nf b/tests/modules/nf-core/bcftools/annotate/main.nf
new file mode 100644
index 00000000000..df59b6465c9
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/annotate/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_ANNOTATE } from '../../../../../modules/nf-core/bcftools/annotate/main.nf'
+
+workflow test_bcftools_annotate_out_vcf {
+
+    input = [ 
+    [ id:'test_compressed_vcf', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+
+    BCFTOOLS_ANNOTATE ( input )
+}
+
+workflow test_bcftools_annotate_out_bcf {
+
+    input = [ 
+    [ id:'test_compressed_bcf', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_bcf'], checkIfExists: true) ]
+
+    BCFTOOLS_ANNOTATE ( input )
+}
diff --git a/tests/modules/bcftools/annotate/nextflow.config b/tests/modules/nf-core/bcftools/annotate/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/annotate/nextflow.config
rename to tests/modules/nf-core/bcftools/annotate/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/annotate/test.yml b/tests/modules/nf-core/bcftools/annotate/test.yml
new file mode 100644
index 00000000000..22027d3e5de
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/annotate/test.yml
@@ -0,0 +1,19 @@
+- name: bcftools annotate test_bcftools_annotate_out_vcf
+  command: nextflow run ./tests/modules/nf-core/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c ./tests/config/nextflow.config
+  tags:
+    - bcftools/annotate
+    - bcftools
+  files:
+    - path: output/bcftools/test_compressed_vcf_annotated.vcf.gz
+    - path: output/bcftools/versions.yml
+      md5sum: ff237d88fce62300fdab66b284e9aa95
+
+- name: bcftools annotate test_bcftools_annotate_out_bcf
+  command: nextflow run ./tests/modules/nf-core/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c ./tests/config/nextflow.config
+  tags:
+    - bcftools/annotate
+    - bcftools
+  files:
+    - path: output/bcftools/test_compressed_bcf_annotated.bcf
+    - path: output/bcftools/versions.yml
+      md5sum: bbcefb8ebfca05c538a92dbfb94d977e
diff --git a/tests/modules/nf-core/bcftools/concat/main.nf b/tests/modules/nf-core/bcftools/concat/main.nf
new file mode 100644
index 00000000000..582af6db550
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/concat/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_CONCAT } from '../../../../../modules/nf-core/bcftools/concat/main.nf'
+
+workflow test_bcftools_concat_tbi {
+    
+    input = [ [ id:'test3' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) ]
+            ]
+
+    BCFTOOLS_CONCAT ( input )
+}
+
+workflow test_bcftools_concat_no_tbi {
+    
+    input = [ [ id:'test3' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
+              []
+            ]
+
+    BCFTOOLS_CONCAT ( input )
+}
diff --git a/tests/modules/bcftools/concat/nextflow.config b/tests/modules/nf-core/bcftools/concat/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/concat/nextflow.config
rename to tests/modules/nf-core/bcftools/concat/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/concat/test.yml b/tests/modules/nf-core/bcftools/concat/test.yml
new file mode 100644
index 00000000000..495676f3086
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/concat/test.yml
@@ -0,0 +1,17 @@
+- name: bcftools concat test_bcftools_concat_tbi
+  command: nextflow run ./tests/modules/nf-core/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcftools/concat/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/concat
+  files:
+    - path: output/bcftools/test3.vcf.gz
+      md5sum: 1f6a3ffdffbc56e0bc1b184e70ee88df
+
+- name: bcftools concat test_bcftools_concat_no_tbi
+  command: nextflow run ./tests/modules/nf-core/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcftools/concat/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/concat
+  files:
+    - path: output/bcftools/test3.vcf.gz
+      md5sum: 1f6a3ffdffbc56e0bc1b184e70ee88df
diff --git a/tests/modules/nf-core/bcftools/consensus/main.nf b/tests/modules/nf-core/bcftools/consensus/main.nf
new file mode 100644
index 00000000000..ffc3c5f9545
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/consensus/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_CONSENSUS } from '../../../../../modules/nf-core/bcftools/consensus/main.nf'
+
+workflow test_bcftools_consensus {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BCFTOOLS_CONSENSUS ( input )
+}
diff --git a/tests/modules/bcftools/consensus/nextflow.config b/tests/modules/nf-core/bcftools/consensus/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/consensus/nextflow.config
rename to tests/modules/nf-core/bcftools/consensus/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/consensus/test.yml b/tests/modules/nf-core/bcftools/consensus/test.yml
new file mode 100644
index 00000000000..26a554217e1
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/consensus/test.yml
@@ -0,0 +1,8 @@
+- name: bcftools consensus test_bcftools_consensus
+  command: nextflow run ./tests/modules/nf-core/bcftools/consensus -entry test_bcftools_consensus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/consensus/nextflow.config
+  tags:
+    - bcftools/consensus
+    - bcftools
+  files:
+    - path: output/bcftools/test.fa
+      md5sum: e57d3e4d113f989bc069c5fd61627091
diff --git a/tests/modules/nf-core/bcftools/convert/main.nf b/tests/modules/nf-core/bcftools/convert/main.nf
new file mode 100644
index 00000000000..5ea3c9a52bb
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/convert/main.nf
@@ -0,0 +1,51 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_GVCF } from '../../../../../modules/nf-core/bcftools/convert/main.nf'
+include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_BCF  } from '../../../../../modules/nf-core/bcftools/convert/main.nf'
+
+workflow test_bcftools_convert_gvcf {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+        []
+    ]
+
+    bed = []
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BCFTOOLS_CONVERT_GVCF ( input, bed, fasta )
+}
+
+workflow test_bcftools_convert_gvcf_bed {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BCFTOOLS_CONVERT_GVCF ( input, bed, fasta )
+}
+
+workflow test_bcftools_convert_gvcf_to_bcf {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+        []
+    ]
+
+    bed = []
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BCFTOOLS_CONVERT_BCF ( input, bed, fasta )
+}
diff --git a/tests/modules/bcftools/convert/nextflow.config b/tests/modules/nf-core/bcftools/convert/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/convert/nextflow.config
rename to tests/modules/nf-core/bcftools/convert/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/convert/test.yml b/tests/modules/nf-core/bcftools/convert/test.yml
new file mode 100644
index 00000000000..5d124c5d989
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/convert/test.yml
@@ -0,0 +1,23 @@
+- name: bcftools convert test_bcftools_convert_gvcf
+  command: nextflow run ./tests/modules/nf-core/bcftools/convert -entry test_bcftools_convert_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/convert/nextflow.config
+  tags:
+    - bcftools/convert
+    - bcftools
+  files:
+    - path: output/bcftools/test.vcf.gz
+
+- name: bcftools convert test_bcftools_convert_gvcf_bed
+  command: nextflow run ./tests/modules/nf-core/bcftools/convert -entry test_bcftools_convert_gvcf_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/convert/nextflow.config
+  tags:
+    - bcftools/convert
+    - bcftools
+  files:
+    - path: output/bcftools/test.vcf.gz
+
+- name: bcftools convert test_bcftools_convert_gvcf_to_bcf
+  command: nextflow run ./tests/modules/nf-core/bcftools/convert -entry test_bcftools_convert_gvcf_to_bcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/convert/nextflow.config
+  tags:
+    - bcftools/convert
+    - bcftools
+  files:
+    - path: output/bcftools/test.bcf.gz
diff --git a/tests/modules/nf-core/bcftools/filter/main.nf b/tests/modules/nf-core/bcftools/filter/main.nf
new file mode 100644
index 00000000000..0fff20eb406
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/filter/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+//keep --no-verson argument, otherwise md5 will change on each execution
+include { BCFTOOLS_FILTER } from '../../../../../modules/nf-core/bcftools/filter/main.nf'
+
+workflow test_bcftools_filter {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+            ]
+
+    BCFTOOLS_FILTER ( input )
+}
diff --git a/tests/modules/bcftools/filter/nextflow.config b/tests/modules/nf-core/bcftools/filter/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/filter/nextflow.config
rename to tests/modules/nf-core/bcftools/filter/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/filter/test.yml b/tests/modules/nf-core/bcftools/filter/test.yml
new file mode 100644
index 00000000000..d877945c9ff
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/filter/test.yml
@@ -0,0 +1,8 @@
+- name: bcftools filter test_bcftools_filter
+  command: nextflow run ./tests/modules/nf-core/bcftools/filter -entry test_bcftools_filter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/filter/nextflow.config
+  tags:
+    - bcftools/filter
+    - bcftools
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: c5f2a6a912964c45e8231140420561f9
diff --git a/tests/modules/nf-core/bcftools/index/main.nf b/tests/modules/nf-core/bcftools/index/main.nf
new file mode 100644
index 00000000000..ba58f4076d7
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/index/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_CSI } from '../../../../../modules/nf-core/bcftools/index/main.nf'
+include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_TBI } from '../../../../../modules/nf-core/bcftools/index/main.nf'
+
+
+workflow test_bcftools_index_csi {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+
+    BCFTOOLS_INDEX_CSI ( input )
+}
+
+workflow test_bcftools_index_tbi {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+
+    BCFTOOLS_INDEX_TBI ( input )
+}
diff --git a/tests/modules/bcftools/index/nextflow.config b/tests/modules/nf-core/bcftools/index/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/index/nextflow.config
rename to tests/modules/nf-core/bcftools/index/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/index/test.yml b/tests/modules/nf-core/bcftools/index/test.yml
new file mode 100644
index 00000000000..6b8112ec08a
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/index/test.yml
@@ -0,0 +1,17 @@
+- name: bcftools index
+  command: nextflow run ./tests/modules/nf-core/bcftools/index -entry test_bcftools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/index/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/index
+  files:
+    - path: output/bcftools/test.vcf.gz.csi
+      md5sum: 9c49464e5983cc02ba89c862c2f33cf8
+
+- name: bcftools index tbi
+  command: nextflow run ./tests/modules/nf-core/bcftools/index -entry test_bcftools_index_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/index/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/index
+  files:
+    - path: output/bcftools/test.vcf.gz.tbi
+      md5sum: a5c54806112b6b2464d4985b96b176c0
diff --git a/tests/modules/nf-core/bcftools/isec/main.nf b/tests/modules/nf-core/bcftools/isec/main.nf
new file mode 100644
index 00000000000..42012448d2c
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/isec/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_ISEC } from '../../../../../modules/nf-core/bcftools/isec/main.nf'
+
+workflow test_bcftools_isec {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)],
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)]
+            ]
+
+    BCFTOOLS_ISEC ( input )
+}
diff --git a/tests/modules/bcftools/isec/nextflow.config b/tests/modules/nf-core/bcftools/isec/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/isec/nextflow.config
rename to tests/modules/nf-core/bcftools/isec/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/isec/test.yml b/tests/modules/nf-core/bcftools/isec/test.yml
new file mode 100644
index 00000000000..9fe3d064e29
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/isec/test.yml
@@ -0,0 +1,18 @@
+- name: bcftools isec test_bcftools_isec
+  command: nextflow run ./tests/modules/nf-core/bcftools/isec -entry test_bcftools_isec -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/isec/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/isec
+  files:
+    - path: output/bcftools/test/0000.vcf.gz
+      md5sum: c5f2a6a912964c45e8231140420561f9
+    - path: output/bcftools/test/0001.vcf.gz.tbi
+      md5sum: a596568a2bbab1acd817427bf3ceb20e
+    - path: output/bcftools/test/sites.txt
+      md5sum: 1cea3fbde7f6d3c97f3d39036f9690df
+    - path: output/bcftools/test/0000.vcf.gz.tbi
+      md5sum: a596568a2bbab1acd817427bf3ceb20e
+    - path: output/bcftools/test/0001.vcf.gz
+      md5sum: c5f2a6a912964c45e8231140420561f9
+    - path: output/bcftools/test/README.txt
+      md5sum: 10fc33b66522645600d44afbd41fb792
diff --git a/tests/modules/nf-core/bcftools/merge/main.nf b/tests/modules/nf-core/bcftools/merge/main.nf
new file mode 100644
index 00000000000..2b3df3f4d32
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/merge/main.nf
@@ -0,0 +1,68 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+//keep --no-verson argument, otherwise md5 will change on each execution
+include { BCFTOOLS_MERGE                        } from '../../../../../modules/nf-core/bcftools/merge/main.nf'
+include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_GVCF } from '../../../../../modules/nf-core/bcftools/merge/main.nf'
+include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_BCF  } from '../../../../../modules/nf-core/bcftools/merge/main.nf'
+
+workflow test_bcftools_merge {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
+              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
+            ]
+
+    bed = []
+    fasta = []
+    fasta_fai = []
+
+    BCFTOOLS_MERGE ( input, bed, fasta, fasta_fai )
+}
+
+workflow test_bcftools_merge_bed {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
+              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
+            ]
+
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    fasta = []
+    fasta_fai = []
+
+    BCFTOOLS_MERGE ( input, bed, fasta, fasta_fai )
+}
+
+workflow test_bcftools_merge_gvcf {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ],
+              [ file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz_tbi'], checkIfExists: true) ]
+            ]
+
+    bed = []
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    BCFTOOLS_MERGE_GVCF ( input, bed, fasta, fasta_fai )
+}
+
+workflow test_bcftools_merge_bcf {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
+              [ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
+            ]
+
+    bed = []
+    fasta = []
+    fasta_fai = []
+
+    BCFTOOLS_MERGE_BCF ( input, bed, fasta, fasta_fai )
+}
diff --git a/tests/modules/bcftools/merge/nextflow.config b/tests/modules/nf-core/bcftools/merge/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/merge/nextflow.config
rename to tests/modules/nf-core/bcftools/merge/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/merge/test.yml b/tests/modules/nf-core/bcftools/merge/test.yml
new file mode 100644
index 00000000000..edd7eeafee6
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/merge/test.yml
@@ -0,0 +1,35 @@
+- name: bcftools merge test_bcftools_merge
+  command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcftools/merge/nextflow.config
+  tags:
+    - bcftools/merge
+    - bcftools
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: 744b28bef1469aabdcfd354293ef725d
+
+- name: bcftools merge test_bcftools_merge_bed
+  command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_bed -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcftools/merge/nextflow.config
+  tags:
+    - bcftools/merge
+    - bcftools
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: 9597e71ae1706f76f00707687be43240
+
+- name: bcftools merge test_bcftools_merge_gvcf
+  command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_gvcf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcftools/merge/nextflow.config
+  tags:
+    - bcftools/merge
+    - bcftools
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: 8aef4d860228cb651e0cb920376f5118
+
+- name: bcftools merge test_bcftools_merge_bcf
+  command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_bcf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcftools/merge/nextflow.config
+  tags:
+    - bcftools/merge
+    - bcftools
+  files:
+    - path: output/bcftools/test.bcf.gz
+      md5sum: 3ca1ab0d9a6ede049c6eeadf88177eb9
diff --git a/tests/modules/nf-core/bcftools/mpileup/main.nf b/tests/modules/nf-core/bcftools/mpileup/main.nf
new file mode 100644
index 00000000000..02da43cc9c6
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/mpileup/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_MPILEUP } from '../../../../../modules/nf-core/bcftools/mpileup/main.nf'
+
+workflow test_bcftools_mpileup {
+
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = false
+
+    BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
+}
+
+workflow test_bcftools_save_mpileup {
+
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = true
+
+    BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
+}
diff --git a/tests/modules/bcftools/mpileup/nextflow.config b/tests/modules/nf-core/bcftools/mpileup/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/mpileup/nextflow.config
rename to tests/modules/nf-core/bcftools/mpileup/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/mpileup/test.yml b/tests/modules/nf-core/bcftools/mpileup/test.yml
new file mode 100644
index 00000000000..d6d0cd6ec2c
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/mpileup/test.yml
@@ -0,0 +1,27 @@
+- name: bcftools mpileup test_bcftools_mpileup
+  command: nextflow run ./tests/modules/nf-core/bcftools/mpileup -entry test_bcftools_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/mpileup/nextflow.config
+  tags:
+    - bcftools/mpileup
+    - bcftools
+  files:
+    - path: output/bcftools/test.bcftools_stats.txt
+      md5sum: 4bb496a523ce6b35432d3bbb6b24a885
+    - path: output/bcftools/test.vcf.gz.tbi
+      md5sum: f5e9c86c2269138663c9fb3effe840da
+    - path: output/bcftools/test.vcf.gz
+      md5sum: f37c4bdb0b7a4330477d6716ae2778c2
+
+- name: bcftools mpileup test_bcftools_save_mpileup
+  command: nextflow run ./tests/modules/nf-core/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/mpileup/nextflow.config
+  tags:
+    - bcftools/mpileup
+    - bcftools
+  files:
+    - path: output/bcftools/test.bcftools_stats.txt
+      md5sum: 4bb496a523ce6b35432d3bbb6b24a885
+    - path: output/bcftools/test.vcf.gz.tbi
+      md5sum: f5e9c86c2269138663c9fb3effe840da
+    - path: output/bcftools/test.vcf.gz
+      md5sum: f37c4bdb0b7a4330477d6716ae2778c2
+    - path: output/bcftools/test.mpileup
+      md5sum: d7c55262aa6637487ba1c621983cfb49
diff --git a/tests/modules/nf-core/bcftools/norm/main.nf b/tests/modules/nf-core/bcftools/norm/main.nf
new file mode 100644
index 00000000000..53363bec82b
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/norm/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_NORM } from '../../../../../modules/nf-core/bcftools/norm/main.nf'
+
+workflow test_bcftools_norm_no_tbi {
+    
+    input = [ [ id:'test2', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+            []
+            ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BCFTOOLS_NORM ( input, fasta )
+}
+
+workflow test_bcftools_norm_tbi {
+    
+    input = [ [ id:'test2', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)            
+            ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BCFTOOLS_NORM ( input, fasta )
+}
diff --git a/tests/modules/bcftools/norm/nextflow.config b/tests/modules/nf-core/bcftools/norm/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/norm/nextflow.config
rename to tests/modules/nf-core/bcftools/norm/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/norm/test.yml b/tests/modules/nf-core/bcftools/norm/test.yml
new file mode 100644
index 00000000000..b0d57ec1e9e
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/norm/test.yml
@@ -0,0 +1,15 @@
+- name: bcftools norm test_bcftools_norm_no_tbi
+  command: nextflow run ./tests/modules/nf-core/bcftools/norm -entry test_bcftools_norm_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/norm/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/norm
+  files:
+    - path: output/bcftools/test2.vcf.gz
+
+- name: bcftools norm test_bcftools_norm_tbi
+  command: nextflow run ./tests/modules/nf-core/bcftools/norm -entry test_bcftools_norm_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/norm/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/norm
+  files:
+    - path: output/bcftools/test2.vcf.gz
diff --git a/tests/modules/nf-core/bcftools/query/main.nf b/tests/modules/nf-core/bcftools/query/main.nf
new file mode 100644
index 00000000000..d1ad7e96aae
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/query/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_QUERY } from '../../../../../modules/nf-core/bcftools/query/main.nf'
+
+workflow test_bcftools_query {
+
+    input = [ [ id:'out' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_QUERY ( input, regions, targets, samples )
+}
+
+workflow test_bcftools_query_with_optional_files {
+
+    input = [ [ id:'out' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+    regions = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
+    targets = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+    samples = []
+
+    BCFTOOLS_QUERY ( input, regions, targets, samples )
+}
diff --git a/tests/modules/bcftools/query/nextflow.config b/tests/modules/nf-core/bcftools/query/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/query/nextflow.config
rename to tests/modules/nf-core/bcftools/query/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/query/test.yml b/tests/modules/nf-core/bcftools/query/test.yml
new file mode 100644
index 00000000000..829ee630e4d
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/query/test.yml
@@ -0,0 +1,17 @@
+- name: bcftools query
+  command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/query
+  files:
+    - path: output/bcftools/out.txt
+      md5sum: c32a6d28f185822d8fe1eeb7e42ec155
+
+- name: bcftools query with optional files
+  command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/query
+  files:
+    - path: output/bcftools/out.txt
+      md5sum: 5a87e0865df2f0ab2884fc113ec2a70d
diff --git a/tests/modules/nf-core/bcftools/reheader/main.nf b/tests/modules/nf-core/bcftools/reheader/main.nf
new file mode 100644
index 00000000000..8fdafb33429
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/reheader/main.nf
@@ -0,0 +1,40 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_REHEADER } from '../../../../../modules/nf-core/bcftools/reheader/main.nf'
+
+workflow test_bcftools_reheader_update_sequences {
+
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
+    ]
+    fai    = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    header = []
+    BCFTOOLS_REHEADER ( input, fai, header )
+}
+
+workflow test_bcftools_reheader_new_header {
+
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
+    ]
+    fai    = []
+    header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+
+    BCFTOOLS_REHEADER ( input, fai, header )
+}
+
+workflow test_bcftools_reheader_new_header_update_sequences {
+
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
+    ]
+    fai    = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+
+    BCFTOOLS_REHEADER ( input, fai, header )
+}
diff --git a/tests/modules/bcftools/reheader/nextflow.config b/tests/modules/nf-core/bcftools/reheader/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/reheader/nextflow.config
rename to tests/modules/nf-core/bcftools/reheader/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/reheader/test.yml b/tests/modules/nf-core/bcftools/reheader/test.yml
new file mode 100644
index 00000000000..84deb70d2c1
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/reheader/test.yml
@@ -0,0 +1,26 @@
+- name: bcftools reheader test_bcftools_reheader_update_sequences
+  command: nextflow run ./tests/modules/nf-core/bcftools/reheader -entry test_bcftools_reheader_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/reheader/nextflow.config
+  tags:
+    - bcftools/reheader
+    - bcftools
+  files:
+    - path: output/bcftools/test.updated.vcf.gz
+      md5sum: c8a732976911c0c0815d973d5974769a
+
+- name: bcftools reheader test_bcftools_reheader_new_header
+  command: nextflow run ./tests/modules/nf-core/bcftools/reheader -entry test_bcftools_reheader_new_header -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/reheader/nextflow.config
+  tags:
+    - bcftools/reheader
+    - bcftools
+  files:
+    - path: output/bcftools/test.updated.vcf.gz
+      md5sum: aba91c9ec58e38d73657f02df8457b66
+
+- name: bcftools reheader test_bcftools_reheader_new_header_update_sequences
+  command: nextflow run ./tests/modules/nf-core/bcftools/reheader -entry test_bcftools_reheader_new_header_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/reheader/nextflow.config
+  tags:
+    - bcftools/reheader
+    - bcftools
+  files:
+    - path: output/bcftools/test.updated.vcf.gz
+      md5sum: c8a732976911c0c0815d973d5974769a
diff --git a/tests/modules/nf-core/bcftools/roh/main.nf b/tests/modules/nf-core/bcftools/roh/main.nf
new file mode 100644
index 00000000000..d18a0aecefc
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/roh/main.nf
@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_ROH } from '../../../../../modules/nf-core/bcftools/roh/main.nf'
+
+workflow test_bcftools_roh {
+
+    input = [ [ id:'test' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+
+    af_file = [[],[]]
+    gen_map = []
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
+}
+
+workflow test_bcftools_roh_stub {
+
+    input = [ [ id:'test' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+
+    af_file = [[],[]]
+    gen_map = []
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
+}
diff --git a/tests/modules/bcftools/roh/nextflow.config b/tests/modules/nf-core/bcftools/roh/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/roh/nextflow.config
rename to tests/modules/nf-core/bcftools/roh/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/roh/test.yml b/tests/modules/nf-core/bcftools/roh/test.yml
new file mode 100644
index 00000000000..3ea272dd53a
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/roh/test.yml
@@ -0,0 +1,17 @@
+- name: "bcftools roh"
+  command: nextflow run ./tests/modules/nf-core/bcftools/roh -entry test_bcftools_roh -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/roh/nextflow.config
+  tags:
+    - "bcftools"
+    - "bcftools/roh"
+  files:
+    - path: "output/bcftools/test.roh"
+    - path: "output/bcftools/versions.yml"
+
+- name: "bcftools roh stub"
+  command: nextflow run ./tests/modules/nf-core/bcftools/roh -entry test_bcftools_roh_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/roh/nextflow.config
+  tags:
+    - "bcftools"
+    - "bcftools/roh"
+  files:
+    - path: "output/bcftools/test.roh"
+    - path: "output/bcftools/versions.yml"
diff --git a/tests/modules/nf-core/bcftools/sort/main.nf b/tests/modules/nf-core/bcftools/sort/main.nf
new file mode 100644
index 00000000000..d4960fccd97
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/sort/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_SORT } from '../../../../../modules/nf-core/bcftools/sort/main.nf'
+
+workflow test_bcftools_sort {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    BCFTOOLS_SORT ( input )
+}
diff --git a/tests/modules/bcftools/sort/nextflow.config b/tests/modules/nf-core/bcftools/sort/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/sort/nextflow.config
rename to tests/modules/nf-core/bcftools/sort/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/sort/test.yml b/tests/modules/nf-core/bcftools/sort/test.yml
new file mode 100644
index 00000000000..c51da8b2441
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/sort/test.yml
@@ -0,0 +1,10 @@
+- name: bcftools sort test_bcftools_sort
+  command: nextflow run ./tests/modules/nf-core/bcftools/sort -entry test_bcftools_sort -c ./tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/sort
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: c5f2a6a912964c45e8231140420561f9
+    - path: output/bcftools/versions.yml
+      md5sum: 70cbb59e64c37a6ab6131b0e470892f4
diff --git a/tests/modules/nf-core/bcftools/stats/main.nf b/tests/modules/nf-core/bcftools/stats/main.nf
new file mode 100644
index 00000000000..c8ceb924c2d
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/stats/main.nf
@@ -0,0 +1,38 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_STATS } from '../../../../../modules/nf-core/bcftools/stats/main.nf'
+
+workflow test_bcftools_stats {
+    input = [ [ id:'test' ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+            []]
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_STATS ( input, regions, targets, samples )
+}
+
+workflow test_bcftools_stats_regions {
+    input = [ [ id:'test' ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+    regions = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
+    targets = []
+    samples = []
+
+    BCFTOOLS_STATS ( input, regions, targets, samples )
+}
+
+workflow test_bcftools_stats_targets {
+    input = [ [ id:'test' ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+            []]
+    regions = []
+    targets = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+    samples = []
+
+    BCFTOOLS_STATS ( input, regions, targets, samples )
+}
diff --git a/tests/modules/bcftools/stats/nextflow.config b/tests/modules/nf-core/bcftools/stats/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/stats/nextflow.config
rename to tests/modules/nf-core/bcftools/stats/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/stats/test.yml b/tests/modules/nf-core/bcftools/stats/test.yml
new file mode 100644
index 00000000000..92f3aec93b0
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/stats/test.yml
@@ -0,0 +1,26 @@
+- name: bcftools stats test_bcftools_stats
+  command: nextflow run ./tests/modules/nf-core/bcftools/stats -entry test_bcftools_stats -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcftools/stats/nextflow.config
+  tags:
+    - bcftools/stats
+    - bcftools
+  files:
+    - path: output/bcftools/test.bcftools_stats.txt
+      contains: ["TSTV	0	6	2	3.00	6	2	3.00", "DP	0	1	0	0.000000	5	55.555556"]
+
+- name: bcftools stats test_bcftools_stats_regions
+  command: nextflow run ./tests/modules/nf-core/bcftools/stats -entry test_bcftools_stats_regions -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcftools/stats/nextflow.config
+  tags:
+    - bcftools/stats
+    - bcftools
+  files:
+    - path: output/bcftools/test.bcftools_stats.txt
+      contains: ["TSTV	0	5	1	5.00	5	1	5.00", "DP	0	1	0	0.000000	3	42.857143"]
+
+- name: bcftools stats test_bcftools_stats_targets
+  command: nextflow run ./tests/modules/nf-core/bcftools/stats -entry test_bcftools_stats_targets -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcftools/stats/nextflow.config
+  tags:
+    - bcftools/stats
+    - bcftools
+  files:
+    - path: output/bcftools/test.bcftools_stats.txt
+      contains: ["TSTV	0	6	2	3.00	6	2	3.00", "DP	0	1	0	0.000000	5	55.555556"]
diff --git a/tests/modules/nf-core/bcftools/view/main.nf b/tests/modules/nf-core/bcftools/view/main.nf
new file mode 100644
index 00000000000..d06a242111f
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/view/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_VIEW } from '../../../../../modules/nf-core/bcftools/view/main.nf'
+
+workflow test_bcftools_view {
+
+    regions = []
+    targets = []
+    samples = []
+
+    input = [[ id:'out', single_end:false ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+
+    BCFTOOLS_VIEW ( input, regions, targets, samples )
+}
+
+workflow test_bcftools_view_with_optional_files {
+
+    regions = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
+    targets = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+    samples = []
+
+    input = [[ id:'out', single_end:false ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)]
+
+    BCFTOOLS_VIEW ( input, regions, targets, samples )
+}
diff --git a/tests/modules/bcftools/view/nextflow.config b/tests/modules/nf-core/bcftools/view/nextflow.config
similarity index 100%
rename from tests/modules/bcftools/view/nextflow.config
rename to tests/modules/nf-core/bcftools/view/nextflow.config
diff --git a/tests/modules/nf-core/bcftools/view/test.yml b/tests/modules/nf-core/bcftools/view/test.yml
new file mode 100644
index 00000000000..429a5f56a80
--- /dev/null
+++ b/tests/modules/nf-core/bcftools/view/test.yml
@@ -0,0 +1,17 @@
+- name: bcftools view
+  command: nextflow run ./tests/modules/nf-core/bcftools/view -entry test_bcftools_view -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/view/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/view
+  files:
+    - path: output/bcftools/out.vcf.gz
+      md5sum: c5f2a6a912964c45e8231140420561f9
+
+- name: bcftools view with optional files
+  command: nextflow run ./tests/modules/nf-core/bcftools/view -entry test_bcftools_view_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/view/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/view
+  files:
+    - path: output/bcftools/out.vcf.gz
+      md5sum: 265a36d06f8ac3bf52086e4467e537f8
diff --git a/tests/modules/nf-core/bcl2fastq/main.nf b/tests/modules/nf-core/bcl2fastq/main.nf
new file mode 100644
index 00000000000..9718f573257
--- /dev/null
+++ b/tests/modules/nf-core/bcl2fastq/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCL2FASTQ } from '../../../../modules/nf-core/bcl2fastq/main.nf'
+include { UNTAR      } from '../../../../modules/nf-core/untar/main.nf'
+
+workflow test_bcl2fastq {
+    ch_flowcell = Channel.value([
+            [id:'test', lane:1 ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)])
+
+    ch_flowcell
+    .multiMap { meta, ss, run ->
+        samplesheet: [meta, ss]
+        tar: [meta, run]
+    }.set{ ch_fc_split }
+
+    ch_flowcell_untar = ch_fc_split.samplesheet.join( UNTAR ( ch_fc_split.tar ).untar )
+
+    BCL2FASTQ (ch_flowcell_untar)
+}
diff --git a/tests/modules/bcl2fastq/nextflow.config b/tests/modules/nf-core/bcl2fastq/nextflow.config
similarity index 100%
rename from tests/modules/bcl2fastq/nextflow.config
rename to tests/modules/nf-core/bcl2fastq/nextflow.config
diff --git a/tests/modules/nf-core/bcl2fastq/test.yml b/tests/modules/nf-core/bcl2fastq/test.yml
new file mode 100644
index 00000000000..db222ea8417
--- /dev/null
+++ b/tests/modules/nf-core/bcl2fastq/test.yml
@@ -0,0 +1,33 @@
+- name: bcl2fastq test_bcl2fastq
+  command: nextflow run ./tests/modules/nf-core/bcl2fastq -entry test_bcl2fastq -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bcl2fastq/nextflow.config
+  tags:
+    - bcl2fastq
+  files:
+    - path: output/bcl2fastq/Sample1_S1_L001_R1_001.fastq.gz
+      md5sum: e92fce7b86c6447b053d72c5cb4be89c
+    - path: output/bcl2fastq/Stats/AdapterTrimming.txt
+      md5sum: 48ed2b914b1246c0b5d8667525550946
+    - path: output/bcl2fastq/Stats/ConversionStats.xml
+      md5sum: 8fe0f57f3f5d256a0762dba75ac62d05
+    - path: output/bcl2fastq/Stats/DemultiplexingStats.xml
+      md5sum: 2047ff18f5b9107c084de06e9ff943ad
+    - path: output/bcl2fastq/Stats/DemuxSummaryF1L1.txt
+      md5sum: 03e5fd0c1e3079c5f8c7b4d0501b37ff
+    - path: output/bcl2fastq/Stats/FastqSummaryF1L1.txt
+      md5sum: 0c6f2d87ee183b84d1051cde9a5643d1
+    - path: output/bcl2fastq/Stats/Stats.json
+      md5sum: 8e5f038b8aa9e465599d3575f930e604
+    - path: output/bcl2fastq/flowcell/InterOp/ControlMetricsOut.bin
+      md5sum: 6d77b38d0793a6e1ce1e85706e488953
+    - path: output/bcl2fastq/flowcell/InterOp/CorrectedIntMetricsOut.bin
+      md5sum: 2bbf84d3be72734addaa2fe794711434
+    - path: output/bcl2fastq/flowcell/InterOp/ErrorMetricsOut.bin
+      md5sum: 38c88def138e9bb832539911affdb286
+    - path: output/bcl2fastq/flowcell/InterOp/ExtractionMetricsOut.bin
+      md5sum: 7497c3178837eea8f09350b5cd252e99
+    - path: output/bcl2fastq/flowcell/InterOp/IndexMetricsOut.bin
+      md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
+    - path: output/bcl2fastq/flowcell/InterOp/QMetricsOut.bin
+      md5sum: 7e9f198d53ebdfbb699a5f94cf1ed51c
+    - path: output/bcl2fastq/flowcell/InterOp/TileMetricsOut.bin
+      md5sum: 83891751ec1c91a425a524b476b6ca3c
diff --git a/tests/modules/nf-core/bclconvert/main.nf b/tests/modules/nf-core/bclconvert/main.nf
new file mode 100644
index 00000000000..74640d5a4d6
--- /dev/null
+++ b/tests/modules/nf-core/bclconvert/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCLCONVERT } from '../../../../modules/nf-core/bclconvert/main.nf'
+include { UNTAR      } from '../../../../modules/nf-core/untar/main.nf'
+
+workflow test_bclconvert {
+    ch_flowcell = Channel.value([
+            [id:'test', lane:1 ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)])
+
+    ch_flowcell
+    .multiMap { meta, ss, run ->
+        samplesheet: [meta, ss]
+        tar: [meta, run]
+    }.set{ ch_fc_split }
+
+    ch_flowcell_untar = ch_fc_split.samplesheet.join( UNTAR ( ch_fc_split.tar ).untar )
+
+    BCLCONVERT (ch_flowcell_untar)
+}
diff --git a/tests/modules/bclconvert/nextflow.config b/tests/modules/nf-core/bclconvert/nextflow.config
similarity index 100%
rename from tests/modules/bclconvert/nextflow.config
rename to tests/modules/nf-core/bclconvert/nextflow.config
diff --git a/tests/modules/nf-core/bclconvert/test.yml b/tests/modules/nf-core/bclconvert/test.yml
new file mode 100644
index 00000000000..90a557ae046
--- /dev/null
+++ b/tests/modules/nf-core/bclconvert/test.yml
@@ -0,0 +1,50 @@
+- name: bclconvert test_bclconvert
+  command: nextflow run ./tests/modules/nf-core/bclconvert -entry test_bclconvert -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bclconvert/nextflow.config
+  tags:
+    - bclconvert
+  files:
+    - path: output/bclconvert/Logs/Errors.log
+    - path: output/bclconvert/Logs/FastqComplete.txt
+    - path: output/bclconvert/Logs/Info.log
+    - path: output/bclconvert/Logs/Warnings.log
+    - path: output/bclconvert/Reports/Adapter_Cycle_Metrics.csv
+      md5sum: 5a0c88793b4a0885fe3dda16609b576e
+    - path: output/bclconvert/Reports/Adapter_Metrics.csv
+      md5sum: 989240b8840b2169ac1061f952c90f6c
+    - path: output/bclconvert/Reports/Demultiplex_Stats.csv
+      md5sum: 93949a8cd96f907d83e0808c1ec2a04b
+    - path: output/bclconvert/Reports/Demultiplex_Tile_Stats.csv
+      md5sum: 83120160b0f22a1303fa1db31c19f6e9
+    - path: output/bclconvert/Reports/IndexMetricsOut.bin
+      md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
+    - path: output/bclconvert/Reports/Index_Hopping_Counts.csv
+      md5sum: 1059369e375fd8f8423c0f6c934be978
+    - path: output/bclconvert/Reports/Quality_Metrics.csv
+      md5sum: 6614accb1bb414fe312b17b81f5521f7
+    - path: output/bclconvert/Reports/Quality_Tile_Metrics.csv
+      md5sum: cdc89fd2962bdd4a24f71e186112118a
+    - path: output/bclconvert/Reports/RunInfo.xml
+      md5sum: 03038959f4dd181c86bc97ae71fe270a
+    - path: output/bclconvert/Reports/SampleSheet.csv
+      md5sum: dc0dffd39541dd6cc5b4801d768a8d2b
+    - path: output/bclconvert/Reports/Top_Unknown_Barcodes.csv
+      md5sum: 2e2faba761137f228e56bd3428453ccc
+    - path: output/bclconvert/Reports/fastq_list.csv
+      md5sum: 05bc84f51840f5754cfb8381b36f2cb0
+    - path: output/bclconvert/Sample1_S1_L001_R1_001.fastq.gz
+      md5sum: 0a0341e2990b4fa1d9ad4b4c603144c1
+    - path: output/bclconvert/Undetermined_S0_L001_R1_001.fastq.gz
+      md5sum: febef808ae5397ea4ee7ee40e5fd39e0
+    - path: output/bclconvert/flowcell/InterOp/ControlMetricsOut.bin
+      md5sum: 6d77b38d0793a6e1ce1e85706e488953
+    - path: output/bclconvert/flowcell/InterOp/CorrectedIntMetricsOut.bin
+      md5sum: 2bbf84d3be72734addaa2fe794711434
+    - path: output/bclconvert/flowcell/InterOp/ErrorMetricsOut.bin
+      md5sum: 38c88def138e9bb832539911affdb286
+    - path: output/bclconvert/flowcell/InterOp/ExtractionMetricsOut.bin
+      md5sum: 7497c3178837eea8f09350b5cd252e99
+    - path: output/bclconvert/flowcell/InterOp/IndexMetricsOut.bin
+    - path: output/bclconvert/flowcell/InterOp/QMetricsOut.bin
+      md5sum: 7e9f198d53ebdfbb699a5f94cf1ed51c
+    - path: output/bclconvert/flowcell/InterOp/TileMetricsOut.bin
+      md5sum: 83891751ec1c91a425a524b476b6ca3c
diff --git a/tests/modules/nf-core/bedtools/bamtobed/main.nf b/tests/modules/nf-core/bedtools/bamtobed/main.nf
new file mode 100644
index 00000000000..26db37effa9
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/bamtobed/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_BAMTOBED } from '../../../../../modules/nf-core/bedtools/bamtobed/main.nf'
+
+workflow test_bedtools_bamtobed {
+    input = [ [ id:'test'], //meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+            ]
+
+    BEDTOOLS_BAMTOBED ( input )
+}
diff --git a/tests/modules/bedtools/bamtobed/nextflow.config b/tests/modules/nf-core/bedtools/bamtobed/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/bamtobed/nextflow.config
rename to tests/modules/nf-core/bedtools/bamtobed/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/bamtobed/test.yml b/tests/modules/nf-core/bedtools/bamtobed/test.yml
new file mode 100644
index 00000000000..234f5c54f80
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/bamtobed/test.yml
@@ -0,0 +1,8 @@
+- name: bedtools bamtobed
+  command: nextflow run ./tests/modules/nf-core/bedtools/bamtobed -entry test_bedtools_bamtobed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/bamtobed/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/bamtobed
+  files:
+    - path: ./output/bedtools/test.bed
+      md5sum: 3c6b88e414debd889c10eb972180b687
diff --git a/tests/modules/nf-core/bedtools/complement/main.nf b/tests/modules/nf-core/bedtools/complement/main.nf
new file mode 100644
index 00000000000..e379ee4761d
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/complement/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_COMPLEMENT } from '../../../../../modules/nf-core/bedtools/complement/main.nf'
+
+workflow test_bedtools_complement {
+    input = [ [ id:'test'],
+              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+            ]
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+
+    BEDTOOLS_COMPLEMENT ( input, sizes )
+}
diff --git a/tests/modules/bedtools/complement/nextflow.config b/tests/modules/nf-core/bedtools/complement/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/complement/nextflow.config
rename to tests/modules/nf-core/bedtools/complement/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/complement/test.yml b/tests/modules/nf-core/bedtools/complement/test.yml
new file mode 100644
index 00000000000..d5cf9b54e4d
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/complement/test.yml
@@ -0,0 +1,8 @@
+- name: bedtools complement
+  command: nextflow run ./tests/modules/nf-core/bedtools/complement -entry test_bedtools_complement -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/complement/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/complement
+  files:
+    - path: ./output/bedtools/test_out.bed
+      md5sum: d71df7e47aec0661c27b71e483e727f9
diff --git a/tests/modules/nf-core/bedtools/genomecov/main.nf b/tests/modules/nf-core/bedtools/genomecov/main.nf
new file mode 100644
index 00000000000..c808b1a4b47
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/genomecov/main.nf
@@ -0,0 +1,57 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_GENOMECOV } from '../../../../../modules/nf-core/bedtools/genomecov/main.nf'
+
+workflow test_bedtools_genomecov_noscale {
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+        1
+    ]
+
+    sizes = []
+    extension = 'txt'
+
+    BEDTOOLS_GENOMECOV ( input, sizes, extension )
+}
+
+workflow test_bedtools_genomecov_nonbam_noscale {
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
+        1
+    ]
+
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+    extension = 'txt'
+
+    BEDTOOLS_GENOMECOV ( input, sizes, extension )
+}
+
+workflow test_bedtools_genomecov_scale {
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+        0.5
+    ]
+
+    sizes = file('dummy_chromosome_sizes')
+    extension = 'txt'
+
+    BEDTOOLS_GENOMECOV ( input, sizes, extension )
+}
+
+workflow test_bedtools_genomecov_nonbam_scale {
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
+        0.5
+    ]
+
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+    extension = 'txt'
+
+    BEDTOOLS_GENOMECOV ( input, sizes, extension )
+}
diff --git a/tests/modules/bedtools/genomecov/nextflow.config b/tests/modules/nf-core/bedtools/genomecov/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/genomecov/nextflow.config
rename to tests/modules/nf-core/bedtools/genomecov/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/genomecov/test.yml b/tests/modules/nf-core/bedtools/genomecov/test.yml
new file mode 100644
index 00000000000..1134218c850
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/genomecov/test.yml
@@ -0,0 +1,35 @@
+- name: bedtools genomecov test_bedtools_genomecov_noscale
+  command: nextflow run ./tests/modules/nf-core/bedtools/genomecov -entry test_bedtools_genomecov_noscale -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/genomecov/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/genomecov
+  files:
+    - path: output/bedtools/test_out.txt
+      md5sum: 66083198daca6c001d328ba9616e9b53
+
+- name: bedtools genomecov test_bedtools_genomecov_nonbam_noscale
+  command: nextflow run ./tests/modules/nf-core/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_noscale -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/genomecov/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/genomecov
+  files:
+    - path: output/bedtools/test_out.txt
+      md5sum: f47b58840087426e5b643d8dfd155c1f
+
+- name: bedtools genomecov test_bedtools_genomecov_scale
+  command: nextflow run ./tests/modules/nf-core/bedtools/genomecov -entry test_bedtools_genomecov_scale -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/genomecov/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/genomecov
+  files:
+    - path: output/bedtools/test_out.txt
+      md5sum: 01291b6e1beab72e046653e709eb0e10
+
+- name: bedtools genomecov test_bedtools_genomecov_nonbam_scale
+  command: nextflow run ./tests/modules/nf-core/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_scale -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/genomecov/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/genomecov
+  files:
+    - path: output/bedtools/test_out.txt
+      md5sum: de3c59c0ea123bcdbbad27bc0a0a601e
diff --git a/tests/modules/nf-core/bedtools/getfasta/main.nf b/tests/modules/nf-core/bedtools/getfasta/main.nf
new file mode 100644
index 00000000000..664346cb3da
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/getfasta/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_GETFASTA } from '../../../../../modules/nf-core/bedtools/getfasta/main.nf'
+
+workflow test_bedtools_getfasta {
+    bed   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    
+    BEDTOOLS_GETFASTA ( bed, fasta )
+}
diff --git a/tests/modules/bedtools/getfasta/nextflow.config b/tests/modules/nf-core/bedtools/getfasta/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/getfasta/nextflow.config
rename to tests/modules/nf-core/bedtools/getfasta/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/getfasta/test.yml b/tests/modules/nf-core/bedtools/getfasta/test.yml
new file mode 100644
index 00000000000..8b9f309d02d
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/getfasta/test.yml
@@ -0,0 +1,8 @@
+- name: bedtools getfasta
+  command: nextflow run ./tests/modules/nf-core/bedtools/getfasta -entry test_bedtools_getfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/getfasta/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/getfasta
+  files:
+    - path: ./output/bedtools/test.fa
+      md5sum: 41c3a45a57a16c04f828d8f8bb52df70
diff --git a/tests/modules/nf-core/bedtools/intersect/main.nf b/tests/modules/nf-core/bedtools/intersect/main.nf
new file mode 100644
index 00000000000..cdee9a3c1f7
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/intersect/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_INTERSECT } from '../../../../../modules/nf-core/bedtools/intersect/main.nf'
+
+workflow test_bedtools_intersect {
+    input = [
+        [ id:'test' ],
+        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
+    ]
+
+    extension = 'bed'
+
+    BEDTOOLS_INTERSECT ( input, extension )
+}
+
+workflow test_bedtools_intersect_bam {
+    input = [
+        [ id:'test' ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
+    ]
+
+    extension = 'bam'
+
+    BEDTOOLS_INTERSECT ( input, extension )
+}
diff --git a/tests/modules/bedtools/intersect/nextflow.config b/tests/modules/nf-core/bedtools/intersect/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/intersect/nextflow.config
rename to tests/modules/nf-core/bedtools/intersect/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/intersect/test.yml b/tests/modules/nf-core/bedtools/intersect/test.yml
new file mode 100644
index 00000000000..fc96a00b71e
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/intersect/test.yml
@@ -0,0 +1,17 @@
+- name: bedtools intersect test_bedtools_intersect
+  command: nextflow run ./tests/modules/nf-core/bedtools/intersect -entry test_bedtools_intersect -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/intersect/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/intersect
+  files:
+    - path: output/bedtools/test_out.bed
+      md5sum: afcbf01c2f2013aad71dbe8e34f2c15c
+
+- name: bedtools intersect test_bedtools_intersect_bam
+  command: nextflow run ./tests/modules/nf-core/bedtools/intersect -entry test_bedtools_intersect_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/intersect/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/intersect
+  files:
+    - path: output/bedtools/test_out.bam
+      md5sum: 738324efe2b1e442ceb6539a630c3fe6
diff --git a/tests/modules/nf-core/bedtools/makewindows/main.nf b/tests/modules/nf-core/bedtools/makewindows/main.nf
new file mode 100644
index 00000000000..8928a772b43
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/makewindows/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_MAKEWINDOWS } from '../../../../../modules/nf-core/bedtools/makewindows/main.nf'
+
+workflow test_bedtools_makewindows {
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    ]
+
+    BEDTOOLS_MAKEWINDOWS ( input, true )
+}
diff --git a/tests/modules/bedtools/makewindows/nextflow.config b/tests/modules/nf-core/bedtools/makewindows/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/makewindows/nextflow.config
rename to tests/modules/nf-core/bedtools/makewindows/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/makewindows/test.yml b/tests/modules/nf-core/bedtools/makewindows/test.yml
new file mode 100644
index 00000000000..3fa43b342a1
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/makewindows/test.yml
@@ -0,0 +1,8 @@
+- name: bedtools makewindows test_bedtools_makewindows
+  command: nextflow run ./tests/modules/nf-core/bedtools/makewindows -entry test_bedtools_makewindows -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/makewindows/nextflow.config
+  tags:
+    - bedtools/makewindows
+    - bedtools
+  files:
+    - path: output/bedtools/test.tab
+      md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e
diff --git a/tests/modules/nf-core/bedtools/maskfasta/main.nf b/tests/modules/nf-core/bedtools/maskfasta/main.nf
new file mode 100644
index 00000000000..115a44e6b6e
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/maskfasta/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_MASKFASTA } from '../../../../../modules/nf-core/bedtools/maskfasta/main.nf'
+
+workflow test_bedtools_maskfasta {
+    bed   = [ [ id:'test'],
+              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    
+    BEDTOOLS_MASKFASTA ( bed, fasta )
+}
diff --git a/tests/modules/bedtools/maskfasta/nextflow.config b/tests/modules/nf-core/bedtools/maskfasta/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/maskfasta/nextflow.config
rename to tests/modules/nf-core/bedtools/maskfasta/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/maskfasta/test.yml b/tests/modules/nf-core/bedtools/maskfasta/test.yml
new file mode 100644
index 00000000000..62c834a8c09
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/maskfasta/test.yml
@@ -0,0 +1,8 @@
+- name: bedtools maskfasta
+  command: nextflow run ./tests/modules/nf-core/bedtools/maskfasta -entry test_bedtools_maskfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/maskfasta/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/maskfasta
+  files:
+    - path: ./output/bedtools/test.fa
+      md5sum: f4f6749698f11074228d2c79338e3b9c
diff --git a/tests/modules/nf-core/bedtools/merge/main.nf b/tests/modules/nf-core/bedtools/merge/main.nf
new file mode 100644
index 00000000000..a1a84527fd3
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/merge/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_MERGE } from '../../../../../modules/nf-core/bedtools/merge/main.nf'
+
+workflow test_bedtools_merge {
+    input = [ [ id:'test'],
+              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+            ]
+
+    BEDTOOLS_MERGE ( input )
+}
+
diff --git a/tests/modules/bedtools/merge/nextflow.config b/tests/modules/nf-core/bedtools/merge/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/merge/nextflow.config
rename to tests/modules/nf-core/bedtools/merge/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/merge/test.yml b/tests/modules/nf-core/bedtools/merge/test.yml
new file mode 100644
index 00000000000..bee9b75ba5f
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/merge/test.yml
@@ -0,0 +1,8 @@
+- name: bedtools merge
+  command: nextflow run ./tests/modules/nf-core/bedtools/merge -entry test_bedtools_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/merge/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/merge
+  files:
+    - path: ./output/bedtools/test_out.bed
+      md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e
diff --git a/tests/modules/nf-core/bedtools/slop/main.nf b/tests/modules/nf-core/bedtools/slop/main.nf
new file mode 100644
index 00000000000..40531695034
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/slop/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_SLOP } from '../../../../../modules/nf-core/bedtools/slop/main.nf'
+
+workflow test_bedtools_slop {
+    input = [ [ id:'test'],
+              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+            ]
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+    
+    BEDTOOLS_SLOP ( input, sizes )
+}
+
diff --git a/tests/modules/bedtools/slop/nextflow.config b/tests/modules/nf-core/bedtools/slop/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/slop/nextflow.config
rename to tests/modules/nf-core/bedtools/slop/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/slop/test.yml b/tests/modules/nf-core/bedtools/slop/test.yml
new file mode 100644
index 00000000000..a69dedb6317
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/slop/test.yml
@@ -0,0 +1,8 @@
+- name: bedtools slop
+  command: nextflow run ./tests/modules/nf-core/bedtools/slop -entry test_bedtools_slop -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/slop/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/slop
+  files:
+    - path: ./output/bedtools/test_out.bed
+      md5sum: 4f1d8924925fe5d205c9e1981fe290a4
diff --git a/tests/modules/nf-core/bedtools/sort/main.nf b/tests/modules/nf-core/bedtools/sort/main.nf
new file mode 100644
index 00000000000..b7652a88a07
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/sort/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_SORT } from '../../../../../modules/nf-core/bedtools/sort/main.nf'
+
+workflow test_bedtools_sort {
+    input = [ [ id:'test'],
+              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+            ]
+
+    BEDTOOLS_SORT ( input, "testext" )
+}
diff --git a/tests/modules/bedtools/sort/nextflow.config b/tests/modules/nf-core/bedtools/sort/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/sort/nextflow.config
rename to tests/modules/nf-core/bedtools/sort/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/sort/test.yml b/tests/modules/nf-core/bedtools/sort/test.yml
new file mode 100644
index 00000000000..64336a88af2
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/sort/test.yml
@@ -0,0 +1,8 @@
+- name: bedtools sort
+  command: nextflow run ./tests/modules/nf-core/bedtools/sort -entry test_bedtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/sort/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/sort
+  files:
+    - path: ./output/bedtools/test_out.testext
+      md5sum: fe4053cf4de3aebbdfc3be2efb125a74
diff --git a/tests/modules/nf-core/bedtools/split/main.nf b/tests/modules/nf-core/bedtools/split/main.nf
new file mode 100644
index 00000000000..f4818503a3d
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/split/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_SPLIT } from '../../../../../modules/nf-core/bedtools/split/main.nf'
+
+workflow test_bedtools_split {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)
+    ]
+
+    number_of_files = 2
+
+    BEDTOOLS_SPLIT ( input, number_of_files )
+}
diff --git a/tests/modules/bedtools/split/nextflow.config b/tests/modules/nf-core/bedtools/split/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/split/nextflow.config
rename to tests/modules/nf-core/bedtools/split/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/split/test.yml b/tests/modules/nf-core/bedtools/split/test.yml
new file mode 100644
index 00000000000..330069c25aa
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/split/test.yml
@@ -0,0 +1,10 @@
+- name: bedtools split test_bedtools_split
+  command: nextflow run ./tests/modules/nf-core/bedtools/split -entry test_bedtools_split -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bedtools/split/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/split
+  files:
+    - path: output/bedtools/test.00001.bed
+      md5sum: d58e5e46c2fcc3b8be5db0f023e93cb5
+    - path: output/bedtools/test.00002.bed
+      md5sum: 03caf952e9297a54620d2bbba8dc2823
diff --git a/tests/modules/nf-core/bedtools/subtract/main.nf b/tests/modules/nf-core/bedtools/subtract/main.nf
new file mode 100644
index 00000000000..a86c81a1870
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/subtract/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_SUBTRACT } from '../../../../../modules/nf-core/bedtools/subtract/main.nf'
+
+workflow test_bedtools_subtract {
+    input = [
+        [ id:'test_subtract' ],
+        file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    ]
+
+    BEDTOOLS_SUBTRACT ( input )
+}
diff --git a/tests/modules/bedtools/subtract/nextflow.config b/tests/modules/nf-core/bedtools/subtract/nextflow.config
similarity index 100%
rename from tests/modules/bedtools/subtract/nextflow.config
rename to tests/modules/nf-core/bedtools/subtract/nextflow.config
diff --git a/tests/modules/nf-core/bedtools/subtract/test.yml b/tests/modules/nf-core/bedtools/subtract/test.yml
new file mode 100644
index 00000000000..efb1863cbaa
--- /dev/null
+++ b/tests/modules/nf-core/bedtools/subtract/test.yml
@@ -0,0 +1,8 @@
+- name: bedtools subtract
+  command: nextflow run ./tests/modules/nf-core/bedtools/subtract -entry test_bedtools_subtract -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/subtract/nextflow.config
+  tags:
+    - bedtools
+    - bedtools/subtract
+  files:
+    - path: output/bedtools/test_subtract.bed
+      md5sum: 63513c4dc69e8b481ce3b4b2a9f24259
diff --git a/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf b/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf
new file mode 100644
index 00000000000..2f349907adf
--- /dev/null
+++ b/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BIOBAMBAM_BAMMARKDUPLICATES2 } from '../../../../../modules/nf-core/biobambam/bammarkduplicates2/main.nf'
+
+workflow test_biobambam_bammarkduplicates2 {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
+    ]
+
+    BIOBAMBAM_BAMMARKDUPLICATES2 ( input )
+}
diff --git a/tests/modules/biobambam/bammarkduplicates2/nextflow.config b/tests/modules/nf-core/biobambam/bammarkduplicates2/nextflow.config
similarity index 100%
rename from tests/modules/biobambam/bammarkduplicates2/nextflow.config
rename to tests/modules/nf-core/biobambam/bammarkduplicates2/nextflow.config
diff --git a/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml b/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml
new file mode 100644
index 00000000000..2d838f1fc6e
--- /dev/null
+++ b/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml
@@ -0,0 +1,12 @@
+- name: biobambam bammarkduplicates2 test_biobambam_bammarkduplicates2
+  command: nextflow run ./tests/modules/nf-core/biobambam/bammarkduplicates2 -entry test_biobambam_bammarkduplicates2 -c ./tests/config/nextflow.config
+  tags:
+    - biobambam/bammarkduplicates2
+    - biobambam
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: 603edff09029096ddf2bb8a3f12d7aa7
+    - path: output/biobambam/test.metrics.txt
+      md5sum: 30d6e7d90bb5df46329d4bc0144ce927
+    - path: output/biobambam/versions.yml
+      md5sum: dfdf2b084655d124acac0bfb4eda86cc
diff --git a/tests/modules/nf-core/biobambam/bammerge/main.nf b/tests/modules/nf-core/biobambam/bammerge/main.nf
new file mode 100644
index 00000000000..8c92c7dba70
--- /dev/null
+++ b/tests/modules/nf-core/biobambam/bammerge/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BIOBAMBAM_BAMMERGE } from '../../../../../modules/nf-core/biobambam/bammerge/main.nf'
+
+workflow test_biobambam_bammerge_paired {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+        ]
+    ]
+
+    BIOBAMBAM_BAMMERGE ( input )
+}
+
+workflow test_biobambam_bammerge_single {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+        ]
+    ]
+
+    BIOBAMBAM_BAMMERGE ( input )
+}
diff --git a/tests/modules/biobambam/bammerge/nextflow.config b/tests/modules/nf-core/biobambam/bammerge/nextflow.config
similarity index 100%
rename from tests/modules/biobambam/bammerge/nextflow.config
rename to tests/modules/nf-core/biobambam/bammerge/nextflow.config
diff --git a/tests/modules/nf-core/biobambam/bammerge/test.yml b/tests/modules/nf-core/biobambam/bammerge/test.yml
new file mode 100644
index 00000000000..c886635b878
--- /dev/null
+++ b/tests/modules/nf-core/biobambam/bammerge/test.yml
@@ -0,0 +1,25 @@
+- name: biobambam bammerge test_biobambam_bammerge_paired
+  command: nextflow run ./tests/modules/nf-core/biobambam/bammerge -entry test_biobambam_bammerge_paired -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/biobambam/bammerge/nextflow.config
+  tags:
+    - biobambam/bammerge
+    - biobambam
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: bc3d32ab6a54d1894ca7cc79387dec57
+    - path: output/biobambam/test.bam.bai
+      md5sum: b8ae542a37a73d79de1c15c765207c53
+    - path: output/biobambam/test.md5
+      md5sum: 31c59857990ceb392242136429e30243
+
+- name: biobambam bammerge test_biobambam_bammerge_single
+  command: nextflow run ./tests/modules/nf-core/biobambam/bammerge -entry test_biobambam_bammerge_single -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/biobambam/bammerge/nextflow.config
+  tags:
+    - biobambam/bammerge
+    - biobambam
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: 86185d3d6895a7722d3b3a09c6f91bfc
+    - path: output/biobambam/test.bam.bai
+      md5sum: 973680feb6bc73cd1051ea83c7219418
+    - path: output/biobambam/test.md5
+      md5sum: 244a9d1cbc6d74724285c80220e5e427
diff --git a/tests/modules/nf-core/biobambam/bamsormadup/main.nf b/tests/modules/nf-core/biobambam/bamsormadup/main.nf
new file mode 100644
index 00000000000..1f9adae5ac5
--- /dev/null
+++ b/tests/modules/nf-core/biobambam/bamsormadup/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BIOBAMBAM_BAMSORMADUP } from '../../../../../modules/nf-core/biobambam/bamsormadup/main.nf'
+
+workflow test_biobambam_bamsormadup_multi_input {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
+    ]
+
+    BIOBAMBAM_BAMSORMADUP ( input, [] )
+}
+
+workflow test_biobambam_bamsormadup_single_input {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)],
+    ]
+
+    BIOBAMBAM_BAMSORMADUP ( input, [] )
+}
diff --git a/tests/modules/biobambam/bamsormadup/nextflow.config b/tests/modules/nf-core/biobambam/bamsormadup/nextflow.config
similarity index 100%
rename from tests/modules/biobambam/bamsormadup/nextflow.config
rename to tests/modules/nf-core/biobambam/bamsormadup/nextflow.config
diff --git a/tests/modules/nf-core/biobambam/bamsormadup/test.yml b/tests/modules/nf-core/biobambam/bamsormadup/test.yml
new file mode 100644
index 00000000000..4837c16f042
--- /dev/null
+++ b/tests/modules/nf-core/biobambam/bamsormadup/test.yml
@@ -0,0 +1,21 @@
+- name: biobambam bamsormadup test_biobambam_bamsormadup_multi_input
+  command: nextflow run ./tests/modules/nf-core/biobambam/bamsormadup -entry test_biobambam_bamsormadup_multi_input -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/biobambam/bamsormadup/nextflow.config
+  tags:
+    - biobambam
+    - biobambam/bamsormadup
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: 1d549a00b065584c298594180ca9f3bc
+    - path: output/biobambam/test.metrics.txt
+      md5sum: 1721879bea1f3888ecd33b35e6ee0e72
+
+- name: biobambam bamsormadup test_biobambam_bamsormadup_single_input
+  command: nextflow run ./tests/modules/nf-core/biobambam/bamsormadup -entry test_biobambam_bamsormadup_single_input -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/biobambam/bamsormadup/nextflow.config
+  tags:
+    - biobambam
+    - biobambam/bamsormadup
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: 48e01431daec7fb17471d930a6d1d587
+    - path: output/biobambam/test.metrics.txt
+      md5sum: b97458eff0d4b259055e4902849ee53b
diff --git a/tests/modules/nf-core/biscuit/align/main.nf b/tests/modules/nf-core/biscuit/align/main.nf
new file mode 100644
index 00000000000..00fe14d6bb8
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/align/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX }                     from '../../../../../modules/nf-core/biscuit/index/main.nf'
+include { BISCUIT_ALIGN as BISCUIT_ALIGN_SE } from '../../../../../modules/nf-core/biscuit/align/main.nf'
+include { BISCUIT_ALIGN as BISCUIT_ALIGN_PE } from '../../../../../modules/nf-core/biscuit/align/main.nf'
+
+
+// Single-end test
+workflow test_biscuit_align_single {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_ALIGN_SE (input, BISCUIT_INDEX.out.index )
+}
+
+// paired-end test
+workflow test_biscuit_align_paired {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_ALIGN_SE (input, BISCUIT_INDEX.out.index )
+}
diff --git a/tests/modules/biscuit/align/nextflow.config b/tests/modules/nf-core/biscuit/align/nextflow.config
similarity index 100%
rename from tests/modules/biscuit/align/nextflow.config
rename to tests/modules/nf-core/biscuit/align/nextflow.config
diff --git a/tests/modules/nf-core/biscuit/align/test.yml b/tests/modules/nf-core/biscuit/align/test.yml
new file mode 100644
index 00000000000..95ff9411ce9
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/align/test.yml
@@ -0,0 +1,53 @@
+- name: biscuit align test_biscuit_align_single
+  command: nextflow run ./tests/modules/nf-core/biscuit/align -entry test_biscuit_align_single -c ./tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/align
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: eb36532425cb9b259410d6464a9e523a
+    - path: output/biscuit/versions.yml
+      md5sum: a86c4170bbf90cc75b93eb59ea124acd
+
+- name: biscuit align test_biscuit_align_paired
+  command: nextflow run ./tests/modules/nf-core/biscuit/align -entry test_biscuit_align_paired -c ./tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/align
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: be3f6aa86c499d6a6b2996e5936e4f50
+    - path: output/biscuit/versions.yml
+      md5sum: f0b7dffd28f5e6bb1466fce6661d133f
diff --git a/tests/modules/nf-core/biscuit/biscuitblaster/main.nf b/tests/modules/nf-core/biscuit/biscuitblaster/main.nf
new file mode 100644
index 00000000000..7db9d4c528d
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/biscuitblaster/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX                         } from '../../../../../modules/nf-core/biscuit/index/main.nf'
+include { BISCUIT_BLASTER as BISCUIT_BLASTER_SE } from '../../../../../modules/nf-core/biscuit/biscuitblaster/main.nf'
+include { BISCUIT_BLASTER as BISCUIT_BLASTER_PE } from '../../../../../modules/nf-core/biscuit/biscuitblaster/main.nf'
+
+// Single-end test
+workflow test_biscuit_blaster_single {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_BLASTER_SE (input, BISCUIT_INDEX.out.index )
+}
+
+// paired-end test
+workflow test_biscuit_blaster_paired {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_BLASTER_PE (input, BISCUIT_INDEX.out.index )
+}
diff --git a/tests/modules/biscuit/biscuitblaster/nextflow.config b/tests/modules/nf-core/biscuit/biscuitblaster/nextflow.config
similarity index 100%
rename from tests/modules/biscuit/biscuitblaster/nextflow.config
rename to tests/modules/nf-core/biscuit/biscuitblaster/nextflow.config
diff --git a/tests/modules/nf-core/biscuit/biscuitblaster/test.yml b/tests/modules/nf-core/biscuit/biscuitblaster/test.yml
new file mode 100644
index 00000000000..c1f9abb55db
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/biscuitblaster/test.yml
@@ -0,0 +1,57 @@
+- name: biscuit biscuitblaster test_biscuit_blaster_single
+  command: nextflow run ./tests/modules/nf-core/biscuit/biscuitblaster -entry test_biscuit_blaster_single -c ./tests/config/nextflow.config
+  tags:
+    - biscuit/biscuitblaster
+    - biscuit
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: 9ece50b67349382d38b20c2702e65675
+    - path: output/biscuit/test.bam.bai
+      md5sum: 8f14bb42fd38cc7ce4a3c3a9d7133ea4
+    - path: output/biscuit/versions.yml
+      md5sum: bfb660b5b0d92dde6817a1c6a2a302bb
+
+- name: biscuit biscuitblaster test_biscuit_blaster_paired
+  command: nextflow run ./tests/modules/nf-core/biscuit/biscuitblaster -entry test_biscuit_blaster_paired -c ./tests/config/nextflow.config
+  tags:
+    - biscuit/biscuitblaster
+    - biscuit
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: 0c6de35f38003df6ea5dd036170df91b
+    - path: output/biscuit/test.bam.bai
+      md5sum: 0d76977b2e36046cc176112776c5fa4e
+    - path: output/biscuit/versions.yml
+      md5sum: 82160a7ad29ccc3a21e59b1869399c04
diff --git a/tests/modules/nf-core/biscuit/bsconv/main.nf b/tests/modules/nf-core/biscuit/bsconv/main.nf
new file mode 100644
index 00000000000..14bc0e22439
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/bsconv/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX  } from '../../../../../modules/nf-core/biscuit/index/main.nf'
+include { BISCUIT_BSCONV } from '../../../../../modules/nf-core/biscuit/bsconv/main.nf'
+
+workflow test_biscuit_bsconv {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_BSCONV ( input, BISCUIT_INDEX.out.index )
+}
diff --git a/tests/modules/biscuit/bsconv/nextflow.config b/tests/modules/nf-core/biscuit/bsconv/nextflow.config
similarity index 100%
rename from tests/modules/biscuit/bsconv/nextflow.config
rename to tests/modules/nf-core/biscuit/bsconv/nextflow.config
diff --git a/tests/modules/nf-core/biscuit/bsconv/test.yml b/tests/modules/nf-core/biscuit/bsconv/test.yml
new file mode 100644
index 00000000000..db50a552354
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/bsconv/test.yml
@@ -0,0 +1,26 @@
+- name: biscuit bsconv test_biscuit_bsconv
+  command: nextflow run ./tests/modules/nf-core/biscuit/bsconv -entry test_biscuit_bsconv -c ./tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/bsconv
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: e33e9498d00dd32222b90a6bd981226f
+    - path: output/biscuit/versions.yml
+      md5sum: 7deec1f096203542bbb72ac4fa05f9ba
diff --git a/tests/modules/nf-core/biscuit/epiread/main.nf b/tests/modules/nf-core/biscuit/epiread/main.nf
new file mode 100644
index 00000000000..13eb7afce98
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/epiread/main.nf
@@ -0,0 +1,48 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX   } from '../../../../../modules/nf-core/biscuit/index/main.nf'
+include { BISCUIT_EPIREAD } from '../../../../../modules/nf-core/biscuit/epiread/main.nf'
+
+workflow test_biscuit_epiread_nosnp {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
+        [] //SNP BED file
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
+}
+
+workflow test_biscuit_epiread_snp {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed')
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
+}
+
+workflow test_biscuit_epiread_snp_decompress {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed.gz')
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
+}
diff --git a/tests/modules/biscuit/epiread/nextflow.config b/tests/modules/nf-core/biscuit/epiread/nextflow.config
similarity index 100%
rename from tests/modules/biscuit/epiread/nextflow.config
rename to tests/modules/nf-core/biscuit/epiread/nextflow.config
diff --git a/tests/modules/nf-core/biscuit/epiread/test.yml b/tests/modules/nf-core/biscuit/epiread/test.yml
new file mode 100644
index 00000000000..23ab6aa3b71
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/epiread/test.yml
@@ -0,0 +1,80 @@
+- name: biscuit epiread test_biscuit_epiread_nosnp
+  command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_nosnp -c ./tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/epiread
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bed.gz
+      md5sum: dbb30b59f4ef6fdfdee38630225c0574
+    - path: output/biscuit/versions.yml
+      md5sum: 674a77ac5ca8f4b42d30e58e30c3a9af
+
+- name: biscuit epiread test_biscuit_epiread_snp
+  command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_snp -c ./tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/epiread
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bed.gz
+      md5sum: a29fea6ad74453ec94f8220747dab906
+    - path: output/biscuit/versions.yml
+      md5sum: f2f7c4ff3c6a135b1c8a3aff24a44d81
+
+- name: biscuit epiread test_biscuit_epiread_snp_decompress
+  command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_snp_decompress -c ./tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/epiread
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bed.gz
+      md5sum: a29fea6ad74453ec94f8220747dab906
+    - path: output/biscuit/versions.yml
+      md5sum: cb0258ebf4e1a731a4310ec17c3dc442
diff --git a/tests/modules/nf-core/biscuit/index/main.nf b/tests/modules/nf-core/biscuit/index/main.nf
new file mode 100644
index 00000000000..6ac491306f9
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/index/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX } from '../../../../../modules/nf-core/biscuit/index/main.nf'
+
+workflow test_biscuit_index {
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+}
diff --git a/tests/modules/biscuit/index/nextflow.config b/tests/modules/nf-core/biscuit/index/nextflow.config
similarity index 100%
rename from tests/modules/biscuit/index/nextflow.config
rename to tests/modules/nf-core/biscuit/index/nextflow.config
diff --git a/tests/modules/nf-core/biscuit/index/test.yml b/tests/modules/nf-core/biscuit/index/test.yml
new file mode 100644
index 00000000000..c14a3f00103
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/index/test.yml
@@ -0,0 +1,24 @@
+- name: biscuit index test_biscuit_index
+  command: nextflow run ./tests/modules/nf-core/biscuit/index -entry test_biscuit_index -c ./tests/config/nextflow.config
+  tags:
+    - biscuit/index
+    - biscuit
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/versions.yml
+      md5sum: 5c5873e482a57966db246648ffddf62f
diff --git a/tests/modules/nf-core/biscuit/mergecg/main.nf b/tests/modules/nf-core/biscuit/mergecg/main.nf
new file mode 100644
index 00000000000..9eade987eaa
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/mergecg/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX   } from '../../../../../modules/nf-core/biscuit/index/main.nf'
+include { BISCUIT_MERGECG } from '../../../../../modules/nf-core/biscuit/mergecg/main.nf'
+
+workflow test_biscuit_mergecg {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-cg.bed.gz', checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_MERGECG ( input, BISCUIT_INDEX.out.index )
+}
diff --git a/tests/modules/biscuit/mergecg/nextflow.config b/tests/modules/nf-core/biscuit/mergecg/nextflow.config
similarity index 100%
rename from tests/modules/biscuit/mergecg/nextflow.config
rename to tests/modules/nf-core/biscuit/mergecg/nextflow.config
diff --git a/tests/modules/nf-core/biscuit/mergecg/test.yml b/tests/modules/nf-core/biscuit/mergecg/test.yml
new file mode 100644
index 00000000000..7b16d1646cd
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/mergecg/test.yml
@@ -0,0 +1,26 @@
+- name: biscuit mergecg test_biscuit_mergecg
+  command: nextflow run ./tests/modules/nf-core/biscuit/mergecg -entry test_biscuit_mergecg -c ./tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/mergecg
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bed.gz
+      md5sum: d693b28ddc81265f388860d391fc7c5b
+    - path: output/biscuit/versions.yml
+      md5sum: f670d63671af06bf8654677bf373b3a1
diff --git a/tests/modules/nf-core/biscuit/pileup/main.nf b/tests/modules/nf-core/biscuit/pileup/main.nf
new file mode 100644
index 00000000000..7f9ebb4fb07
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/pileup/main.nf
@@ -0,0 +1,38 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX  } from '../../../../../modules/nf-core/biscuit/index/main.nf'
+include { BISCUIT_PILEUP } from '../../../../../modules/nf-core/biscuit/pileup/main.nf'
+
+workflow test_biscuit_pileup {
+
+    input = [ [ id:'test' ], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)],
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)],    
+	[], //tumor bam 
+	[] //tumor bai
+        ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
+
+}
+
+workflow test_biscuit_pileup_somatic {
+
+    input = [ [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)    
+        ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
+
+}
diff --git a/tests/modules/biscuit/pileup/nextflow.config b/tests/modules/nf-core/biscuit/pileup/nextflow.config
similarity index 100%
rename from tests/modules/biscuit/pileup/nextflow.config
rename to tests/modules/nf-core/biscuit/pileup/nextflow.config
diff --git a/tests/modules/nf-core/biscuit/pileup/test.yml b/tests/modules/nf-core/biscuit/pileup/test.yml
new file mode 100644
index 00000000000..318a662dee1
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/pileup/test.yml
@@ -0,0 +1,53 @@
+- name: biscuit pileup test_biscuit_pileup
+  command: nextflow run ./tests/modules/nf-core/biscuit/pileup -entry test_biscuit_pileup -c ./tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/pileup
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 1891c1de381b3a96d4e72f590fde20c1
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: 668799eea40aefb8013cbf8ed6c47cfe
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 10541b05bbea44d0344b0345a6522ba8
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 2c38edd64234420add133f5fe1ff975d
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 7deee1aac3395d93bef1df11ab38379e
+    - path: output/biscuit/test.vcf.gz
+      md5sum: ef9798c318ead0f8a79ee7fdeb1ffbf9
+    - path: output/biscuit/versions.yml
+      md5sum: ae38b891fdbf9f7ff5c486408f949dc5
+
+- name: biscuit pileup test_biscuit_pileup_somatic
+  command: nextflow run ./tests/modules/nf-core/biscuit/pileup -entry test_biscuit_pileup_somatic -c ./tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/pileup
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 1891c1de381b3a96d4e72f590fde20c1
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: 668799eea40aefb8013cbf8ed6c47cfe
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 10541b05bbea44d0344b0345a6522ba8
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 2c38edd64234420add133f5fe1ff975d
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 7deee1aac3395d93bef1df11ab38379e
+    - path: output/biscuit/test.vcf.gz
+      md5sum: 692b4a6191b08fabe5efa5abe00da420
+    - path: output/biscuit/versions.yml
+      md5sum: cc51fd498d67fdc7cc067686eb855b93
diff --git a/tests/modules/nf-core/biscuit/qc/main.nf b/tests/modules/nf-core/biscuit/qc/main.nf
new file mode 100644
index 00000000000..8f226b1d774
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/qc/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX  } from '../../../../../modules/nf-core/biscuit/index/main.nf'
+include { BISCUIT_QC } from '../../../../../modules/nf-core/biscuit/qc/main.nf'
+
+workflow test_biscuit_qc {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_QC ( input, BISCUIT_INDEX.out.index )
+}
diff --git a/tests/modules/biscuit/qc/nextflow.config b/tests/modules/nf-core/biscuit/qc/nextflow.config
similarity index 100%
rename from tests/modules/biscuit/qc/nextflow.config
rename to tests/modules/nf-core/biscuit/qc/nextflow.config
diff --git a/tests/modules/nf-core/biscuit/qc/test.yml b/tests/modules/nf-core/biscuit/qc/test.yml
new file mode 100644
index 00000000000..2cd8ca7c432
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/qc/test.yml
@@ -0,0 +1,38 @@
+- name: biscuit qc test_biscuit_qc
+  command: nextflow run ./tests/modules/nf-core/biscuit/qc -entry test_biscuit_qc -c ./tests/config/nextflow.config
+  tags:
+    - biscuit/qc
+    - biscuit
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test_CpGRetentionByReadPos.txt
+      md5sum: 498b6c0af196fb34c8835371b9e9b68a
+    - path: output/biscuit/test_CpHRetentionByReadPos.txt
+      md5sum: a266942c5719cecab7f60f63cbe7335d
+    - path: output/biscuit/test_dup_report.txt
+      md5sum: 65bddf4fbe9e40d7c6c976060df53e3b
+    - path: output/biscuit/test_isize_table.txt
+      md5sum: aadf6f2e271abc334b6146cf164bdda3
+    - path: output/biscuit/test_mapq_table.txt
+      md5sum: c8adaac84bb8db3b7f48e1ed4fccad00
+    - path: output/biscuit/test_strand_table.txt
+      md5sum: 27068382ba6b2dbf313169a85c9dbb3a
+    - path: output/biscuit/test_totalReadConversionRate.txt
+      md5sum: 8f0c1fceaebfa74f2757720e3bc85fed
+    - path: output/biscuit/versions.yml
+      md5sum: a730fa4888e6882cf1b8ba92645b04ee
diff --git a/tests/modules/nf-core/biscuit/vcf2bed/main.nf b/tests/modules/nf-core/biscuit/vcf2bed/main.nf
new file mode 100644
index 00000000000..3f9828080f1
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/vcf2bed/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_VCF2BED } from '../../../../../modules/nf-core/biscuit/vcf2bed/main.nf'
+
+workflow test_biscuit_vcf2bed {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test.vcf.gz', checkIfExists: true)
+    ]
+
+    BISCUIT_VCF2BED ( input )
+
+}
diff --git a/tests/modules/biscuit/vcf2bed/nextflow.config b/tests/modules/nf-core/biscuit/vcf2bed/nextflow.config
similarity index 100%
rename from tests/modules/biscuit/vcf2bed/nextflow.config
rename to tests/modules/nf-core/biscuit/vcf2bed/nextflow.config
diff --git a/tests/modules/nf-core/biscuit/vcf2bed/test.yml b/tests/modules/nf-core/biscuit/vcf2bed/test.yml
new file mode 100644
index 00000000000..ad4f9a1aa76
--- /dev/null
+++ b/tests/modules/nf-core/biscuit/vcf2bed/test.yml
@@ -0,0 +1,10 @@
+- name: biscuit vcf2bed test_biscuit_vcf2bed
+  command: nextflow run ./tests/modules/nf-core/biscuit/vcf2bed -entry test_biscuit_vcf2bed -c ./tests/config/nextflow.config
+  tags:
+    - biscuit/vcf2bed
+    - biscuit
+  files:
+    - path: output/biscuit/test.bed.gz
+      md5sum: e2dd492289dc8463f364285e31b9553a
+    - path: output/biscuit/versions.yml
+      md5sum: cd784276e2fb6739d55e1b60d12202cd
diff --git a/tests/modules/nf-core/bismark/align/main.nf b/tests/modules/nf-core/bismark/align/main.nf
new file mode 100644
index 00000000000..c24e751c919
--- /dev/null
+++ b/tests/modules/nf-core/bismark/align/main.nf
@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_GENOMEPREPARATION         } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf'
+include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../../modules/nf-core/bismark/align/main.nf'
+include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../../modules/nf-core/bismark/align/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_bismark_align_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISMARK_GENOMEPREPARATION ( fasta )
+    BISMARK_ALIGN_SE ( input, BISMARK_GENOMEPREPARATION.out.index )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_bismark_align_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISMARK_GENOMEPREPARATION ( fasta )
+    BISMARK_ALIGN_PE ( input, BISMARK_GENOMEPREPARATION.out.index )
+}
diff --git a/tests/modules/bismark/align/nextflow.config b/tests/modules/nf-core/bismark/align/nextflow.config
similarity index 100%
rename from tests/modules/bismark/align/nextflow.config
rename to tests/modules/nf-core/bismark/align/nextflow.config
diff --git a/tests/modules/nf-core/bismark/align/test.yml b/tests/modules/nf-core/bismark/align/test.yml
new file mode 100644
index 00000000000..a7362eb0d2a
--- /dev/null
+++ b/tests/modules/nf-core/bismark/align/test.yml
@@ -0,0 +1,19 @@
+- name: bismark align single-end test workflow
+  command: nextflow run ./tests/modules/nf-core/bismark/align -entry test_bismark_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/align/nextflow.config
+  tags:
+    - bismark
+    - bismark/align
+  files:
+    - path: output/bismark/test.methylated_1_bismark_bt2.bam
+      md5sum: dca4ba9ff705b70446f812e59bdb1a32
+    - path: output/bismark/test.methylated_1_bismark_bt2_SE_report.txt
+
+- name: bismark align paired-end test workflow
+  command: nextflow run ./tests/modules/nf-core/bismark/align -entry test_bismark_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/align/nextflow.config
+  tags:
+    - bismark
+    - bismark/align
+  files:
+    - path: output/bismark/test.methylated_1_bismark_bt2_pe.bam
+      md5sum: 43943b1f30d056fcbd9ed26061ea0583
+    - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.txt
diff --git a/tests/modules/nf-core/bismark/deduplicate/main.nf b/tests/modules/nf-core/bismark/deduplicate/main.nf
new file mode 100644
index 00000000000..7f1ae9c127b
--- /dev/null
+++ b/tests/modules/nf-core/bismark/deduplicate/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_DEDUPLICATE } from '../../../../../modules/nf-core/bismark/deduplicate/main.nf'
+
+workflow test_bismark_deduplicate {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_bam'], checkIfExists: true) ]
+            ]
+
+    BISMARK_DEDUPLICATE ( input )
+}
diff --git a/tests/modules/bismark/deduplicate/nextflow.config b/tests/modules/nf-core/bismark/deduplicate/nextflow.config
similarity index 100%
rename from tests/modules/bismark/deduplicate/nextflow.config
rename to tests/modules/nf-core/bismark/deduplicate/nextflow.config
diff --git a/tests/modules/nf-core/bismark/deduplicate/test.yml b/tests/modules/nf-core/bismark/deduplicate/test.yml
new file mode 100644
index 00000000000..ba4d2de7a3d
--- /dev/null
+++ b/tests/modules/nf-core/bismark/deduplicate/test.yml
@@ -0,0 +1,10 @@
+- name: bismark deduplicate test workflow
+  command: nextflow run ./tests/modules/nf-core/bismark/deduplicate -entry test_bismark_deduplicate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/deduplicate/nextflow.config
+  tags:
+    - bismark
+    - bismark/deduplicate
+  files:
+    - path: output/bismark/test.paired_end.methylated.deduplicated.bam
+      md5sum: 82213a207048bcb5d8cc1cee92703a29
+    - path: output/bismark/test.paired_end.methylated.deduplication_report.txt
+      md5sum: 86aaf87bac9ccdc3cc83628f20b902dc
diff --git a/tests/modules/nf-core/bismark/genomepreparation/main.nf b/tests/modules/nf-core/bismark/genomepreparation/main.nf
new file mode 100644
index 00000000000..71b77805193
--- /dev/null
+++ b/tests/modules/nf-core/bismark/genomepreparation/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_GENOMEPREPARATION } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf'
+
+workflow test_bismark_genomepreparation {
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISMARK_GENOMEPREPARATION ( fasta )
+}
diff --git a/tests/modules/bismark/genomepreparation/nextflow.config b/tests/modules/nf-core/bismark/genomepreparation/nextflow.config
similarity index 100%
rename from tests/modules/bismark/genomepreparation/nextflow.config
rename to tests/modules/nf-core/bismark/genomepreparation/nextflow.config
diff --git a/tests/modules/nf-core/bismark/genomepreparation/test.yml b/tests/modules/nf-core/bismark/genomepreparation/test.yml
new file mode 100644
index 00000000000..8868eed3de5
--- /dev/null
+++ b/tests/modules/nf-core/bismark/genomepreparation/test.yml
@@ -0,0 +1,36 @@
+- name: bismark genomepreparation test workflow
+  command: nextflow run ./tests/modules/nf-core/bismark/genomepreparation -entry test_bismark_genomepreparation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/genomepreparation/nextflow.config
+  tags:
+    - bismark
+    - bismark/genomepreparation
+  files:
+    - path: ./output/bismark/BismarkIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa
+      md5sum: 903b9f357eea4a5f36e21e78e0fe1dfa
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.4.bt2
+      md5sum: 6c4f549575e5882ff3a97ae10ae2e7be
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.1.bt2
+      md5sum: 10a8854e5eeb95629f46d24b0d8da70c
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.3.bt2
+      md5sum: 4ed93abba181d8dfab2e303e33114777
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.2.bt2
+      md5sum: bc5d407e6fce3e1cdb4b23ab2a20f707
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2
+      md5sum: 48bf400de85cd7324fbf6bf38fe2dc95
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2
+      md5sum: d37d586b41b6a36efb25839961d242cb
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2
+      md5sum: 17f51e65f44477962226a83b369b2bc4
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2
+      md5sum: d36044c5dfe37af0411f60d446585bc6
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa
+      md5sum: e529375ec2039112161465b5169fcd59
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.4.bt2
+      md5sum: b1e855685ed634daa7df8e180c9b2fc4
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.1.bt2
+      md5sum: a6fa4068ed10872568f32568c66cb600
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.2.bt2
+      md5sum: fc5b634e2f5137801e3801d62ad05f74
+    - path: ./output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.3.bt2
+      md5sum: 4ed93abba181d8dfab2e303e33114777
diff --git a/tests/modules/nf-core/bismark/methylationextractor/main.nf b/tests/modules/nf-core/bismark/methylationextractor/main.nf
new file mode 100644
index 00000000000..6c11f013bc4
--- /dev/null
+++ b/tests/modules/nf-core/bismark/methylationextractor/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_GENOMEPREPARATION    } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf'
+include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../../modules/nf-core/bismark/methylationextractor/main.nf'
+
+workflow test_bismark_methylationextractor {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_bam'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISMARK_GENOMEPREPARATION ( fasta )
+    BISMARK_METHYLATIONEXTRACTOR ( input, BISMARK_GENOMEPREPARATION.out.index )
+}
diff --git a/tests/modules/bismark/methylationextractor/nextflow.config b/tests/modules/nf-core/bismark/methylationextractor/nextflow.config
similarity index 100%
rename from tests/modules/bismark/methylationextractor/nextflow.config
rename to tests/modules/nf-core/bismark/methylationextractor/nextflow.config
diff --git a/tests/modules/nf-core/bismark/methylationextractor/test.yml b/tests/modules/nf-core/bismark/methylationextractor/test.yml
new file mode 100644
index 00000000000..ef1643dfff6
--- /dev/null
+++ b/tests/modules/nf-core/bismark/methylationextractor/test.yml
@@ -0,0 +1,16 @@
+- name: bismark methylation extractor test workflow
+  command: nextflow run ./tests/modules/nf-core/bismark/methylationextractor -entry test_bismark_methylationextractor -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/methylationextractor/nextflow.config
+  tags:
+    - bismark
+    - bismark/methylationextractor
+  files:
+    - path: output/bismark/CHG_OB_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CHG_OT_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CHH_OB_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CHH_OT_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CpG_OB_test.paired_end.methylated.txt.gz
+    - path: output/bismark/CpG_OT_test.paired_end.methylated.txt.gz
+    - path: output/bismark/test.paired_end.methylated.M-bias.txt
+      md5sum: 0b100924d46b3c35115f1206f34c4a59
+    - path: output/bismark/test.paired_end.methylated_splitting_report.txt
+      md5sum: f28a9dd8de8c42b8900b190b8f79647a
diff --git a/tests/modules/nf-core/bismark/report/main.nf b/tests/modules/nf-core/bismark/report/main.nf
new file mode 100644
index 00000000000..df1567c43a2
--- /dev/null
+++ b/tests/modules/nf-core/bismark/report/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_GENOMEPREPARATION    } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf'
+include { BISMARK_ALIGN                } from '../../../../../modules/nf-core/bismark/align/main.nf'
+include { BISMARK_DEDUPLICATE          } from '../../../../../modules/nf-core/bismark/deduplicate/main.nf'
+include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../../modules/nf-core/bismark/methylationextractor/main.nf'
+include { BISMARK_REPORT               } from '../../../../../modules/nf-core/bismark/report/main.nf'
+
+workflow test_bismark_report {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISMARK_GENOMEPREPARATION ( fasta )
+    BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
+    BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
+    BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
+    BISMARK_REPORT (
+        BISMARK_ALIGN.out.report
+            .join(BISMARK_DEDUPLICATE.out.report)
+            .join(BISMARK_METHYLATIONEXTRACTOR.out.report)
+            .join(BISMARK_METHYLATIONEXTRACTOR.out.mbias)
+    )
+}
diff --git a/tests/modules/bismark/report/nextflow.config b/tests/modules/nf-core/bismark/report/nextflow.config
similarity index 100%
rename from tests/modules/bismark/report/nextflow.config
rename to tests/modules/nf-core/bismark/report/nextflow.config
diff --git a/tests/modules/nf-core/bismark/report/test.yml b/tests/modules/nf-core/bismark/report/test.yml
new file mode 100644
index 00000000000..591d2789a2e
--- /dev/null
+++ b/tests/modules/nf-core/bismark/report/test.yml
@@ -0,0 +1,8 @@
+- name: bismark report test workflow
+  command: nextflow run ./tests/modules/nf-core/bismark/report -entry test_bismark_report -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/report/nextflow.config
+  tags:
+    - bismark
+    - bismark/report
+  files:
+    - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.html
+    - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.txt
diff --git a/tests/modules/nf-core/bismark/summary/main.nf b/tests/modules/nf-core/bismark/summary/main.nf
new file mode 100644
index 00000000000..89bb91a0162
--- /dev/null
+++ b/tests/modules/nf-core/bismark/summary/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_GENOMEPREPARATION    } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf'
+include { BISMARK_ALIGN                } from '../../../../../modules/nf-core/bismark/align/main.nf'
+include { BISMARK_DEDUPLICATE          } from '../../../../../modules/nf-core/bismark/deduplicate/main.nf'
+include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../../modules/nf-core/bismark/methylationextractor/main.nf'
+include { BISMARK_SUMMARY              } from '../../../../../modules/nf-core/bismark/summary/main.nf'
+
+workflow test_bismark_summary {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISMARK_GENOMEPREPARATION ( fasta )
+    BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
+    BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
+    BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
+    BISMARK_SUMMARY (
+        BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam },
+        BISMARK_ALIGN.out.report.collect{ meta, report -> report },
+        BISMARK_DEDUPLICATE.out.report.collect{ meta, bam -> bam },
+        BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report },
+        BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
+    )
+}
diff --git a/tests/modules/bismark/summary/nextflow.config b/tests/modules/nf-core/bismark/summary/nextflow.config
similarity index 100%
rename from tests/modules/bismark/summary/nextflow.config
rename to tests/modules/nf-core/bismark/summary/nextflow.config
diff --git a/tests/modules/nf-core/bismark/summary/test.yml b/tests/modules/nf-core/bismark/summary/test.yml
new file mode 100644
index 00000000000..d4ccddaadaf
--- /dev/null
+++ b/tests/modules/nf-core/bismark/summary/test.yml
@@ -0,0 +1,9 @@
+- name: bismark summary test workflow
+  command: nextflow run ./tests/modules/nf-core/bismark/summary -entry test_bismark_summary -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/summary/nextflow.config
+  tags:
+    - bismark
+    - bismark/summary
+  files:
+    - path: output/bismark/bismark_summary_report.html
+    - path: output/bismark/bismark_summary_report.txt
+      md5sum: fdfadd5399c4e7b2108da100e72036eb
diff --git a/tests/modules/nf-core/blast/blastn/main.nf b/tests/modules/nf-core/blast/blastn/main.nf
new file mode 100644
index 00000000000..cb0f8bdf52c
--- /dev/null
+++ b/tests/modules/nf-core/blast/blastn/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BLAST_MAKEBLASTDB } from '../../../../../modules/nf-core/blast/makeblastdb/main.nf'
+include { BLAST_BLASTN      } from '../../../../../modules/nf-core/blast/blastn/main.nf'
+
+workflow test_blast_blastn {
+    input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    BLAST_MAKEBLASTDB ( input )
+    BLAST_BLASTN ( [ [id:'test'], input ], BLAST_MAKEBLASTDB.out.db )
+}
diff --git a/tests/modules/blast/blastn/nextflow.config b/tests/modules/nf-core/blast/blastn/nextflow.config
similarity index 100%
rename from tests/modules/blast/blastn/nextflow.config
rename to tests/modules/nf-core/blast/blastn/nextflow.config
diff --git a/tests/modules/nf-core/blast/blastn/test.yml b/tests/modules/nf-core/blast/blastn/test.yml
new file mode 100644
index 00000000000..2c3492a1b07
--- /dev/null
+++ b/tests/modules/nf-core/blast/blastn/test.yml
@@ -0,0 +1,22 @@
+- name: blast_blastn
+  command: nextflow run ./tests/modules/nf-core/blast/blastn -entry test_blast_blastn -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/blast/blastn/nextflow.config
+  tags:
+    - blast
+    - blast/blastn
+  files:
+    - path: ./output/blast/test.blastn.txt
+    - path: ./output/blast/blast_db/genome.fasta.nsq
+      md5sum: 982cbc7d9e38743b9b1037588862b9da
+    - path: ./output/blast/blast_db/genome.fasta.nin
+    - path: ./output/blast/blast_db/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: ./output/blast/blast_db/genome.fasta.nhr
+      md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
+    - path: ./output/blast/blast_db/genome.fasta.ndb
+      md5sum: 0d553c830656469211de113c5022f06d
+    - path: ./output/blast/blast_db/genome.fasta.not
+      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
+    - path: ./output/blast/blast_db/genome.fasta.nto
+      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
+    - path: ./output/blast/blast_db/genome.fasta.ntf
+      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
diff --git a/tests/modules/nf-core/blast/makeblastdb/main.nf b/tests/modules/nf-core/blast/makeblastdb/main.nf
new file mode 100644
index 00000000000..6822a9fb4ab
--- /dev/null
+++ b/tests/modules/nf-core/blast/makeblastdb/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BLAST_MAKEBLASTDB } from '../../../../../modules/nf-core/blast/makeblastdb/main.nf'
+
+workflow test_blast_makeblastdb {
+    input =  [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    BLAST_MAKEBLASTDB ( input )
+}
diff --git a/tests/modules/blast/makeblastdb/nextflow.config b/tests/modules/nf-core/blast/makeblastdb/nextflow.config
similarity index 100%
rename from tests/modules/blast/makeblastdb/nextflow.config
rename to tests/modules/nf-core/blast/makeblastdb/nextflow.config
diff --git a/tests/modules/nf-core/blast/makeblastdb/test.yml b/tests/modules/nf-core/blast/makeblastdb/test.yml
new file mode 100644
index 00000000000..a1f527fb430
--- /dev/null
+++ b/tests/modules/nf-core/blast/makeblastdb/test.yml
@@ -0,0 +1,21 @@
+- name: blast_makeblastdb
+  command: nextflow run ./tests/modules/nf-core/blast/makeblastdb -entry test_blast_makeblastdb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/blast/makeblastdb/nextflow.config
+  tags:
+    - blast
+    - blast/makeblastdb
+  files:
+    - path: ./output/blast/blast_db/genome.fasta.nsq
+      md5sum: 982cbc7d9e38743b9b1037588862b9da
+    - path: ./output/blast/blast_db/genome.fasta.nin
+    - path: ./output/blast/blast_db/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: ./output/blast/blast_db/genome.fasta.nhr
+      md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
+    - path: ./output/blast/blast_db/genome.fasta.ndb
+      md5sum: 0d553c830656469211de113c5022f06d
+    - path: ./output/blast/blast_db/genome.fasta.not
+      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
+    - path: ./output/blast/blast_db/genome.fasta.nto
+      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
+    - path: ./output/blast/blast_db/genome.fasta.ntf
+      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
diff --git a/tests/modules/nf-core/blast/tblastn/main.nf b/tests/modules/nf-core/blast/tblastn/main.nf
new file mode 100644
index 00000000000..ee40d8386f0
--- /dev/null
+++ b/tests/modules/nf-core/blast/tblastn/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BLAST_TBLASTN } from '../../../../../modules/nf-core/blast/tblastn/main.nf'
+include { BLAST_MAKEBLASTDB } from '../../../../../modules/nf-core/blast/makeblastdb/main.nf'
+
+workflow test_blast_tblastn {
+
+    input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    input_pep = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+
+    BLAST_MAKEBLASTDB ( input )
+    BLAST_TBLASTN ( [ [id:'test'], input_pep ], BLAST_MAKEBLASTDB.out.db )
+}
diff --git a/tests/modules/blast/tblastn/nextflow.config b/tests/modules/nf-core/blast/tblastn/nextflow.config
similarity index 100%
rename from tests/modules/blast/tblastn/nextflow.config
rename to tests/modules/nf-core/blast/tblastn/nextflow.config
diff --git a/tests/modules/nf-core/blast/tblastn/test.yml b/tests/modules/nf-core/blast/tblastn/test.yml
new file mode 100644
index 00000000000..89887a007b8
--- /dev/null
+++ b/tests/modules/nf-core/blast/tblastn/test.yml
@@ -0,0 +1,25 @@
+- name: blast tblastn
+  command: nextflow run ./tests/modules/nf-core/blast/tblastn -entry test_blast_tblastn -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/blast/tblastn/nextflow.config
+  tags:
+    - blast
+    - blast/tblastn
+  files:
+    - path: ./output/blast/test.tblastn.txt
+      md5sum: c26ccfa5ceae82fc6affdc77f5505b62
+    - path: ./output/blast/versions.yml
+      md5sum: 6d23563b8d75e2fe1e03d3fbe10098a9
+    - path: ./output/blast/blast_db/genome.fasta.nsq
+      md5sum: 982cbc7d9e38743b9b1037588862b9da
+    - path: ./output/blast/blast_db/genome.fasta.nin
+    - path: ./output/blast/blast_db/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: ./output/blast/blast_db/genome.fasta.nhr
+      md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
+    - path: ./output/blast/blast_db/genome.fasta.ndb
+      md5sum: 0d553c830656469211de113c5022f06d
+    - path: ./output/blast/blast_db/genome.fasta.not
+      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
+    - path: ./output/blast/blast_db/genome.fasta.nto
+      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
+    - path: ./output/blast/blast_db/genome.fasta.ntf
+      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
diff --git a/tests/modules/nf-core/bowtie/align/main.nf b/tests/modules/nf-core/bowtie/align/main.nf
new file mode 100644
index 00000000000..96863814855
--- /dev/null
+++ b/tests/modules/nf-core/bowtie/align/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE_BUILD } from '../../../../../modules/nf-core/bowtie/build/main.nf'
+include { BOWTIE_ALIGN } from '../../../../../modules/nf-core/bowtie/align/main.nf'
+
+workflow test_bowtie_align_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BOWTIE_BUILD ( fasta )
+    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
+}
+
+workflow test_bowtie_align_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BOWTIE_BUILD ( fasta )
+    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
+}
diff --git a/tests/modules/bowtie/align/nextflow.config b/tests/modules/nf-core/bowtie/align/nextflow.config
similarity index 100%
rename from tests/modules/bowtie/align/nextflow.config
rename to tests/modules/nf-core/bowtie/align/nextflow.config
diff --git a/tests/modules/nf-core/bowtie/align/test.yml b/tests/modules/nf-core/bowtie/align/test.yml
new file mode 100644
index 00000000000..45ebb7598f7
--- /dev/null
+++ b/tests/modules/nf-core/bowtie/align/test.yml
@@ -0,0 +1,42 @@
+- name: bowtie align single-end
+  command: nextflow run ./tests/modules/nf-core/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie/align/nextflow.config
+  tags:
+    - bowtie
+    - bowtie/align
+  files:
+    - path: ./output/bowtie/test.bam
+    - path: ./output/bowtie/test.out
+      md5sum: 4b9140ceadb8a18ae9330885370f8a0b
+    - path: ./output/bowtie/bowtie/genome.3.ebwt
+      md5sum: 4ed93abba181d8dfab2e303e33114777
+    - path: ./output/bowtie/bowtie/genome.2.ebwt
+      md5sum: 02b44af9f94c62ecd3c583048e25d4cf
+    - path: ./output/bowtie/bowtie/genome.rev.2.ebwt
+      md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
+    - path: ./output/bowtie/bowtie/genome.4.ebwt
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
+    - path: ./output/bowtie/bowtie/genome.rev.1.ebwt
+      md5sum: b37aaf11853e65a3b13561f27a912b06
+    - path: ./output/bowtie/bowtie/genome.1.ebwt
+      md5sum: d9b76ecf9fd0413240173273b38d8199
+
+- name: bowtie align paired-end
+  command: nextflow run ./tests/modules/nf-core/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie/align/nextflow.config
+  tags:
+    - bowtie
+    - bowtie/align
+  files:
+    - path: ./output/bowtie/test.bam
+    - path: ./output/bowtie/test.out
+    - path: ./output/bowtie/bowtie/genome.3.ebwt
+      md5sum: 4ed93abba181d8dfab2e303e33114777
+    - path: ./output/bowtie/bowtie/genome.2.ebwt
+      md5sum: 02b44af9f94c62ecd3c583048e25d4cf
+    - path: ./output/bowtie/bowtie/genome.rev.2.ebwt
+      md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
+    - path: ./output/bowtie/bowtie/genome.4.ebwt
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
+    - path: ./output/bowtie/bowtie/genome.rev.1.ebwt
+      md5sum: b37aaf11853e65a3b13561f27a912b06
+    - path: ./output/bowtie/bowtie/genome.1.ebwt
+      md5sum: d9b76ecf9fd0413240173273b38d8199
diff --git a/tests/modules/bowtie/build b/tests/modules/nf-core/bowtie/build
similarity index 100%
rename from tests/modules/bowtie/build
rename to tests/modules/nf-core/bowtie/build
diff --git a/tests/modules/nf-core/bowtie/build_test/main.nf b/tests/modules/nf-core/bowtie/build_test/main.nf
new file mode 100644
index 00000000000..23356ec35f5
--- /dev/null
+++ b/tests/modules/nf-core/bowtie/build_test/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE_BUILD } from '../../../../../modules/nf-core/bowtie/build/main.nf'
+
+workflow test_bowtie_build {
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BOWTIE_BUILD ( fasta )
+}
diff --git a/tests/modules/bowtie/build_test/nextflow.config b/tests/modules/nf-core/bowtie/build_test/nextflow.config
similarity index 100%
rename from tests/modules/bowtie/build_test/nextflow.config
rename to tests/modules/nf-core/bowtie/build_test/nextflow.config
diff --git a/tests/modules/nf-core/bowtie/build_test/test.yml b/tests/modules/nf-core/bowtie/build_test/test.yml
new file mode 100644
index 00000000000..04a48375e3c
--- /dev/null
+++ b/tests/modules/nf-core/bowtie/build_test/test.yml
@@ -0,0 +1,18 @@
+- name: bowtie build
+  command: nextflow run ./tests/modules/nf-core/bowtie/build_test -entry test_bowtie_build -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie/build/nextflow.config
+  tags:
+    - bowtie
+    - bowtie/build
+  files:
+    - path: ./output/bowtie/bowtie/genome.3.ebwt
+      md5sum: 4ed93abba181d8dfab2e303e33114777
+    - path: ./output/bowtie/bowtie/genome.2.ebwt
+      md5sum: 02b44af9f94c62ecd3c583048e25d4cf
+    - path: ./output/bowtie/bowtie/genome.rev.2.ebwt
+      md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
+    - path: ./output/bowtie/bowtie/genome.4.ebwt
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
+    - path: ./output/bowtie/bowtie/genome.rev.1.ebwt
+      md5sum: b37aaf11853e65a3b13561f27a912b06
+    - path: ./output/bowtie/bowtie/genome.1.ebwt
+      md5sum: d9b76ecf9fd0413240173273b38d8199
diff --git a/tests/modules/nf-core/bowtie2/align/main.nf b/tests/modules/nf-core/bowtie2/align/main.nf
new file mode 100644
index 00000000000..40f46b227b6
--- /dev/null
+++ b/tests/modules/nf-core/bowtie2/align/main.nf
@@ -0,0 +1,99 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE2_BUILD } from '../../../../../modules/nf-core/bowtie2/build/main.nf'
+include { BOWTIE2_ALIGN } from '../../../../../modules/nf-core/bowtie2/align/main.nf'
+
+workflow test_bowtie2_align_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false
+    sort = false
+
+    BOWTIE2_BUILD ( fasta )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
+}
+
+workflow test_bowtie2_align_single_end_sorted {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false
+    sort = true
+
+    BOWTIE2_BUILD ( fasta )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
+}
+
+workflow test_bowtie2_align_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false
+    sort = false
+
+    BOWTIE2_BUILD ( fasta )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
+}
+
+workflow test_bowtie2_align_paired_end_sorted {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false
+    sort = true
+
+    BOWTIE2_BUILD ( fasta )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
+}
+
+workflow test_bowtie2_align_single_end_large_index {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false
+    sort = false
+
+    BOWTIE2_BUILD ( fasta )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
+}
+
+workflow test_bowtie2_align_paired_end_large_index {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false
+    sort = false
+
+    BOWTIE2_BUILD ( fasta )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
+}
diff --git a/tests/modules/bowtie2/align/nextflow.config b/tests/modules/nf-core/bowtie2/align/nextflow.config
similarity index 100%
rename from tests/modules/bowtie2/align/nextflow.config
rename to tests/modules/nf-core/bowtie2/align/nextflow.config
diff --git a/tests/modules/nf-core/bowtie2/align/test.yml b/tests/modules/nf-core/bowtie2/align/test.yml
new file mode 100644
index 00000000000..5ec73575c51
--- /dev/null
+++ b/tests/modules/nf-core/bowtie2/align/test.yml
@@ -0,0 +1,49 @@
+- name: bowtie2 align test_bowtie2_align_single_end
+  command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2/align
+  files:
+    - path: ./output/bowtie2/test.bam
+    - path: ./output/bowtie2/test.bowtie2.log
+    - path: ./output/bowtie2/versions.yml
+
+- name: bowtie2 align test_bowtie2_align_single_end_sorted
+  command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_single_end_sorted -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2/align
+  files:
+    - path: ./output/bowtie2/test.bam
+    - path: ./output/bowtie2/test.bowtie2.log
+    - path: ./output/bowtie2/versions.yml
+
+- name: bowtie2 align test_bowtie2_align_paired_end
+  command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2/align
+  files:
+    - path: ./output/bowtie2/test.bam
+    - path: ./output/bowtie2/test.bowtie2.log
+    - path: ./output/bowtie2/versions.yml
+
+- name: bowtie2 align test_bowtie2_align_single_end_large_index
+  command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config --force_large_index
+  tags:
+    - bowtie2
+    - bowtie2/align
+  files:
+    - path: ./output/bowtie2/test.bam
+    - path: ./output/bowtie2/test.bowtie2.log
+    - path: ./output/bowtie2/versions.yml
+
+- name: bowtie2 align test_bowtie2_align_paired_end_large_index
+  command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config --force_large_index
+  tags:
+    - bowtie2
+    - bowtie2/align
+  files:
+    - path: ./output/bowtie2/test.bam
+    - path: ./output/bowtie2/test.bowtie2.log
+    - path: ./output/bowtie2/versions.yml
diff --git a/tests/modules/bowtie2/build b/tests/modules/nf-core/bowtie2/build
similarity index 100%
rename from tests/modules/bowtie2/build
rename to tests/modules/nf-core/bowtie2/build
diff --git a/tests/modules/nf-core/bowtie2/build_test/main.nf b/tests/modules/nf-core/bowtie2/build_test/main.nf
new file mode 100644
index 00000000000..350010dd619
--- /dev/null
+++ b/tests/modules/nf-core/bowtie2/build_test/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE2_BUILD } from '../../../../../modules/nf-core/bowtie2/build/main.nf'
+
+workflow test_bowtie2_build {
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BOWTIE2_BUILD ( fasta )
+}
diff --git a/tests/modules/bowtie2/build_test/nextflow.config b/tests/modules/nf-core/bowtie2/build_test/nextflow.config
similarity index 100%
rename from tests/modules/bowtie2/build_test/nextflow.config
rename to tests/modules/nf-core/bowtie2/build_test/nextflow.config
diff --git a/tests/modules/nf-core/bowtie2/build_test/test.yml b/tests/modules/nf-core/bowtie2/build_test/test.yml
new file mode 100644
index 00000000000..fe5817e2642
--- /dev/null
+++ b/tests/modules/nf-core/bowtie2/build_test/test.yml
@@ -0,0 +1,18 @@
+- name: bowtie2 build
+  command: nextflow run ./tests/modules/nf-core/bowtie2/build_test -entry test_bowtie2_build -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/build/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2/build
+  files:
+    - path: ./output/bowtie2/bowtie2/genome.3.bt2
+      md5sum: 4ed93abba181d8dfab2e303e33114777
+    - path: ./output/bowtie2/bowtie2/genome.2.bt2
+      md5sum: 47b153cd1319abc88dda532462651fcf
+    - path: ./output/bowtie2/bowtie2/genome.1.bt2
+      md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
+    - path: ./output/bowtie2/bowtie2/genome.4.bt2
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
+    - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
+      md5sum: 52be6950579598a990570fbcf5372184
+    - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
+      md5sum: e3b4ef343dea4dd571642010a7d09597
diff --git a/tests/modules/nf-core/bracken/bracken/main.nf b/tests/modules/nf-core/bracken/bracken/main.nf
new file mode 100644
index 00000000000..abd4b62cc53
--- /dev/null
+++ b/tests/modules/nf-core/bracken/bracken/main.nf
@@ -0,0 +1,57 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR           } from '../../../../../modules/nf-core/untar/main.nf'
+include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main.nf'
+include { BRACKEN_BRACKEN } from '../../../../../modules/nf-core/bracken/bracken/main.nf'
+
+workflow test_bracken_bracken_single_end_default_args {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
+}
+
+workflow test_bracken_bracken_single_end_custom_args {
+    input = [ [ id:'test', single_end:true, threshold:0, taxonomic_level:'G', read_length:100 ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
+}
+
+workflow test_bracken_bracken_paired_end_default_args {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
+}
+
+workflow test_bracken_bracken_paired_end_custom_args {
+    input = [ [ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
+}
diff --git a/tests/modules/bracken/bracken/nextflow.config b/tests/modules/nf-core/bracken/bracken/nextflow.config
similarity index 100%
rename from tests/modules/bracken/bracken/nextflow.config
rename to tests/modules/nf-core/bracken/bracken/nextflow.config
diff --git a/tests/modules/nf-core/bracken/bracken/test.yml b/tests/modules/nf-core/bracken/bracken/test.yml
new file mode 100644
index 00000000000..c35a12a7a48
--- /dev/null
+++ b/tests/modules/nf-core/bracken/bracken/test.yml
@@ -0,0 +1,43 @@
+- name: bracken bracken test_bracken_bracken_single_end_default_args
+  command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_single_end_default_args -c ./tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_S.tsv
+      md5sum: 4a21ae14ff8a0311d55f139af5247838
+    - path: output/bracken/versions.yml
+      md5sum: e0abdac999c0d58becd8c868dd12028b
+
+- name: bracken bracken test_bracken_bracken_single_end_custom_args
+  command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_single_end_custom_args -c ./tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_G.tsv
+      md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
+    - path: output/bracken/versions.yml
+      md5sum: 7d0a1629ece197a8062271d39ed8ef74
+
+- name: bracken bracken test_bracken_bracken_paired_end_default_args
+  command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_paired_end_default_args -c ./tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_S.tsv
+      md5sum: 4a21ae14ff8a0311d55f139af5247838
+    - path: output/bracken/versions.yml
+      md5sum: 7b58898d0b9cce1ca170ac5a82d8ecf1
+
+- name: bracken bracken test_bracken_bracken_paired_end_custom_args
+  command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_paired_end_custom_args -c ./tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_G.tsv
+      md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
+    - path: output/bracken/versions.yml
+      md5sum: 3c9160394af663ae7808c0f77fcedae8
diff --git a/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf
new file mode 100644
index 00000000000..333156d4d8f
--- /dev/null
+++ b/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR           } from '../../../../../modules/nf-core/untar/main.nf'
+include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main.nf'
+include { BRACKEN_BRACKEN } from '../../../../../modules/nf-core/bracken/bracken/main.nf'
+include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../../../../modules/nf-core/bracken/combinebrackenoutputs/main.nf'
+
+workflow test_bracken_combinebrackenoutputs {
+
+    input = Channel.of(
+        [[ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
+        [[ id:'test2', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
+    )
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
+
+    BRACKEN_COMBINEBRACKENOUTPUTS ( BRACKEN_BRACKEN.out.reports.map{it[1]}.collect() )
+}
+
diff --git a/tests/modules/bracken/combinebrackenoutputs/nextflow.config b/tests/modules/nf-core/bracken/combinebrackenoutputs/nextflow.config
similarity index 100%
rename from tests/modules/bracken/combinebrackenoutputs/nextflow.config
rename to tests/modules/nf-core/bracken/combinebrackenoutputs/nextflow.config
diff --git a/tests/modules/nf-core/bracken/combinebrackenoutputs/test.yml b/tests/modules/nf-core/bracken/combinebrackenoutputs/test.yml
new file mode 100644
index 00000000000..ebf64da70e2
--- /dev/null
+++ b/tests/modules/nf-core/bracken/combinebrackenoutputs/test.yml
@@ -0,0 +1,9 @@
+- name: bracken combinebrackenoutputs test_bracken_combinebrackenoutputs
+  command: nextflow run ./tests/modules/nf-core/bracken/combinebrackenoutputs -entry test_bracken_combinebrackenoutputs -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/bracken/combinebrackenoutputs/nextflow.config
+  tags:
+    - bracken/combinebrackenoutputs
+    - bracken
+  files:
+    - path: output/bracken/bracken_combined.txt
+      contains:
+        - "name	taxonomy_id	taxonomy_lvl"
diff --git a/tests/modules/nf-core/busco/main.nf b/tests/modules/nf-core/busco/main.nf
new file mode 100644
index 00000000000..6618b589af2
--- /dev/null
+++ b/tests/modules/nf-core/busco/main.nf
@@ -0,0 +1,104 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BUSCO } from '../../../../modules/nf-core/busco/main.nf'
+
+workflow test_busco_genome_single_fasta {
+
+    input = [
+        [ id:'test' ], // meta map
+        file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10', // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
+        [], // Download busco lineage
+        [] // No config
+    )
+
+}
+
+workflow test_busco_genome_multi_fasta {
+
+    input = [
+        [ id:'test' ], // meta map
+        [
+            file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
+            file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
+        ]
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10',
+        [], // Download busco lineage
+        [] // No config
+    )
+
+}
+
+workflow test_busco_eukaryote_metaeuk {
+
+    input = [
+        [ id:'test' ], // meta map
+        file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'eukaryota_odb10',
+        [], // Download busco lineage
+        [] // No config
+    )
+
+}
+
+workflow test_busco_eukaryote_augustus {
+
+    input = [
+        [ id:'test' ], // meta map
+        file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'eukaryota_odb10',
+        [], // Download busco lineage
+        [] // No config
+    )
+
+}
+
+workflow test_busco_protein {
+
+    input = [
+        [ id:'test' ], // meta map
+        file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10',
+        [], // Download busco lineage
+        [] // No config
+    )
+
+}
+
+workflow test_busco_transcriptome {
+
+    input = [
+        [ id:'test' ], // meta map
+        file( params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10',
+        [], // Download busco lineage
+        [] // No config
+    )
+
+}
diff --git a/tests/modules/busco/nextflow.config b/tests/modules/nf-core/busco/nextflow.config
similarity index 100%
rename from tests/modules/busco/nextflow.config
rename to tests/modules/nf-core/busco/nextflow.config
diff --git a/tests/modules/nf-core/busco/test.yml b/tests/modules/nf-core/busco/test.yml
new file mode 100644
index 00000000000..caaaba1b182
--- /dev/null
+++ b/tests/modules/nf-core/busco/test.yml
@@ -0,0 +1,610 @@
+- name: busco test_busco_genome_single_fasta
+  command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_genome_single_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/busco/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
+    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
+      md5sum: bc2440f8a68d7fbf931ff911c1c3fdfa
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
+      contains:
+        - "Tool: prodigal"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
+      md5sum: 275a7ece09ef61aa59ee7a811289e3d8
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: ab574cde031a3fbff471976ea61e215d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "lineage_dataset"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
+
+- name: busco test_busco_genome_multi_fasta
+  command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_genome_multi_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/busco/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
+    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
+      contains:
+        - "Input_file"
+        - "genome.fna"
+        - "genome.fasta"
+        - "bacteria_odb10"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_err.log
+      md5sum: c1fdc6977332f53dfe7f632733bb4585
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_out.log
+      md5sum: 50752acb1c5a20be886bfdfc06635bcb
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/.checkpoint
+      contains:
+        - "Tool: prodigal"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.faa
+      md5sum: 8166471fc5f08c82fd5643ab42327f9d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.fna
+      md5sum: ddc508a18f60e7f3314534df50cdf8ca
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
+      md5sum: 8166471fc5f08c82fd5643ab42327f9d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
+      md5sum: ddc508a18f60e7f3314534df50cdf8ca
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
+      md5sum: c1fdc6977332f53dfe7f632733bb4585
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
+      md5sum: 50752acb1c5a20be886bfdfc06635bcb
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.faa
+      md5sum: e56fd59c38248dc21ac94355dca98121
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.fna
+      md5sum: b365f84bf99c68357952e0b98ed7ce42
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_err.log
+      md5sum: e5f14d7925ba14a0f9850542f3739894
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_out.log
+      md5sum: d41971bfc1b621d4ffd2633bc47017ea
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/full_table.tsv
+      md5sum: f473ded1f1db2463533d51be6ed6fd2d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
+      contains:
+        - "Tool: prodigal"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
+      md5sum: 275a7ece09ef61aa59ee7a811289e3d8
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: ab574cde031a3fbff471976ea61e215d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
+
+- name: busco test_busco_eukaryote_metaeuk
+  command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_eukaryote_metaeuk -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/busco/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
+    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
+      md5sum: ff6d8277e452a83ce9456bbee666feb6
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_out.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_out.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_out.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/full_table.tsv
+      md5sum: ff1b64c2adadcf9f0a954a19893e421b
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/.checkpoint
+      contains:
+        - "Tool: metaeuk"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/combined_pred_proteins.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.codon.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.gff
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.headersMap.tsv
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/refseq_db_rerun.faa
+      md5sum: d80b8fa4cb5ed0d47d63d6aa93635bc2
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.codon.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.gff
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.headersMap.tsv
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/missing_busco_list.tsv
+      md5sum: 6c17c7e06991db898b318b932d686406
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
+
+- name: busco test_busco_eukaryote_augustus
+  command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_eukaryote_augustus -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/busco/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
+      md5sum: cdd3ffd590a778cdd2f0f367ee86eba7
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/.checkpoint
+      contains:
+        - "Tool: makeblastdb"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ndb
+      md5sum: 0d553c830656469211de113c5022f06d
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nhr
+      md5sum: 82396da5130a85faf6d454e2889a1d45
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nin
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.njs
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.not
+      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nsq
+      md5sum: 4bc119903ac72152363f47612645046a
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ntf
+      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nto
+      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_out.log
+      contains:
+        - "Building a new DB"
+        - "Adding sequences from FASTA"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_out.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/.checkpoint
+      contains:
+        - "Tool: tblastn"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/coordinates.tsv
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/tblastn.tsv
+      contains:
+        - "TBLASTN"
+        - "BLAST processed"
+        - "queries"
+    - path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Running Augustus gene predictor"
+
+- name: busco test_busco_protein
+  command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_protein -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/busco/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
+    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
+      md5sum: 7a65e6cbb6c56a2ea4e739ae0aa3297d
+    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/full_table.tsv
+      md5sum: 81e0e9a5897bb72fffbb1866779f6834
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+
+- name: busco test_busco_transcriptome
+  command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_transcriptome -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/busco/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
+    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
+      md5sum: 46118ecf60d1b87d22b96d80f4f03632
+    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/.checkpoint
+      contains:
+        - "Tool: makeblastdb"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ndb
+      md5sum: 3788c017fe5e6f0f58224e9cdd21822b
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nhr
+      md5sum: 8ecd2ce392bb5e25ddbe1d85f879582e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nin
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.njs
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.not
+      md5sum: 0c340e376c7e85d19f82ec1a833e6a6e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nsq
+      md5sum: 532d5c0a7ea00fe95ca3c97cb3be6198
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ntf
+      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nto
+      md5sum: ff74bd41f9cc9b011c63a32c4f7693bf
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_err.log
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_out.log
+      contains:
+        - "Building a new DB"
+        - "Adding sequences from FASTA"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_err.log
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_out.log
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/.checkpoint
+      contains:
+        - "Tool: tblastn"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/coordinates.tsv
+      md5sum: cc30eed321944af293452bdbcfc24292
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_101.temp
+      md5sum: 73e9c65fc83fedc58f57f09b08f08238
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_119.temp
+      md5sum: 7fa4cc7955ec0cc36330a221c579b975
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_129.temp
+      md5sum: 6f1601c875d019e3f6f1f98ed8e988d4
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_138.temp
+      md5sum: 3f8e034686cd240c2330650d791bcae2
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_143.temp
+      md5sum: df3dfa8e9ba30ed70cf75b5e7abf2179
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_172.temp
+      md5sum: 7d463e0e6cf7169bc9077d8dc776dda1
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_178.temp
+      md5sum: 2288edf7fa4f88f51b4cf4d94086f77e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_188.temp
+      md5sum: 029906abbad6d87fc57830dd548cac24
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_195.temp
+      md5sum: 4937f3b348774a31b1160a00297c29cc
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_210.temp
+      md5sum: afcb20ba4c466479d6b91c8c62251e1f
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_232.temp
+      md5sum: 2e1e823ce017345bd998191a39fa9924
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_268.temp
+      md5sum: 08c2d82c34ecffbe1c638b410349412e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_29.temp
+      md5sum: cd9b63cf93524284781535c888313764
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_44.temp
+      md5sum: d1929b742b24ebe379bf4801ca882dca
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_58.temp
+      md5sum: 69215765b010c05336538cb322c900b3
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_72.temp
+      md5sum: 6feaa1cc3b0899a147ea9d466878f3e3
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_80.temp
+      md5sum: 13625eae14e860a96ce17cd4e37e9d01
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_81.temp
+      md5sum: e14b2484649b0dbc8926815c207b806d
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_93.temp
+      md5sum: 6902c93691df00e690faea914c71839e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_97.temp
+      md5sum: 0a0d9d38a83acbd5ad43c29cdf429988
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/tblastn.tsv
+      contains:
+        - "TBLASTN"
+        - "BLAST processed"
+        - "queries"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/full_table.tsv
+      md5sum: 14bb2d7788bd0aa547e4a99df6659f1e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: 485902b7b62403985ee9f781e17b20ab
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/single_copy_proteins.faa
+      md5sum: e04b9465733577ae6e4bccb7aa01e720
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1024388at2.faa
+      md5sum: 7333c39a20258f20c7019ea0cd83157c
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1054741at2.faa
+      md5sum: ebb481e77a824685fbe04d8a2f3a0d7d
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1093223at2.faa
+      md5sum: 34621c7d499034e8f8e6b92fd4020a93
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1151822at2.faa
+      md5sum: aa89ca381c1c70c9c4e1380351ca7c2a
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/143460at2.faa
+      md5sum: f2e91d78b8dd3722840378789f29e8c8
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1491686at2.faa
+      md5sum: 73c25aef5c9cba7f4151804941b146ea
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1504821at2.faa
+      md5sum: cda556018d1f84ebe517e89f6fc107d0
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1574817at2.faa
+      md5sum: a9096c9fb8b25c78a72871ab0463acdc
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1592033at2.faa
+      md5sum: e463d25ce186c0cebfd749474f3a4c64
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1623045at2.faa
+      md5sum: f2cfd241590c6d8377286d6135480937
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1661836at2.faa
+      md5sum: 586569546fb9861502468e3d9ba2775c
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1674344at2.faa
+      md5sum: 24c658bee14ad84b062d81ad96642eb8
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1698718at2.faa
+      md5sum: 0b8e26ddf5149bbd8805be7af125208d
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1990650at2.faa
+      md5sum: 159320712ee01fb2ccb31a25df44eead
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/223233at2.faa
+      md5sum: 812629c0b06ac3d18661c2ca78de0c08
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/402899at2.faa
+      md5sum: f7ff4e1591342d30b77392a2e84b57d9
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/505485at2.faa
+      md5sum: 7b34a24fc49c540d46fcf96ff5129564
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/665824at2.faa
+      md5sum: 4cff2df64f6bcaff8bc19c234c8bcccd
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/776861at2.faa
+      md5sum: 613af7a3fea30ea2bece66f603b9284a
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/874197at2.faa
+      md5sum: a7cd1b13c9ef91c7ef4e31614166f197
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/932854at2.faa
+      md5sum: fe313ffd5efdb0fed887a04fba352552
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/95696at2.faa
+      md5sum: 4e1f30a2fea4dfbf9bb7fae2700622a0
diff --git a/tests/modules/nf-core/bwa/aln/main.nf b/tests/modules/nf-core/bwa/aln/main.nf
new file mode 100644
index 00000000000..0b5458d66b4
--- /dev/null
+++ b/tests/modules/nf-core/bwa/aln/main.nf
@@ -0,0 +1,39 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf'
+include { BWA_ALN   } from '../../../../../modules/nf-core/bwa/aln/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_bwa_aln_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+    BWA_ALN ( input, BWA_INDEX.out.index )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_bwa_aln_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+    BWA_ALN ( input, BWA_INDEX.out.index )
+}
diff --git a/tests/modules/bwa/aln/nextflow.config b/tests/modules/nf-core/bwa/aln/nextflow.config
similarity index 100%
rename from tests/modules/bwa/aln/nextflow.config
rename to tests/modules/nf-core/bwa/aln/nextflow.config
diff --git a/tests/modules/nf-core/bwa/aln/test.yml b/tests/modules/nf-core/bwa/aln/test.yml
new file mode 100644
index 00000000000..8a3bec17ae2
--- /dev/null
+++ b/tests/modules/nf-core/bwa/aln/test.yml
@@ -0,0 +1,39 @@
+- name: bwa aln single-end
+  command: nextflow run ./tests/modules/nf-core/bwa/aln -entry test_bwa_aln_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/aln/nextflow.config
+  tags:
+    - bwa
+    - bwa/aln
+  files:
+    - path: ./output/bwa/test.sai
+      md5sum: aaaf39b6814c96ca1a5eacc662adf926
+    - path: ./output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: ./output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: ./output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+
+- name: bwa aln paired-end
+  command: nextflow run ./tests/modules/nf-core/bwa/aln -entry test_bwa_aln_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/aln/nextflow.config
+  tags:
+    - bwa
+    - bwa/aln
+  files:
+    - path: ./output/bwa/test.1.sai
+      md5sum: aaaf39b6814c96ca1a5eacc662adf926
+    - path: ./output/bwa/test.2.sai
+      md5sum: b4f185d9b4cb256dd5c377070a536124
+    - path: ./output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: ./output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: ./output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
diff --git a/tests/modules/nf-core/bwa/index/main.nf b/tests/modules/nf-core/bwa/index/main.nf
new file mode 100644
index 00000000000..956ba083c91
--- /dev/null
+++ b/tests/modules/nf-core/bwa/index/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf'
+
+workflow test_bwa_index {
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+}
diff --git a/tests/modules/bwa/index/nextflow.config b/tests/modules/nf-core/bwa/index/nextflow.config
similarity index 100%
rename from tests/modules/bwa/index/nextflow.config
rename to tests/modules/nf-core/bwa/index/nextflow.config
diff --git a/tests/modules/nf-core/bwa/index/test.yml b/tests/modules/nf-core/bwa/index/test.yml
new file mode 100644
index 00000000000..7d313195fad
--- /dev/null
+++ b/tests/modules/nf-core/bwa/index/test.yml
@@ -0,0 +1,16 @@
+- name: bwa index test_bwa_index
+  command: nextflow run ./tests/modules/nf-core/bwa/index -entry test_bwa_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/index/nextflow.config
+  tags:
+    - bwa
+    - bwa/index
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
diff --git a/tests/modules/nf-core/bwa/mem/main.nf b/tests/modules/nf-core/bwa/mem/main.nf
new file mode 100644
index 00000000000..2378144581a
--- /dev/null
+++ b/tests/modules/nf-core/bwa/mem/main.nf
@@ -0,0 +1,72 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf'
+include { BWA_MEM   } from '../../../../../modules/nf-core/bwa/mem/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_bwa_mem_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+    BWA_MEM ( input, BWA_INDEX.out.index, false )
+}
+
+//
+// Test with single-end data and sort
+//
+workflow test_bwa_mem_single_end_sort {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+    BWA_MEM ( input, BWA_INDEX.out.index, true )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_bwa_mem_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+    BWA_MEM ( input, BWA_INDEX.out.index, false )
+}
+
+//
+// Test with paired-end data and sort
+//
+workflow test_bwa_mem_paired_end_sort {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+    BWA_MEM ( input, BWA_INDEX.out.index, true )
+}
diff --git a/tests/modules/bwa/mem/nextflow.config b/tests/modules/nf-core/bwa/mem/nextflow.config
similarity index 100%
rename from tests/modules/bwa/mem/nextflow.config
rename to tests/modules/nf-core/bwa/mem/nextflow.config
diff --git a/tests/modules/nf-core/bwa/mem/test.yml b/tests/modules/nf-core/bwa/mem/test.yml
new file mode 100644
index 00000000000..7e8157b8bec
--- /dev/null
+++ b/tests/modules/nf-core/bwa/mem/test.yml
@@ -0,0 +1,71 @@
+- name: bwa mem single-end
+  command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config
+  tags:
+    - bwa
+    - bwa/mem
+  files:
+    - path: ./output/bwa/test.bam
+    - path: ./output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: ./output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: ./output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+
+- name: bwa mem single-end sort
+  command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config
+  tags:
+    - bwa
+    - bwa/mem
+  files:
+    - path: ./output/bwa/test.bam
+    - path: ./output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: ./output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: ./output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+
+- name: bwa mem paired-end
+  command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config
+  tags:
+    - bwa
+    - bwa/mem
+  files:
+    - path: ./output/bwa/test.bam
+    - path: ./output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: ./output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: ./output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+
+- name: bwa mem paired-end sort
+  command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config
+  tags:
+    - bwa
+    - bwa/mem
+  files:
+    - path: ./output/bwa/test.bam
+    - path: ./output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: ./output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: ./output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
diff --git a/tests/modules/nf-core/bwa/sampe/main.nf b/tests/modules/nf-core/bwa/sampe/main.nf
new file mode 100644
index 00000000000..a250d5a9664
--- /dev/null
+++ b/tests/modules/nf-core/bwa/sampe/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf'
+include { BWA_ALN   } from '../../../../../modules/nf-core/bwa/aln/main.nf'
+include { BWA_SAMPE } from '../../../../../modules/nf-core/bwa/sampe/main.nf'
+
+workflow test_bwa_sampe {
+
+    Channel
+        .fromList(
+            [
+                [ id:'test', single_end:false ],
+                [ [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
+            ]
+        ).collect()
+        .set { input }
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+    BWA_ALN ( input, BWA_INDEX.out.index )
+    BWA_SAMPE ( input.join(BWA_ALN.out.sai), BWA_INDEX.out.index )
+}
diff --git a/tests/modules/bwa/sampe/nextflow.config b/tests/modules/nf-core/bwa/sampe/nextflow.config
similarity index 100%
rename from tests/modules/bwa/sampe/nextflow.config
rename to tests/modules/nf-core/bwa/sampe/nextflow.config
diff --git a/tests/modules/nf-core/bwa/sampe/test.yml b/tests/modules/nf-core/bwa/sampe/test.yml
new file mode 100644
index 00000000000..1fbc1f9fb1f
--- /dev/null
+++ b/tests/modules/nf-core/bwa/sampe/test.yml
@@ -0,0 +1,8 @@
+- name: bwa sampe
+  command: nextflow run ./tests/modules/nf-core/bwa/sampe -entry test_bwa_sampe -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/sampe/nextflow.config
+  tags:
+    - bwa
+    - bwa/sampe
+  files:
+    - path: output/bwa/test.bam
+      md5sum: 67528d633a1a78e3d0e8d1486c1a960a
diff --git a/tests/modules/nf-core/bwa/samse/main.nf b/tests/modules/nf-core/bwa/samse/main.nf
new file mode 100644
index 00000000000..b8cc2e2b5e1
--- /dev/null
+++ b/tests/modules/nf-core/bwa/samse/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf'
+include { BWA_ALN   } from '../../../../../modules/nf-core/bwa/aln/main.nf'
+include { BWA_SAMSE } from '../../../../../modules/nf-core/bwa/samse/main.nf'
+
+workflow test_bwa_samse {
+
+    Channel
+        .fromList(
+            [ [ id:'test', single_end:true ],
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+        ).collect()
+        .set { input }
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX ( fasta )
+    BWA_ALN ( input, BWA_INDEX.out.index )
+    BWA_SAMSE ( input.join(BWA_ALN.out.sai, by:[0]), BWA_INDEX.out.index )
+}
diff --git a/tests/modules/bwa/samse/nextflow.config b/tests/modules/nf-core/bwa/samse/nextflow.config
similarity index 100%
rename from tests/modules/bwa/samse/nextflow.config
rename to tests/modules/nf-core/bwa/samse/nextflow.config
diff --git a/tests/modules/nf-core/bwa/samse/test.yml b/tests/modules/nf-core/bwa/samse/test.yml
new file mode 100644
index 00000000000..db3a8bf2450
--- /dev/null
+++ b/tests/modules/nf-core/bwa/samse/test.yml
@@ -0,0 +1,8 @@
+- name: bwa samse
+  command: nextflow run ./tests/modules/nf-core/bwa/samse -entry test_bwa_samse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/samse/nextflow.config
+  tags:
+    - bwa
+    - bwa/samse
+  files:
+    - path: output/bwa/test.bam
+      md5sum: 9a0ca9678a03e6fa4bda459c04c99bd6
diff --git a/tests/modules/nf-core/bwamem2/index/main.nf b/tests/modules/nf-core/bwamem2/index/main.nf
new file mode 100644
index 00000000000..c4c16298aa0
--- /dev/null
+++ b/tests/modules/nf-core/bwamem2/index/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWAMEM2_INDEX } from '../../../../../modules/nf-core/bwamem2/index/main.nf'
+
+workflow test_bwamem2_index {
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWAMEM2_INDEX ( [ [id:'test'], fasta] )
+}
diff --git a/tests/modules/bwamem2/index/nextflow.config b/tests/modules/nf-core/bwamem2/index/nextflow.config
similarity index 100%
rename from tests/modules/bwamem2/index/nextflow.config
rename to tests/modules/nf-core/bwamem2/index/nextflow.config
diff --git a/tests/modules/nf-core/bwamem2/index/test.yml b/tests/modules/nf-core/bwamem2/index/test.yml
new file mode 100644
index 00000000000..be000b25857
--- /dev/null
+++ b/tests/modules/nf-core/bwamem2/index/test.yml
@@ -0,0 +1,16 @@
+- name: bwamem2 index
+  command: nextflow run ./tests/modules/nf-core/bwamem2/index -entry test_bwamem2_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/index/nextflow.config
+  tags:
+    - bwamem2
+    - bwamem2/index
+  files:
+    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
+      md5sum: b02870de80106104abcb03cd9463e7d8
+    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
+      md5sum: d097a1b82dee375d41a1ea69895a9216
+    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
diff --git a/tests/modules/nf-core/bwamem2/mem/main.nf b/tests/modules/nf-core/bwamem2/mem/main.nf
new file mode 100644
index 00000000000..e53446a845d
--- /dev/null
+++ b/tests/modules/nf-core/bwamem2/mem/main.nf
@@ -0,0 +1,73 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWAMEM2_INDEX } from '../../../../../modules/nf-core/bwamem2/index/main.nf'
+include { BWAMEM2_MEM   } from '../../../../../modules/nf-core/bwamem2/mem/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_bwamem2_mem_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWAMEM2_INDEX ( [ [:], fasta ] )
+    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
+}
+
+//
+// Test with single-end data and sort
+//
+workflow test_bwamem2_mem_single_end_sort {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWAMEM2_INDEX ( [ [:], fasta ] )
+    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
+}
+
+
+//
+// Test with paired-end data
+//
+workflow test_bwamem2_mem_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWAMEM2_INDEX ( [ [:], fasta ] )
+    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
+}
+
+//
+// Test with paired-end data and sort
+//
+workflow test_bwamem2_mem_paired_end_sort {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWAMEM2_INDEX ( [ [:], fasta ] )
+    BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
+}
diff --git a/tests/modules/bwamem2/mem/nextflow.config b/tests/modules/nf-core/bwamem2/mem/nextflow.config
similarity index 100%
rename from tests/modules/bwamem2/mem/nextflow.config
rename to tests/modules/nf-core/bwamem2/mem/nextflow.config
diff --git a/tests/modules/nf-core/bwamem2/mem/test.yml b/tests/modules/nf-core/bwamem2/mem/test.yml
new file mode 100644
index 00000000000..d693fc72840
--- /dev/null
+++ b/tests/modules/nf-core/bwamem2/mem/test.yml
@@ -0,0 +1,71 @@
+- name: bwamem2 mem single-end
+  command: nextflow run ./tests/modules/nf-core/bwamem2/mem -entry test_bwamem2_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/mem/nextflow.config
+  tags:
+    - bwamem2
+    - bwamem2/mem
+  files:
+    - path: ./output/bwamem2/test.bam
+    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
+      md5sum: b02870de80106104abcb03cd9463e7d8
+    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
+      md5sum: d097a1b82dee375d41a1ea69895a9216
+    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+
+- name: bwamem2 mem single-end sort
+  command: nextflow run ./tests/modules/nf-core/bwamem2/mem -entry test_bwamem2_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/mem/nextflow.config
+  tags:
+    - bwamem2
+    - bwamem2/mem
+  files:
+    - path: ./output/bwamem2/test.bam
+    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
+      md5sum: b02870de80106104abcb03cd9463e7d8
+    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
+      md5sum: d097a1b82dee375d41a1ea69895a9216
+    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+
+- name: bwamem2 mem paired-end
+  command: nextflow run ./tests/modules/nf-core/bwamem2/mem -entry test_bwamem2_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/mem/nextflow.config
+  tags:
+    - bwamem2
+    - bwamem2/mem
+  files:
+    - path: ./output/bwamem2/test.bam
+    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
+      md5sum: b02870de80106104abcb03cd9463e7d8
+    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
+      md5sum: d097a1b82dee375d41a1ea69895a9216
+    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+
+- name: bwamem2 mem paired-end sort
+  command: nextflow run ./tests/modules/nf-core/bwamem2/mem -entry test_bwamem2_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/mem/nextflow.config
+  tags:
+    - bwamem2
+    - bwamem2/mem
+  files:
+    - path: ./output/bwamem2/test.bam
+    - path: ./output/bwamem2/bwamem2/genome.fasta.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: ./output/bwamem2/bwamem2/genome.fasta.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: ./output/bwamem2/bwamem2/genome.fasta.0123
+      md5sum: b02870de80106104abcb03cd9463e7d8
+    - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
+      md5sum: d097a1b82dee375d41a1ea69895a9216
+    - path: ./output/bwamem2/bwamem2/genome.fasta.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
diff --git a/tests/modules/nf-core/bwameth/align/main.nf b/tests/modules/nf-core/bwameth/align/main.nf
new file mode 100644
index 00000000000..5128ab8bdf3
--- /dev/null
+++ b/tests/modules/nf-core/bwameth/align/main.nf
@@ -0,0 +1,39 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWAMETH_INDEX } from '../../../../../modules/nf-core/bwameth/index/main.nf'
+include { BWAMETH_ALIGN } from '../../../../../modules/nf-core/bwameth/align/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_bwameth_align_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWAMETH_INDEX ( fasta )
+    BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_bwameth_align_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWAMETH_INDEX ( fasta )
+    BWAMETH_ALIGN ( input, BWAMETH_INDEX.out.index )
+}
diff --git a/tests/modules/bwameth/align/nextflow.config b/tests/modules/nf-core/bwameth/align/nextflow.config
similarity index 100%
rename from tests/modules/bwameth/align/nextflow.config
rename to tests/modules/nf-core/bwameth/align/nextflow.config
diff --git a/tests/modules/nf-core/bwameth/align/test.yml b/tests/modules/nf-core/bwameth/align/test.yml
new file mode 100644
index 00000000000..6474091306e
--- /dev/null
+++ b/tests/modules/nf-core/bwameth/align/test.yml
@@ -0,0 +1,15 @@
+- name: bwameth align single-end test workflow
+  command: nextflow run ./tests/modules/nf-core/bwameth/align -entry test_bwameth_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwameth/align/nextflow.config
+  tags:
+    - bwameth
+    - bwameth/align
+  files:
+    - path: output/bwameth/test.bam
+
+- name: bwameth align paired-end test workflow
+  command: nextflow run ./tests/modules/nf-core/bwameth/align -entry test_bwameth_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwameth/align/nextflow.config
+  tags:
+    - bwameth
+    - bwameth/align
+  files:
+    - path: output/bwameth/test.bam
diff --git a/tests/modules/nf-core/bwameth/index/main.nf b/tests/modules/nf-core/bwameth/index/main.nf
new file mode 100644
index 00000000000..14f27490bb2
--- /dev/null
+++ b/tests/modules/nf-core/bwameth/index/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWAMETH_INDEX } from '../../../../../modules/nf-core/bwameth/index/main.nf'
+
+workflow test_bwameth_index {
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWAMETH_INDEX ( fasta )
+}
diff --git a/tests/modules/bwameth/index/nextflow.config b/tests/modules/nf-core/bwameth/index/nextflow.config
similarity index 100%
rename from tests/modules/bwameth/index/nextflow.config
rename to tests/modules/nf-core/bwameth/index/nextflow.config
diff --git a/tests/modules/nf-core/bwameth/index/test.yml b/tests/modules/nf-core/bwameth/index/test.yml
new file mode 100644
index 00000000000..9d35893640c
--- /dev/null
+++ b/tests/modules/nf-core/bwameth/index/test.yml
@@ -0,0 +1,18 @@
+- name: bwameth index test workflow
+  command: nextflow run ./tests/modules/nf-core/bwameth/index -entry test_bwameth_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwameth/index/nextflow.config
+  tags:
+    - bwameth
+    - bwameth/index
+  files:
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t
+      md5sum: 98039984526a41d04d6bd92fcc040c62
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.pac
+      md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.amb
+      md5sum: 249a4195069071ce47cd0bae68abe376
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.ann
+      md5sum: 46524d4359dcdfb203a235ab3b930dbb
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.bwt
+      md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b
+    - path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.sa
+      md5sum: d25f6486f5134f57ed5b258f6fbb8673
diff --git a/tests/modules/nf-core/cat/cat/main.nf b/tests/modules/nf-core/cat/cat/main.nf
new file mode 100644
index 00000000000..da8823c2c63
--- /dev/null
+++ b/tests/modules/nf-core/cat/cat/main.nf
@@ -0,0 +1,61 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CAT_CAT                        } from '../../../../../modules/nf-core/cat/cat/main.nf'
+include { CAT_CAT as CAT_UNZIPPED_ZIPPED } from '../../../../../modules/nf-core/cat/cat/main.nf'
+include { CAT_CAT as CAT_ZIPPED_UNZIPPED } from '../../../../../modules/nf-core/cat/cat/main.nf'
+
+workflow test_cat_unzipped_unzipped {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) ]
+    ]
+
+    CAT_CAT ( input )
+}
+
+workflow test_cat_zipped_zipped {
+
+    input = [
+         [ id:'test', single_end:true ], // meta map
+        [file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
+    ]
+
+    CAT_CAT ( input )
+}
+
+workflow test_cat_zipped_unzipped {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
+    ]
+
+    CAT_ZIPPED_UNZIPPED ( input )
+}
+
+workflow test_cat_unzipped_zipped {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)]
+    ]
+
+    CAT_UNZIPPED_ZIPPED ( input )
+}
+
+workflow test_cat_one_file_unzipped_zipped {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    CAT_UNZIPPED_ZIPPED ( input )
+}
diff --git a/tests/modules/cat/cat/nextflow.config b/tests/modules/nf-core/cat/cat/nextflow.config
similarity index 100%
rename from tests/modules/cat/cat/nextflow.config
rename to tests/modules/nf-core/cat/cat/nextflow.config
diff --git a/tests/modules/nf-core/cat/cat/test.yml b/tests/modules/nf-core/cat/cat/test.yml
new file mode 100644
index 00000000000..6c2b7aa5061
--- /dev/null
+++ b/tests/modules/nf-core/cat/cat/test.yml
@@ -0,0 +1,81 @@
+- name: cat unzipped unzipped
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/test.fasta
+      md5sum: f44b33a0e441ad58b2d3700270e2dbe2
+
+- name: cat unzipped unzipped stub
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/test.fasta
+
+- name: cat zipped zipped
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/test.gz
+
+- name: cat zipped zipped stub
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/test.gz
+
+- name: cat zipped unzipped
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt
+      md5sum: c439d3b60e7bc03e8802a451a0d9a5d9
+
+- name: cat zipped unzipped stub
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt
+
+- name: cat unzipped zipped
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt.gz
+
+- name: cat unzipped zipped stub
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt.gz
+
+- name: cat one file unzipped zipped
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt.gz
+
+- name: cat one file unzipped zipped stub
+  command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt.gz
diff --git a/tests/modules/nf-core/cat/fastq/main.nf b/tests/modules/nf-core/cat/fastq/main.nf
new file mode 100644
index 00000000000..dbd61f8441e
--- /dev/null
+++ b/tests/modules/nf-core/cat/fastq/main.nf
@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CAT_FASTQ } from '../../../../../modules/nf-core/cat/fastq/main.nf'
+
+workflow test_cat_fastq_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    CAT_FASTQ ( input )
+}
+
+workflow test_cat_fastq_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    CAT_FASTQ ( input )
+}
+
+workflow test_cat_fastq_single_end_same_name {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    CAT_FASTQ ( input )
+}
+
+workflow test_cat_fastq_paired_end_same_name {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    CAT_FASTQ ( input )
+}
+
+workflow test_cat_fastq_single_end_single_file {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+    ]
+
+    CAT_FASTQ ( input )
+}
diff --git a/tests/modules/cat/fastq/nextflow.config b/tests/modules/nf-core/cat/fastq/nextflow.config
similarity index 100%
rename from tests/modules/cat/fastq/nextflow.config
rename to tests/modules/nf-core/cat/fastq/nextflow.config
diff --git a/tests/modules/nf-core/cat/fastq/test.yml b/tests/modules/nf-core/cat/fastq/test.yml
new file mode 100644
index 00000000000..51085494010
--- /dev/null
+++ b/tests/modules/nf-core/cat/fastq/test.yml
@@ -0,0 +1,82 @@
+- name: cat fastq single-end
+  command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test.merged.fastq.gz
+      md5sum: f9cf5e375f7de81a406144a2c70cc64d
+
+- name: cat fastq fastqc_paired_end
+  command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test_2.merged.fastq.gz
+      md5sum: 77c8e966e130d8c6b6ec9be52fcb2bda
+    - path: ./output/cat/test_1.merged.fastq.gz
+      md5sum: f9cf5e375f7de81a406144a2c70cc64d
+
+- name: cat fastq single-end-same-name
+  command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test.merged.fastq.gz
+      md5sum: 63f817db7a29a03eb538104495556f66
+
+- name: cat fastq fastqc_paired_end_same_name
+  command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test_1.merged.fastq.gz
+      md5sum: 63f817db7a29a03eb538104495556f66
+    - path: ./output/cat/test_2.merged.fastq.gz
+      md5sum: fe9f266f43a6fc3dcab690a18419a56e
+
+- name: cat fastq single-end-single-file
+  command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end_single_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test.merged.fastq.gz
+      md5sum: e325ef7deb4023447a1f074e285761af
+
+- name: cat fastq single-end stub
+  command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test.merged.fastq.gz
+
+- name: cat fastq fastqc_paired_end stub
+  command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test_2.merged.fastq.gz
+    - path: ./output/cat/test_1.merged.fastq.gz
+
+- name: cat fastq single-end-same-name stub
+  command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test.merged.fastq.gz
+
+- name: cat fastq fastqc_paired_end_same_name stub
+  command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test_1.merged.fastq.gz
+    - path: ./output/cat/test_2.merged.fastq.gz
diff --git a/tests/modules/nf-core/cellranger/count/main.nf b/tests/modules/nf-core/cellranger/count/main.nf
new file mode 100644
index 00000000000..f4746db4bfd
--- /dev/null
+++ b/tests/modules/nf-core/cellranger/count/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CELLRANGER_MKGTF } from '../../../../../modules/nf-core/cellranger/mkgtf/main.nf'
+include { CELLRANGER_MKREF } from '../../../../../modules/nf-core/cellranger/mkref/main.nf'
+include { CELLRANGER_COUNT } from '../../../../../modules/nf-core/cellranger/count/main.nf'
+
+workflow test_cellranger_count {
+
+    input = [ [ id:'test', single_end:true, strandedness:'forward', gem: '123', samples: ["test_10x"] ], // meta map
+             [ file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    reference_name = "homo_sapiens_chr22_reference"
+
+    CELLRANGER_MKGTF ( gtf )
+
+    CELLRANGER_MKREF (
+        fasta,
+        CELLRANGER_MKGTF.out.gtf,
+        reference_name
+    )
+
+    CELLRANGER_COUNT(
+        input,
+        CELLRANGER_MKREF.out.reference
+    )
+}
diff --git a/tests/modules/cellranger/count/nextflow.config b/tests/modules/nf-core/cellranger/count/nextflow.config
similarity index 100%
rename from tests/modules/cellranger/count/nextflow.config
rename to tests/modules/nf-core/cellranger/count/nextflow.config
diff --git a/tests/modules/nf-core/cellranger/count/test.yml b/tests/modules/nf-core/cellranger/count/test.yml
new file mode 100644
index 00000000000..1621c1af39b
--- /dev/null
+++ b/tests/modules/nf-core/cellranger/count/test.yml
@@ -0,0 +1,65 @@
+- name: cellranger count test_cellranger_count
+  command: nextflow run ./tests/modules/nf-core/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cellranger/count/nextflow.config
+  tags:
+    - cellranger/count
+    - cellranger
+  files:
+    - path: output/cellranger/genome.filtered.gtf
+      md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
+    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
+      md5sum: 3520cd30e1b100e55f578db9c855f685
+    - path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
+      md5sum: d1e05cd46684fa26d852b6bc9f05e31f
+    - path: output/cellranger/homo_sapiens_chr22_reference/reference.json
+      md5sum: 8405fd7f527a944eafb9c2909045840b
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
+      md5sum: 897cec2d191945335f8b320438bd9135
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/SA
+      md5sum: 7961129ac5d0e1706105be1d31c6b30c
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
+      md5sum: dcceb480b30cda93fb8c63ddc339093b
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
+      md5sum: bc73df776dd3d5bb9cfcbcba60880519
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
+      md5sum: 9129691eeb4ed0d02b17be879fa3edb0
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
+      md5sum: 209b82f0683efd03e17d2c729676554f
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
+      md5sum: 02a8f4575bdfcd4a42b4d8d07f2e9369
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
+      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
+      md5sum: cedcb5f4e7d97bc548cd5daa022e092c
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
+      md5sum: f8b6b7cc8248151a98c46d4ebec450c6
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/features.tsv.gz
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
+    - path: output/cellranger/sample-123/outs/metrics_summary.csv
+      md5sum: 707df0f101d479d93f412ca74f9c4131
+    - path: output/cellranger/sample-123/outs/molecule_info.h5
+      md5sum: a13bd7425f441c8d0eac8ffc50082996
+    - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
+      md5sum: 15441da9cfceea0bb48c8b66b1b860df
+    - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
+      md5sum: 7c3d49c77016a09535aff61a027f750c
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
+      md5sum: a5290f3e300a4070f3d68a0c2e215f54
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/barcodes.tsv.gz
+      md5sum: 5cc39ef0c7ac85f2b758b164aabf9157
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/features.tsv.gz
+      md5sum: 07d497c7ce3e22f374af7b2cf9b97d72
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/matrix.mtx.gz
+      md5sum: bdce94a51f16e22d40301724080b76ee
+    - path: output/cellranger/sample-123/outs/web_summary.html
diff --git a/tests/modules/nf-core/cellranger/mkfastq/main.nf b/tests/modules/nf-core/cellranger/mkfastq/main.nf
new file mode 100644
index 00000000000..80434d5d5e8
--- /dev/null
+++ b/tests/modules/nf-core/cellranger/mkfastq/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR          } from '../../../../../modules/nf-core/untar/main.nf'
+include { CELLRANGER_MKFASTQ } from '../../../../../modules/nf-core/cellranger/mkfastq/main.nf'
+
+workflow test_cellranger_mkfastq_simple {
+
+    simple_csv = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true)
+    tiny_bcl = [ [], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true) ]
+
+    UNTAR ( tiny_bcl )
+
+    CELLRANGER_MKFASTQ ( UNTAR.out.untar.map{ it[1] }, simple_csv)
+}
+
+workflow test_cellranger_mkfastq_illumina {
+
+    samplesheet_csv = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv", checkIfExists: true)
+    tiny_bcl = [ [], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true) ]
+
+    UNTAR ( tiny_bcl )
+
+    CELLRANGER_MKFASTQ ( UNTAR.out.untar.map{ it[1] }, samplesheet_csv)
+}
diff --git a/tests/modules/cellranger/mkfastq/nextflow.config b/tests/modules/nf-core/cellranger/mkfastq/nextflow.config
similarity index 100%
rename from tests/modules/cellranger/mkfastq/nextflow.config
rename to tests/modules/nf-core/cellranger/mkfastq/nextflow.config
diff --git a/tests/modules/nf-core/cellranger/mkfastq/test.yml b/tests/modules/nf-core/cellranger/mkfastq/test.yml
new file mode 100644
index 00000000000..2279c842729
--- /dev/null
+++ b/tests/modules/nf-core/cellranger/mkfastq/test.yml
@@ -0,0 +1,14 @@
+- name: cellranger mkfastq test_cellranger_mkfastq_simple
+  command: nextflow run ./tests/modules/nf-core/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkfastq/nextflow.config -stub-run
+  tags:
+    - cellranger
+    - cellranger/mkfastq
+  files:
+    - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
+- name: cellranger mkfastq test_cellranger_mkfastq_illumina
+  command: nextflow run ./tests/modules/nf-core/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkfastq/nextflow.config -stub-run
+  tags:
+    - cellranger
+    - cellranger/mkfastq
+  files:
+    - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
diff --git a/tests/modules/nf-core/cellranger/mkgtf/main.nf b/tests/modules/nf-core/cellranger/mkgtf/main.nf
new file mode 100644
index 00000000000..cb281beee37
--- /dev/null
+++ b/tests/modules/nf-core/cellranger/mkgtf/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CELLRANGER_MKGTF } from '../../../../../modules/nf-core/cellranger/mkgtf/main.nf'
+
+workflow test_cellranger_mkgtf {
+    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+
+    CELLRANGER_MKGTF ( gtf )
+}
diff --git a/tests/modules/cellranger/mkgtf/nextflow.config b/tests/modules/nf-core/cellranger/mkgtf/nextflow.config
similarity index 100%
rename from tests/modules/cellranger/mkgtf/nextflow.config
rename to tests/modules/nf-core/cellranger/mkgtf/nextflow.config
diff --git a/tests/modules/nf-core/cellranger/mkgtf/test.yml b/tests/modules/nf-core/cellranger/mkgtf/test.yml
new file mode 100644
index 00000000000..b9ae76a7f9c
--- /dev/null
+++ b/tests/modules/nf-core/cellranger/mkgtf/test.yml
@@ -0,0 +1,8 @@
+- name: cellranger mkgtf test_cellranger_mkgtf
+  command: nextflow run ./tests/modules/nf-core/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cellranger/mkgtf/nextflow.config
+  tags:
+    - cellranger/mkgtf
+    - cellranger
+  files:
+    - path: output/cellranger/genome.filtered.gtf
+      md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
diff --git a/tests/modules/nf-core/cellranger/mkref/main.nf b/tests/modules/nf-core/cellranger/mkref/main.nf
new file mode 100644
index 00000000000..05f85805a01
--- /dev/null
+++ b/tests/modules/nf-core/cellranger/mkref/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CELLRANGER_MKREF } from '../../../../../modules/nf-core/cellranger/mkref/main.nf'
+
+workflow test_cellranger_mkref {
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    reference_name = "homo_sapiens_chr22_reference"
+
+    CELLRANGER_MKREF ( fasta,
+                        gtf,
+                        reference_name )
+}
diff --git a/tests/modules/cellranger/mkref/nextflow.config b/tests/modules/nf-core/cellranger/mkref/nextflow.config
similarity index 100%
rename from tests/modules/cellranger/mkref/nextflow.config
rename to tests/modules/nf-core/cellranger/mkref/nextflow.config
diff --git a/tests/modules/nf-core/cellranger/mkref/test.yml b/tests/modules/nf-core/cellranger/mkref/test.yml
new file mode 100644
index 00000000000..6dea68de629
--- /dev/null
+++ b/tests/modules/nf-core/cellranger/mkref/test.yml
@@ -0,0 +1,43 @@
+- name: cellranger mkref test_cellranger_mkref
+  command: nextflow run ./tests/modules/nf-core/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cellranger/mkref/nextflow.config
+  tags:
+    - cellranger/mkref
+    - cellranger
+  files:
+    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
+      md5sum: 3520cd30e1b100e55f578db9c855f685
+    - path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
+      md5sum: 6d9b5f409bfea95022bc25b9590e194e
+    - path: output/cellranger/homo_sapiens_chr22_reference/reference.json
+      md5sum: 6cc817f0923062e780e6573806840cea
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
+      md5sum: 22102926fadf5890e905ca71b2da3f35
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/SA
+      md5sum: bcf3e1a855783105150b46c905465333
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
+      md5sum: b93fb07d342e6c32a00ebc4311c0ad38
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
+      md5sum: bc73df776dd3d5bb9cfcbcba60880519
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
+      md5sum: d04497f69d6ef889efd4d34fe63edcc4
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
+      md5sum: 0d560290fab688b7268d88d5494bf9fe
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
+      md5sum: 8b608537307443ffaee4927d2b428805
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
+      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
+      md5sum: 8760c33e966dad0b39f440301ebbdee4
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
+      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
+      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
diff --git a/tests/modules/nf-core/centrifuge/centrifuge/main.nf b/tests/modules/nf-core/centrifuge/centrifuge/main.nf
new file mode 100644
index 00000000000..ab91d9f001e
--- /dev/null
+++ b/tests/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR                 } from '../../../../../modules/nf-core/untar/main.nf'
+include { CENTRIFUGE_CENTRIFUGE } from '../../../../../modules/nf-core/centrifuge/centrifuge/main.nf'
+
+workflow test_centrifuge_centrifuge_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
+    save_unaligned = true
+    save_aligned = false
+    sam_format = false
+
+    UNTAR ( db )
+    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
+
+}
+
+workflow test_centrifuge_centrifuge_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+     db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
+     save_unaligned = true
+     save_aligned = false
+     sam_format = false
+
+    UNTAR ( db )
+    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
+
+
+}
diff --git a/tests/modules/centrifuge/centrifuge/nextflow.config b/tests/modules/nf-core/centrifuge/centrifuge/nextflow.config
similarity index 100%
rename from tests/modules/centrifuge/centrifuge/nextflow.config
rename to tests/modules/nf-core/centrifuge/centrifuge/nextflow.config
diff --git a/tests/modules/nf-core/centrifuge/centrifuge/test.yml b/tests/modules/nf-core/centrifuge/centrifuge/test.yml
new file mode 100644
index 00000000000..6d1a64a5e33
--- /dev/null
+++ b/tests/modules/nf-core/centrifuge/centrifuge/test.yml
@@ -0,0 +1,22 @@
+- name: centrifuge centrifuge test_centrifuge_centrifuge_single_end
+  command: nextflow run ./tests/modules/nf-core/centrifuge/centrifuge -entry test_centrifuge_centrifuge_single_end -c ./tests/config/nextflow.config
+  tags:
+    - centrifuge
+    - centrifuge/centrifuge
+  files:
+    - path: output/centrifuge/test.report.txt
+    - path: output/centrifuge/test.results.txt
+    - path: output/centrifuge/test.unmapped.fastq.gz
+    - path: output/centrifuge/versions.yml
+
+- name: centrifuge centrifuge test_centrifuge_centrifuge_paired_end
+  command: nextflow run ./tests/modules/nf-core/centrifuge/centrifuge -entry test_centrifuge_centrifuge_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - centrifuge
+    - centrifuge/centrifuge
+  files:
+    - path: output/centrifuge/test.report.txt
+    - path: output/centrifuge/test.results.txt
+    - path: output/centrifuge/test.unmapped.fastq.1.gz
+    - path: output/centrifuge/test.unmapped.fastq.2.gz
+    - path: output/centrifuge/versions.yml
diff --git a/tests/modules/nf-core/centrifuge/kreport/main.nf b/tests/modules/nf-core/centrifuge/kreport/main.nf
new file mode 100644
index 00000000000..517b72a5aec
--- /dev/null
+++ b/tests/modules/nf-core/centrifuge/kreport/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR                } from '../../../../../modules/nf-core/untar/main.nf'
+include { CENTRIFUGE_CENTRIFUGE } from '../../../../../modules/nf-core/centrifuge/centrifuge/main.nf'
+include { CENTRIFUGE_KREPORT    } from '../../../../../modules/nf-core/centrifuge/kreport/main.nf'
+
+workflow test_centrifuge_kreport_single_end {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
+
+    ch_db = UNTAR ( db )
+    CENTRIFUGE_CENTRIFUGE ( input, ch_db.untar.map{ it[1] }, false, false, false )
+    CENTRIFUGE_KREPORT ( CENTRIFUGE_CENTRIFUGE.out.results, ch_db.untar.map{ it[1] } )
+}
+
+workflow test_centrifuge_kreport_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+     db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
+
+    ch_db = UNTAR ( db )
+    CENTRIFUGE_CENTRIFUGE ( input, ch_db.untar.map{ it[1] }, false, false, false )
+    CENTRIFUGE_KREPORT ( CENTRIFUGE_CENTRIFUGE.out.results, ch_db.untar.map{ it[1] } )
+}
+
diff --git a/tests/modules/centrifuge/kreport/nextflow.config b/tests/modules/nf-core/centrifuge/kreport/nextflow.config
similarity index 100%
rename from tests/modules/centrifuge/kreport/nextflow.config
rename to tests/modules/nf-core/centrifuge/kreport/nextflow.config
diff --git a/tests/modules/nf-core/centrifuge/kreport/test.yml b/tests/modules/nf-core/centrifuge/kreport/test.yml
new file mode 100644
index 00000000000..d28da916edb
--- /dev/null
+++ b/tests/modules/nf-core/centrifuge/kreport/test.yml
@@ -0,0 +1,19 @@
+- name: centrifuge kreport test_centrifuge_kreport_single_end
+  command: nextflow run ./tests/modules/nf-core/centrifuge/kreport -entry test_centrifuge_kreport_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/centrifuge/kreport/nextflow.config
+  tags:
+    - centrifuge/kreport
+    - centrifuge
+  files:
+    - path: output/centrifuge/test.report.txt
+    - path: output/centrifuge/test.results.txt
+    - path: output/centrifuge/test.txt
+
+- name: centrifuge kreport test_centrifuge_kreport_paired_end
+  command: nextflow run ./tests/modules/nf-core/centrifuge/kreport -entry test_centrifuge_kreport_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/centrifuge/kreport/nextflow.config
+  tags:
+    - centrifuge/kreport
+    - centrifuge
+  files:
+    - path: output/centrifuge/test.report.txt
+    - path: output/centrifuge/test.results.txt
+    - path: output/centrifuge/test.txt
diff --git a/tests/modules/nf-core/checkm/lineagewf/main.nf b/tests/modules/nf-core/checkm/lineagewf/main.nf
new file mode 100644
index 00000000000..eb7bedd8110
--- /dev/null
+++ b/tests/modules/nf-core/checkm/lineagewf/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CHECKM_LINEAGEWF } from '../../../../../modules/nf-core/checkm/lineagewf/main.nf'
+
+workflow test_checkm_lineagewf {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
+    fasta_ext = 'fasta'
+
+    CHECKM_LINEAGEWF ( input, fasta_ext, [] )
+}
+
+workflow test_checkm_lineagewf_multi {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ]
+    fasta_ext = 'fasta'
+
+    CHECKM_LINEAGEWF ( input, fasta_ext, [] )
+}
diff --git a/tests/modules/checkm/lineagewf/nextflow.config b/tests/modules/nf-core/checkm/lineagewf/nextflow.config
similarity index 100%
rename from tests/modules/checkm/lineagewf/nextflow.config
rename to tests/modules/nf-core/checkm/lineagewf/nextflow.config
diff --git a/tests/modules/nf-core/checkm/lineagewf/test.yml b/tests/modules/nf-core/checkm/lineagewf/test.yml
new file mode 100644
index 00000000000..8fcaf067293
--- /dev/null
+++ b/tests/modules/nf-core/checkm/lineagewf/test.yml
@@ -0,0 +1,34 @@
+- name: checkm lineagewf
+  command: nextflow run ./tests/modules/nf-core/checkm/lineagewf -entry test_checkm_lineagewf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/checkm/lineagewf/nextflow.config
+  tags:
+    - checkm
+    - checkm/lineagewf
+  files:
+    - path: output/checkm/test.tsv
+      md5sum: d5559764f563c4b55223e4e4a3dc1ec9
+    - path: output/checkm/test/checkm.log
+      contains:
+        - "INFO: Parsing HMM hits to marker genes:"
+    - path: output/checkm/test/lineage.ms
+      contains:
+        - "# [Lineage Marker File]"
+        - "contigs"
+        - "UID1"
+
+- name: checkm lineagewf_multi
+  command: nextflow run ./tests/modules/nf-core/checkm/lineagewf -entry test_checkm_lineagewf_multi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/checkm/lineagewf/nextflow.config
+  tags:
+    - checkm
+    - checkm/lineagewf
+  files:
+    - path: output/checkm/test.tsv
+      md5sum: 7e0fa177dcf151b84b7751813fbde3d1
+    - path: output/checkm/test/checkm.log
+      contains:
+        - "INFO: Parsing HMM hits to marker genes:"
+    - path: output/checkm/test/lineage.ms
+      contains:
+        - "# [Lineage Marker File]"
+        - "contigs"
+        - "UID1"
+        - "genome"
diff --git a/tests/modules/nf-core/checkm/qa/main.nf b/tests/modules/nf-core/checkm/qa/main.nf
new file mode 100644
index 00000000000..8f4c64e5630
--- /dev/null
+++ b/tests/modules/nf-core/checkm/qa/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CHECKM_LINEAGEWF              } from '../../../../../modules/nf-core/checkm/lineagewf/main.nf'
+include { CHECKM_LINEAGEWF as CHECKM_LINEAGEWF_FASTA        } from '../../../../../modules/nf-core/checkm/lineagewf/main.nf'
+include { CHECKM_QA                     } from '../../../../../modules/nf-core/checkm/qa/main.nf'
+include { CHECKM_QA as CHECKM_QA_FASTA  } from '../../../../../modules/nf-core/checkm/qa/main.nf'
+
+workflow test_checkm_qa {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
+    fasta_ext = 'fasta'
+
+    CHECKM_LINEAGEWF ( input, fasta_ext, [] )
+
+    ch_checkmqa_input = CHECKM_LINEAGEWF.out.checkm_output
+        .join(CHECKM_LINEAGEWF.out.marker_file)
+        .map{
+            meta, dir, marker ->
+            [ meta, dir, marker, []]
+        }
+
+    CHECKM_QA ( ch_checkmqa_input, [] )
+}
+
+workflow test_checkm_qa_fasta {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
+    fasta_ext = 'fasta'
+
+    CHECKM_LINEAGEWF_FASTA ( input, fasta_ext, [] )
+
+    ch_checkmqa_input =  CHECKM_LINEAGEWF_FASTA.out.checkm_output
+        .join(CHECKM_LINEAGEWF_FASTA.out.marker_file)
+        .map{
+            meta, dir, marker ->
+            [ meta, dir, marker, []]
+        }
+
+    CHECKM_QA_FASTA ( ch_checkmqa_input, [] )
+}
diff --git a/tests/modules/checkm/qa/nextflow.config b/tests/modules/nf-core/checkm/qa/nextflow.config
similarity index 100%
rename from tests/modules/checkm/qa/nextflow.config
rename to tests/modules/nf-core/checkm/qa/nextflow.config
diff --git a/tests/modules/nf-core/checkm/qa/test.yml b/tests/modules/nf-core/checkm/qa/test.yml
new file mode 100644
index 00000000000..bee7dedeb23
--- /dev/null
+++ b/tests/modules/nf-core/checkm/qa/test.yml
@@ -0,0 +1,16 @@
+- name: checkm qa test_checkm_qa
+  command: nextflow run ./tests/modules/nf-core/checkm/qa -entry test_checkm_qa -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/checkm/qa/nextflow.config
+  tags:
+    - checkm/qa
+    - checkm
+  files:
+    - path: output/checkm/test.qa.txt
+      md5sum: 645f4282569afb4b171396732b2d2582
+
+- name: checkm qa test_checkm_qa_fasta
+  command: nextflow run ./tests/modules/nf-core/checkm/qa -entry test_checkm_qa_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/checkm/qa/nextflow.config
+  tags:
+    - checkm/qa
+    - checkm
+  files:
+    - path: output/checkm/test.qa.fasta
diff --git a/tests/modules/nf-core/chromap/chromap/main.nf b/tests/modules/nf-core/chromap/chromap/main.nf
new file mode 100644
index 00000000000..97f5f737ed6
--- /dev/null
+++ b/tests/modules/nf-core/chromap/chromap/main.nf
@@ -0,0 +1,78 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CHROMAP_INDEX                           } from '../../../../../modules/nf-core/chromap/index/main.nf'
+include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_BASE } from '../../../../../modules/nf-core/chromap/chromap/main.nf'
+include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_SAM  } from '../../../../../modules/nf-core/chromap/chromap/main.nf'
+
+workflow test_chromap_chromap_single_end {
+
+    // Test single-end and gz compressed output
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    CHROMAP_INDEX ( fasta )
+    CHROMAP_CHROMAP_BASE (
+        input,                      // meta + read data
+        fasta,                      // reference genome
+        CHROMAP_INDEX.out.index,    // reference index
+        [],                         // barcode file
+        [],                         // barcode whitelist
+        [],                         // chromosome order file
+        []                          // pairs chromosome order file
+    )
+}
+
+workflow test_chromap_chromap_paired_end {
+
+    // Test paired-end and gz compressed output
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    CHROMAP_INDEX ( fasta )
+    CHROMAP_CHROMAP_BASE (
+        input,                      // meta + read data
+        fasta,                      // reference genome
+        CHROMAP_INDEX.out.index,    // reference index
+        [],                         // barcode file
+        [],                         // barcode whitelist
+        [],                         // chromosome order file
+        []                          // pairs chromosome order file
+    )
+}
+
+workflow test_chromap_chromap_paired_bam {
+
+    // Test paired-end and bam output
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    CHROMAP_INDEX ( fasta )
+    CHROMAP_CHROMAP_SAM (
+        input,                      // meta + read data
+        fasta,                      // reference genome
+        CHROMAP_INDEX.out.index,    // reference index
+        [],                         // barcode file
+        [],                         // barcode whitelist
+        [],                         // chromosome order file
+        []                          // pairs chromosome order file
+    )
+}
diff --git a/tests/modules/chromap/chromap/nextflow.config b/tests/modules/nf-core/chromap/chromap/nextflow.config
similarity index 100%
rename from tests/modules/chromap/chromap/nextflow.config
rename to tests/modules/nf-core/chromap/chromap/nextflow.config
diff --git a/tests/modules/nf-core/chromap/chromap/test.yml b/tests/modules/nf-core/chromap/chromap/test.yml
new file mode 100644
index 00000000000..073bcdcfe08
--- /dev/null
+++ b/tests/modules/nf-core/chromap/chromap/test.yml
@@ -0,0 +1,32 @@
+- name: chromap chromap test_chromap_chromap_single_end
+  command: nextflow run ./tests/modules/nf-core/chromap/chromap -entry test_chromap_chromap_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chromap/chromap/nextflow.config
+  tags:
+    - chromap/chromap
+    - chromap
+  files:
+    - path: output/chromap/genome.index
+    - path: output/chromap/test.bed.gz
+      md5sum: 25e40bde24c7b447292cd68573728694
+    - path: output/chromap/versions.yml
+
+- name: chromap chromap test_chromap_chromap_paired_end
+  command: nextflow run ./tests/modules/nf-core/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chromap/chromap/nextflow.config
+  tags:
+    - chromap/chromap
+    - chromap
+  files:
+    - path: output/chromap/genome.index
+    - path: output/chromap/test.bed.gz
+      md5sum: 7cdc8448882b75811e0c784f5f20aef2
+    - path: output/chromap/versions.yml
+
+- name: chromap chromap test_chromap_chromap_paired_bam
+  command: nextflow run ./tests/modules/nf-core/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chromap/chromap/nextflow.config
+  tags:
+    - chromap/chromap
+    - chromap
+  files:
+    - path: output/chromap/genome.index
+    - path: output/chromap/test.bam
+      md5sum: 0cb45628d1abe4b4359650040c501aef
+    - path: output/chromap/versions.yml
diff --git a/tests/modules/nf-core/chromap/index/main.nf b/tests/modules/nf-core/chromap/index/main.nf
new file mode 100644
index 00000000000..11987851c56
--- /dev/null
+++ b/tests/modules/nf-core/chromap/index/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CHROMAP_INDEX } from '../../../../../modules/nf-core/chromap/index/main.nf'
+
+workflow test_chromap_index {
+
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    CHROMAP_INDEX ( input )
+}
diff --git a/tests/modules/chromap/index/nextflow.config b/tests/modules/nf-core/chromap/index/nextflow.config
similarity index 100%
rename from tests/modules/chromap/index/nextflow.config
rename to tests/modules/nf-core/chromap/index/nextflow.config
diff --git a/tests/modules/nf-core/chromap/index/test.yml b/tests/modules/nf-core/chromap/index/test.yml
new file mode 100644
index 00000000000..d71767471d8
--- /dev/null
+++ b/tests/modules/nf-core/chromap/index/test.yml
@@ -0,0 +1,9 @@
+- name: chromap index test_chromap_index
+  command: nextflow run ./tests/modules/nf-core/chromap/index -entry test_chromap_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chromap/index/nextflow.config
+  tags:
+    - chromap/index
+    - chromap
+  files:
+    - path: output/chromap/genome.index
+    - path: output/chromap/versions.yml
+      md5sum: fc5c80190d0622ea3e979e6862f8e32b
diff --git a/tests/modules/nf-core/clonalframeml/main.nf b/tests/modules/nf-core/clonalframeml/main.nf
new file mode 100644
index 00000000000..fdd7d8ae911
--- /dev/null
+++ b/tests/modules/nf-core/clonalframeml/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CLONALFRAMEML } from '../../../../modules/nf-core/clonalframeml/main.nf'
+
+workflow test_clonalframeml {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_aln_nwk'], checkIfExists: true),
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_aln_gz'], checkIfExists: true)
+    ]
+
+    CLONALFRAMEML ( input )
+}
diff --git a/tests/modules/clonalframeml/nextflow.config b/tests/modules/nf-core/clonalframeml/nextflow.config
similarity index 100%
rename from tests/modules/clonalframeml/nextflow.config
rename to tests/modules/nf-core/clonalframeml/nextflow.config
diff --git a/tests/modules/nf-core/clonalframeml/test.yml b/tests/modules/nf-core/clonalframeml/test.yml
new file mode 100644
index 00000000000..1b880ec1a64
--- /dev/null
+++ b/tests/modules/nf-core/clonalframeml/test.yml
@@ -0,0 +1,15 @@
+- name: clonalframeml test_clonalframeml
+  command: nextflow run ./tests/modules/nf-core/clonalframeml -entry test_clonalframeml -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/clonalframeml/nextflow.config
+  tags:
+    - clonalframeml
+  files:
+    - path: output/clonalframeml/test.ML_sequence.fasta
+      md5sum: 1b75cdaea78f5920ebb92125422a2589
+    - path: output/clonalframeml/test.em.txt
+      md5sum: 5439d59897a9a90390bb175207bf2b9b
+    - path: output/clonalframeml/test.importation_status.txt
+      md5sum: 6ce9dbc7746b1c884af042fa02311fba
+    - path: output/clonalframeml/test.labelled_tree.newick
+      md5sum: aa47754eea8a3b6bab56bd7c83ba78db
+    - path: output/clonalframeml/test.position_cross_reference.txt
+      md5sum: 8ff60768b348fc6f7a1e787aca72f596
diff --git a/tests/modules/nf-core/cmseq/polymut/main.nf b/tests/modules/nf-core/cmseq/polymut/main.nf
new file mode 100644
index 00000000000..c4535090ba0
--- /dev/null
+++ b/tests/modules/nf-core/cmseq/polymut/main.nf
@@ -0,0 +1,38 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CMSEQ_POLYMUT } from '../../../../../modules/nf-core/cmseq/polymut/main.nf'
+
+workflow test_cmseq_polymut_1 {
+
+    input_1 = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              [],
+              file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
+              [] ]
+
+    CMSEQ_POLYMUT( input_1 )
+    
+}
+
+workflow test_cmseq_polymut_2 {
+    input_2 = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
+              [] ]
+
+    CMSEQ_POLYMUT( input_2 )
+}
+
+workflow test_cmseq_polymut_3 {
+    input_3 = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), ]
+
+    CMSEQ_POLYMUT( input_3 )
+}
+    
diff --git a/tests/modules/cmseq/polymut/nextflow.config b/tests/modules/nf-core/cmseq/polymut/nextflow.config
similarity index 100%
rename from tests/modules/cmseq/polymut/nextflow.config
rename to tests/modules/nf-core/cmseq/polymut/nextflow.config
diff --git a/tests/modules/nf-core/cmseq/polymut/test.yml b/tests/modules/nf-core/cmseq/polymut/test.yml
new file mode 100644
index 00000000000..41ba04471bb
--- /dev/null
+++ b/tests/modules/nf-core/cmseq/polymut/test.yml
@@ -0,0 +1,26 @@
+- name: cmseq polymut test_cmseq_polymut_1
+  command: nextflow run ./tests/modules/nf-core/cmseq/polymut -entry test_cmseq_polymut_1 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cmseq/polymut/nextflow.config
+  tags:
+    - cmseq/polymut
+    - cmseq
+  files:
+    - path: output/cmseq/test.txt
+      md5sum: fd325c1724ee23d132a9115c64494efc
+
+- name: cmseq polymut test_cmseq_polymut_2
+  command: nextflow run ./tests/modules/nf-core/cmseq/polymut -entry test_cmseq_polymut_2 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cmseq/polymut/nextflow.config
+  tags:
+    - cmseq/polymut
+    - cmseq
+  files:
+    - path: output/cmseq/test.txt
+      md5sum: fd325c1724ee23d132a9115c64494efc
+
+- name: cmseq polymut test_cmseq_polymut_3
+  command: nextflow run ./tests/modules/nf-core/cmseq/polymut -entry test_cmseq_polymut_3 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cmseq/polymut/nextflow.config
+  tags:
+    - cmseq/polymut
+    - cmseq
+  files:
+    - path: output/cmseq/test.txt
+      md5sum: fd325c1724ee23d132a9115c64494efc
diff --git a/tests/modules/nf-core/cnvkit/antitarget/main.nf b/tests/modules/nf-core/cnvkit/antitarget/main.nf
new file mode 100644
index 00000000000..6edce1d848d
--- /dev/null
+++ b/tests/modules/nf-core/cnvkit/antitarget/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVKIT_ANTITARGET } from '../../../../../modules/nf-core/cnvkit/antitarget/main.nf'
+
+workflow test_cnvkit_antitarget {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    ]
+
+    CNVKIT_ANTITARGET ( input )
+}
+
diff --git a/tests/modules/cnvkit/antitarget/nextflow.config b/tests/modules/nf-core/cnvkit/antitarget/nextflow.config
similarity index 100%
rename from tests/modules/cnvkit/antitarget/nextflow.config
rename to tests/modules/nf-core/cnvkit/antitarget/nextflow.config
diff --git a/tests/modules/nf-core/cnvkit/antitarget/test.yml b/tests/modules/nf-core/cnvkit/antitarget/test.yml
new file mode 100644
index 00000000000..2d0a4ce576f
--- /dev/null
+++ b/tests/modules/nf-core/cnvkit/antitarget/test.yml
@@ -0,0 +1,8 @@
+- name: cnvkit antitarget test_cnvkit_antitarget
+  command: nextflow run ./tests/modules/nf-core/cnvkit/antitarget -entry test_cnvkit_antitarget -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cnvkit/antitarget/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/antitarget
+  files:
+    - path: output/cnvkit/test.antitarget.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
diff --git a/tests/modules/nf-core/cnvkit/batch/main.nf b/tests/modules/nf-core/cnvkit/batch/main.nf
new file mode 100755
index 00000000000..c1fed0ed59e
--- /dev/null
+++ b/tests/modules/nf-core/cnvkit/batch/main.nf
@@ -0,0 +1,99 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVKIT_BATCH as CNVKIT_HYBRID    } from '../../../../../modules/nf-core/cnvkit/batch/main.nf'
+include { CNVKIT_BATCH as CNVKIT_WGS       } from '../../../../../modules/nf-core/cnvkit/batch/main.nf'
+include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../../modules/nf-core/cnvkit/batch/main.nf'
+include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../../modules/nf-core/cnvkit/batch/main.nf'
+
+workflow test_cnvkit_hybrid_somatic {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
+    ]
+    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
+
+    CNVKIT_HYBRID ( input, fasta, [], targets, [] )
+}
+
+workflow test_cnvkit_wgs_somatic {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    CNVKIT_WGS ( input, fasta, [], [], [] )
+}
+
+workflow test_cnvkit_cram_wgs_somatic {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+    ]
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    CNVKIT_WGS ( input, fasta, fasta_fai, [], [] )
+}
+
+
+workflow test_cnvkit_tumoronly_hybrid_bam {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+        []
+    ]
+    reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
+
+    CNVKIT_TUMORONLY ( input, [], [],  [], reference )
+}
+
+workflow test_cnvkit_tumoronly_hybrid_cram {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        []
+    ]
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
+
+    CNVKIT_TUMORONLY ( input, fasta, [], [], reference )
+}
+
+workflow test_cnvkit_germline_hybrid_cram {
+
+    input = [
+        [ id:'test'], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
+    ]
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    CNVKIT_GERMLINE ( input, fasta, fasta_fai, targets,  [])
+}
+
+workflow test_cnvkit_germline_hybrid_bam {
+
+    input = [
+        [ id:'test'], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
+    ]
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    CNVKIT_GERMLINE ( input, fasta, [], targets,  [])
+}
diff --git a/tests/modules/cnvkit/batch/nextflow.config b/tests/modules/nf-core/cnvkit/batch/nextflow.config
similarity index 100%
rename from tests/modules/cnvkit/batch/nextflow.config
rename to tests/modules/nf-core/cnvkit/batch/nextflow.config
diff --git a/tests/modules/nf-core/cnvkit/batch/test.yml b/tests/modules/nf-core/cnvkit/batch/test.yml
new file mode 100755
index 00000000000..4b14f412fd4
--- /dev/null
+++ b/tests/modules/nf-core/cnvkit/batch/test.yml
@@ -0,0 +1,183 @@
+- name: cnvkit batch test_cnvkit_hybrid_somatic
+  command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_hybrid_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/baits.antitarget.bed
+    - path: output/cnvkit/baits.target.bed
+      md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
+    - path: output/cnvkit/reference.cnn
+      md5sum: 035d031f54c5f1b43b903da96559b475
+    - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
+      md5sum: 203caf8cef6935bb50b4138097955cb8
+    - path: output/cnvkit/test.paired_end.sorted.bintest.cns
+      md5sum: 6544d979475def8a9f69ba42a985668d
+    - path: output/cnvkit/test.paired_end.sorted.call.cns
+      md5sum: f2ca59b4d50b0c317adc526c1b99b622
+    - path: output/cnvkit/test.paired_end.sorted.cnr
+      md5sum: 7e37d73ab604dbc3fe4ebb56aca9bdc3
+    - path: output/cnvkit/test.paired_end.sorted.cns
+      md5sum: 060af1aa637ed51812af19bcce24fcfe
+    - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
+      md5sum: 3fe80b6013ffc3e9968345e810158215
+    - path: output/cnvkit/test.single_end.sorted.antitargetcoverage.cnn
+      md5sum: 203caf8cef6935bb50b4138097955cb8
+    - path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
+      md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
+
+- name: cnvkit batch test_cnvkit_wgs_somatic
+  command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/genome.antitarget.bed
+    - path: output/cnvkit/genome.bed
+      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
+    - path: output/cnvkit/genome.target.bed
+      md5sum: a13353ae9c8405e701390c069255bbd2
+    - path: output/cnvkit/reference.cnn
+      md5sum: 1606a85410bfaa79464be6e98699aa83
+    - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
+      md5sum: 203caf8cef6935bb50b4138097955cb8
+    - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
+      md5sum: ff526714696aa49bdc1dc8d00d965266
+    - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
+      md5sum: 203caf8cef6935bb50b4138097955cb8
+    - path: output/cnvkit/test2.paired_end.sorted.bintest.cns
+      md5sum: 6544d979475def8a9f69ba42a985668d
+    - path: output/cnvkit/test2.paired_end.sorted.call.cns
+      md5sum: f6de754c34f780e6befee5b3ff0893f8
+    - path: output/cnvkit/test2.paired_end.sorted.cnr
+      md5sum: 80318d06c6b095945a0fb0e85e887cbc
+    - path: output/cnvkit/test2.paired_end.sorted.cns
+      md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
+    - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
+      md5sum: 6ae6b3fce7299eedca6133d911c38fe1
+
+- name: cnvkit batch test_cnvkit_cram_wgs_somatic
+  command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/genome.antitarget.bed
+    - path: output/cnvkit/genome.bed
+      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
+    - path: output/cnvkit/genome.target.bed
+      md5sum: a13353ae9c8405e701390c069255bbd2
+    - path: output/cnvkit/reference.cnn
+      md5sum: 1606a85410bfaa79464be6e98699aa83
+    - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
+      md5sum: 203caf8cef6935bb50b4138097955cb8
+    - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
+      md5sum: ff526714696aa49bdc1dc8d00d965266
+    - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
+      md5sum: 203caf8cef6935bb50b4138097955cb8
+    - path: output/cnvkit/test2.paired_end.sorted.bintest.cns
+      md5sum: 6544d979475def8a9f69ba42a985668d
+    - path: output/cnvkit/test2.paired_end.sorted.call.cns
+      md5sum: f6de754c34f780e6befee5b3ff0893f8
+    - path: output/cnvkit/test2.paired_end.sorted.cnr
+      md5sum: 80318d06c6b095945a0fb0e85e887cbc
+    - path: output/cnvkit/test2.paired_end.sorted.cns
+      md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
+    - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
+      md5sum: 6ae6b3fce7299eedca6133d911c38fe1
+
+- name: cnvkit batch test_cnvkit_tumoronly_hybrid_bam
+  command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/reference_chr21.target-tmp.bed
+      md5sum: 657b25dbda8516624efa8cb2cf3716ca
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: f7caeca04aba28b125ce26b511f42afb
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: d9bdb71ce807051369577ee7f807a40c
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 2b56aac606ba6183d018b30ca58afcec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
+
+- name: cnvkit batch test_cnvkit_tumoronly_hybrid_cram
+  command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/reference_chr21.target-tmp.bed
+      md5sum: 657b25dbda8516624efa8cb2cf3716ca
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: f7caeca04aba28b125ce26b511f42afb
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: d9bdb71ce807051369577ee7f807a40c
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 2b56aac606ba6183d018b30ca58afcec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
+
+- name: cnvkit batch test_cnvkit_germline_hybrid_cram
+  command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/multi_intervals.antitarget.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/multi_intervals.target.bed
+      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
+    - path: output/cnvkit/reference.cnn
+      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: 68b62b75cd91b2ffe5633686fb943490
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: df196edd72613c59186f4d87df3dc4a4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: 3b4fc0cc73be78f978cfe2422470753e
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
+
+- name: cnvkit batch test_cnvkit_germline_hybrid_bam
+  command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/multi_intervals.antitarget.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/multi_intervals.target.bed
+      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
+    - path: output/cnvkit/reference.cnn
+      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: 68b62b75cd91b2ffe5633686fb943490
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: df196edd72613c59186f4d87df3dc4a4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: 3b4fc0cc73be78f978cfe2422470753e
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
diff --git a/tests/modules/nf-core/cnvkit/reference/main.nf b/tests/modules/nf-core/cnvkit/reference/main.nf
new file mode 100644
index 00000000000..16358378e64
--- /dev/null
+++ b/tests/modules/nf-core/cnvkit/reference/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVKIT_REFERENCE } from '../../../../../modules/nf-core/cnvkit/reference/main.nf'
+
+workflow test_cnvkit_reference {
+
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    targets     = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    antitargets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_antitarget_bed'], checkIfExists: true)
+
+    CNVKIT_REFERENCE ( fasta, targets, antitargets )
+}
diff --git a/tests/modules/cnvkit/reference/nextflow.config b/tests/modules/nf-core/cnvkit/reference/nextflow.config
similarity index 100%
rename from tests/modules/cnvkit/reference/nextflow.config
rename to tests/modules/nf-core/cnvkit/reference/nextflow.config
diff --git a/tests/modules/nf-core/cnvkit/reference/test.yml b/tests/modules/nf-core/cnvkit/reference/test.yml
new file mode 100644
index 00000000000..14b6d077b5f
--- /dev/null
+++ b/tests/modules/nf-core/cnvkit/reference/test.yml
@@ -0,0 +1,8 @@
+- name: cnvkit reference test_cnvkit_reference
+  command: nextflow run ./tests/modules/nf-core/cnvkit/reference -entry test_cnvkit_reference -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/cnvkit/reference/nextflow.config
+  tags:
+    - cnvkit/reference
+    - cnvkit
+  files:
+    - path: output/cnvkit/multi_intervals.reference.cnn
+      md5sum: 7c4a7902f5ab101b1f9d6038d331b3d9
diff --git a/tests/modules/nf-core/cnvpytor/callcnvs/main.nf b/tests/modules/nf-core/cnvpytor/callcnvs/main.nf
new file mode 100644
index 00000000000..cbbd83c4040
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/callcnvs/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_CALLCNVS } from '../../../../../modules/nf-core/cnvpytor/callcnvs/main.nf'
+
+workflow test_cnvpytor_callcnvs {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    CNVPYTOR_CALLCNVS ( input )
+}
diff --git a/tests/modules/cnvpytor/callcnvs/nextflow.config b/tests/modules/nf-core/cnvpytor/callcnvs/nextflow.config
similarity index 100%
rename from tests/modules/cnvpytor/callcnvs/nextflow.config
rename to tests/modules/nf-core/cnvpytor/callcnvs/nextflow.config
diff --git a/tests/modules/nf-core/cnvpytor/callcnvs/test.yml b/tests/modules/nf-core/cnvpytor/callcnvs/test.yml
new file mode 100644
index 00000000000..7d3f8fe1ffd
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/callcnvs/test.yml
@@ -0,0 +1,17 @@
+- name: cnvpytor callcnvs test_cnvpytor_callcnvs
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c ./tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/callcnvs
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor callcnvs test_cnvpytor_callcnvs stub
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/callcnvs
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/nf-core/cnvpytor/histogram/main.nf b/tests/modules/nf-core/cnvpytor/histogram/main.nf
new file mode 100644
index 00000000000..12214e87653
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/histogram/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_HISTOGRAM } from '../../../../../modules/nf-core/cnvpytor/histogram/main.nf'
+
+workflow test_cnvpytor_histogram {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true),
+    ]
+
+    CNVPYTOR_HISTOGRAM ( input )
+}
diff --git a/tests/modules/cnvpytor/histogram/nextflow.config b/tests/modules/nf-core/cnvpytor/histogram/nextflow.config
similarity index 100%
rename from tests/modules/cnvpytor/histogram/nextflow.config
rename to tests/modules/nf-core/cnvpytor/histogram/nextflow.config
diff --git a/tests/modules/nf-core/cnvpytor/histogram/test.yml b/tests/modules/nf-core/cnvpytor/histogram/test.yml
new file mode 100644
index 00000000000..a25fc3902af
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/histogram/test.yml
@@ -0,0 +1,17 @@
+- name: cnvpytor histogram test_cnvpytor_histogram
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/histogram -entry test_cnvpytor_histogram -c ./tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/histogram
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor histogram test_cnvpytor_histogram stub
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/histogram -entry test_cnvpytor_histogram -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/histogram
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf b/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf
new file mode 100644
index 00000000000..b2d3f5592d2
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_IMPORTREADDEPTH } from '../../../../../modules/nf-core/cnvpytor/importreaddepth/main.nf'
+
+
+workflow test_cnvpytor_importreaddepth {
+
+    input = [
+        [ id: 'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    CNVPYTOR_IMPORTREADDEPTH (input, [], [])
+}
+
+workflow test_cnvpytor_importreaddepth_cram {
+
+    input = [
+        [ id: 'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    CNVPYTOR_IMPORTREADDEPTH (input, fasta, fai)
+}
diff --git a/tests/modules/cnvpytor/importreaddepth/nextflow.config b/tests/modules/nf-core/cnvpytor/importreaddepth/nextflow.config
similarity index 100%
rename from tests/modules/cnvpytor/importreaddepth/nextflow.config
rename to tests/modules/nf-core/cnvpytor/importreaddepth/nextflow.config
diff --git a/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml b/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml
new file mode 100644
index 00000000000..9e62d1c1df0
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml
@@ -0,0 +1,35 @@
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c ./tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth stub
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c ./tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram stub
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/nf-core/cnvpytor/partition/main.nf b/tests/modules/nf-core/cnvpytor/partition/main.nf
new file mode 100644
index 00000000000..bd46cec0b9f
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/partition/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_PARTITION } from '../../../../../modules/nf-core/cnvpytor/partition/main.nf'
+
+workflow test_cnvpytor_partition {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    CNVPYTOR_PARTITION ( input )
+}
diff --git a/tests/modules/cnvpytor/partition/nextflow.config b/tests/modules/nf-core/cnvpytor/partition/nextflow.config
similarity index 100%
rename from tests/modules/cnvpytor/partition/nextflow.config
rename to tests/modules/nf-core/cnvpytor/partition/nextflow.config
diff --git a/tests/modules/nf-core/cnvpytor/partition/test.yml b/tests/modules/nf-core/cnvpytor/partition/test.yml
new file mode 100644
index 00000000000..88eff3b6bd4
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/partition/test.yml
@@ -0,0 +1,17 @@
+- name: cnvpytor partition test_cnvpytor_partition
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/partition -entry test_cnvpytor_partition -c ./tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/partition
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor partition test_cnvpytor_partition stub
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/partition -entry test_cnvpytor_partition -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/partition
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/nf-core/cnvpytor/view/main.nf b/tests/modules/nf-core/cnvpytor/view/main.nf
new file mode 100644
index 00000000000..799234b0e55
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/view/main.nf
@@ -0,0 +1,42 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_VIEW } from '../../../../../modules/nf-core/cnvpytor/view/main.nf'
+
+workflow test_cnvpytor_view {
+
+    input = [
+        [ id:'test'], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
+    ]
+
+    bin_sizes = "10000 100000"
+
+    CNVPYTOR_VIEW ( input, bin_sizes, [] )
+}
+
+workflow test_cnvpytor_view_tsvout {
+
+    input = [
+        [ id:'test'], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
+    ]
+
+    output_suffix = "tsv"
+
+    CNVPYTOR_VIEW ( input, [], output_suffix )
+}
+
+workflow test_cnvpytor_view_stub {
+
+    input = [
+        [ id:'test'], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
+    ]
+
+    bin_sizes = []
+    output_suffix = []
+
+    CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
+}
diff --git a/tests/modules/cnvpytor/view/nextflow.config b/tests/modules/nf-core/cnvpytor/view/nextflow.config
similarity index 100%
rename from tests/modules/cnvpytor/view/nextflow.config
rename to tests/modules/nf-core/cnvpytor/view/nextflow.config
diff --git a/tests/modules/nf-core/cnvpytor/view/test.yml b/tests/modules/nf-core/cnvpytor/view/test.yml
new file mode 100644
index 00000000000..f8b54e2d7c1
--- /dev/null
+++ b/tests/modules/nf-core/cnvpytor/view/test.yml
@@ -0,0 +1,27 @@
+- name: cnvpytor view test_cnvpytor_view
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view -c ./tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/view
+  files:
+    - path: output/cnvpytor/test_10000.vcf
+    - path: output/cnvpytor/test_100000.vcf
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor view test_cnvpytor_view tsv
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view_tsvout -c ./tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/view
+  files:
+    - path: output/cnvpytor/test_1000.tsv
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor view test_cnvpytor_view stub
+  command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view_stub -c ./tests/config/nextflow.config  -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/view
+  files:
+    - path: output/cnvpytor/test.vcf
+    - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/nf-core/controlfreec/assesssignificance/main.nf b/tests/modules/nf-core/controlfreec/assesssignificance/main.nf
new file mode 100644
index 00000000000..f1add9072d0
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/assesssignificance/main.nf
@@ -0,0 +1,77 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CONTROLFREEC_ASSESSSIGNIFICANCE } from '../../../../../modules/nf-core/controlfreec/assesssignificance/main.nf'
+include { CONTROLFREEC_FREEC              } from '../../../../../modules/nf-core/controlfreec/freec/main.nf'
+include { UNTAR                           }        from '../../../../../modules/nf-core/untar/main.nf'
+
+workflow test_controlfreec_assesssignificance {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
+    CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
+}
+
+workflow test_controlfreec_assesssignificance_single {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
+    CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
+}
diff --git a/tests/modules/controlfreec/assesssignificance/nextflow.config b/tests/modules/nf-core/controlfreec/assesssignificance/nextflow.config
similarity index 100%
rename from tests/modules/controlfreec/assesssignificance/nextflow.config
rename to tests/modules/nf-core/controlfreec/assesssignificance/nextflow.config
diff --git a/tests/modules/nf-core/controlfreec/assesssignificance/test.yml b/tests/modules/nf-core/controlfreec/assesssignificance/test.yml
new file mode 100644
index 00000000000..94740f8fa0a
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/assesssignificance/test.yml
@@ -0,0 +1,18 @@
+- name: controlfreec assesssignificance test_controlfreec_assesssignificance
+  command: nextflow run ./tests/modules/nf-core/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance -c ./tests/config/nextflow.config
+  tags:
+    - controlfreec/assesssignificance
+    - controlfreec
+  files:
+    - path: output/controlfreec/test.p.value.txt
+      md5sum: 44e23b916535fbc1a3f47b57fad292df
+    - path: output/controlfreec/versions.yml
+
+- name: controlfreec assesssignificance test_controlfreec_assesssignificance_single
+  command: nextflow run ./tests/modules/nf-core/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance_single -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec/assesssignificance
+    - controlfreec
+  files:
+    - path: output/controlfreec/test.p.value.txt
+    - path: output/controlfreec/versions.yml
diff --git a/tests/modules/nf-core/controlfreec/freec/main.nf b/tests/modules/nf-core/controlfreec/freec/main.nf
new file mode 100644
index 00000000000..3b9af3f5318
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/freec/main.nf
@@ -0,0 +1,71 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CONTROLFREEC_FREEC } from '../../../../../modules/nf-core/controlfreec/freec/main.nf'
+include { UNTAR              }        from '../../../../../modules/nf-core/untar/main.nf'
+
+workflow test_controlfreec_freec {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+}
+
+workflow test_controlfreec_freec_single {
+
+    input = [
+        [ id:'test2', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+}
+
diff --git a/tests/modules/controlfreec/freec/nextflow.config b/tests/modules/nf-core/controlfreec/freec/nextflow.config
similarity index 100%
rename from tests/modules/controlfreec/freec/nextflow.config
rename to tests/modules/nf-core/controlfreec/freec/nextflow.config
diff --git a/tests/modules/nf-core/controlfreec/freec/test.yml b/tests/modules/nf-core/controlfreec/freec/test.yml
new file mode 100644
index 00000000000..c0096876bc9
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/freec/test.yml
@@ -0,0 +1,37 @@
+- name: controlfreec test_controlfreec_freec
+  command: nextflow run ./tests/modules/nf-core/controlfreec/freec -entry test_controlfreec_freec -c ./tests/config/nextflow.config
+  tags:
+    - controlfreec
+    - controlfreec/freec
+  files:
+    - path: output/controlfreec/config.txt
+    - path: output/controlfreec/test.mpileup.gz_control.cpn
+      md5sum: 1768b571677c418560e5a8fe203bdc79
+    - path: output/controlfreec/test2.mpileup.gz_BAF.txt
+      md5sum: 3bb7437001cf061a77eaf87b8558c48d
+    - path: output/controlfreec/test2.mpileup.gz_CNVs
+      md5sum: 1f4f5834dbd1490afdb22f6d3091c4c9
+    - path: output/controlfreec/test2.mpileup.gz_info.txt
+      md5sum: 1a3055d35028525ccc9e693cc9f335e0
+    - path: output/controlfreec/test2.mpileup.gz_ratio.BedGraph
+      md5sum: 8ba455b232be20cdcc5bf1e4035e8032
+    - path: output/controlfreec/test2.mpileup.gz_ratio.txt
+      md5sum: b76b2434de710325069e37fb1e132760
+    - path: output/controlfreec/test2.mpileup.gz_sample.cpn
+      md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
+    - path: output/controlfreec/versions.yml
+
+- name: controlfreec test_controlfreec_freec_single
+  command: nextflow run ./tests/modules/nf-core/controlfreec/freec -entry test_controlfreec_freec_single -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec
+    - controlfreec/freec
+  files:
+    - path: output/controlfreec/config.txt
+    - path: output/controlfreec/test2_BAF.txt
+    - path: output/controlfreec/test2_CNVs
+    - path: output/controlfreec/test2_info.txt
+    - path: output/controlfreec/test2_ratio.BedGraph
+    - path: output/controlfreec/test2_ratio.txt
+    - path: output/controlfreec/test2_sample.cpn
+    - path: output/controlfreec/versions.yml
diff --git a/tests/modules/nf-core/controlfreec/freec2bed/main.nf b/tests/modules/nf-core/controlfreec/freec2bed/main.nf
new file mode 100644
index 00000000000..16ae2a89759
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/freec2bed/main.nf
@@ -0,0 +1,75 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CONTROLFREEC_FREEC2BED } from '../../../../../modules/nf-core/controlfreec/freec2bed/main.nf'
+include { CONTROLFREEC_FREEC     } from '../../../../../modules/nf-core/controlfreec/freec/main.nf'
+include { UNTAR                  } from '../../../../../modules/nf-core/untar/main.nf'
+
+workflow test_controlfreec_freec2bed {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
+}
+
+workflow test_controlfreec_freec2bed_single {
+
+      input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
+}
diff --git a/tests/modules/controlfreec/freec2bed/nextflow.config b/tests/modules/nf-core/controlfreec/freec2bed/nextflow.config
similarity index 100%
rename from tests/modules/controlfreec/freec2bed/nextflow.config
rename to tests/modules/nf-core/controlfreec/freec2bed/nextflow.config
diff --git a/tests/modules/nf-core/controlfreec/freec2bed/test.yml b/tests/modules/nf-core/controlfreec/freec2bed/test.yml
new file mode 100644
index 00000000000..9a632817e00
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/freec2bed/test.yml
@@ -0,0 +1,16 @@
+- name: controlfreec freec2bed test_controlfreec_freec2bed
+  command: nextflow run ./tests/modules/nf-core/controlfreec/freec2bed -entry test_controlfreec_freec2bed -c ./tests/config/nextflow.config
+  tags:
+    - controlfreec/freec2bed
+    - controlfreec
+  files:
+    - path: output/controlfreec/test.bed
+      md5sum: abe10b7ce94ba903503e697394c17297
+
+- name: controlfreec freec2bed test_controlfreec_freec2bed_single
+  command: nextflow run ./tests/modules/nf-core/controlfreec/freec2bed -entry test_controlfreec_freec2bed_single -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec/freec2bed
+    - controlfreec
+  files:
+    - path: output/controlfreec/test.bed
diff --git a/tests/modules/nf-core/controlfreec/freec2circos/main.nf b/tests/modules/nf-core/controlfreec/freec2circos/main.nf
new file mode 100644
index 00000000000..2de1cb8fc1a
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/freec2circos/main.nf
@@ -0,0 +1,75 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CONTROLFREEC_FREEC2CIRCOS } from '../../../../../modules/nf-core/controlfreec/freec2circos/main.nf'
+include { CONTROLFREEC_FREEC     } from '../../../../../modules/nf-core/controlfreec/freec/main.nf'
+include { UNTAR                  } from '../../../../../modules/nf-core/untar/main.nf'
+
+workflow test_controlfreec_freec2circos {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
+}
+
+workflow test_controlfreec_freec2circos_single {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
+}
diff --git a/tests/modules/controlfreec/freec2circos/nextflow.config b/tests/modules/nf-core/controlfreec/freec2circos/nextflow.config
similarity index 100%
rename from tests/modules/controlfreec/freec2circos/nextflow.config
rename to tests/modules/nf-core/controlfreec/freec2circos/nextflow.config
diff --git a/tests/modules/nf-core/controlfreec/freec2circos/test.yml b/tests/modules/nf-core/controlfreec/freec2circos/test.yml
new file mode 100644
index 00000000000..6fa51b7ec1c
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/freec2circos/test.yml
@@ -0,0 +1,16 @@
+- name: controlfreec freec2circos test_controlfreec_freec2circos
+  command: nextflow run ./tests/modules/nf-core/controlfreec/freec2circos -entry test_controlfreec_freec2circos -c ./tests/config/nextflow.config
+  tags:
+    - controlfreec
+    - controlfreec/freec2circos
+  files:
+    - path: output/controlfreec/test.circos.txt
+      md5sum: 19cf35f2c36b46f717dc8342b8a5a645
+
+- name: controlfreec freec2circos test_controlfreec_freec2circos_single
+  command: nextflow run ./tests/modules/nf-core/controlfreec/freec2circos -entry test_controlfreec_freec2circos_single -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec
+    - controlfreec/freec2circos
+  files:
+    - path: output/controlfreec/test.circos.txt
diff --git a/tests/modules/nf-core/controlfreec/makegraph/main.nf b/tests/modules/nf-core/controlfreec/makegraph/main.nf
new file mode 100644
index 00000000000..a87285df741
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/makegraph/main.nf
@@ -0,0 +1,77 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CONTROLFREEC_MAKEGRAPH } from '../../../../../modules/nf-core/controlfreec/makegraph/main.nf'
+include { CONTROLFREEC_FREEC     } from '../../../../../modules/nf-core/controlfreec/freec/main.nf'
+include { UNTAR                  } from '../../../../../modules/nf-core/untar/main.nf'
+
+workflow test_controlfreec_makegraph {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
+    CONTROLFREEC_MAKEGRAPH ( makegraph_in )
+}
+
+workflow test_controlfreec_makegraph_single {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
+    CONTROLFREEC_MAKEGRAPH ( makegraph_in )
+}
diff --git a/tests/modules/controlfreec/makegraph/nextflow.config b/tests/modules/nf-core/controlfreec/makegraph/nextflow.config
similarity index 100%
rename from tests/modules/controlfreec/makegraph/nextflow.config
rename to tests/modules/nf-core/controlfreec/makegraph/nextflow.config
diff --git a/tests/modules/nf-core/controlfreec/makegraph/test.yml b/tests/modules/nf-core/controlfreec/makegraph/test.yml
new file mode 100644
index 00000000000..803b0889336
--- /dev/null
+++ b/tests/modules/nf-core/controlfreec/makegraph/test.yml
@@ -0,0 +1,22 @@
+- name: controlfreec makegraph test_controlfreec_makegraph
+  command: nextflow run ./tests/modules/nf-core/controlfreec/makegraph -entry test_controlfreec_makegraph -c ./tests/config/nextflow.config
+  tags:
+    - controlfreec
+    - controlfreec/makegraph
+  files:
+    - path: output/controlfreec/test_BAF.png
+      md5sum: f9d977839e09c7e2472d970bd4aa834c
+    - path: output/controlfreec/test_ratio.log2.png
+      md5sum: b3c7916b1b4951a0cc3da20d8e9e0262
+    - path: output/controlfreec/test_ratio.png
+      md5sum: 1435b29536b3b1555b4c423f8f4fb000
+
+- name: controlfreec makegraph test_controlfreec_makegraph_single
+  command: nextflow run ./tests/modules/nf-core/controlfreec/makegraph -entry test_controlfreec_makegraph_single -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec
+    - controlfreec/makegraph
+  files:
+    - path: output/controlfreec/test_BAF.png
+    - path: output/controlfreec/test_ratio.log2.png
+    - path: output/controlfreec/test_ratio.png
diff --git a/tests/modules/nf-core/cooler/cload/main.nf b/tests/modules/nf-core/cooler/cload/main.nf
new file mode 100644
index 00000000000..baa0ea26272
--- /dev/null
+++ b/tests/modules/nf-core/cooler/cload/main.nf
@@ -0,0 +1,52 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { COOLER_CLOAD }                       from '../../../../../modules/nf-core/cooler/cload/main.nf'
+include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../../modules/nf-core/cooler/cload/main.nf'
+include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../../modules/nf-core/cooler/cload/main.nf'
+include { COOLER_DUMP }                        from '../../../../../modules/nf-core/cooler/dump/main.nf'
+include { COOLER_DUMP as COOLER_DUMP_PAIRS}    from '../../../../../modules/nf-core/cooler/dump/main.nf'
+include { COOLER_DUMP as COOLER_DUMP_TABIX}    from '../../../../../modules/nf-core/cooler/dump/main.nf'
+
+workflow test_cooler_cload_pairix {
+
+    input = [ [ id:'test_pairix', single_end:false ], // meta map
+             file(params.test_data['generic']['cooler']['test_pairix_pair_gz'], checkIfExists: true),
+             file(params.test_data['generic']['cooler']['test_pairix_pair_gz_px2'], checkIfExists: true)]
+
+    sizes    = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
+    bin_size = 2000000
+
+    COOLER_CLOAD ( input, bin_size, sizes )
+    COOLER_DUMP(COOLER_CLOAD.out.cool.map{[it[0], it[2]]}, [])
+
+}
+
+workflow test_cooler_cload_pairs {
+
+    input = [ [ id:'test_pairs', single_end:false ], // meta map
+             file(params.test_data['generic']['cooler']['test_pairs_pair'], checkIfExists: true),
+             []]
+
+    sizes    = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
+    bin_size = 2000000
+
+    COOLER_CLOAD_PAIRS ( input, bin_size, sizes )
+    COOLER_DUMP_PAIRS(COOLER_CLOAD_PAIRS.out.cool.map{[it[0], it[2]]}, [])
+
+}
+
+workflow test_cooler_cload_tabix {
+
+    input = [ [ id:'test_tabix', single_end:false ], // meta map
+             file(params.test_data['generic']['cooler']['test_tabix_pair_gz'], checkIfExists: true),
+             file(params.test_data['generic']['cooler']['test_tabix_pair_gz_tbi'], checkIfExists: true)]
+
+    sizes    = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
+    bin_size = 2000000
+
+    COOLER_CLOAD_TABIX ( input, bin_size, sizes )
+    COOLER_DUMP_TABIX(COOLER_CLOAD_TABIX.out.cool.map{[it[0], it[2]]}, [])
+
+}
diff --git a/tests/modules/cooler/cload/nextflow.config b/tests/modules/nf-core/cooler/cload/nextflow.config
similarity index 100%
rename from tests/modules/cooler/cload/nextflow.config
rename to tests/modules/nf-core/cooler/cload/nextflow.config
diff --git a/tests/modules/nf-core/cooler/cload/test.yml b/tests/modules/nf-core/cooler/cload/test.yml
new file mode 100644
index 00000000000..83552db836c
--- /dev/null
+++ b/tests/modules/nf-core/cooler/cload/test.yml
@@ -0,0 +1,29 @@
+- name: cooler cload test_cooler_cload_pairix
+  command: nextflow run ./tests/modules/nf-core/cooler/cload -entry test_cooler_cload_pairix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/cload/nextflow.config
+  tags:
+    - cooler/cload
+    - cooler
+  files:
+    - path: output/cooler/test_pairix.2000000.cool
+    - path: output/cooler/test_pairix.bedpe
+      md5sum: 0cd85311089669688ec17468eae02111
+
+- name: cooler cload test_cooler_cload_pairs
+  command: nextflow run ./tests/modules/nf-core/cooler/cload -entry test_cooler_cload_pairs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/cload/nextflow.config
+  tags:
+    - cooler/cload
+    - cooler
+  files:
+    - path: output/cooler/test_pairs.2000000.cool
+    - path: output/cooler/test_pairs.bedpe
+      md5sum: 7f832733fc7853ebb1937b33e4c1e0de
+
+- name: cooler cload test_cooler_cload_tabix
+  command: nextflow run ./tests/modules/nf-core/cooler/cload -entry test_cooler_cload_tabix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/cload/nextflow.config
+  tags:
+    - cooler/cload
+    - cooler
+  files:
+    - path: output/cooler/test_tabix.2000000.cool
+    - path: output/cooler/test_tabix.bedpe
+      md5sum: 0cd85311089669688ec17468eae02111
diff --git a/tests/modules/nf-core/cooler/digest/main.nf b/tests/modules/nf-core/cooler/digest/main.nf
new file mode 100644
index 00000000000..bd2fd8a9ef7
--- /dev/null
+++ b/tests/modules/nf-core/cooler/digest/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { COOLER_DIGEST } from '../../../../../modules/nf-core/cooler/digest/main.nf'
+
+workflow test_cooler_digest {
+
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+    enzyme = "CviQI"
+
+    COOLER_DIGEST ( input, sizes, enzyme )
+}
diff --git a/tests/modules/cooler/digest/nextflow.config b/tests/modules/nf-core/cooler/digest/nextflow.config
similarity index 100%
rename from tests/modules/cooler/digest/nextflow.config
rename to tests/modules/nf-core/cooler/digest/nextflow.config
diff --git a/tests/modules/nf-core/cooler/digest/test.yml b/tests/modules/nf-core/cooler/digest/test.yml
new file mode 100644
index 00000000000..3ddf058736b
--- /dev/null
+++ b/tests/modules/nf-core/cooler/digest/test.yml
@@ -0,0 +1,8 @@
+- name: cooler digest test_cooler_digest
+  command: nextflow run ./tests/modules/nf-core/cooler/digest -entry test_cooler_digest -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/digest/nextflow.config
+  tags:
+    - cooler/digest
+    - cooler
+  files:
+    - path: output/cooler/genome_CviQI.bed
+      md5sum: f02d3cfaf642b27d4cc197209845e096
diff --git a/tests/modules/nf-core/cooler/dump/main.nf b/tests/modules/nf-core/cooler/dump/main.nf
new file mode 100644
index 00000000000..0b3c5e9fdb5
--- /dev/null
+++ b/tests/modules/nf-core/cooler/dump/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { COOLER_DUMP } from '../../../../../modules/nf-core/cooler/dump/main.nf'
+
+workflow test_cooler_dump {
+
+    input = [ [ id:'test' ], // meta map
+              file("https://raw.githubusercontent.com/open2c/cooler/master/tests/data/toy.asymm.16.cool", checkIfExists: true) ]
+
+    COOLER_DUMP ( input, [:] )
+}
diff --git a/tests/modules/cooler/dump/nextflow.config b/tests/modules/nf-core/cooler/dump/nextflow.config
similarity index 100%
rename from tests/modules/cooler/dump/nextflow.config
rename to tests/modules/nf-core/cooler/dump/nextflow.config
diff --git a/tests/modules/nf-core/cooler/dump/test.yml b/tests/modules/nf-core/cooler/dump/test.yml
new file mode 100644
index 00000000000..fa41e2eb018
--- /dev/null
+++ b/tests/modules/nf-core/cooler/dump/test.yml
@@ -0,0 +1,8 @@
+- name: cooler dump test_cooler_dump
+  command: nextflow run ./tests/modules/nf-core/cooler/dump -entry test_cooler_dump -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/dump/nextflow.config
+  tags:
+    - cooler/dump
+    - cooler
+  files:
+    - path: output/cooler/test.bedpe
+      md5sum: 38e9b0b8cc74f55a15e8ab01023048bd
diff --git a/tests/modules/nf-core/cooler/merge/main.nf b/tests/modules/nf-core/cooler/merge/main.nf
new file mode 100644
index 00000000000..58ac789c264
--- /dev/null
+++ b/tests/modules/nf-core/cooler/merge/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { COOLER_MERGE } from '../../../../../modules/nf-core/cooler/merge/main.nf'
+include { COOLER_DUMP  } from '../../../../../modules/nf-core/cooler/dump/main.nf'
+
+workflow test_cooler_merge {
+
+    input = [
+        [ id:'test' ], // meta map
+        [
+            file(params.test_data['generic']['cooler']['test_merge_cool'], checkIfExists: true),
+            file(params.test_data['generic']['cooler']['test_merge_cool_cp2'], checkIfExists: true)
+        ]
+    ]
+
+    COOLER_MERGE ( input )
+    COOLER_DUMP ( COOLER_MERGE.out.cool, "" )
+}
diff --git a/tests/modules/cooler/merge/nextflow.config b/tests/modules/nf-core/cooler/merge/nextflow.config
similarity index 100%
rename from tests/modules/cooler/merge/nextflow.config
rename to tests/modules/nf-core/cooler/merge/nextflow.config
diff --git a/tests/modules/nf-core/cooler/merge/test.yml b/tests/modules/nf-core/cooler/merge/test.yml
new file mode 100644
index 00000000000..735f94ab66f
--- /dev/null
+++ b/tests/modules/nf-core/cooler/merge/test.yml
@@ -0,0 +1,8 @@
+- name: cooler merge test_cooler_merge
+  command: nextflow run ./tests/modules/nf-core/cooler/merge -entry test_cooler_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/merge/nextflow.config
+  tags:
+    - cooler/merge
+    - cooler
+  files:
+    - path: output/cooler/test.bedpe
+      md5sum: 0ce5e715bfc4674cdda02f2d7e7e3170
diff --git a/tests/modules/nf-core/cooler/zoomify/main.nf b/tests/modules/nf-core/cooler/zoomify/main.nf
new file mode 100644
index 00000000000..5ec0a3296e2
--- /dev/null
+++ b/tests/modules/nf-core/cooler/zoomify/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { COOLER_ZOOMIFY } from '../../../../../modules/nf-core/cooler/zoomify/main.nf'
+
+workflow test_cooler_zoomify {
+
+   input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['generic']['cooler']['test_merge_cool'], checkIfExists: true)
+    ]
+
+    COOLER_ZOOMIFY ( input )
+}
diff --git a/tests/modules/cooler/zoomify/nextflow.config b/tests/modules/nf-core/cooler/zoomify/nextflow.config
similarity index 100%
rename from tests/modules/cooler/zoomify/nextflow.config
rename to tests/modules/nf-core/cooler/zoomify/nextflow.config
diff --git a/tests/modules/nf-core/cooler/zoomify/test.yml b/tests/modules/nf-core/cooler/zoomify/test.yml
new file mode 100644
index 00000000000..c39deee2baf
--- /dev/null
+++ b/tests/modules/nf-core/cooler/zoomify/test.yml
@@ -0,0 +1,8 @@
+- name: cooler zoomify test_cooler_zoomify
+  command: nextflow run ./tests/modules/nf-core/cooler/zoomify -entry test_cooler_zoomify -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/zoomify/nextflow.config
+  tags:
+    - cooler
+    - cooler/zoomify
+  files:
+    - path: output/cooler/test.bedpe
+      md5sum: 0ce5e715bfc4674cdda02f2d7e7e3170
diff --git a/tests/modules/nf-core/csvtk/concat/main.nf b/tests/modules/nf-core/csvtk/concat/main.nf
new file mode 100644
index 00000000000..688e1258342
--- /dev/null
+++ b/tests/modules/nf-core/csvtk/concat/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CSVTK_CONCAT } from '../../../../../modules/nf-core/csvtk/concat/main.nf'
+
+workflow test_csvtk_concat {
+
+    input = [ 
+        [ id:'test' ], // meta map
+        [ file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_hybrid.csv", checkIfExists: true),
+          file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_long.csv", checkIfExists: true),
+          file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_short.csv", checkIfExists: true) ]
+    ]
+
+    in_format = "tsv"
+    out_format = "csv"
+
+    CSVTK_CONCAT ( input, in_format, out_format )
+}
diff --git a/tests/modules/csvtk/concat/nextflow.config b/tests/modules/nf-core/csvtk/concat/nextflow.config
similarity index 100%
rename from tests/modules/csvtk/concat/nextflow.config
rename to tests/modules/nf-core/csvtk/concat/nextflow.config
diff --git a/tests/modules/nf-core/csvtk/concat/test.yml b/tests/modules/nf-core/csvtk/concat/test.yml
new file mode 100644
index 00000000000..08639640589
--- /dev/null
+++ b/tests/modules/nf-core/csvtk/concat/test.yml
@@ -0,0 +1,8 @@
+- name: csvtk concat
+  command: nextflow run ./tests/modules/nf-core/csvtk/concat -entry test_csvtk_concat -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/csvtk/concat/nextflow.config
+  tags:
+    - csvtk
+    - csvtk/concat
+  files:
+    - path: output/csvtk/test.csv
+      md5sum: 917fe5d857f04b58e0f49c384d167cec
diff --git a/tests/modules/nf-core/csvtk/split/main.nf b/tests/modules/nf-core/csvtk/split/main.nf
new file mode 100644
index 00000000000..3d373442ebb
--- /dev/null
+++ b/tests/modules/nf-core/csvtk/split/main.nf
@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CSVTK_SPLIT } from '../../../../../modules/nf-core/csvtk/split/main.nf'
+
+workflow test_csvtk_split_tsv {
+
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['generic']['tsv']['test_tsv'], checkIfExists: true) ]
+    ]
+    in_format = "tsv"
+    out_format = "tsv"
+    CSVTK_SPLIT ( input, in_format, out_format )
+}
+
+workflow test_csvtk_split_csv {
+
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['generic']['csv']['test_csv'], checkIfExists: true) ]
+    ]
+    in_format = "csv"
+    out_format = "csv"
+    CSVTK_SPLIT( input, in_format, out_format )
+}
diff --git a/tests/modules/csvtk/split/nextflow.config b/tests/modules/nf-core/csvtk/split/nextflow.config
similarity index 100%
rename from tests/modules/csvtk/split/nextflow.config
rename to tests/modules/nf-core/csvtk/split/nextflow.config
diff --git a/tests/modules/nf-core/csvtk/split/test.yml b/tests/modules/nf-core/csvtk/split/test.yml
new file mode 100644
index 00000000000..d9b1e85d671
--- /dev/null
+++ b/tests/modules/nf-core/csvtk/split/test.yml
@@ -0,0 +1,25 @@
+- name: csvtk split test_csvtk_split_tsv
+  command: nextflow run ./tests/modules/nf-core/csvtk/split -entry test_csvtk_split_tsv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/csvtk/split/nextflow.config
+  tags:
+    - csvtk/split
+    - csvtk
+  files:
+    - path: output/csvtk/test-Ken.tsv
+      md5sum: 589a2add7f0b8e998d4959e5d883e7d5
+    - path: output/csvtk/test-Rob.tsv
+      md5sum: 6c5555d689c4e685d35d6e394ad6e1e6
+    - path: output/csvtk/test-Robert.tsv
+      md5sum: 45ae6da8111096746d1736d34220a3ec
+
+- name: csvtk split test_csvtk_split_csv
+  command: nextflow run ./tests/modules/nf-core/csvtk/split -entry test_csvtk_split_csv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/csvtk/split/nextflow.config
+  tags:
+    - csvtk/split
+    - csvtk
+  files:
+    - path: output/csvtk/test-Ken.csv
+      md5sum: 71a931dae6f15f5ddb0318c7d4afe81e
+    - path: output/csvtk/test-Rob.csv
+      md5sum: efc4bc507021043a3bf2fb0724c4a216
+    - path: output/csvtk/test-Robert.csv
+      md5sum: 8de2f076e64252c2abed69b9c2a3a386
diff --git a/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf b/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf
new file mode 100644
index 00000000000..33464d2ef51
--- /dev/null
+++ b/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -0,0 +1,55 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTQC                      } from '../../../../../modules/nf-core/fastqc/main.nf'
+include { MULTIQC                     } from '../../../../../modules/nf-core/multiqc/main.nf'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../../modules/nf-core/custom/dumpsoftwareversions/main.nf'
+
+workflow fastqc1 {
+    take:
+    input
+
+    main:
+    FASTQC ( input )
+
+    emit:
+    versions = FASTQC.out.versions
+}
+
+workflow fastqc2 {
+    take:
+    input
+
+    main:
+    FASTQC ( input )
+
+    emit:
+    versions = FASTQC.out.versions
+    zip = FASTQC.out.zip
+}
+
+workflow test_custom_dumpsoftwareversions {
+    input = [
+        [ id: 'test', single_end: false ],
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    // Using subworkflows to ensure that the script can properly handle
+    // cases where subworkflows have a module with the same name.
+    fastqc1 ( input )
+    fastqc2 ( input )
+    MULTIQC ( fastqc2.out.zip.collect { it[1] }, [], [], [] )
+
+    fastqc1
+        .out
+        .versions
+        .mix(fastqc2.out.versions)
+        .mix(MULTIQC.out.versions)
+        .set { ch_software_versions }
+
+    CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
+}
diff --git a/tests/modules/custom/dumpsoftwareversions/nextflow.config b/tests/modules/nf-core/custom/dumpsoftwareversions/nextflow.config
similarity index 100%
rename from tests/modules/custom/dumpsoftwareversions/nextflow.config
rename to tests/modules/nf-core/custom/dumpsoftwareversions/nextflow.config
diff --git a/tests/modules/nf-core/custom/dumpsoftwareversions/test.yml b/tests/modules/nf-core/custom/dumpsoftwareversions/test.yml
new file mode 100644
index 00000000000..7a2fad5a374
--- /dev/null
+++ b/tests/modules/nf-core/custom/dumpsoftwareversions/test.yml
@@ -0,0 +1,14 @@
+- name: custom dumpsoftwareversions
+  command: nextflow run ./tests/modules/nf-core/custom/dumpsoftwareversions -entry test_custom_dumpsoftwareversions -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/dumpsoftwareversions/nextflow.config
+  tags:
+    - custom
+    - custom/dumpsoftwareversions
+  files:
+    - path: output/custom/software_versions.yml
+      contains:
+        - FASTQC
+        - MULTIQC
+      must_not_contain:
+        - fastqc1
+        - fastqc2
+    - path: output/custom/software_versions_mqc.yml
diff --git a/tests/modules/nf-core/custom/getchromsizes/main.nf b/tests/modules/nf-core/custom/getchromsizes/main.nf
new file mode 100644
index 00000000000..94413afcd5d
--- /dev/null
+++ b/tests/modules/nf-core/custom/getchromsizes/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CUSTOM_GETCHROMSIZES } from '../../../../../modules/nf-core/custom/getchromsizes/main.nf'
+
+workflow test_custom_getchromsizes {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    CUSTOM_GETCHROMSIZES ( input )
+}
+
+workflow test_custom_getchromsizes_bgzip {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) ]
+
+    CUSTOM_GETCHROMSIZES ( input )
+}
diff --git a/tests/modules/custom/getchromsizes/nextflow.config b/tests/modules/nf-core/custom/getchromsizes/nextflow.config
similarity index 100%
rename from tests/modules/custom/getchromsizes/nextflow.config
rename to tests/modules/nf-core/custom/getchromsizes/nextflow.config
diff --git a/tests/modules/nf-core/custom/getchromsizes/test.yml b/tests/modules/nf-core/custom/getchromsizes/test.yml
new file mode 100644
index 00000000000..bc870ff9dbf
--- /dev/null
+++ b/tests/modules/nf-core/custom/getchromsizes/test.yml
@@ -0,0 +1,26 @@
+- name: custom getchromsizes
+  command: nextflow run ./tests/modules/nf-core/custom/getchromsizes -entry test_custom_getchromsizes -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/getchromsizes/nextflow.config
+  tags:
+    - custom
+    - custom/getchromsizes
+  files:
+    - path: output/custom/genome.fasta.fai
+      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
+    - path: output/custom/genome.fasta.sizes
+      md5sum: a57c401f27ae5133823fb09fb21c8a3c
+    - path: output/custom/versions.yml
+      md5sum: 3e4a23a0852f4ec34296224d87446d9a
+- name: custom getchromsizes_bgzip
+  command: nextflow run ./tests/modules/nf-core/custom/getchromsizes -entry test_custom_getchromsizes_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/getchromsizes/nextflow.config
+  tags:
+    - custom
+    - custom/getchromsizes
+  files:
+    - path: output/custom/genome.fasta.gz.fai
+      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
+    - path: output/custom/genome.fasta.gz.gzi
+      md5sum: 7dea362b3fac8e00956a4952a3d4f474
+    - path: output/custom/genome.fasta.gz.sizes
+      md5sum: a57c401f27ae5133823fb09fb21c8a3c
+    - path: output/custom/versions.yml
+      md5sum: 22871934dfac30a6109068fd79b2d0ba
diff --git a/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf b/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf
new file mode 100644
index 00000000000..399abb6eaec
--- /dev/null
+++ b/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../../../modules/nf-core/custom/sratoolsncbisettings/main.nf'
+
+workflow test_sratoolsncbisettings_with_good_existing {
+
+    file(params.settings_path).mkdirs()
+    def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+    settings.copyTo(params.settings_file)
+
+    CUSTOM_SRATOOLSNCBISETTINGS()
+}
+
+workflow test_sratoolsncbisettings_with_bad_existing {
+
+    file(params.settings_path).mkdirs()
+    def settings = file(params.settings_file)
+    settings.text = '''
+    ## auto-generated configuration file - DO NOT EDIT ##
+
+    config/default = "false"
+    /repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
+    /repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
+    /repository/user/ad/public/apps/file/volumes/flatAd = "."
+    /repository/user/ad/public/apps/refseq/volumes/refseqAd = "."
+    /repository/user/ad/public/apps/sra/volumes/sraAd = "."
+    /repository/user/ad/public/apps/sraPileup/volumes/ad = "."
+    /repository/user/ad/public/apps/sraRealign/volumes/ad = "."
+    /repository/user/ad/public/apps/wgs/volumes/wgsAd = "."
+    /repository/user/ad/public/root = "."
+    /repository/user/default-path = "/root/ncbi"
+    '''.stripIndent()
+
+    CUSTOM_SRATOOLSNCBISETTINGS()
+}
+
+workflow test_sratoolsncbisettings_with_nonexisting {
+    def settings = file(params.settings_file)
+    settings.delete()
+
+    CUSTOM_SRATOOLSNCBISETTINGS()
+}
diff --git a/tests/modules/custom/sratoolsncbisettings/nextflow.config b/tests/modules/nf-core/custom/sratoolsncbisettings/nextflow.config
similarity index 100%
rename from tests/modules/custom/sratoolsncbisettings/nextflow.config
rename to tests/modules/nf-core/custom/sratoolsncbisettings/nextflow.config
diff --git a/tests/modules/custom/sratoolsncbisettings/nextflow_mount.config b/tests/modules/nf-core/custom/sratoolsncbisettings/nextflow_mount.config
similarity index 100%
rename from tests/modules/custom/sratoolsncbisettings/nextflow_mount.config
rename to tests/modules/nf-core/custom/sratoolsncbisettings/nextflow_mount.config
diff --git a/tests/modules/nf-core/custom/sratoolsncbisettings/test.yml b/tests/modules/nf-core/custom/sratoolsncbisettings/test.yml
new file mode 100644
index 00000000000..beb1580fe0e
--- /dev/null
+++ b/tests/modules/nf-core/custom/sratoolsncbisettings/test.yml
@@ -0,0 +1,44 @@
+- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_good_existing"
+  command: nextflow run ./tests/modules/nf-core/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_good_existing -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/sratoolsncbisettings/nextflow_mount.config
+  tags:
+    - "custom"
+    - "custom/sratoolsncbisettings"
+  files:
+    - path: "output/custom/user-settings.mkfg"
+      md5sum: 955e27aff2c277c2f1f0943a098888c1
+    - path: output/custom/versions.yml
+      contains:
+        - "sratools: 2.11.0"
+
+- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_bad_existing"
+  command: nextflow run ./tests/modules/nf-core/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_bad_existing -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/sratoolsncbisettings/nextflow_mount.config
+  tags:
+    - "custom"
+    - "custom/sratoolsncbisettings"
+  exit_code: 1
+  stdout:
+    contains:
+      - "Command error:"
+      - "missing the required entries"
+      - "/LIBS/GUID"
+      - "/libs/cloud/report_instance_identity"
+      - "Feel free to add the following"
+  files:
+    - path: "output/custom/user-settings.mkfg"
+      should_exist: false
+    - path: output/custom/versions.yml
+      should_exist: false
+
+- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_nonexisting"
+  command: nextflow run ./tests/modules/nf-core/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_nonexisting -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/sratoolsncbisettings/nextflow.config
+  tags:
+    - "custom"
+    - "custom/sratoolsncbisettings"
+  files:
+    - path: "output/custom/user-settings.mkfg"
+      contains:
+        - "/LIBS/GUID"
+        - "/libs/cloud/report_instance_identity"
+    - path: output/custom/versions.yml
+      contains:
+        - "sratools: 2.11.0"
diff --git a/tests/modules/nf-core/cutadapt/main.nf b/tests/modules/nf-core/cutadapt/main.nf
new file mode 100644
index 00000000000..edd1cde1a63
--- /dev/null
+++ b/tests/modules/nf-core/cutadapt/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CUTADAPT } from '../../../../modules/nf-core/cutadapt/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_cutadapt_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    CUTADAPT ( input )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_cutadapt_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    CUTADAPT ( input )
+}
+
diff --git a/tests/modules/cutadapt/nextflow.config b/tests/modules/nf-core/cutadapt/nextflow.config
similarity index 100%
rename from tests/modules/cutadapt/nextflow.config
rename to tests/modules/nf-core/cutadapt/nextflow.config
diff --git a/tests/modules/nf-core/cutadapt/test.yml b/tests/modules/nf-core/cutadapt/test.yml
new file mode 100644
index 00000000000..94c0715b706
--- /dev/null
+++ b/tests/modules/nf-core/cutadapt/test.yml
@@ -0,0 +1,16 @@
+- name: cutadapt single-end
+  command: nextflow run ./tests/modules/nf-core/cutadapt -entry test_cutadapt_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cutadapt/nextflow.config
+  tags:
+    - cutadapt
+  files:
+    - path: ./output/cutadapt/test.cutadapt.log
+    - path: ./output/cutadapt/test.trim.fastq.gz
+
+- name: cutadapt paired-end
+  command: nextflow run ./tests/modules/nf-core/cutadapt -entry test_cutadapt_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cutadapt/nextflow.config
+  tags:
+    - cutadapt
+  files:
+    - path: ./output/cutadapt/test.cutadapt.log
+    - path: ./output/cutadapt/test_1.trim.fastq.gz
+    - path: ./output/cutadapt/test_2.trim.fastq.gz
diff --git a/tests/modules/nf-core/damageprofiler/main.nf b/tests/modules/nf-core/damageprofiler/main.nf
new file mode 100644
index 00000000000..128bc52124f
--- /dev/null
+++ b/tests/modules/nf-core/damageprofiler/main.nf
@@ -0,0 +1,39 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DAMAGEPROFILER } from '../../../../modules/nf-core/damageprofiler/main.nf'
+
+workflow test_damageprofiler {
+
+    input        = [ [ id:'test', single_end:false ], // meta map
+                   [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
+    fasta        = []
+    fai          = []
+    species_list = []
+
+
+    DAMAGEPROFILER ( input, fasta, fai, species_list )
+}
+
+workflow test_damageprofiler_reference {
+
+    input        = [ [ id:'test', single_end:false ], // meta map
+                   [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
+    fasta        = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai          = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    species_list = []
+
+    DAMAGEPROFILER ( input, fasta, fai, species_list )
+}
+
+workflow test_damageprofiler_specieslist {
+
+    input        = [ [ id:'test', single_end:false ], // meta map
+                   [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
+    fasta        = []
+    fai          = []
+    species_list = file(params.test_data['homo_sapiens']['genome']['genome_header'], checkIfExists: true)
+
+    DAMAGEPROFILER ( input, fasta, fai, species_list )
+}
diff --git a/tests/modules/damageprofiler/nextflow.config b/tests/modules/nf-core/damageprofiler/nextflow.config
similarity index 100%
rename from tests/modules/damageprofiler/nextflow.config
rename to tests/modules/nf-core/damageprofiler/nextflow.config
diff --git a/tests/modules/nf-core/damageprofiler/test.yml b/tests/modules/nf-core/damageprofiler/test.yml
new file mode 100644
index 00000000000..bbaa31c0f82
--- /dev/null
+++ b/tests/modules/nf-core/damageprofiler/test.yml
@@ -0,0 +1,77 @@
+- name: damageprofiler test_damageprofiler
+  command: nextflow run ./tests/modules/nf-core/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/damageprofiler/nextflow.config
+  tags:
+    - damageprofiler
+  files:
+    - path: output/damageprofiler/test/3pGtoA_freq.txt
+      md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
+    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
+      md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
+    - path: output/damageprofiler/test/5pCtoT_freq.txt
+      md5sum: 38b5d7c87ec2d8422bc5587095711c5f
+    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
+      md5sum: 05e041ff47e7c6d08ede51f5c81a2464
+    - path: output/damageprofiler/test/DNA_comp_genome.txt
+      md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
+    - path: output/damageprofiler/test/DNA_composition_sample.txt
+      md5sum: 16be9c91a06fa7defee376230b12862f
+    - path: output/damageprofiler/test/DamagePlot.pdf
+    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
+    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
+    - path: output/damageprofiler/test/DamageProfiler.log
+    - path: output/damageprofiler/test/Length_plot.pdf
+    - path: output/damageprofiler/test/Length_plot_combined_data.svg
+    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
+    - path: output/damageprofiler/test/dmgprof.json
+      md5sum: a011a47edaadb3a07527c329a6492570
+    - path: output/damageprofiler/test/editDistance.txt
+      md5sum: 7590dac007633ee11025cc99ec9f009b
+    - path: output/damageprofiler/test/edit_distance.pdf
+    - path: output/damageprofiler/test/edit_distance.svg
+    - path: output/damageprofiler/test/lgdistribution.txt
+      md5sum: 583fd98094de3fb462b133daeaadcf52
+    - path: output/damageprofiler/test/misincorporation.txt
+      md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
+
+- name: damageprofiler test_damageprofiler_reference
+  command: nextflow run ./tests/modules/nf-core/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/damageprofiler/nextflow.config
+  tags:
+    - damageprofiler
+  files:
+    - path: output/damageprofiler/test/3pGtoA_freq.txt
+      md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
+    - path: output/damageprofiler/test/3p_freq_misincorporations.txt
+      md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
+    - path: output/damageprofiler/test/5pCtoT_freq.txt
+      md5sum: 38b5d7c87ec2d8422bc5587095711c5f
+    - path: output/damageprofiler/test/5p_freq_misincorporations.txt
+      md5sum: 05e041ff47e7c6d08ede51f5c81a2464
+    - path: output/damageprofiler/test/DNA_comp_genome.txt
+      md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
+    - path: output/damageprofiler/test/DNA_composition_sample.txt
+      md5sum: 16be9c91a06fa7defee376230b12862f
+    - path: output/damageprofiler/test/DamagePlot.pdf
+    - path: output/damageprofiler/test/DamagePlot_five_prime.svg
+    - path: output/damageprofiler/test/DamagePlot_three_prime.svg
+    - path: output/damageprofiler/test/DamageProfiler.log
+    - path: output/damageprofiler/test/Length_plot.pdf
+    - path: output/damageprofiler/test/Length_plot_combined_data.svg
+    - path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
+    - path: output/damageprofiler/test/dmgprof.json
+      md5sum: a011a47edaadb3a07527c329a6492570
+    - path: output/damageprofiler/test/editDistance.txt
+      md5sum: 7590dac007633ee11025cc99ec9f009b
+    - path: output/damageprofiler/test/edit_distance.pdf
+    - path: output/damageprofiler/test/edit_distance.svg
+    - path: output/damageprofiler/test/lgdistribution.txt
+      md5sum: 583fd98094de3fb462b133daeaadcf52
+    - path: output/damageprofiler/test/misincorporation.txt
+      md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
+
+- name: damageprofiler test_damageprofiler_specieslist
+  command: nextflow run ./tests/modules/nf-core/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/damageprofiler/nextflow.config
+  tags:
+    - damageprofiler
+  files:
+    - path: output/damageprofiler/test/DamageProfiler.log
+      #contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
diff --git a/tests/modules/nf-core/dastool/dastool/main.nf b/tests/modules/nf-core/dastool/dastool/main.nf
new file mode 100644
index 00000000000..efea6dc8436
--- /dev/null
+++ b/tests/modules/nf-core/dastool/dastool/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl = 2
+
+include { METABAT2_METABAT2 } from '../../../../../modules/nf-core/metabat2/metabat2/main.nf'
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf'
+include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../../modules/nf-core/dastool/fastatocontig2bin/main.nf'
+include { DASTOOL_DASTOOL } from '../../../../../modules/nf-core/dastool/dastool/main.nf'
+
+workflow test_dastool_dastool {
+
+    input_depth = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
+
+    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+        .map { it -> [[ id:'test', single_end:false ], it] }
+        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+        .set { input_metabat2 }
+
+    METABAT2_METABAT2 ( input_metabat2 )
+
+    DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
+
+    Channel.of([ [ id:'test', single_end:false ], // meta map
+                      file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)])
+        .join( DASTOOL_FASTATOCONTIG2BIN.out.fastatocontig2bin )
+        .set {input_dastool}
+
+
+    DASTOOL_DASTOOL ( input_dastool, [], [] )
+}
diff --git a/tests/modules/dastool/dastool/nextflow.config b/tests/modules/nf-core/dastool/dastool/nextflow.config
similarity index 100%
rename from tests/modules/dastool/dastool/nextflow.config
rename to tests/modules/nf-core/dastool/dastool/nextflow.config
diff --git a/tests/modules/nf-core/dastool/dastool/test.yml b/tests/modules/nf-core/dastool/dastool/test.yml
new file mode 100644
index 00000000000..de6609ca158
--- /dev/null
+++ b/tests/modules/nf-core/dastool/dastool/test.yml
@@ -0,0 +1,28 @@
+- name: dastool dastool test_dastool_dastool
+  command: nextflow run ./tests/modules/nf-core/dastool/dastool -entry test_dastool_dastool -c ./tests/config/nextflow.config
+  tags:
+    - dastool/dastool
+    - dastool
+  files:
+    - path: output/dastool/test.seqlength
+      md5sum: b815a5811008c36808a59b1d0dcfab24
+    - path: output/dastool/test.tsv
+      md5sum: 6e46c0be14dded7cb13af38f54feea47
+    - path: output/dastool/test_DASTool.log
+    - path: output/dastool/test_DASTool_contig2bin.tsv
+      md5sum: 6e46c0be14dded7cb13af38f54feea47
+    - path: output/dastool/test_DASTool_summary.tsv
+      md5sum: ab9dd3709a59a69bc66030b9e0ff3d5b
+    - path: output/dastool/test_proteins.faa
+    - path: output/dastool/test_proteins.faa.all.b6
+      md5sum: 39c11237ef22ac73109aaac267e185d0
+    - path: output/dastool/test_proteins.faa.archaea.scg
+      md5sum: e79d82eecee25821d1658ea4f082601d
+    - path: output/dastool/test_proteins.faa.bacteria.scg
+      md5sum: 8132cfb17cf398d41c036ead55c96ffe
+    - path: output/dastool/test_proteins.faa.findSCG.b6
+      md5sum: 48e90e12cd6c88d00608777dbc48a82a
+    - path: output/dastool/test_proteins.faa.scg.candidates.faa
+      md5sum: d94b7bed0f8aa9cf2824d72c548c537c
+    - path: output/dastool/versions.yml
+      md5sum: 004e04c6a38652df2e0c59c44e29c9de
diff --git a/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf b/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf
new file mode 100644
index 00000000000..70ea9bdafa8
--- /dev/null
+++ b/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf
@@ -0,0 +1,48 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP                                } from '../../../../../modules/nf-core/gunzip/main.nf'
+include { METABAT2_METABAT2                     } from '../../../../../modules/nf-core/metabat2/metabat2/main.nf'
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS  } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf'
+include { DASTOOL_FASTATOCONTIG2BIN                 } from '../../../../../modules/nf-core/dastool/fastatocontig2bin/main.nf'
+
+workflow test_dastool_fastatocontig2bin {
+
+    input_depth = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
+
+    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+        .map { it -> [[ id:'test', single_end:false ], it] }
+        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+        .set { input_metabat2 }
+
+    METABAT2_METABAT2 ( input_metabat2 )
+
+    DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
+}
+
+workflow test_dastool_fastatocontig2bin_ungzipped {
+
+    input_depth = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+
+    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
+
+    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+        .map { it -> [[ id:'test', single_end:false ], it] }
+        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+        .set { input_metabat2 }
+
+    METABAT2_METABAT2 ( input_metabat2 )
+
+    // TODO test unzipped input files
+    ch_input_2_fastatocontig2bin = GUNZIP( METABAT2_METABAT2.out.fasta  ).gunzip
+
+    DASTOOL_FASTATOCONTIG2BIN ( ch_input_2_fastatocontig2bin, "fa")
+}
diff --git a/tests/modules/dastool/fastatocontig2bin/nextflow.config b/tests/modules/nf-core/dastool/fastatocontig2bin/nextflow.config
similarity index 100%
rename from tests/modules/dastool/fastatocontig2bin/nextflow.config
rename to tests/modules/nf-core/dastool/fastatocontig2bin/nextflow.config
diff --git a/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml b/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml
new file mode 100644
index 00000000000..4333a72594a
--- /dev/null
+++ b/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml
@@ -0,0 +1,20 @@
+- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin
+  command: nextflow run ./tests/modules/nf-core/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin -c ./tests/config/nextflow.config
+  tags:
+    - dastool
+    - dastool/fastatocontig2bin
+  files:
+    - path: output/dastool/test.tsv
+      md5sum: 6e46c0be14dded7cb13af38f54feea47
+    - path: output/dastool/versions.yml
+      md5sum: ff4b6f14bee4548bf09b5e602c306595
+
+- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin_ungzipped
+  command: nextflow run ./tests/modules/nf-core/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin_ungzipped -c ./tests/config/nextflow.config
+  tags:
+    - dastool
+    - dastool/fastatocontig2bin
+  files:
+    - path: output/dastool/test.tsv
+      md5sum: 6e46c0be14dded7cb13af38f54feea47
+    - path: output/dastool/versions.yml
diff --git a/tests/modules/nf-core/dastool/scaffolds2bin/main.nf b/tests/modules/nf-core/dastool/scaffolds2bin/main.nf
new file mode 100644
index 00000000000..272b7abf685
--- /dev/null
+++ b/tests/modules/nf-core/dastool/scaffolds2bin/main.nf
@@ -0,0 +1,48 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP                                } from '../../../../../modules/nf-core/gunzip/main.nf'
+include { METABAT2_METABAT2                     } from '../../../../../modules/nf-core/metabat2/metabat2/main.nf'
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS  } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf'
+include { DASTOOL_SCAFFOLDS2BIN                 } from '../../../../../modules/nf-core/dastool/scaffolds2bin/main.nf'
+
+workflow test_dastool_scaffolds2bin {
+
+    input_depth = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
+
+    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+        .map { it -> [[ id:'test', single_end:false ], it] }
+        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+        .set { input_metabat2 }
+
+    METABAT2_METABAT2 ( input_metabat2 )
+
+    DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
+}
+
+workflow test_dastool_scaffolds2bin_ungzipped {
+
+    input_depth = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+
+    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
+
+    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+        .map { it -> [[ id:'test', single_end:false ], it] }
+        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+        .set { input_metabat2 }
+
+    METABAT2_METABAT2 ( input_metabat2 )
+
+    // TODO test unzipped input files
+    ch_input_2_scaffolds2bin = GUNZIP( METABAT2_METABAT2.out.fasta  ).gunzip
+
+    DASTOOL_SCAFFOLDS2BIN ( ch_input_2_scaffolds2bin, "fa")
+}
diff --git a/tests/modules/dastool/scaffolds2bin/nextflow.config b/tests/modules/nf-core/dastool/scaffolds2bin/nextflow.config
similarity index 100%
rename from tests/modules/dastool/scaffolds2bin/nextflow.config
rename to tests/modules/nf-core/dastool/scaffolds2bin/nextflow.config
diff --git a/tests/modules/nf-core/dastool/scaffolds2bin/test.yml b/tests/modules/nf-core/dastool/scaffolds2bin/test.yml
new file mode 100644
index 00000000000..2dcf828f1ae
--- /dev/null
+++ b/tests/modules/nf-core/dastool/scaffolds2bin/test.yml
@@ -0,0 +1,20 @@
+- name: dastool scaffolds2bin test_dastool_scaffolds2bin
+  command: nextflow run ./tests/modules/nf-core/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c ./tests/config/nextflow.config
+  tags:
+    - dastool
+    - dastool/scaffolds2bin
+  files:
+    - path: output/dastool/test.tsv
+      md5sum: 6e46c0be14dded7cb13af38f54feea47
+    - path: output/dastool/versions.yml
+      md5sum: d0831ed159eb5a1a1565d1d211012ad6
+- name: dastool scaffolds2bin test_dastool_scaffolds2bin_ungzipped
+  command: nextflow run ./tests/modules/nf-core/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c ./tests/config/nextflow.config
+  tags:
+    - dastool
+    - dastool/scaffolds2bin
+  files:
+    - path: output/dastool/test.tsv
+      md5sum: 6e46c0be14dded7cb13af38f54feea47
+    - path: output/dastool/versions.yml
+      md5sum: da58e477b7f4c16a9ea495ec1a4a4d4f
diff --git a/tests/modules/nf-core/dedup/main.nf b/tests/modules/nf-core/dedup/main.nf
new file mode 100644
index 00000000000..0d8b89b9626
--- /dev/null
+++ b/tests/modules/nf-core/dedup/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEDUP } from '../../../../modules/nf-core/dedup/main.nf'
+
+workflow test_dedup {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+
+    DEDUP ( input )
+}
diff --git a/tests/modules/dedup/nextflow.config b/tests/modules/nf-core/dedup/nextflow.config
similarity index 100%
rename from tests/modules/dedup/nextflow.config
rename to tests/modules/nf-core/dedup/nextflow.config
diff --git a/tests/modules/nf-core/dedup/test.yml b/tests/modules/nf-core/dedup/test.yml
new file mode 100644
index 00000000000..0d9445f8fdb
--- /dev/null
+++ b/tests/modules/nf-core/dedup/test.yml
@@ -0,0 +1,13 @@
+- name: dedup test_dedup
+  command: nextflow run ./tests/modules/nf-core/dedup -entry test_dedup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dedup/nextflow.config
+  tags:
+    - dedup
+  files:
+    - path: output/dedup/test.paired_end.dedup.json
+      md5sum: 2def0b54aba1fafa21b274f260de1b6f
+    - path: output/dedup/test.paired_end.hist
+      md5sum: df3492273a1db0d8152e35d9d5e38aa6
+    - path: output/dedup/test.paired_end.log
+      md5sum: 4b8855bd63b2f4b37da4cfb17e61fb00
+    - path: output/dedup/test.paired_end_rmdup.bam
+      md5sum: 8b0408fe3e258989095303a47e5b5061
diff --git a/tests/modules/nf-core/deeparg/downloaddata/main.nf b/tests/modules/nf-core/deeparg/downloaddata/main.nf
new file mode 100644
index 00000000000..eecbdabc8da
--- /dev/null
+++ b/tests/modules/nf-core/deeparg/downloaddata/main.nf
@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPARG_DOWNLOADDATA } from '../../../../../modules/nf-core/deeparg/downloaddata/main.nf'
+
+workflow test_deeparg_downloaddata {
+    DEEPARG_DOWNLOADDATA ( )
+}
diff --git a/tests/modules/deeparg/downloaddata/nextflow.config b/tests/modules/nf-core/deeparg/downloaddata/nextflow.config
similarity index 100%
rename from tests/modules/deeparg/downloaddata/nextflow.config
rename to tests/modules/nf-core/deeparg/downloaddata/nextflow.config
diff --git a/tests/modules/nf-core/deeparg/downloaddata/test.yml b/tests/modules/nf-core/deeparg/downloaddata/test.yml
new file mode 100644
index 00000000000..bae89614206
--- /dev/null
+++ b/tests/modules/nf-core/deeparg/downloaddata/test.yml
@@ -0,0 +1,9 @@
+- name: deeparg downloaddata test_deeparg_downloaddata
+  command: nextflow run ./tests/modules/nf-core/deeparg/downloaddata -entry test_deeparg_downloaddata -c ./tests/config/nextflow.config
+  tags:
+    - deeparg
+    - deeparg/downloaddata
+  files:
+    - path: output/deeparg/db/
+    - path: output/deeparg/db/data/gg13/dataset.rev.2.bt2
+      md5sum: 99d90f132fc2795d5a527ce31f1c4d30
diff --git a/tests/modules/nf-core/deeparg/predict/main.nf b/tests/modules/nf-core/deeparg/predict/main.nf
new file mode 100644
index 00000000000..5037e398d1e
--- /dev/null
+++ b/tests/modules/nf-core/deeparg/predict/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPARG_DOWNLOADDATA } from '../../../../../modules/nf-core/deeparg/downloaddata/main.nf'
+include { DEEPARG_PREDICT      } from '../../../../../modules/nf-core/deeparg/predict/main.nf'
+
+workflow test_deeparg_predict {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
+        'LS'
+    ]
+
+    DEEPARG_DOWNLOADDATA( )
+    DEEPARG_PREDICT ( input, DEEPARG_DOWNLOADDATA.out.db )
+
+}
diff --git a/tests/modules/deeparg/predict/nextflow.config b/tests/modules/nf-core/deeparg/predict/nextflow.config
similarity index 100%
rename from tests/modules/deeparg/predict/nextflow.config
rename to tests/modules/nf-core/deeparg/predict/nextflow.config
diff --git a/tests/modules/nf-core/deeparg/predict/test.yml b/tests/modules/nf-core/deeparg/predict/test.yml
new file mode 100644
index 00000000000..fc8398aa20a
--- /dev/null
+++ b/tests/modules/nf-core/deeparg/predict/test.yml
@@ -0,0 +1,17 @@
+- name: deeparg predict test_deeparg_predict
+  command: nextflow run ./tests/modules/nf-core/deeparg/predict -entry test_deeparg_predict -c ./tests/config/nextflow.config
+  tags:
+    - deeparg/predict
+    - deeparg
+  files:
+    - path: output/deeparg/test.align.daa
+      md5sum: c52d0af8362244f214da25bc45f2bf42
+    - path: output/deeparg/test.align.daa.tsv
+      md5sum: a4aa1da2db98274ede2b927fa8227e5a
+    - path: output/deeparg/test.mapping.ARG
+      md5sum: 0e049e99eab4c55666062df21707d5b9
+    - path: output/deeparg/test.mapping.potential.ARG
+      contains:
+        - "#ARG"
+    - path: output/deeparg/versions.yml
+      md5sum: e848ddab324e8c6fd18eaa6b2656f195
diff --git a/tests/modules/nf-core/deepbgc/download/main.nf b/tests/modules/nf-core/deepbgc/download/main.nf
new file mode 100644
index 00000000000..cfa71428370
--- /dev/null
+++ b/tests/modules/nf-core/deepbgc/download/main.nf
@@ -0,0 +1,10 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPBGC_DOWNLOAD } from '../../../../../modules/nf-core/deepbgc/download/main.nf'
+
+workflow test_deepbgc_download {
+
+    DEEPBGC_DOWNLOAD (  )
+}
diff --git a/tests/modules/deepbgc/download/nextflow.config b/tests/modules/nf-core/deepbgc/download/nextflow.config
similarity index 100%
rename from tests/modules/deepbgc/download/nextflow.config
rename to tests/modules/nf-core/deepbgc/download/nextflow.config
diff --git a/tests/modules/nf-core/deepbgc/download/test.yml b/tests/modules/nf-core/deepbgc/download/test.yml
new file mode 100644
index 00000000000..aa71b99596f
--- /dev/null
+++ b/tests/modules/nf-core/deepbgc/download/test.yml
@@ -0,0 +1,30 @@
+- name: deepbgc download test_deepbgc_download
+  command: nextflow run ./tests/modules/nf-core/deepbgc/download -entry test_deepbgc_download -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/deepbgc/download/nextflow.config
+  tags:
+    - deepbgc
+    - deepbgc/download
+  files:
+    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_activity.pkl
+      md5sum: 90f0c010460e9df882cb057664a49f30
+    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_class.pkl
+      md5sum: f78a2eda240403d2f40643d42202f3ac
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_geneborder.pkl
+      md5sum: ca4be7031ae9f70780f17c616a4fa5b5
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_original.pkl
+      md5sum: 2ca2429bb9bc99a401d1093c376b37aa
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_retrained.pkl
+      md5sum: 65679a3b61c562ff4b84bdb574bb6d93
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/deepbgc.pkl
+      md5sum: 7e9218be79ba45bc9adb23bed3845dc1
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.clans.tsv
+      md5sum: a0a4590ffb2b33b83ef2b28f6ead886b
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm
+      md5sum: 79a3328e4c95b13949a4489b19959fc5
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3f
+      md5sum: cbca323cf8dd4e5e7c109114ec444162
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3i
+      md5sum: 5242332a3f6a60cd1ab634cd9331afd6
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3m
+      md5sum: 1fe946fa2b3bcde1d4b2bad732bce612
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3p
+      md5sum: 27b98a1ded123b6a1ef72db01927017c
diff --git a/tests/modules/nf-core/deepbgc/pipeline/main.nf b/tests/modules/nf-core/deepbgc/pipeline/main.nf
new file mode 100644
index 00000000000..41b103d9e2a
--- /dev/null
+++ b/tests/modules/nf-core/deepbgc/pipeline/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf'
+include { PRODIGAL } from '../../../../modules/nf-core/prodigal/main.nf'
+include { DEEPBGC_DOWNLOAD } from '../../../../../modules/nf-core/deepbgc/download/main.nf'
+include { DEEPBGC_PIPELINE } from '../../../../../modules/nf-core/deepbgc/pipeline/main.nf'
+
+workflow test_deepbgc_pipeline_gbk {
+
+    input = [
+        [ id:'test_gbk', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
+    ]
+
+    DEEPBGC_DOWNLOAD ()
+    GUNZIP ( input )
+    PRODIGAL ( GUNZIP.out.gunzip, 'gbk' )
+    DEEPBGC_PIPELINE ( PRODIGAL.out.gene_annotations, DEEPBGC_DOWNLOAD.out.db )
+}
+
+workflow test_deepbgc_pipeline_fa {
+
+    input = [
+        [ id:'test_fa', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
+    ]
+
+    DEEPBGC_DOWNLOAD ()
+    GUNZIP ( input )
+    DEEPBGC_PIPELINE ( GUNZIP.out.gunzip, DEEPBGC_DOWNLOAD.out.db )
+}
diff --git a/tests/modules/deepbgc/pipeline/nextflow.config b/tests/modules/nf-core/deepbgc/pipeline/nextflow.config
similarity index 100%
rename from tests/modules/deepbgc/pipeline/nextflow.config
rename to tests/modules/nf-core/deepbgc/pipeline/nextflow.config
diff --git a/tests/modules/nf-core/deepbgc/pipeline/test.yml b/tests/modules/nf-core/deepbgc/pipeline/test.yml
new file mode 100644
index 00000000000..0923aad76b7
--- /dev/null
+++ b/tests/modules/nf-core/deepbgc/pipeline/test.yml
@@ -0,0 +1,97 @@
+- name: deepbgc pipeline test_deepbgc_pipeline_gbk
+  command: nextflow run ./tests/modules/nf-core/deepbgc/pipeline -entry test_deepbgc_pipeline_gbk -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/deepbgc/pipeline/nextflow.config
+  tags:
+    - deepbgc/pipeline
+    - deepbgc
+  files:
+    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_activity.pkl
+      md5sum: 90f0c010460e9df882cb057664a49f30
+    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_class.pkl
+      md5sum: f78a2eda240403d2f40643d42202f3ac
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_geneborder.pkl
+      md5sum: ca4be7031ae9f70780f17c616a4fa5b5
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_original.pkl
+      md5sum: 2ca2429bb9bc99a401d1093c376b37aa
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_retrained.pkl
+      md5sum: 65679a3b61c562ff4b84bdb574bb6d93
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/deepbgc.pkl
+      md5sum: 7e9218be79ba45bc9adb23bed3845dc1
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.clans.tsv
+      md5sum: a0a4590ffb2b33b83ef2b28f6ead886b
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm
+      md5sum: 79a3328e4c95b13949a4489b19959fc5
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3f
+      md5sum: cbca323cf8dd4e5e7c109114ec444162
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3i
+      md5sum: 5242332a3f6a60cd1ab634cd9331afd6
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3m
+      md5sum: 1fe946fa2b3bcde1d4b2bad732bce612
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3p
+      md5sum: 27b98a1ded123b6a1ef72db01927017c
+    - path: output/deepbgc/test_gbk/LOG.txt
+      contains: ["Saved DeepBGC result to:"]
+    - path: output/deepbgc/test_gbk/README.txt
+    - path: output/deepbgc/test_gbk/test_gbk.antismash.json
+      md5sum: 7dba3996cf38756b05e7612de8433c23
+    - path: output/deepbgc/test_gbk/test_gbk.bgc.gbk
+    - path: output/deepbgc/test_gbk/test_gbk.full.gbk
+    - path: output/gunzip/test1.contigs.fa
+      md5sum: 80c4d78f2810f6d9e90fa6da9bb9c4f9
+    - path: output/prodigal/test_gbk.faa
+      md5sum: b140ca303ff9ee32e615bfcc4b05038c
+    - path: output/prodigal/test_gbk.fna
+      md5sum: 28232dd696754fb95308874c9528296f
+    - path: output/prodigal/test_gbk.gbk
+      md5sum: b5c309b0296e7cdc21d1e71f33400f20
+    - path: output/prodigal/test_gbk_all.txt
+      md5sum: 8fe56fcf4d9e839e83be7523cd3efa02
+
+- name: deepbgc pipeline test_deepbgc_pipeline_fa
+  command: nextflow run ./tests/modules/nf-core/deepbgc/pipeline -entry test_deepbgc_pipeline_fa -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/deepbgc/pipeline/nextflow.config
+  tags:
+    - deepbgc/pipeline
+    - deepbgc
+  files:
+    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_activity.pkl
+      md5sum: 90f0c010460e9df882cb057664a49f30
+    - path: output/deepbgc/deepbgc_db/0.1.0/classifier/product_class.pkl
+      md5sum: f78a2eda240403d2f40643d42202f3ac
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_geneborder.pkl
+      md5sum: ca4be7031ae9f70780f17c616a4fa5b5
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_original.pkl
+      md5sum: 2ca2429bb9bc99a401d1093c376b37aa
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/clusterfinder_retrained.pkl
+      md5sum: 65679a3b61c562ff4b84bdb574bb6d93
+    - path: output/deepbgc/deepbgc_db/0.1.0/detector/deepbgc.pkl
+      md5sum: 7e9218be79ba45bc9adb23bed3845dc1
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.clans.tsv
+      md5sum: a0a4590ffb2b33b83ef2b28f6ead886b
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm
+      md5sum: 79a3328e4c95b13949a4489b19959fc5
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3f
+      md5sum: cbca323cf8dd4e5e7c109114ec444162
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3i
+      md5sum: 5242332a3f6a60cd1ab634cd9331afd6
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3m
+      md5sum: 1fe946fa2b3bcde1d4b2bad732bce612
+    - path: output/deepbgc/deepbgc_db/common/Pfam-A.31.0.hmm.h3p
+      md5sum: 27b98a1ded123b6a1ef72db01927017c
+    - path: output/deepbgc/test1.contigs/LOG.txt
+      contains: ["Saved DeepBGC result to:"]
+    - path: output/deepbgc/test1.contigs/README.txt
+    - path: output/deepbgc/test1.contigs/evaluation/test1.contigs.bgc.png
+      md5sum: f4a0fc6cd260e2d7ad16f7a1fa103f96
+    - path: output/deepbgc/test1.contigs/evaluation/test1.contigs.score.png
+      md5sum: 572e8882031f667580d8c8e13c2cbb91
+    - path: output/deepbgc/test1.contigs/test1.contigs.antismash.json
+      contains: ['"name": "DeepBGC"']
+    - path: output/deepbgc/test1.contigs/test1.contigs.bgc.gbk
+      md5sum: 7fc70dd034903622dae273bf71b402f2
+    - path: output/deepbgc/test1.contigs/test1.contigs.bgc.tsv
+      contains: ["sequence_id"]
+    - path: output/deepbgc/test1.contigs/test1.contigs.full.gbk
+      contains: ["LOCUS"]
+    - path: output/deepbgc/test1.contigs/test1.contigs.pfam.tsv
+      md5sum: 1179eb4e6df0c83aaeec18d7d34e7524
+    - path: output/gunzip/test1.contigs.fa
+      md5sum: 80c4d78f2810f6d9e90fa6da9bb9c4f9
diff --git a/tests/modules/nf-core/deeptools/bamcoverage/main.nf b/tests/modules/nf-core/deeptools/bamcoverage/main.nf
new file mode 100644
index 00000000000..170476944e8
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/bamcoverage/main.nf
@@ -0,0 +1,41 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPTOOLS_BAMCOVERAGE } from '../../../../../modules/nf-core/deeptools/bamcoverage/main.nf'
+
+workflow test_deeptools_bamcoverage_bam {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+        ]
+
+    DEEPTOOLS_BAMCOVERAGE ( input, [], [] )
+}
+
+workflow test_deeptools_bamcoverage_cram {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+        ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    DEEPTOOLS_BAMCOVERAGE ( input, fasta, fasta_fai)
+}
+
+workflow test_deeptools_bamcoverage_cram_no_fasta_fai {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+        ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    DEEPTOOLS_BAMCOVERAGE ( input, fasta, [])
+}
diff --git a/tests/modules/deeptools/bamcoverage/nextflow.config b/tests/modules/nf-core/deeptools/bamcoverage/nextflow.config
similarity index 100%
rename from tests/modules/deeptools/bamcoverage/nextflow.config
rename to tests/modules/nf-core/deeptools/bamcoverage/nextflow.config
diff --git a/tests/modules/nf-core/deeptools/bamcoverage/test.yml b/tests/modules/nf-core/deeptools/bamcoverage/test.yml
new file mode 100644
index 00000000000..e777e6a87cc
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/bamcoverage/test.yml
@@ -0,0 +1,26 @@
+- name: deeptools bamcoverage test_deeptools_bamcoverage_bam
+  command: nextflow run ./tests/modules/nf-core/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/deeptools/bamcoverage/nextflow.config
+  tags:
+    - deeptools/bamcoverage
+    - deeptools
+  files:
+    - path: output/deeptools/test.bigWig
+      md5sum: 95fe9383a9e6c02aea6b785cf074274f
+
+- name: deeptools bamcoverage test_deeptools_bamcoverage_cram
+  command: nextflow run ./tests/modules/nf-core/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/deeptools/bamcoverage/nextflow.config
+  tags:
+    - deeptools/bamcoverage
+    - deeptools
+  files:
+    - path: output/deeptools/test.bigWig
+      md5sum: 95fe9383a9e6c02aea6b785cf074274f
+
+- name: deeptools bamcoverage test_deeptools_bamcoverage_cram_no_fasta_fai
+  command: nextflow run ./tests/modules/nf-core/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram_no_fasta_fai -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/deeptools/bamcoverage/nextflow.config
+  tags:
+    - deeptools/bamcoverage
+    - deeptools
+  files:
+    - path: output/deeptools/test.bigWig
+      md5sum: 95fe9383a9e6c02aea6b785cf074274f
diff --git a/tests/modules/nf-core/deeptools/computematrix/main.nf b/tests/modules/nf-core/deeptools/computematrix/main.nf
new file mode 100644
index 00000000000..57a2baf20cf
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/computematrix/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPTOOLS_COMPUTEMATRIX } from '../../../../../modules/nf-core/deeptools/computematrix/main.nf'
+
+workflow test_deeptools_computematrix {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_bigwig'], checkIfExists: true)
+            ]
+
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+
+    DEEPTOOLS_COMPUTEMATRIX ( input, bed )
+}
diff --git a/tests/modules/deeptools/computematrix/nextflow.config b/tests/modules/nf-core/deeptools/computematrix/nextflow.config
similarity index 100%
rename from tests/modules/deeptools/computematrix/nextflow.config
rename to tests/modules/nf-core/deeptools/computematrix/nextflow.config
diff --git a/tests/modules/nf-core/deeptools/computematrix/test.yml b/tests/modules/nf-core/deeptools/computematrix/test.yml
new file mode 100644
index 00000000000..b49144f6836
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/computematrix/test.yml
@@ -0,0 +1,9 @@
+- name: deeptools computematrix
+  command: nextflow run ./tests/modules/nf-core/deeptools/computematrix -entry test_deeptools_computematrix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/computematrix/nextflow.config
+  tags:
+    - deeptools
+    - deeptools/computematrix
+  files:
+    - path: output/deeptools/test.computeMatrix.mat.gz
+    - path: output/deeptools/test.computeMatrix.vals.mat.tab
+      md5sum: 19e22051cc44edb7db3e0f8345330d90
diff --git a/tests/modules/nf-core/deeptools/plotfingerprint/main.nf b/tests/modules/nf-core/deeptools/plotfingerprint/main.nf
new file mode 100644
index 00000000000..6b77c173b3d
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/plotfingerprint/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+params.fragment_size = 1000
+
+include { DEEPTOOLS_PLOTFINGERPRINT } from '../../../../../modules/nf-core/deeptools/plotfingerprint/main.nf'
+
+workflow test_deeptools_plotfingerprint {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+            ]
+
+    DEEPTOOLS_PLOTFINGERPRINT ( input )
+}
diff --git a/tests/modules/deeptools/plotfingerprint/nextflow.config b/tests/modules/nf-core/deeptools/plotfingerprint/nextflow.config
similarity index 100%
rename from tests/modules/deeptools/plotfingerprint/nextflow.config
rename to tests/modules/nf-core/deeptools/plotfingerprint/nextflow.config
diff --git a/tests/modules/nf-core/deeptools/plotfingerprint/test.yml b/tests/modules/nf-core/deeptools/plotfingerprint/test.yml
new file mode 100644
index 00000000000..080c595b02c
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/plotfingerprint/test.yml
@@ -0,0 +1,13 @@
+- name: deeptools plotfingerprint
+  command: nextflow run ./tests/modules/nf-core/deeptools/plotfingerprint -entry test_deeptools_plotfingerprint -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/plotfingerprint/nextflow.config
+  tags:
+    - deeptools
+    - deeptools/plotfingerprint
+  files:
+    - path: output/deeptools/test.plotFingerprint.pdf
+    - path: output/deeptools/test.plotFingerprint.qcmetrics.txt
+      contains:
+        - "AUC"
+        - "0.24184576629880325"
+    - path: output/deeptools/test.plotFingerprint.raw.txt
+      md5sum: aff8e53de0ddd893aa9d8f9d4ce7e291
diff --git a/tests/modules/nf-core/deeptools/plotheatmap/main.nf b/tests/modules/nf-core/deeptools/plotheatmap/main.nf
new file mode 100644
index 00000000000..7c178278cbe
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/plotheatmap/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPTOOLS_PLOTHEATMAP } from '../../../../../modules/nf-core/deeptools/plotheatmap/main.nf'
+
+workflow test_deeptools_plotheatmap {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_computematrix_mat_gz'], checkIfExists: true)
+            ]
+
+    DEEPTOOLS_PLOTHEATMAP ( input )
+}
diff --git a/tests/modules/deeptools/plotheatmap/nextflow.config b/tests/modules/nf-core/deeptools/plotheatmap/nextflow.config
similarity index 100%
rename from tests/modules/deeptools/plotheatmap/nextflow.config
rename to tests/modules/nf-core/deeptools/plotheatmap/nextflow.config
diff --git a/tests/modules/nf-core/deeptools/plotheatmap/test.yml b/tests/modules/nf-core/deeptools/plotheatmap/test.yml
new file mode 100644
index 00000000000..eaad3135faa
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/plotheatmap/test.yml
@@ -0,0 +1,8 @@
+- name: deeptools plotheatmap
+  command: nextflow run ./tests/modules/nf-core/deeptools/plotheatmap -entry test_deeptools_plotheatmap -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/plotheatmap/nextflow.config
+  tags:
+    - deeptools
+    - deeptools/plotheatmap
+  files:
+    - path: output/deeptools/test.plotHeatmap.mat.tab
+    - path: output/deeptools/test.plotHeatmap.pdf
diff --git a/tests/modules/nf-core/deeptools/plotprofile/main.nf b/tests/modules/nf-core/deeptools/plotprofile/main.nf
new file mode 100644
index 00000000000..d1bff6276a8
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/plotprofile/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPTOOLS_PLOTPROFILE } from '../../../../../modules/nf-core/deeptools/plotprofile/main.nf'
+
+workflow test_deeptools_plotprofile {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_computematrix_mat_gz'], checkIfExists: true)
+            ]
+
+    DEEPTOOLS_PLOTPROFILE ( input )
+}
diff --git a/tests/modules/deeptools/plotprofile/nextflow.config b/tests/modules/nf-core/deeptools/plotprofile/nextflow.config
similarity index 100%
rename from tests/modules/deeptools/plotprofile/nextflow.config
rename to tests/modules/nf-core/deeptools/plotprofile/nextflow.config
diff --git a/tests/modules/nf-core/deeptools/plotprofile/test.yml b/tests/modules/nf-core/deeptools/plotprofile/test.yml
new file mode 100644
index 00000000000..1c457ab93e3
--- /dev/null
+++ b/tests/modules/nf-core/deeptools/plotprofile/test.yml
@@ -0,0 +1,9 @@
+- name: deeptools plotprofile
+  command: nextflow run ./tests/modules/nf-core/deeptools/plotprofile -entry test_deeptools_plotprofile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/plotprofile/nextflow.config
+  tags:
+    - deeptools
+    - deeptools/plotprofile
+  files:
+    - path: output/deeptools/test.plotProfile.pdf
+    - path: output/deeptools/test.plotProfile.tab
+      md5sum: d561cb659a292cef973ea631c7d440cb
diff --git a/tests/modules/nf-core/deepvariant/main.nf b/tests/modules/nf-core/deepvariant/main.nf
new file mode 100644
index 00000000000..f6fb857c848
--- /dev/null
+++ b/tests/modules/nf-core/deepvariant/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPVARIANT                          } from '../../../../modules/nf-core/deepvariant/main.nf'
+include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../../modules/nf-core/deepvariant/main.nf'
+
+workflow test_deepvariant {
+
+    bam_tuple_ch = Channel.of([ [ id:'test', single_end:false ], // meta map
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                               []
+                                ])
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    DEEPVARIANT ( bam_tuple_ch, fasta, fai)
+}
+
+workflow test_deepvariant_cram_intervals {
+
+    cram_tuple_ch = Channel.of([[ id:'test', single_end:false ], // meta map
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                               file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                            ])
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    DEEPVARIANT_INTERVALS ( cram_tuple_ch, fasta, fai)
+}
diff --git a/tests/modules/deepvariant/nextflow.config b/tests/modules/nf-core/deepvariant/nextflow.config
similarity index 100%
rename from tests/modules/deepvariant/nextflow.config
rename to tests/modules/nf-core/deepvariant/nextflow.config
diff --git a/tests/modules/nf-core/deepvariant/test.yml b/tests/modules/nf-core/deepvariant/test.yml
new file mode 100644
index 00000000000..e5901cb743f
--- /dev/null
+++ b/tests/modules/nf-core/deepvariant/test.yml
@@ -0,0 +1,23 @@
+- name: deepvariant test_deepvariant
+  command: nextflow run ./tests/modules/nf-core/deepvariant -entry test_deepvariant -c ./tests/config/nextflow.config
+  tags:
+    - deepvariant
+  files:
+    - path: output/deepvariant/test_out.g.vcf.gz
+      md5sum: c4c65a3eaf62d6fbe0aba0a414318c8d
+    - path: output/deepvariant/test_out.vcf.gz
+      md5sum: ad964f68ac1d1b2720a9a4e0b6a3a389
+    - path: output/deepvariant/versions.yml
+      md5sum: 51572055ca5c07fc4001b25a9c273bf8
+
+- name: deepvariant test_deepvariant_cram_intervals
+  command: nextflow run ./tests/modules/nf-core/deepvariant -entry test_deepvariant_cram_intervals -c ./tests/config/nextflow.config
+  tags:
+    - deepvariant
+  files:
+    - path: output/deepvariant/test_out.g.vcf.gz
+      md5sum: c4c65a3eaf62d6fbe0aba0a414318c8d
+    - path: output/deepvariant/test_out.vcf.gz
+      md5sum: ad964f68ac1d1b2720a9a4e0b6a3a389
+    - path: output/deepvariant/versions.yml
+      md5sum: 7d9293db0d44423b114abc7116feb967
diff --git a/tests/modules/nf-core/delly/call/main.nf b/tests/modules/nf-core/delly/call/main.nf
new file mode 100644
index 00000000000..8be4b492c1f
--- /dev/null
+++ b/tests/modules/nf-core/delly/call/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DELLY_CALL } from '../../../../../modules/nf-core/delly/call/main.nf'
+
+workflow test_delly_call_bam {
+    input     = [ [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                    []
+                ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    DELLY_CALL ( input, fasta, fai )
+}
+
+workflow test_delly_call_cram {
+    input     = [ [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                    []
+                ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    DELLY_CALL ( input, fasta, fai )
+}
+
+workflow test_delly_call_exclude_regions {
+    input     = [ [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+                ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    DELLY_CALL ( input, fasta, fai )
+}
diff --git a/tests/modules/delly/call/nextflow.config b/tests/modules/nf-core/delly/call/nextflow.config
similarity index 100%
rename from tests/modules/delly/call/nextflow.config
rename to tests/modules/nf-core/delly/call/nextflow.config
diff --git a/tests/modules/nf-core/delly/call/test.yml b/tests/modules/nf-core/delly/call/test.yml
new file mode 100644
index 00000000000..0b1564c12a6
--- /dev/null
+++ b/tests/modules/nf-core/delly/call/test.yml
@@ -0,0 +1,32 @@
+- name: delly call test_delly_call_bam
+  command: nextflow run ./tests/modules/nf-core/delly/call -entry test_delly_call_bam -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/delly/call/nextflow.config
+  tags:
+    - delly
+    - delly/call
+  files:
+    - path: output/delly/test.bcf
+      md5sum: 82be17d3b18b80ef5f37627bb579b07b
+    - path: output/delly/test.bcf.csi
+      md5sum: c198abfc14584c5ac69c004057927e0b
+
+- name: delly call test_delly_call_cram
+  command: nextflow run ./tests/modules/nf-core/delly/call -entry test_delly_call_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/delly/call/nextflow.config
+  tags:
+    - delly
+    - delly/call
+  files:
+    - path: output/delly/test.bcf
+      md5sum: 4f6ae6b5800ae824ba35674f2903cd5c
+    - path: output/delly/test.bcf.csi
+      md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271
+
+- name: delly call test_delly_call_exclude_regions
+  command: nextflow run ./tests/modules/nf-core/delly/call -entry test_delly_call_exclude_regions -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/delly/call/nextflow.config
+  tags:
+    - delly
+    - delly/call
+  files:
+    - path: output/delly/test.bcf
+      md5sum: 4f6ae6b5800ae824ba35674f2903cd5c
+    - path: output/delly/test.bcf.csi
+      md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271
diff --git a/tests/modules/nf-core/diamond/blastp/main.nf b/tests/modules/nf-core/diamond/blastp/main.nf
new file mode 100644
index 00000000000..0e890f5a5a0
--- /dev/null
+++ b/tests/modules/nf-core/diamond/blastp/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DIAMOND_MAKEDB } from '../../../../../modules/nf-core/diamond/makedb/main.nf'
+include { DIAMOND_BLASTP } from '../../../../../modules/nf-core/diamond/blastp/main.nf'
+
+workflow test_diamond_blastp {
+
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    out_ext = 'txt'
+    blast_columns = 'qseqid qlen'
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
+}
+
+workflow test_diamond_blastp_daa {
+
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    out_ext = 'daa'
+    blast_columns = []
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
+}
diff --git a/tests/modules/diamond/blastp/nextflow.config b/tests/modules/nf-core/diamond/blastp/nextflow.config
similarity index 100%
rename from tests/modules/diamond/blastp/nextflow.config
rename to tests/modules/nf-core/diamond/blastp/nextflow.config
diff --git a/tests/modules/nf-core/diamond/blastp/test.yml b/tests/modules/nf-core/diamond/blastp/test.yml
new file mode 100644
index 00000000000..910a464c43d
--- /dev/null
+++ b/tests/modules/nf-core/diamond/blastp/test.yml
@@ -0,0 +1,17 @@
+- name: diamond blastp test_diamond_blastp
+  command: nextflow run ./tests/modules/nf-core/diamond/blastp -entry test_diamond_blastp -c ./tests/config/nextflow.config
+  tags:
+    - diamond/blastp
+    - diamond
+  files:
+    - path: output/diamond/test.diamond_blastp.txt
+    - path: output/diamond/versions.yml
+
+- name: diamond blastp test_diamond_blastp_daa
+  command: nextflow run ./tests/modules/nf-core/diamond/blastp -entry test_diamond_blastp_daa -c ./tests/config/nextflow.config
+  tags:
+    - diamond/blastp
+    - diamond
+  files:
+    - path: output/diamond/test.diamond_blastp.daa
+    - path: output/diamond/versions.yml
diff --git a/tests/modules/nf-core/diamond/blastx/main.nf b/tests/modules/nf-core/diamond/blastx/main.nf
new file mode 100644
index 00000000000..5fdc8e63c7e
--- /dev/null
+++ b/tests/modules/nf-core/diamond/blastx/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DIAMOND_MAKEDB } from '../../../../../modules/nf-core/diamond/makedb/main.nf'
+include { DIAMOND_BLASTX } from '../../../../../modules/nf-core/diamond/blastx/main.nf'
+
+workflow test_diamond_blastx {
+
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    out_ext = 'tfdfdt'  // Nonsense file extension to check default case.
+    blast_columns = 'qseqid qlen'
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
+}
+
+workflow test_diamond_blastx_daa {
+
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    out_ext = 'daa'
+    blast_columns = []
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
+}
diff --git a/tests/modules/diamond/blastx/nextflow.config b/tests/modules/nf-core/diamond/blastx/nextflow.config
similarity index 100%
rename from tests/modules/diamond/blastx/nextflow.config
rename to tests/modules/nf-core/diamond/blastx/nextflow.config
diff --git a/tests/modules/nf-core/diamond/blastx/test.yml b/tests/modules/nf-core/diamond/blastx/test.yml
new file mode 100644
index 00000000000..adbdff9a14c
--- /dev/null
+++ b/tests/modules/nf-core/diamond/blastx/test.yml
@@ -0,0 +1,21 @@
+- name: diamond blastx test_diamond_blastx
+  command: nextflow run ./tests/modules/nf-core/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/diamond/blastx/nextflow.config
+  tags:
+    - diamond
+    - diamond/blastx
+  files:
+    - path: output/diamond/proteome.fasta.dmnd
+    - path: output/diamond/test.diamond_blastx.log
+      contains: ["queries aligned"]
+    - path: output/diamond/test.diamond_blastx.txt
+
+- name: diamond blastx test_diamond_blastx_daa
+  command: nextflow run ./tests/modules/nf-core/diamond/blastx -entry test_diamond_blastx_daa -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/diamond/blastx/nextflow.config
+  tags:
+    - diamond
+    - diamond/blastx
+  files:
+    - path: output/diamond/proteome.fasta.dmnd
+    - path: output/diamond/test.diamond_blastx.daa
+    - path: output/diamond/test.diamond_blastx.log
+      contains: ["queries aligned"]
diff --git a/tests/modules/nf-core/diamond/makedb/main.nf b/tests/modules/nf-core/diamond/makedb/main.nf
new file mode 100644
index 00000000000..6276ba4733c
--- /dev/null
+++ b/tests/modules/nf-core/diamond/makedb/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DIAMOND_MAKEDB } from '../../../../../modules/nf-core/diamond/makedb/main.nf'
+
+workflow test_diamond_makedb {
+
+    input = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+
+    DIAMOND_MAKEDB ( input )
+}
diff --git a/tests/modules/diamond/makedb/nextflow.config b/tests/modules/nf-core/diamond/makedb/nextflow.config
similarity index 100%
rename from tests/modules/diamond/makedb/nextflow.config
rename to tests/modules/nf-core/diamond/makedb/nextflow.config
diff --git a/tests/modules/nf-core/diamond/makedb/test.yml b/tests/modules/nf-core/diamond/makedb/test.yml
new file mode 100644
index 00000000000..e62ccc2c8eb
--- /dev/null
+++ b/tests/modules/nf-core/diamond/makedb/test.yml
@@ -0,0 +1,9 @@
+- name: diamond makedb test_diamond_makedb
+  command: nextflow run ./tests/modules/nf-core/diamond/makedb -entry test_diamond_makedb -c ./tests/config/nextflow.config
+  tags:
+    - diamond/makedb
+    - diamond
+  files:
+    - path: output/diamond/proteome.fasta.dmnd
+      md5sum: fc28c50b202dd7a7c5451cddff2ba1f4
+    - path: output/diamond/versions.yml
diff --git a/tests/modules/nf-core/dragmap/align/main.nf b/tests/modules/nf-core/dragmap/align/main.nf
new file mode 100644
index 00000000000..55d47fa5c4e
--- /dev/null
+++ b/tests/modules/nf-core/dragmap/align/main.nf
@@ -0,0 +1,60 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DRAGMAP_HASHTABLE } from '../../../../../modules/nf-core/dragmap/hashtable/main.nf'
+include { DRAGMAP_ALIGN     } from '../../../../../modules/nf-core/dragmap/align/main.nf'
+
+workflow test_dragmap_align_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    DRAGMAP_HASHTABLE ( fasta )
+    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
+}
+
+workflow test_dragmap_align_single_end_sort {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    DRAGMAP_HASHTABLE ( fasta )
+    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
+}
+
+workflow test_dragmap_align_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    DRAGMAP_HASHTABLE ( fasta )
+    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
+}
+
+workflow test_dragmap_align_paired_end_sort {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    DRAGMAP_HASHTABLE ( fasta )
+    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
+}
diff --git a/tests/modules/dragmap/align/nextflow.config b/tests/modules/nf-core/dragmap/align/nextflow.config
similarity index 100%
rename from tests/modules/dragmap/align/nextflow.config
rename to tests/modules/nf-core/dragmap/align/nextflow.config
diff --git a/tests/modules/nf-core/dragmap/align/test.yml b/tests/modules/nf-core/dragmap/align/test.yml
new file mode 100644
index 00000000000..bfc23508118
--- /dev/null
+++ b/tests/modules/nf-core/dragmap/align/test.yml
@@ -0,0 +1,35 @@
+- name: dragmap align single-end
+  command: nextflow run ./tests/modules/nf-core/dragmap/align -entry test_dragmap_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/align/nextflow.config
+  tags:
+    - dragmap
+    - dragmap/align
+  files:
+    - path: output/dragmap/test.bam
+    - path: output/dragmap/test.dragmap.log
+
+- name: dragmap align single-end_sort
+  command: nextflow run ./tests/modules/nf-core/dragmap/align -entry test_dragmap_align_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/align/nextflow.config
+  tags:
+    - dragmap
+    - dragmap/align
+  files:
+    - path: output/dragmap/test.bam
+    - path: output/dragmap/test.dragmap.log
+
+- name: dragmap align paired-end
+  command: nextflow run ./tests/modules/nf-core/dragmap/align -entry test_dragmap_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/align/nextflow.config
+  tags:
+    - dragmap
+    - dragmap/align
+  files:
+    - path: output/dragmap/test.bam
+    - path: output/dragmap/test.dragmap.log
+
+- name: dragmap align paired-end_sort
+  command: nextflow run ./tests/modules/nf-core/dragmap/align -entry test_dragmap_align_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/align/nextflow.config
+  tags:
+    - dragmap
+    - dragmap/align
+  files:
+    - path: output/dragmap/test.bam
+    - path: output/dragmap/test.dragmap.log
diff --git a/tests/modules/nf-core/dragmap/hashtable/main.nf b/tests/modules/nf-core/dragmap/hashtable/main.nf
new file mode 100644
index 00000000000..7e72f66f828
--- /dev/null
+++ b/tests/modules/nf-core/dragmap/hashtable/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DRAGMAP_HASHTABLE } from '../../../../../modules/nf-core/dragmap/hashtable/main.nf'
+
+workflow test_dragmap_hashtable {
+    
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    DRAGMAP_HASHTABLE ( fasta )
+}
+
+// TODO Add test using alt-masked bed file
+// https://github.com/Illumina/dragmap#build-hash-table-using-an-alt-masked-bed-file
diff --git a/tests/modules/dragmap/hashtable/nextflow.config b/tests/modules/nf-core/dragmap/hashtable/nextflow.config
similarity index 100%
rename from tests/modules/dragmap/hashtable/nextflow.config
rename to tests/modules/nf-core/dragmap/hashtable/nextflow.config
diff --git a/tests/modules/nf-core/dragmap/hashtable/test.yml b/tests/modules/nf-core/dragmap/hashtable/test.yml
new file mode 100644
index 00000000000..553799047b2
--- /dev/null
+++ b/tests/modules/nf-core/dragmap/hashtable/test.yml
@@ -0,0 +1,19 @@
+- name: dragmap hashtable
+  command: nextflow run ./tests/modules/nf-core/dragmap/hashtable -entry test_dragmap_hashtable -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/hashtable/nextflow.config
+  tags:
+    - dragmap
+    - dragmap/hashtable
+  files:
+    - path: output/dragmap/dragmap/hash_table.cfg
+    - path: output/dragmap/dragmap/hash_table.cfg.bin
+    - path: output/dragmap/dragmap/hash_table.cmp
+      md5sum: bc210e5358fd65656f9aea297b59ec7d
+    - path: output/dragmap/dragmap/hash_table_stats.txt
+    - path: output/dragmap/dragmap/reference.bin
+      md5sum: b6b5c12a42416b990cd2844de8f33c5d
+    - path: output/dragmap/dragmap/ref_index.bin
+      md5sum: 8470be9566ecee77eb4aea6a38922a66
+    - path: output/dragmap/dragmap/repeat_mask.bin
+      md5sum: 2439259a2fd32a1d0f4c53d585f3da3a
+    - path: output/dragmap/dragmap/str_table.bin
+      md5sum: 302e2b30993973527e69c6bcd1f093d0
diff --git a/tests/modules/nf-core/dragonflye/main.nf b/tests/modules/nf-core/dragonflye/main.nf
new file mode 100644
index 00000000000..a52287c1c25
--- /dev/null
+++ b/tests/modules/nf-core/dragonflye/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DRAGONFLYE  } from '../../../../modules/nf-core/dragonflye/main.nf'
+include { DRAGONFLYE as DRAGONFLYE_RAVEN   } from '../../../../modules/nf-core/dragonflye/main.nf'
+
+workflow test_dragonflye {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("https://github.com/nf-core/test-datasets/raw/bacass/nanopore/subset15000.fq.gz", checkIfExists: true) ]
+            ]
+
+    DRAGONFLYE ( input )
+}
+
+workflow test_dragonflye_raven {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("https://github.com/nf-core/test-datasets/raw/bacass/nanopore/subset15000.fq.gz", checkIfExists: true) ]
+            ]
+
+    DRAGONFLYE_RAVEN ( input )
+}
diff --git a/tests/modules/dragonflye/nextflow.config b/tests/modules/nf-core/dragonflye/nextflow.config
similarity index 100%
rename from tests/modules/dragonflye/nextflow.config
rename to tests/modules/nf-core/dragonflye/nextflow.config
diff --git a/tests/modules/nf-core/dragonflye/test.yml b/tests/modules/nf-core/dragonflye/test.yml
new file mode 100644
index 00000000000..47a3ce8d41f
--- /dev/null
+++ b/tests/modules/nf-core/dragonflye/test.yml
@@ -0,0 +1,25 @@
+- name: dragonflye with miniasm
+  command: nextflow run ./tests/modules/nf-core/dragonflye -entry test_dragonflye -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragonflye/nextflow.config
+  tags:
+    - dragonflye
+  files:
+    - path: output/dragonflye/miniasm.fasta
+      md5sum: 6b8903ba09592df99f43ed05fda488f6
+    - path: output/dragonflye/miniasm-unpolished.gfa
+      md5sum: 40ab03a417eafab0cb4ac2c32bd006e1
+    # MD5sum not reproducible (timestamp, contig order)
+    - path: output/dragonflye/contigs.fa
+    - path: output/dragonflye/dragonflye.log
+
+- name: dragonflye with raven
+  command: nextflow run ./tests/modules/nf-core/dragonflye -entry test_dragonflye_raven -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragonflye/nextflow.config
+  tags:
+    - dragonflye
+  files:
+    - path: output/dragonflye/raven.fasta
+      md5sum: bd4ba5b0dda110a7ccbea9581c97a898
+    - path: output/dragonflye/raven-unpolished.gfa
+      md5sum: 62c21791dbf9b2c7375dc52d7bab5be2
+    # MD5sum not reproducible (timestamp, contig order)
+    - path: output/dragonflye/contigs.fa
+    - path: output/dragonflye/dragonflye.log
diff --git a/tests/modules/nf-core/dshbio/exportsegments/main.nf b/tests/modules/nf-core/dshbio/exportsegments/main.nf
new file mode 100644
index 00000000000..2d1a3d98d4c
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/exportsegments/main.nf
@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DSHBIO_EXPORTSEGMENTS } from '../../../../../modules/nf-core/dshbio/exportsegments/main.nf'
+
+workflow test_dshbio_exportsegments {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_EXPORTSEGMENTS ( input )
+}
+
+workflow test_dshbio_exportsegments_bgz {
+    input = [ [ id:'test_bgz' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa_bgz'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_EXPORTSEGMENTS ( input )
+}
+
+workflow test_dshbio_exportsegments_gz {
+    input = [ [ id:'test_gz' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa_gz'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_EXPORTSEGMENTS ( input )
+}
+
+workflow test_dshbio_exportsegments_zst {
+    input = [ [ id:'test_zst' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa_zst'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_EXPORTSEGMENTS ( input )
+}
diff --git a/tests/modules/dshbio/exportsegments/nextflow.config b/tests/modules/nf-core/dshbio/exportsegments/nextflow.config
similarity index 100%
rename from tests/modules/dshbio/exportsegments/nextflow.config
rename to tests/modules/nf-core/dshbio/exportsegments/nextflow.config
diff --git a/tests/modules/nf-core/dshbio/exportsegments/test.yml b/tests/modules/nf-core/dshbio/exportsegments/test.yml
new file mode 100644
index 00000000000..aaf46bd6eb7
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/exportsegments/test.yml
@@ -0,0 +1,35 @@
+- name: dshbio exportsegments
+  command: nextflow run ./tests/modules/nf-core/dshbio/exportsegments -entry test_dshbio_exportsegments -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/exportsegments/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/exportsegments
+  files:
+    - path: ./output/dshbio/test.fa.gz
+      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
+
+- name: dshbio exportsegments bgz
+  command: nextflow run ./tests/modules/nf-core/dshbio/exportsegments -entry test_dshbio_exportsegments_bgz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/exportsegments/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/exportsegments
+  files:
+    - path: ./output/dshbio/test_bgz.fa.gz
+      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
+
+- name: dshbio exportsegments gz
+  command: nextflow run ./tests/modules/nf-core/dshbio/exportsegments -entry test_dshbio_exportsegments_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/exportsegments/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/exportsegments
+  files:
+    - path: ./output/dshbio/test_gz.fa.gz
+      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
+
+- name: dshbio exportsegments zst
+  command: nextflow run ./tests/modules/nf-core/dshbio/exportsegments -entry test_dshbio_exportsegments_zst -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/exportsegments/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/exportsegments
+  files:
+    - path: ./output/dshbio/test_zst.fa.gz
+      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
diff --git a/tests/modules/nf-core/dshbio/filterbed/main.nf b/tests/modules/nf-core/dshbio/filterbed/main.nf
new file mode 100644
index 00000000000..9b0313fe42c
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/filterbed/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DSHBIO_FILTERBED } from '../../../../../modules/nf-core/dshbio/filterbed/main.nf'
+
+workflow test_dshbio_filterbed {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_FILTERBED ( input )
+}
diff --git a/tests/modules/dshbio/filterbed/nextflow.config b/tests/modules/nf-core/dshbio/filterbed/nextflow.config
similarity index 100%
rename from tests/modules/dshbio/filterbed/nextflow.config
rename to tests/modules/nf-core/dshbio/filterbed/nextflow.config
diff --git a/tests/modules/nf-core/dshbio/filterbed/test.yml b/tests/modules/nf-core/dshbio/filterbed/test.yml
new file mode 100644
index 00000000000..5c87e42926d
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/filterbed/test.yml
@@ -0,0 +1,8 @@
+- name: dshbio filterbed
+  command: nextflow run ./tests/modules/nf-core/dshbio/filterbed -entry test_dshbio_filterbed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/filterbed/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/filterbed
+  files:
+    - path: ./output/dshbio/test.filtered.bed.gz
+      md5sum: 163be0a88c70ca629fd516dbaadad96a
diff --git a/tests/modules/nf-core/dshbio/filtergff3/main.nf b/tests/modules/nf-core/dshbio/filtergff3/main.nf
new file mode 100644
index 00000000000..5d679b77a6d
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/filtergff3/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DSHBIO_FILTERGFF3 } from '../../../../../modules/nf-core/dshbio/filtergff3/main.nf'
+
+workflow test_dshbio_filtergff3 {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_FILTERGFF3 ( input )
+}
diff --git a/tests/modules/dshbio/filtergff3/nextflow.config b/tests/modules/nf-core/dshbio/filtergff3/nextflow.config
similarity index 100%
rename from tests/modules/dshbio/filtergff3/nextflow.config
rename to tests/modules/nf-core/dshbio/filtergff3/nextflow.config
diff --git a/tests/modules/nf-core/dshbio/filtergff3/test.yml b/tests/modules/nf-core/dshbio/filtergff3/test.yml
new file mode 100644
index 00000000000..0a649dc1571
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/filtergff3/test.yml
@@ -0,0 +1,8 @@
+- name: dshbio filtergff3
+  command: nextflow run ./tests/modules/nf-core/dshbio/filtergff3 -entry test_dshbio_filtergff3 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/filtergff3/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/filtergff3
+  files:
+    - path: ./output/dshbio/test.filtered.gff3.gz
+      md5sum: 89d320cf91c0ca8fd200cfa9688954e3
diff --git a/tests/modules/nf-core/dshbio/splitbed/main.nf b/tests/modules/nf-core/dshbio/splitbed/main.nf
new file mode 100644
index 00000000000..bc9bd7acbeb
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/splitbed/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DSHBIO_SPLITBED } from '../../../../../modules/nf-core/dshbio/splitbed/main.nf'
+
+workflow test_dshbio_splitbed {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_SPLITBED ( input )
+}
diff --git a/tests/modules/dshbio/splitbed/nextflow.config b/tests/modules/nf-core/dshbio/splitbed/nextflow.config
similarity index 100%
rename from tests/modules/dshbio/splitbed/nextflow.config
rename to tests/modules/nf-core/dshbio/splitbed/nextflow.config
diff --git a/tests/modules/nf-core/dshbio/splitbed/test.yml b/tests/modules/nf-core/dshbio/splitbed/test.yml
new file mode 100644
index 00000000000..6d0a8ee654e
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/splitbed/test.yml
@@ -0,0 +1,10 @@
+- name: dshbio splitbed
+  command: nextflow run ./tests/modules/nf-core/dshbio/splitbed -entry test_dshbio_splitbed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/splitbed/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/splitbed
+  files:
+    - path: ./output/dshbio/test.1.bed.gz
+      md5sum: 967ba338f361740eb015304003ababe7
+    - path: ./output/dshbio/test.0.bed.gz
+      md5sum: 8b884d8cf5c57955f218f1c6dbf02d54
diff --git a/tests/modules/nf-core/dshbio/splitgff3/main.nf b/tests/modules/nf-core/dshbio/splitgff3/main.nf
new file mode 100644
index 00000000000..4cdc70f6701
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/splitgff3/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DSHBIO_SPLITGFF3 } from '../../../../../modules/nf-core/dshbio/splitgff3/main.nf'
+
+workflow test_dshbio_splitgff3 {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_SPLITGFF3 ( input )
+}
diff --git a/tests/modules/dshbio/splitgff3/nextflow.config b/tests/modules/nf-core/dshbio/splitgff3/nextflow.config
similarity index 100%
rename from tests/modules/dshbio/splitgff3/nextflow.config
rename to tests/modules/nf-core/dshbio/splitgff3/nextflow.config
diff --git a/tests/modules/nf-core/dshbio/splitgff3/test.yml b/tests/modules/nf-core/dshbio/splitgff3/test.yml
new file mode 100644
index 00000000000..1302afd42ee
--- /dev/null
+++ b/tests/modules/nf-core/dshbio/splitgff3/test.yml
@@ -0,0 +1,10 @@
+- name: dshbio splitgff3
+  command: nextflow run ./tests/modules/nf-core/dshbio/splitgff3 -entry test_dshbio_splitgff3 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/splitgff3/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/splitgff3
+  files:
+    - path: ./output/dshbio/test.1.gff3.gz
+      md5sum: 0742895e81fe080c01f43f9dd616baae
+    - path: ./output/dshbio/test.0.gff3.gz
+      md5sum: 9aed611b89093f5e0db4e63cb56d8416
diff --git a/tests/modules/nf-core/ectyper/main.nf b/tests/modules/nf-core/ectyper/main.nf
new file mode 100644
index 00000000000..4f23616e918
--- /dev/null
+++ b/tests/modules/nf-core/ectyper/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ECTYPER } from '../../../../modules/nf-core/ectyper/main.nf'
+
+workflow test_ectyper {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    ECTYPER ( input )
+}
diff --git a/tests/modules/ectyper/nextflow.config b/tests/modules/nf-core/ectyper/nextflow.config
similarity index 100%
rename from tests/modules/ectyper/nextflow.config
rename to tests/modules/nf-core/ectyper/nextflow.config
diff --git a/tests/modules/nf-core/ectyper/test.yml b/tests/modules/nf-core/ectyper/test.yml
new file mode 100644
index 00000000000..16970b3d3c5
--- /dev/null
+++ b/tests/modules/nf-core/ectyper/test.yml
@@ -0,0 +1,11 @@
+- name: ectyper test_ectyper
+  command: nextflow run ./tests/modules/nf-core/ectyper -entry test_ectyper -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ectyper/nextflow.config
+  tags:
+    - ectyper
+  files:
+    - path: output/ectyper/blast_output_alleles.txt
+      md5sum: 27f3f5e84f7da451b2948d61589cdb06
+    - path: output/ectyper/ectyper.log
+      contains: ["Serotype", "RefSeq", "O-type", "finished"]
+    - path: output/ectyper/test.tsv
+      md5sum: ba923d7c7ee7d1047466aafc9a9df208
diff --git a/tests/modules/nf-core/eido/convert/main.nf b/tests/modules/nf-core/eido/convert/main.nf
new file mode 100644
index 00000000000..6af8cff274b
--- /dev/null
+++ b/tests/modules/nf-core/eido/convert/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EIDO_CONVERT } from '../../../../../modules/nf-core/eido/convert/main.nf'
+
+workflow test_eido_convert_nextflow_samplesheet {
+
+    nextflow_samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
+    format = "csv"
+    pep_input_base_dir = []
+
+    EIDO_CONVERT ( nextflow_samplesheet, format, pep_input_base_dir )
+}
+
+
+workflow test_eido_convert_pep_project {
+
+    pep_project = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
+    format = "csv"
+    pep_input_base_dir = []
+
+    EIDO_CONVERT ( pep_project, format, pep_input_base_dir )
+}
diff --git a/tests/modules/eido/convert/nextflow.config b/tests/modules/nf-core/eido/convert/nextflow.config
similarity index 100%
rename from tests/modules/eido/convert/nextflow.config
rename to tests/modules/nf-core/eido/convert/nextflow.config
diff --git a/tests/modules/nf-core/eido/convert/test.yml b/tests/modules/nf-core/eido/convert/test.yml
new file mode 100644
index 00000000000..11cdb157b3e
--- /dev/null
+++ b/tests/modules/nf-core/eido/convert/test.yml
@@ -0,0 +1,17 @@
+- name: eido convert test_eido_convert_nextflow_samplesheet
+  command: nextflow run ./tests/modules/nf-core/eido/convert -entry test_eido_convert_nextflow_samplesheet -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/eido/convert/nextflow.config
+  tags:
+    - eido/convert
+    - eido
+  files:
+    - path: output/eido/samplesheet_converted.csv
+      md5sum: 7aa4da4944650b9c7c451c5dfbeae663
+
+- name: eido convert test_eido_convert_pep_project
+  command: nextflow run ./tests/modules/nf-core/eido/convert -entry test_eido_convert_pep_project -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/eido/convert/nextflow.config
+  tags:
+    - eido/convert
+    - eido
+  files:
+    - path: output/eido/samplesheet_converted.csv
+      md5sum: 2191ccc9c9c1ac4577726ea24cdb9fda
diff --git a/tests/modules/nf-core/eido/validate/main.nf b/tests/modules/nf-core/eido/validate/main.nf
new file mode 100644
index 00000000000..3867adc123b
--- /dev/null
+++ b/tests/modules/nf-core/eido/validate/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EIDO_VALIDATE } from '../../../../../modules/nf-core/eido/validate/main.nf'
+
+workflow test_eido_validate_on_nextflow_samplesheet {
+
+    samplesheet = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
+    schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
+    pep_input_base_dir = []
+
+    EIDO_VALIDATE ( samplesheet, schema, pep_input_base_dir )
+}
+
+workflow test_eido_validate_on_pep_config {
+
+    samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
+    schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
+    pep_input_base_dir = []
+
+    EIDO_VALIDATE ( samplesheet, schema, pep_input_base_dir )
+}
diff --git a/tests/modules/eido/validate/nextflow.config b/tests/modules/nf-core/eido/validate/nextflow.config
similarity index 100%
rename from tests/modules/eido/validate/nextflow.config
rename to tests/modules/nf-core/eido/validate/nextflow.config
diff --git a/tests/modules/nf-core/eido/validate/test.yml b/tests/modules/nf-core/eido/validate/test.yml
new file mode 100644
index 00000000000..5071faa502c
--- /dev/null
+++ b/tests/modules/nf-core/eido/validate/test.yml
@@ -0,0 +1,17 @@
+- name: eido validate test_eido_validate_on_nextflow_samplesheet
+  command: nextflow run ./tests/modules/nf-core/eido/validate -entry test_eido_validate_on_nextflow_samplesheet -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/eido/validate/nextflow.config
+  tags:
+    - eido/validate
+    - eido
+  files:
+    - path: output/eido/validation.log
+      md5sum: 3a197c21ebf411aac7616bf9b4470de3
+
+- name: eido validate test_eido_validate_on_pep_config
+  command: nextflow run ./tests/modules/nf-core/eido/validate -entry test_eido_validate_on_pep_config -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/eido/validate/nextflow.config
+  tags:
+    - eido/validate
+    - eido
+  files:
+    - path: output/eido/validation.log
+      md5sum: 3a197c21ebf411aac7616bf9b4470de3
diff --git a/tests/modules/nf-core/elprep/filter/main.nf b/tests/modules/nf-core/elprep/filter/main.nf
new file mode 100644
index 00000000000..834198a46fa
--- /dev/null
+++ b/tests/modules/nf-core/elprep/filter/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ELPREP_FILTER } from '../../../../../modules/nf-core/elprep/filter/main.nf'
+
+workflow test_elprep_filter {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+    reference_elfasta = file(params.test_data['homo_sapiens']['genome']['genome_elfasta'], checkIfExists: true)
+    known_sites_elsites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_elsites'], checkIfExists: true)
+    target_regions_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    ELPREP_FILTER ( input, true, true, [],  [], reference_elfasta, known_sites_elsites, target_regions_bed, [], [], true, true)
+}
diff --git a/tests/modules/elprep/filter/nextflow.config b/tests/modules/nf-core/elprep/filter/nextflow.config
similarity index 100%
rename from tests/modules/elprep/filter/nextflow.config
rename to tests/modules/nf-core/elprep/filter/nextflow.config
diff --git a/tests/modules/nf-core/elprep/filter/test.yml b/tests/modules/nf-core/elprep/filter/test.yml
new file mode 100644
index 00000000000..8425e30406c
--- /dev/null
+++ b/tests/modules/nf-core/elprep/filter/test.yml
@@ -0,0 +1,13 @@
+- name: elprep filter test_elprep_filter
+  command: nextflow run ./tests/modules/nf-core/elprep/filter -entry test_elprep_filter -c ./tests/config/nextflow.config
+  tags:
+    - elprep
+    - elprep/filter
+  files:
+    - path: output/elprep/test.activity_profile.igv
+    - path: output/elprep/test.assembly_regions.igv
+    - path: output/elprep/output/test.bam
+    - path: output/elprep/test.g.vcf.gz
+    - path: output/elprep/test.metrics.txt
+    - path: output/elprep/test.recall
+    - path: output/elprep/versions.yml
diff --git a/tests/modules/nf-core/elprep/merge/main.nf b/tests/modules/nf-core/elprep/merge/main.nf
new file mode 100644
index 00000000000..71dfb0708d1
--- /dev/null
+++ b/tests/modules/nf-core/elprep/merge/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ELPREP_SPLIT } from '../../../../../modules/nf-core/elprep/split/main.nf'
+include { ELPREP_MERGE } from '../../../../../modules/nf-core/elprep/merge/main.nf'
+
+workflow test_elprep_merge {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+
+    ELPREP_SPLIT ( input )
+    ELPREP_MERGE ( ELPREP_SPLIT.out.bam )
+}
diff --git a/tests/modules/elprep/merge/nextflow.config b/tests/modules/nf-core/elprep/merge/nextflow.config
similarity index 100%
rename from tests/modules/elprep/merge/nextflow.config
rename to tests/modules/nf-core/elprep/merge/nextflow.config
diff --git a/tests/modules/nf-core/elprep/merge/test.yml b/tests/modules/nf-core/elprep/merge/test.yml
new file mode 100644
index 00000000000..a0b95b8d0bf
--- /dev/null
+++ b/tests/modules/nf-core/elprep/merge/test.yml
@@ -0,0 +1,8 @@
+- name: elprep merge test_elprep_merge
+  command: nextflow run ./tests/modules/nf-core/elprep/merge -entry test_elprep_merge -c ./tests/config/nextflow.config
+  tags:
+    - elprep
+    - elprep/merge
+  files:
+    - path: output/elprep/output/test.bam
+    - path: output/elprep/versions.yml
diff --git a/tests/modules/nf-core/elprep/split/main.nf b/tests/modules/nf-core/elprep/split/main.nf
new file mode 100644
index 00000000000..3fc26986417
--- /dev/null
+++ b/tests/modules/nf-core/elprep/split/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ELPREP_SPLIT } from '../../../../../modules/nf-core/elprep/split/main.nf'
+
+workflow test_elprep_split {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+
+    ELPREP_SPLIT ( input )
+}
diff --git a/tests/modules/elprep/split/nextflow.config b/tests/modules/nf-core/elprep/split/nextflow.config
similarity index 100%
rename from tests/modules/elprep/split/nextflow.config
rename to tests/modules/nf-core/elprep/split/nextflow.config
diff --git a/tests/modules/nf-core/elprep/split/test.yml b/tests/modules/nf-core/elprep/split/test.yml
new file mode 100644
index 00000000000..cda8d91ec4d
--- /dev/null
+++ b/tests/modules/nf-core/elprep/split/test.yml
@@ -0,0 +1,10 @@
+- name: elprep split test_elprep_split
+  command: nextflow run ./tests/modules/nf-core/elprep/split -entry test_elprep_split -c ./tests/config/nextflow.config
+  tags:
+    - elprep
+    - elprep/split
+  files:
+    - path: output/elprep/output/splits/test-group00001.bam
+    - path: output/elprep/output/splits/test-unmapped.bam
+    - path: output/elprep/output/test-spread.bam
+    - path: output/elprep/versions.yml
diff --git a/tests/modules/nf-core/emboss/seqret/main.nf b/tests/modules/nf-core/emboss/seqret/main.nf
new file mode 100644
index 00000000000..1648c0d1677
--- /dev/null
+++ b/tests/modules/nf-core/emboss/seqret/main.nf
@@ -0,0 +1,50 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EMBOSS_SEQRET } from '../../../../../modules/nf-core/emboss/seqret/main.nf'
+include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf'
+
+workflow test_emboss_seqret_gb2embl {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+    ]
+
+    GUNZIP ( input )
+    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'embl' )
+}
+
+workflow test_emboss_seqret_gb2gff {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+    ]
+
+    GUNZIP ( input )
+    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'gff' )
+}
+
+workflow test_emboss_seqret_gb2pir {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+    ]
+
+    GUNZIP ( input )
+    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'pir' )
+}
+
+workflow test_emboss_seqret_gb2fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+    ]
+
+    GUNZIP ( input )
+    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'fasta' )
+}
diff --git a/tests/modules/emboss/seqret/nextflow.config b/tests/modules/nf-core/emboss/seqret/nextflow.config
similarity index 100%
rename from tests/modules/emboss/seqret/nextflow.config
rename to tests/modules/nf-core/emboss/seqret/nextflow.config
diff --git a/tests/modules/nf-core/emboss/seqret/test.yml b/tests/modules/nf-core/emboss/seqret/test.yml
new file mode 100644
index 00000000000..ac6c9ea0712
--- /dev/null
+++ b/tests/modules/nf-core/emboss/seqret/test.yml
@@ -0,0 +1,40 @@
+- name: emboss seqret test_emboss_seqret_gb2embl
+  command: nextflow run ./tests/modules/nf-core/emboss/seqret -entry test_emboss_seqret_gb2embl -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/emboss/seqret/nextflow.config
+  tags:
+    - emboss
+    - emboss/seqret
+  files:
+    - path: output/emboss/test.embl
+      md5sum: 4810933b1b2174f7067d9afa1da8b01b
+      contains: ["ID   NZ_CP069563;"] # Human-readable test for correct format and sequence
+
+- name: emboss seqret test_emboss_seqret_gb2gff
+  command: nextflow run ./tests/modules/nf-core/emboss/seqret -entry test_emboss_seqret_gb2gff -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/emboss/seqret/nextflow.config
+  tags:
+    - emboss
+    - emboss/seqret
+  files:
+    - path: output/emboss/test.gff
+      contains:
+        - "##gff-version 3" # Human-readable test for correct format
+        - ">NZ_CP069563" # Human-readable test for correct sequence
+
+- name: emboss seqret test_emboss_seqret_gb2pir
+  command: nextflow run ./tests/modules/nf-core/emboss/seqret -entry test_emboss_seqret_gb2pir -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/emboss/seqret/nextflow.config
+  tags:
+    - emboss
+    - emboss/seqret
+  files:
+    - path: output/emboss/test.pir
+      md5sum: 49f4a28533e970aa2438d8adf55a26bb
+      contains: [">D1;NZ_CP069563"] # Human-readable test for correct format and sequence
+
+- name: emboss seqret test_emboss_seqret_gb2fasta
+  command: nextflow run ./tests/modules/nf-core/emboss/seqret -entry test_emboss_seqret_gb2fasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/emboss/seqret/nextflow.config
+  tags:
+    - emboss
+    - emboss/seqret
+  files:
+    - path: output/emboss/test.fasta
+      md5sum: 0694275f05780aeb0b54d46687603f44
+      contains: [">NZ_CP069563"] # Human-readable test for correct format and sequence
diff --git a/tests/modules/nf-core/emmtyper/main.nf b/tests/modules/nf-core/emmtyper/main.nf
new file mode 100644
index 00000000000..b2cd94d552b
--- /dev/null
+++ b/tests/modules/nf-core/emmtyper/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EMMTYPER } from '../../../../modules/nf-core/emmtyper/main.nf'
+
+workflow test_emmtyper {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    EMMTYPER ( input )
+}
diff --git a/tests/modules/emmtyper/nextflow.config b/tests/modules/nf-core/emmtyper/nextflow.config
similarity index 100%
rename from tests/modules/emmtyper/nextflow.config
rename to tests/modules/nf-core/emmtyper/nextflow.config
diff --git a/tests/modules/nf-core/emmtyper/test.yml b/tests/modules/nf-core/emmtyper/test.yml
new file mode 100644
index 00000000000..61b53fd3118
--- /dev/null
+++ b/tests/modules/nf-core/emmtyper/test.yml
@@ -0,0 +1,7 @@
+- name: emmtyper test_emmtyper
+  command: nextflow run ./tests/modules/nf-core/emmtyper -entry test_emmtyper -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/emmtyper/nextflow.config
+  tags:
+    - emmtyper
+  files:
+    - path: output/emmtyper/test.tsv
+      md5sum: c727ba859adec9ca8ff0e091ecf79c62
diff --git a/tests/modules/nf-core/endorspy/main.nf b/tests/modules/nf-core/endorspy/main.nf
new file mode 100644
index 00000000000..0b9da1335ab
--- /dev/null
+++ b/tests/modules/nf-core/endorspy/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ENDORSPY } from '../../../../modules/nf-core/endorspy/main.nf'
+include { SAMTOOLS_FLAGSTAT } from '../../../../modules/nf-core/samtools/flagstat/main.nf'
+include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT2 } from '../../../../modules/nf-core/samtools/flagstat/main.nf'
+include { SAMTOOLS_VIEW } from '../../../../modules/nf-core/samtools/view/main.nf'
+include { SAMTOOLS_INDEX } from '../../../../modules/nf-core/samtools/index/main.nf'
+
+workflow test_endorspy {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+    
+
+    SAMTOOLS_FLAGSTAT ( input )
+    SAMTOOLS_VIEW ( input, [] )
+    SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
+    input2 = SAMTOOLS_VIEW.out.bam
+       .mix(SAMTOOLS_INDEX.out.bai)
+       .groupTuple(by:0)
+       .map{
+            def meta = it[0]
+            def bam = it[1][0]
+            def bai = it[1][1]
+
+            [meta, bam, bai]
+       }
+    SAMTOOLS_FLAGSTAT2 ( input2 )
+    ch_input_flagstat = SAMTOOLS_FLAGSTAT.out.flagstat.join(SAMTOOLS_FLAGSTAT2.out.flagstat)
+    ENDORSPY ( ch_input_flagstat )
+}
diff --git a/tests/modules/endorspy/nextflow.config b/tests/modules/nf-core/endorspy/nextflow.config
similarity index 100%
rename from tests/modules/endorspy/nextflow.config
rename to tests/modules/nf-core/endorspy/nextflow.config
diff --git a/tests/modules/nf-core/endorspy/test.yml b/tests/modules/nf-core/endorspy/test.yml
new file mode 100644
index 00000000000..f81f8e88588
--- /dev/null
+++ b/tests/modules/nf-core/endorspy/test.yml
@@ -0,0 +1,7 @@
+- name: endorspy test_endorspy
+  command: nextflow run ./tests/modules/nf-core/endorspy -entry test_endorspy -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/endorspy/nextflow.config
+  tags:
+    - endorspy
+  files:
+    - path: output/endorspy/test_endogenous_dna_mqc.json
+      md5sum: fe7bea111d966db321dcde7fbfb062b1
diff --git a/tests/modules/nf-core/ensemblvep/main.nf b/tests/modules/nf-core/ensemblvep/main.nf
new file mode 100644
index 00000000000..c1f89406a5f
--- /dev/null
+++ b/tests/modules/nf-core/ensemblvep/main.nf
@@ -0,0 +1,86 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ENSEMBLVEP } from '../../../../modules/nf-core/ensemblvep/main.nf'
+
+include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../../modules/nf-core/ensemblvep/main.nf'
+include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../../modules/nf-core/ensemblvep/main.nf'
+include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../../modules/nf-core/ensemblvep/main.nf'
+include { ENSEMBLVEP as ENSEMBLVEP_VCF_BGZIP } from '../../../../modules/nf-core/ensemblvep/main.nf'
+include { ENSEMBLVEP as ENSEMBLVEP_VCF_GZIP  } from '../../../../modules/nf-core/ensemblvep/main.nf'
+
+workflow test_ensemblvep_fasta_json {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    ENSEMBLVEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
+}
+
+workflow test_ensemblvep_fasta_tab {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    ENSEMBLVEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
+}
+
+workflow test_ensemblvep_fasta_vcf {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
+}
+
+workflow test_ensemblvep_fasta_vcf_bgzip {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    ENSEMBLVEP_VCF_BGZIP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
+}
+
+workflow test_ensemblvep_fasta_vcf_gzip {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    ENSEMBLVEP_VCF_GZIP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
+}
+
+workflow test_ensemblvep_fasta {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
+}
+
+workflow test_ensemblvep_no_fasta {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], [], [] )
+}
diff --git a/tests/modules/ensemblvep/nextflow.config b/tests/modules/nf-core/ensemblvep/nextflow.config
similarity index 100%
rename from tests/modules/ensemblvep/nextflow.config
rename to tests/modules/nf-core/ensemblvep/nextflow.config
diff --git a/tests/modules/nf-core/ensemblvep/test.yml b/tests/modules/nf-core/ensemblvep/test.yml
new file mode 100644
index 00000000000..5c3f4fccf44
--- /dev/null
+++ b/tests/modules/nf-core/ensemblvep/test.yml
@@ -0,0 +1,63 @@
+- name: ensemblvep test_ensemblvep_fasta_json
+  command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_json -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ensemblvep/nextflow.config
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.json
+    - path: output/ensemblvep/test.summary.html
+
+- name: ensemblvep test_ensemblvep_fasta_tab
+  command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_tab -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ensemblvep/nextflow.config
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.tab
+    - path: output/ensemblvep/test.summary.html
+
+- name: ensemblvep test_ensemblvep_fasta_vcf
+  command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ensemblvep/nextflow.config
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.vcf
+    - path: output/ensemblvep/test.summary.html
+
+- name: ensemblvep test_ensemblvep_fasta_vcf_bgzip
+  command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf_bgzip -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ensemblvep/nextflow.config
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.vcf.gz
+    - path: output/ensemblvep/test.summary.html
+
+- name: ensemblvep test_ensemblvep_fasta_vcf_gzip
+  command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf_gzip -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ensemblvep/nextflow.config
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.vcf.gz
+    - path: output/ensemblvep/test.summary.html
+
+- name: ensemblvep test_ensemblvep_fasta
+  command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ensemblvep/nextflow.config
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.vcf
+    - path: output/ensemblvep/test.summary.html
+
+- name: ensemblvep test_ensemblvep_no_fasta
+  command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ensemblvep/nextflow.config
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.vcf
+    - path: output/ensemblvep/test.summary.html
+
+- name: ensemblvep test_ensemblvep_fasta_vcf_stub
+  command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ensemblvep/nextflow.config -stub
+  tags:
+    - ensemblvep
+  files:
+    - path: output/ensemblvep/test.ann.vcf
+    - path: output/ensemblvep/test.summary.html
diff --git a/tests/modules/entrezdirect/esearch/main.nf b/tests/modules/nf-core/entrezdirect/esearch/main.nf
similarity index 100%
rename from tests/modules/entrezdirect/esearch/main.nf
rename to tests/modules/nf-core/entrezdirect/esearch/main.nf
diff --git a/tests/modules/entrezdirect/esearch/nextflow.config b/tests/modules/nf-core/entrezdirect/esearch/nextflow.config
similarity index 100%
rename from tests/modules/entrezdirect/esearch/nextflow.config
rename to tests/modules/nf-core/entrezdirect/esearch/nextflow.config
diff --git a/tests/modules/nf-core/entrezdirect/esearch/test.yml b/tests/modules/nf-core/entrezdirect/esearch/test.yml
new file mode 100644
index 00000000000..0dbe1e31df3
--- /dev/null
+++ b/tests/modules/nf-core/entrezdirect/esearch/test.yml
@@ -0,0 +1,47 @@
+- name: entrezdirect esearch test_entrezdirect_esearch_pubmed
+  command: nextflow run ./tests/modules/nf-core/entrezdirect/esearch -entry test_entrezdirect_esearch_pubmed -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/entrezdirect/esearch/nextflow.config
+  tags:
+    - entrezdirect/esearch
+    - entrezdirect
+  files:
+    - path: output/entrezdirect/test_pubmed.xml
+      contains:
+        - "<ENTREZ_DIRECT>"
+        - "<Db>pubmed</Db>"
+        - "<WebEnv>"
+        - "<QueryKey>"
+        - "<Step>"
+        - "<Count>"
+        - "</ENTREZ_DIRECT>"
+
+- name: entrezdirect esearch test_entrezdirect_esearch_genome
+  command: nextflow run ./tests/modules/nf-core/entrezdirect/esearch -entry test_entrezdirect_esearch_genome -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/entrezdirect/esearch/nextflow.config
+  tags:
+    - entrezdirect/esearch
+    - entrezdirect
+  files:
+    - path: output/entrezdirect/test_genome.xml
+      contains:
+        - "<ENTREZ_DIRECT>"
+        - "<Db>genome</Db>"
+        - "<WebEnv>"
+        - "<QueryKey>"
+        - "<Count>"
+        - "<Step>"
+        - "</ENTREZ_DIRECT>"
+
+- name: entrezdirect esearch test_entrezdirect_esearch_assembly
+  command: nextflow run ./tests/modules/nf-core/entrezdirect/esearch -entry test_entrezdirect_esearch_assembly -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/entrezdirect/esearch/nextflow.config
+  tags:
+    - entrezdirect/esearch
+    - entrezdirect
+  files:
+    - path: output/entrezdirect/test_assembly.xml
+      contains:
+        - "<ENTREZ_DIRECT>"
+        - "<Db>assembly</Db>"
+        - "<WebEnv>"
+        - "<QueryKey>"
+        - "<Count>"
+        - "<Step>"
+        - "</ENTREZ_DIRECT>"
diff --git a/tests/modules/nf-core/entrezdirect/esummary/main.nf b/tests/modules/nf-core/entrezdirect/esummary/main.nf
new file mode 100644
index 00000000000..a951496f42a
--- /dev/null
+++ b/tests/modules/nf-core/entrezdirect/esummary/main.nf
@@ -0,0 +1,50 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ENTREZDIRECT_ESUMMARY } from '../../../../../modules/nf-core/entrezdirect/esummary/main.nf'
+
+//
+// Test with SRA database
+//
+workflow test_entrezdirect_esummary_sra {
+
+    input = [
+        [ id:'test_sra' ], // meta map
+        uid = '5135484',
+        []
+    ]
+    database = 'sra'
+
+    ENTREZDIRECT_ESUMMARY ( input, database )
+}
+
+//
+// Test with Genome database
+//
+workflow test_entrezdirect_esummary_genome {
+
+    input = [
+        [ id:'test_genome' ], // meta map
+        uid = '768',
+        []
+    ]
+    database = 'genome'
+
+    ENTREZDIRECT_ESUMMARY ( input, database )
+}
+
+//
+// Test with Assembly database
+//
+workflow test_entrezdirect_esummary_assembly {
+
+    input = [
+        [ id:'test_assembly' ], // meta map
+        uid = '191021',
+        []
+    ]
+    database = 'assembly'
+
+    ENTREZDIRECT_ESUMMARY ( input, database )
+}
diff --git a/tests/modules/entrezdirect/esummary/nextflow.config b/tests/modules/nf-core/entrezdirect/esummary/nextflow.config
similarity index 100%
rename from tests/modules/entrezdirect/esummary/nextflow.config
rename to tests/modules/nf-core/entrezdirect/esummary/nextflow.config
diff --git a/tests/modules/nf-core/entrezdirect/esummary/test.yml b/tests/modules/nf-core/entrezdirect/esummary/test.yml
new file mode 100644
index 00000000000..635a9449233
--- /dev/null
+++ b/tests/modules/nf-core/entrezdirect/esummary/test.yml
@@ -0,0 +1,26 @@
+- name: entrezdirect esummary test_entrezdirect_esummary_sra
+  command: nextflow run ./tests/modules/nf-core/entrezdirect/esummary -entry test_entrezdirect_esummary_sra -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/entrezdirect/esummary/nextflow.config
+  tags:
+    - entrezdirect
+    - entrezdirect/esummary
+  files:
+    - path: output/entrezdirect/test_sra.xml
+      contains: ["WGS of ornithorhynchus anatinus"]
+
+- name: entrezdirect esummary test_entrezdirect_esummary_genome
+  command: nextflow run ./tests/modules/nf-core/entrezdirect/esummary -entry test_entrezdirect_esummary_genome -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/entrezdirect/esummary/nextflow.config
+  tags:
+    - entrezdirect
+    - entrezdirect/esummary
+  files:
+    - path: output/entrezdirect/test_genome.xml
+      contains: ["Hypsibius dujardini"]
+
+- name: entrezdirect esummary test_entrezdirect_esummary_assembly
+  command: nextflow run ./tests/modules/nf-core/entrezdirect/esummary -entry test_entrezdirect_esummary_assembly -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/entrezdirect/esummary/nextflow.config
+  tags:
+    - entrezdirect
+    - entrezdirect/esummary
+  files:
+    - path: output/entrezdirect/test_assembly.xml
+      contains: ["ContigN50"]
diff --git a/tests/modules/nf-core/entrezdirect/xtract/main.nf b/tests/modules/nf-core/entrezdirect/xtract/main.nf
new file mode 100644
index 00000000000..f56ef23f50c
--- /dev/null
+++ b/tests/modules/nf-core/entrezdirect/xtract/main.nf
@@ -0,0 +1,46 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ENTREZDIRECT_ESUMMARY } from '../../../../../modules/nf-core/entrezdirect/esummary/main.nf'
+include { ENTREZDIRECT_XTRACT   } from '../../../../../modules/nf-core/entrezdirect/xtract/main.nf'
+
+//
+// Test with Assembly database
+//
+workflow test_entrezdirect_xtract_assembly {
+
+    input = [
+        [ id:'test_assembly' ], // meta map
+        uid = '191021',
+        []
+    ]
+    database = 'assembly'
+
+    pattern_in = 'DocumentSummary'
+    element_in = 'SpeciesName BioprojectAccn FtpPath_GenBank'
+    delim = ","
+
+    ENTREZDIRECT_ESUMMARY ( input, database )
+    ENTREZDIRECT_XTRACT ( ENTREZDIRECT_ESUMMARY.out.xml, pattern_in, element_in, delim )
+}
+
+//
+// Test with Genome database
+//
+workflow test_entrezdirect_xtract_genome {
+
+    input = [
+        [ id:'test_genome' ], // meta map
+        uid = '768',
+        []
+    ]
+    database = 'genome'
+
+    pattern_in = 'DocumentSummary'
+    element_in = 'TaxId Organism_Name Project_Accession Assembly_Accession'
+    delim = ","
+
+    ENTREZDIRECT_ESUMMARY ( input, database )
+    ENTREZDIRECT_XTRACT ( ENTREZDIRECT_ESUMMARY.out.xml, pattern_in, element_in, delim )
+}
diff --git a/tests/modules/entrezdirect/xtract/nextflow.config b/tests/modules/nf-core/entrezdirect/xtract/nextflow.config
similarity index 100%
rename from tests/modules/entrezdirect/xtract/nextflow.config
rename to tests/modules/nf-core/entrezdirect/xtract/nextflow.config
diff --git a/tests/modules/nf-core/entrezdirect/xtract/test.yml b/tests/modules/nf-core/entrezdirect/xtract/test.yml
new file mode 100644
index 00000000000..58f60d21b81
--- /dev/null
+++ b/tests/modules/nf-core/entrezdirect/xtract/test.yml
@@ -0,0 +1,17 @@
+- name: entrezdirect xtract test_entrezdirect_xtract_assembly
+  command: nextflow run ./tests/modules/nf-core/entrezdirect/xtract -entry test_entrezdirect_xtract_assembly -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/entrezdirect/xtract/nextflow.config
+  tags:
+    - entrezdirect
+    - entrezdirect/xtract
+  files:
+    - path: output/entrezdirect/test_assembly.txt
+      md5sum: 17073db7c14890aef30f5e3f2d003d32
+
+- name: entrezdirect xtract test_entrezdirect_xtract_genome
+  command: nextflow run ./tests/modules/nf-core/entrezdirect/xtract -entry test_entrezdirect_xtract_genome -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/entrezdirect/xtract/nextflow.config
+  tags:
+    - entrezdirect
+    - entrezdirect/xtract
+  files:
+    - path: output/entrezdirect/test_genome.txt
+      md5sum: 931279db7c80c5bb9ed523815898a9cd
diff --git a/tests/modules/nf-core/epang/main.nf b/tests/modules/nf-core/epang/main.nf
new file mode 100644
index 00000000000..9cb84cdcc89
--- /dev/null
+++ b/tests/modules/nf-core/epang/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EPANG } from '../../../../modules/nf-core/epang/main.nf'
+
+workflow test_epang {
+    
+    input = [
+        [ id:'test', model:'LG' ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/query.alnfaa.gz', checkIfExists: true)
+    ]
+
+    EPANG ( 
+        input,
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/reference.alnfaa.gz', checkIfExists: true),
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/reference.newick', checkIfExists: true),
+        [],
+        [],
+        []
+    )
+}
diff --git a/tests/modules/epang/nextflow.config b/tests/modules/nf-core/epang/nextflow.config
similarity index 100%
rename from tests/modules/epang/nextflow.config
rename to tests/modules/nf-core/epang/nextflow.config
diff --git a/tests/modules/nf-core/epang/test.yml b/tests/modules/nf-core/epang/test.yml
new file mode 100644
index 00000000000..c7048570984
--- /dev/null
+++ b/tests/modules/nf-core/epang/test.yml
@@ -0,0 +1,12 @@
+- name: epang test_epang
+  command: nextflow run ./tests/modules/nf-core/epang -entry test_epang -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/epang/nextflow.config
+  tags:
+    - epang
+  files:
+    - path: output/epang/test.epa_info.log
+      contains:
+        - "INFO 3 Sequences done"
+    - path: output/epang/test.epa_result.jplace.gz
+      contains:
+        - '"placements":'
+        - '"metadata": {"invocation": "epa-ng --model LG --threads 2 --query query.alnfaa.gz --ref-msa reference.alnfaa.gz --tree reference.newick "}'
diff --git a/tests/modules/nf-core/expansionhunter/main.nf b/tests/modules/nf-core/expansionhunter/main.nf
new file mode 100644
index 00000000000..2674e54b163
--- /dev/null
+++ b/tests/modules/nf-core/expansionhunter/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EXPANSIONHUNTER } from '../../../../modules/nf-core/expansionhunter/main.nf'
+
+workflow test_expansionhunter {
+
+    input = [ [ id:'test', gender:'male' ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
+
+    EXPANSIONHUNTER ( input, fasta, variant_catalog )
+}
diff --git a/tests/modules/expansionhunter/nextflow.config b/tests/modules/nf-core/expansionhunter/nextflow.config
similarity index 100%
rename from tests/modules/expansionhunter/nextflow.config
rename to tests/modules/nf-core/expansionhunter/nextflow.config
diff --git a/tests/modules/nf-core/expansionhunter/test.yml b/tests/modules/nf-core/expansionhunter/test.yml
new file mode 100644
index 00000000000..0f49183590e
--- /dev/null
+++ b/tests/modules/nf-core/expansionhunter/test.yml
@@ -0,0 +1,7 @@
+- name: expansionhunter test_expansionhunter
+  command: nextflow run ./tests/modules/nf-core/expansionhunter -entry test_expansionhunter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/expansionhunter/nextflow.config
+  tags:
+    - expansionhunter
+  files:
+    - path: output/expansionhunter/test.vcf
+      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
diff --git a/tests/modules/nf-core/faqcs/main.nf b/tests/modules/nf-core/faqcs/main.nf
new file mode 100644
index 00000000000..1f374c1c343
--- /dev/null
+++ b/tests/modules/nf-core/faqcs/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FAQCS } from '../../../../modules/nf-core/faqcs/main.nf'
+
+
+//
+// Test with single-end data
+//
+workflow test_fastp_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    FAQCS ( input )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_fastp_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    FAQCS ( input )
+}
+
diff --git a/tests/modules/faqcs/nextflow.config b/tests/modules/nf-core/faqcs/nextflow.config
similarity index 100%
rename from tests/modules/faqcs/nextflow.config
rename to tests/modules/nf-core/faqcs/nextflow.config
diff --git a/tests/modules/nf-core/faqcs/test.yml b/tests/modules/nf-core/faqcs/test.yml
new file mode 100644
index 00000000000..1a06fab7af2
--- /dev/null
+++ b/tests/modules/nf-core/faqcs/test.yml
@@ -0,0 +1,55 @@
+- name: faqcs test_fastp_single_end
+  command: nextflow run ./tests/modules/nf-core/faqcs -entry test_fastp_single_end -c ./tests/config/nextflow.config
+  tags:
+    - faqcs
+  files:
+    - path: output/faqcs/qa.test.base_content.txt
+      md5sum: f992603f01ca430c03c8aae02eba2f5d
+    - path: output/faqcs/qa.test.for_qual_histogram.txt
+      md5sum: a3d462ab84151e982f99f85f52c21de3
+    - path: output/faqcs/qa.test.length_count.txt
+      md5sum: 80915f09fbaf5884c32e95acab2d031c
+    - path: output/faqcs/test.base_content.txt
+      md5sum: f992603f01ca430c03c8aae02eba2f5d
+    - path: output/faqcs/test.fastp.log
+      md5sum: be79dc893f87de1f82faf749cdfb848c
+    - path: output/faqcs/test.for_qual_histogram.txt
+      md5sum: a3d462ab84151e982f99f85f52c21de3
+    - path: output/faqcs/test.length_count.txt
+      md5sum: 80915f09fbaf5884c32e95acab2d031c
+    - path: output/faqcs/test.stats.txt
+      md5sum: ea20e93706b2e4c676004253baa3cec6
+    - path: output/faqcs/test.trimmed.fastq.gz
+      md5sum: 875863b402f67403dac63ef59b9c9a8a
+    - path: output/faqcs/test_qc_report.pdf
+    - path: output/faqcs/versions.yml
+      md5sum: 2a38d7e7ab5299336e9669c393c9da6c
+
+- name: faqcs test_fastp_paired_end
+  command: nextflow run ./tests/modules/nf-core/faqcs -entry test_fastp_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - faqcs
+  files:
+    - path: output/faqcs/qa.test.base_content.txt
+      md5sum: 99aa9a775ccd8d6503f0cf80f775203c
+    - path: output/faqcs/qa.test.for_qual_histogram.txt
+      md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
+    - path: output/faqcs/qa.test.length_count.txt
+      md5sum: 420298983c762754d5b0ef32c9d5dad4
+    - path: output/faqcs/test.base_content.txt
+      md5sum: 99aa9a775ccd8d6503f0cf80f775203c
+    - path: output/faqcs/test.fastp.log
+      md5sum: be79dc893f87de1f82faf749cdfb848c
+    - path: output/faqcs/test.for_qual_histogram.txt
+      md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
+    - path: output/faqcs/test.length_count.txt
+      md5sum: 420298983c762754d5b0ef32c9d5dad4
+    - path: output/faqcs/test.stats.txt
+      md5sum: 9a693f8af94ab8c485519d9a523aa622
+    - path: output/faqcs/test_1.trimmed.fastq.gz
+      md5sum: 875863b402f67403dac63ef59b9c9a8a
+    - path: output/faqcs/test_2.trimmed.fastq.gz
+      md5sum: 375aeb74819ca3d72203135ac80df78c
+    - path: output/faqcs/test_qc_report.pdf
+    - path: output/faqcs/versions.yml
+      md5sum: 208d54c0cf6dfc54e719b81b990afac9
diff --git a/tests/modules/nf-core/fargene/main.nf b/tests/modules/nf-core/fargene/main.nf
new file mode 100644
index 00000000000..daebcb3aa37
--- /dev/null
+++ b/tests/modules/nf-core/fargene/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf'
+include { FARGENE } from '../../../../modules/nf-core/fargene/main.nf'
+
+workflow test_fargene {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) ]
+    hmm_model = 'class_a'
+
+    GUNZIP ( input )
+    FARGENE ( GUNZIP.out.gunzip, hmm_model )
+}
diff --git a/tests/modules/fargene/nextflow.config b/tests/modules/nf-core/fargene/nextflow.config
similarity index 100%
rename from tests/modules/fargene/nextflow.config
rename to tests/modules/nf-core/fargene/nextflow.config
diff --git a/tests/modules/nf-core/fargene/test.yml b/tests/modules/nf-core/fargene/test.yml
new file mode 100644
index 00000000000..9801d63a28d
--- /dev/null
+++ b/tests/modules/nf-core/fargene/test.yml
@@ -0,0 +1,13 @@
+- name: fargene
+  command: nextflow run ./tests/modules/nf-core/fargene -entry test_fargene -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fargene/nextflow.config
+  tags:
+    - fargene
+  files:
+    - path: output/fargene/fargene_analysis.log
+    - path: output/fargene/test/hmmsearchresults/test1.contigs-class_A-hmmsearched.out
+    - path: output/fargene/test/results_summary.txt
+      md5sum: 690d351cfc52577263ef4cfab1c81f50
+    - path: output/fargene/test/tmpdir/test1.contigs-positives.out
+    - path: output/fargene/test/tmpdir/tmp.out
+    - path: output/gunzip/test1.contigs.fa
+      md5sum: 80c4d78f2810f6d9e90fa6da9bb9c4f9
diff --git a/tests/modules/nf-core/fastani/main.nf b/tests/modules/nf-core/fastani/main.nf
new file mode 100644
index 00000000000..8538ebc369e
--- /dev/null
+++ b/tests/modules/nf-core/fastani/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTANI } from '../../../../modules/nf-core/fastani/main.nf'
+
+workflow test_fastani {
+
+    query = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    reference = file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+
+    FASTANI ( [[ id:'test' ], query], reference )
+}
diff --git a/tests/modules/fastani/nextflow.config b/tests/modules/nf-core/fastani/nextflow.config
similarity index 100%
rename from tests/modules/fastani/nextflow.config
rename to tests/modules/nf-core/fastani/nextflow.config
diff --git a/tests/modules/nf-core/fastani/test.yml b/tests/modules/nf-core/fastani/test.yml
new file mode 100644
index 00000000000..2ac0adc0949
--- /dev/null
+++ b/tests/modules/nf-core/fastani/test.yml
@@ -0,0 +1,7 @@
+- name: fastani
+  command: nextflow run ./tests/modules/nf-core/fastani -entry test_fastani -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastani/nextflow.config
+  tags:
+    - fastani
+  files:
+    - path: output/fastani/test.ani.txt
+      md5sum: 31d4f04e8cffe13080c86db3f9f3a589
diff --git a/tests/modules/nf-core/fastawindows/main.nf b/tests/modules/nf-core/fastawindows/main.nf
new file mode 100644
index 00000000000..b3448fc3855
--- /dev/null
+++ b/tests/modules/nf-core/fastawindows/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTAWINDOWS } from '../../../../modules/nf-core/fastawindows/main.nf'
+
+workflow test_fastawindows {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    FASTAWINDOWS ( input )
+}
diff --git a/tests/modules/fastawindows/nextflow.config b/tests/modules/nf-core/fastawindows/nextflow.config
similarity index 100%
rename from tests/modules/fastawindows/nextflow.config
rename to tests/modules/nf-core/fastawindows/nextflow.config
diff --git a/tests/modules/nf-core/fastawindows/test.yml b/tests/modules/nf-core/fastawindows/test.yml
new file mode 100644
index 00000000000..677dc8ca66f
--- /dev/null
+++ b/tests/modules/nf-core/fastawindows/test.yml
@@ -0,0 +1,15 @@
+- name: fastawindows test_fastawindows
+  command: nextflow run ./tests/modules/nf-core/fastawindows -entry test_fastawindows -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastawindows/nextflow.config
+  tags:
+    - fastawindows
+  files:
+    - path: output/fastawindows/fw_out/test_freq_windows.tsv
+      md5sum: 237d50ac5ec2bef3142020d569fa5765
+    - path: output/fastawindows/fw_out/test_mononuc_windows.tsv
+      md5sum: a1b4437d0c71d9cfd676de6bda2633f0
+    - path: output/fastawindows/fw_out/test_dinuc_windows.tsv
+      md5sum: 696a9f2a4b2114dfbd6b414694f56a11
+    - path: output/fastawindows/fw_out/test_trinuc_windows.tsv
+      md5sum: dfb05b758f0474e937e2d6ba6fe46dae
+    - path: output/fastawindows/fw_out/test_tetranuc_windows.tsv
+      md5sum: e621537175ee8019360f8b6e8f4330b7
diff --git a/tests/modules/nf-core/fastk/fastk/main.nf b/tests/modules/nf-core/fastk/fastk/main.nf
new file mode 100644
index 00000000000..aa30d58890a
--- /dev/null
+++ b/tests/modules/nf-core/fastk/fastk/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTK_FASTK } from '../../../../../modules/nf-core/fastk/fastk/main.nf'
+
+workflow test_fastk_fastk_single_end {
+
+    input = [
+        [ id:'test' , single_end: true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    FASTK_FASTK ( input )
+}
+
+workflow test_fastk_fastk_paired_end {
+
+    input = [
+        [ id:'test' , single_end: false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FASTK_FASTK ( input )
+}
diff --git a/tests/modules/fastk/fastk/nextflow.config b/tests/modules/nf-core/fastk/fastk/nextflow.config
similarity index 100%
rename from tests/modules/fastk/fastk/nextflow.config
rename to tests/modules/nf-core/fastk/fastk/nextflow.config
diff --git a/tests/modules/nf-core/fastk/fastk/test.yml b/tests/modules/nf-core/fastk/fastk/test.yml
new file mode 100644
index 00000000000..fa075ca7f76
--- /dev/null
+++ b/tests/modules/nf-core/fastk/fastk/test.yml
@@ -0,0 +1,45 @@
+- name: fastk fastk test_fastk_fastk_single_end
+  command: nextflow run ./tests/modules/nf-core/fastk/fastk -entry test_fastk_fastk_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastk/fastk/nextflow.config
+  tags:
+    - fastk
+    - fastk/fastk
+  files:
+    - path: output/fastk/.test_fk.ktab.1
+      md5sum: ceeacd0cb3aa69bf9b2a402830b40e26
+    - path: output/fastk/.test_fk.ktab.2
+      md5sum: f2629fd15b285aed3dc2d5fe546edf3f
+    - path: output/fastk/.test_fk.pidx.1
+      md5sum: 90bc384f61d2ecdb4586ab52ab04fddf
+    - path: output/fastk/.test_fk.prof.1
+      md5sum: ebd48923a724cf79934f0b2ed42ba73d
+    - path: output/fastk/test_fk.hist
+      md5sum: c80e12f7321e62dba4b437d7bff36ec0
+    - path: output/fastk/test_fk.ktab
+      md5sum: a605a58931a4b5029469e1c2575c8cee
+    - path: output/fastk/test_fk.prof
+      md5sum: 43d426c95d277b8148406624d513bd40
+
+- name: fastk fastk test_fastk_fastk_paired_end
+  command: nextflow run ./tests/modules/nf-core/fastk/fastk -entry test_fastk_fastk_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastk/fastk/nextflow.config
+  tags:
+    - fastk
+    - fastk/fastk
+  files:
+    - path: output/fastk/.test_fk.ktab.1
+      md5sum: 7f28fb44940fda799797e3069f5d7263
+    - path: output/fastk/.test_fk.ktab.2
+      md5sum: c14a85c128926ace78372f09029977b1
+    - path: output/fastk/.test_fk.pidx.1
+      md5sum: e7e760f714070a4afefb38ffff559684
+    - path: output/fastk/.test_fk.pidx.2
+      md5sum: a549612bbdba2506eb3311237638c4b0
+    - path: output/fastk/.test_fk.prof.1
+      md5sum: 46a5fd9e297262b058f8c1fd062fcf56
+    - path: output/fastk/.test_fk.prof.2
+      md5sum: 80326a7406f41ccf2e51e341fc804132
+    - path: output/fastk/test_fk.hist
+      md5sum: 4f75b550d87ed4f26a2b10a05ac7e98c
+    - path: output/fastk/test_fk.ktab
+      md5sum: fddd5be0c36ad1d2131b8d8774f7657a
+    - path: output/fastk/test_fk.prof
+      md5sum: d3c7d8decd4ea6e298291b8be0e2de85
diff --git a/tests/modules/nf-core/fastk/histex/main.nf b/tests/modules/nf-core/fastk/histex/main.nf
new file mode 100644
index 00000000000..cc0f3f8ae79
--- /dev/null
+++ b/tests/modules/nf-core/fastk/histex/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTK_FASTK } from '../../../../../modules/nf-core/fastk/fastk/main.nf'
+include { FASTK_HISTEX } from '../../../../../modules/nf-core/fastk/histex/main.nf'
+
+workflow test_fastk_histex {
+
+    input = [
+        [ id:'test' , single_end: true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    FASTK_FASTK ( input )
+    FASTK_HISTEX ( FASTK_FASTK.out.hist )
+}
diff --git a/tests/modules/fastk/histex/nextflow.config b/tests/modules/nf-core/fastk/histex/nextflow.config
similarity index 100%
rename from tests/modules/fastk/histex/nextflow.config
rename to tests/modules/nf-core/fastk/histex/nextflow.config
diff --git a/tests/modules/nf-core/fastk/histex/test.yml b/tests/modules/nf-core/fastk/histex/test.yml
new file mode 100644
index 00000000000..df8e0d914e5
--- /dev/null
+++ b/tests/modules/nf-core/fastk/histex/test.yml
@@ -0,0 +1,8 @@
+- name: fastk histex test_fastk_histex
+  command: nextflow run ./tests/modules/nf-core/fastk/histex -entry test_fastk_histex -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastk/histex/nextflow.config
+  tags:
+    - fastk/histex
+    - fastk
+  files:
+    - path: output/fastk/test.hist
+      md5sum: e3f0c9e7641a46525123312008e4ae86
diff --git a/tests/modules/nf-core/fastk/merge/main.nf b/tests/modules/nf-core/fastk/merge/main.nf
new file mode 100644
index 00000000000..9ff9b338bae
--- /dev/null
+++ b/tests/modules/nf-core/fastk/merge/main.nf
@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTK_FASTK } from '../../../../../modules/nf-core/fastk/fastk/main.nf'
+include { FASTK_MERGE } from '../../../../../modules/nf-core/fastk/merge/main.nf'
+
+workflow test_fastk_merge_hist_only {
+
+    input1 = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    input2= [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FASTK_FASTK ( Channel.of( input1, input2 ) )
+    FASTK_MERGE (
+        FASTK_FASTK.out.hist.groupTuple()
+            .join( FASTK_FASTK.out.ktab.groupTuple(), remainder: true )
+            .join( FASTK_FASTK.out.prof.groupTuple(), remainder: true )
+            .map { meta, hist, ktab, prof -> [meta, hist, ktab ? ktab.flatten() : [] , prof ? prof.flatten() : [] ] }
+    )
+}
+
+workflow test_fastk_merge_all_files {
+
+    input1 = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    input2= [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FASTK_FASTK ( Channel.of( input1, input2 ) )
+    FASTK_MERGE (
+        FASTK_FASTK.out.hist.groupTuple()
+            .join( FASTK_FASTK.out.ktab.groupTuple(), remainder: true )
+            .join( FASTK_FASTK.out.prof.groupTuple(), remainder: true )
+            .map { meta, hist, ktab, prof -> [meta, hist, ktab ? ktab.flatten() : [] , prof ? prof.flatten() : [] ] }
+    )
+}
diff --git a/tests/modules/fastk/merge/nextflow.config b/tests/modules/nf-core/fastk/merge/nextflow.config
similarity index 100%
rename from tests/modules/fastk/merge/nextflow.config
rename to tests/modules/nf-core/fastk/merge/nextflow.config
diff --git a/tests/modules/nf-core/fastk/merge/test.yml b/tests/modules/nf-core/fastk/merge/test.yml
new file mode 100644
index 00000000000..d8fe5ccc666
--- /dev/null
+++ b/tests/modules/nf-core/fastk/merge/test.yml
@@ -0,0 +1,39 @@
+- name: fastk merge test_fastk_merge_hist_only
+  command: nextflow run ./tests/modules/nf-core/fastk/merge -entry test_fastk_merge_hist_only -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastk/merge/nextflow.config
+  tags:
+    - fastk/merge
+    - fastk
+  files:
+    - path: output/fastk/.test.ktab.1
+      md5sum: dff1e9d326aea87778645235cfa3380f
+    - path: output/fastk/.test.ktab.2
+      md5sum: 438e7807dcc2eb8120e1338838147600
+    - path: output/fastk/test.hist
+      md5sum: 75d41eb0e3f8af5456711a95966e2b00
+    - path: output/fastk/test.ktab
+      md5sum: 7d882f4e3542df1a2f5cb0858b12dc03
+
+- name: fastk merge test_fastk_merge_all_files
+  command: nextflow run ./tests/modules/nf-core/fastk/merge -entry test_fastk_merge_all_files -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastk/merge/nextflow.config
+  tags:
+    - fastk/merge
+    - fastk
+  files:
+    - path: output/fastk/.test.ktab.1
+      md5sum: dff1e9d326aea87778645235cfa3380f
+    - path: output/fastk/.test.ktab.2
+      md5sum: 438e7807dcc2eb8120e1338838147600
+    - path: output/fastk/.test.pidx.1
+      md5sum: 7553344778f6571192f04c7e659b967c
+    - path: output/fastk/.test.pidx.2
+      md5sum: 09bb65fb10db58d1fd5bb0a123fccfc6
+    - path: output/fastk/.test.prof.1
+      md5sum: 7f0f84a62c89063ec18c9b0e447afe93
+    - path: output/fastk/.test.prof.2
+      md5sum: 7f0f84a62c89063ec18c9b0e447afe93
+    - path: output/fastk/test.hist
+      md5sum: 75d41eb0e3f8af5456711a95966e2b00
+    - path: output/fastk/test.ktab
+      md5sum: 7d882f4e3542df1a2f5cb0858b12dc03
+    - path: output/fastk/test.prof
+      md5sum: d3c7d8decd4ea6e298291b8be0e2de85
diff --git a/tests/modules/nf-core/fastp/main.nf b/tests/modules/nf-core/fastp/main.nf
new file mode 100644
index 00000000000..6d433e25825
--- /dev/null
+++ b/tests/modules/nf-core/fastp/main.nf
@@ -0,0 +1,86 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTP } from '../../../../modules/nf-core/fastp/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_fastp_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    save_trimmed_fail = false
+    save_merged       = false
+
+    FASTP ( input, save_trimmed_fail, save_merged )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_fastp_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    save_trimmed_fail = false
+    save_merged       = false
+
+    FASTP ( input, save_trimmed_fail, save_merged )
+}
+
+//
+// Test with intereleaved data
+//
+workflow test_fastp_interleaved {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ]
+            ]
+    save_trimmed_fail = false
+    save_merged       = false
+
+    FASTP ( input, save_trimmed_fail, save_merged )
+}
+
+//
+// Test with single-end data with saving trimming fails
+//
+workflow test_fastp_single_end_trim_fail {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    save_trimmed_fail = true
+    save_merged       = false
+
+    FASTP ( input, save_trimmed_fail, save_merged )
+}
+
+//
+// Test with paired-end data with saving trimming fails
+//
+workflow test_fastp_paired_end_trim_fail {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    save_trimmed_fail = true
+    save_merged       = false
+
+    FASTP ( input, save_trimmed_fail, save_merged )
+}
+
+//
+// Test with paired-end data with merging
+//
+workflow test_fastp_paired_end_merged {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    save_trimmed_fail = false
+    save_merged       = true
+
+    FASTP ( input, save_trimmed_fail, save_merged )
+}
diff --git a/tests/modules/fastp/nextflow.config b/tests/modules/nf-core/fastp/nextflow.config
similarity index 100%
rename from tests/modules/fastp/nextflow.config
rename to tests/modules/nf-core/fastp/nextflow.config
diff --git a/tests/modules/nf-core/fastp/test.yml b/tests/modules/nf-core/fastp/test.yml
new file mode 100644
index 00000000000..c8e93ad7f9a
--- /dev/null
+++ b/tests/modules/nf-core/fastp/test.yml
@@ -0,0 +1,191 @@
+- name: fastp test_fastp_single_end
+  command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+  tags:
+    - fastp
+  files:
+    - path: output/fastp/test.fastp.fastq.gz
+      contains:
+        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
+        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
+        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
+        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
+        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
+        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
+    - path: output/fastp/test.fastp.html
+      contains:
+        - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
+        - "single end (151 cycles)"
+    - path: output/fastp/test.fastp.json
+      md5sum: 2616b6791fd89fb1cc2d16a73b9463b0
+    - path: output/fastp/test.fastp.log
+      contains:
+        - "Q20 bases: 12922(92.9841%)"
+        - "reads passed filter: 99"
+
+- name: fastp test_fastp_paired_end
+  command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+  tags:
+    - fastp
+  files:
+    - path: output/fastp/test.fastp.html
+      contains:
+        - "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
+        - "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
+    - path: output/fastp/test.fastp.json
+      contains:
+        - '"passed_filter_reads": 198'
+    - path: output/fastp/test.fastp.log
+      contains:
+        - "No adapter detected for read1"
+        - "Q30 bases: 12281(88.3716%)"
+    - path: output/fastp/test_1.fastp.fastq.gz
+      contains:
+        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
+        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
+        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
+        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
+        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
+        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
+    - path: output/fastp/test_2.fastp.fastq.gz
+      contains:
+        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
+        - "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
+        - "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
+        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/2"
+        - "GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT"
+        - "AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE"
+
+- name: fastp test_fastp_interleaved
+  command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_interleaved -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+  tags:
+    - fastp
+  files:
+    - path: output/fastp/test.fastp.fastq.gz
+      contains:
+        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
+        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
+        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
+        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
+        - "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
+        - "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
+    - path: output/fastp/test.fastp.html
+      contains:
+        - "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
+        - "paired end (151 cycles + 151 cycles)"
+    - path: output/fastp/test.fastp.json
+      md5sum: 25ec85e3534f380ca2109c894671f1ed
+    - path: output/fastp/test.fastp.log
+      contains:
+        - "Q20 bases: 12922(92.9841%)"
+        - "reads passed filter: 198"
+
+- name: fastp test_fastp_single_end_trim_fail
+  command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+  tags:
+    - fastp
+  files:
+    - path: output/fastp/test.fail.fastq.gz
+      contains:
+        - "@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/1 failed_quality_filter"
+        - "GTCTAATCATAATTTCTTGGTACAGGCTGGTATTGTTCATCTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTT"
+        - "AAA//E/EAA/E//E//E//E/E//AE/A/E//EAEA///AE//E///E/EEE6EEEAEEA///E/AEE/EAEE/E//E"
+    - path: output/fastp/test.fastp.fastq.gz
+      contains:
+        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
+        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
+        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
+        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
+        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
+        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
+    - path: output/fastp/test.fastp.html
+      contains:
+        - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
+        - "single end (151 cycles)"
+    - path: output/fastp/test.fastp.json
+      md5sum: 7e10b0b12fab5cff620fdeb1a32392f8
+    - path: output/fastp/test.fastp.log
+      contains:
+        - "Q20 bases: 12922(92.9841%)"
+        - "reads passed filter: 99"
+
+- name: fastp test_fastp_paired_end_trim_fail
+  command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+  tags:
+    - fastp
+  files:
+    - path: output/fastp/test.fastp.html
+      contains:
+        - "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
+        - "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
+    - path: output/fastp/test.fastp.log
+      contains:
+        - "No adapter detected for read1"
+        - "Q30 bases: 12281(88.3716%)"
+    - path: output/fastp/test.fastp.json
+      contains:
+        - '"passed_filter_reads": 198'
+    - path: output/fastp/test_1.fastp.fastq.gz
+      contains:
+        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
+        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
+        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
+        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
+        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
+        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
+    - path: output/fastp/test_2.fastp.fastq.gz
+      contains:
+        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
+        - "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
+        - "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
+        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/2"
+        - "GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT"
+        - "AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE"
+    - path: output/fastp/test_1.fail.fastq.gz
+    - path: output/fastp/test_2.fail.fastq.gz
+      contains:
+        - "@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/2"
+        - "CTTAGGTCTTAGGATTGGCTGTATCAACCTTAAGCTTAAGTACACAATTTTGCATAGAATGTCCAATAA"
+        - "A//AA6EEAEEEEE6EEE/EEA/EA///AAE/EAEEEAE6AE/E/E/EEAAE/EAA/E/E/<EA//E/6"
+
+- name: fastp test_fastp_paired_end_merged
+  command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+  tags:
+    - fastp
+  files:
+    - path: output/fastp/test.fastp.html
+      contains:
+        - "<div id='After_filtering__merged__quality'>"
+    - path: output/fastp/test.fastp.json
+      contains:
+        - '"merged_and_filtered": {'
+        - '"total_reads": 75'
+        - '"total_bases": 13683'
+    - path: output/fastp/test.fastp.log
+      contains:
+        - "Merged and filtered:"
+        - "total reads: 75"
+        - "total bases: 13683"
+    - path: output/fastp/test_1.fastp.fastq.gz
+      contains:
+        - "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1"
+        - "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC"
+        - "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE<AEEAEEEAEAEEEAEAEEAE/AEEEEAEEEEAEA"
+        - "@ERR5069949.324865 NS500628:121:HK3MMAFX2:1:11102:17526:14721/1"
+        - "CACAAACTCTAAAAGAATGTATAGGGTCAGCACCAAAAATACCAGCAGATAATAATGTTGCAAGTAGAACTTCGTGCAGATTAAAATTTTCATAAGCACTCTAAAGAAGTTGAATGTCTTCAAATTTCTTAACATTAGGGCCCACAACAAG"
+        - "AAAAAEA/A<EAA/AE/EE/EE//////EA/EEE/E/EEEE//E/6//EA//<AA/A/EEEAA/EEEE/EEEA/E/</AEE////AEEEE//<E//EAE/A///<EEE//<E<<EEE<///A//E/E/EEEAA/<A////<A/AEAAA//E"
+    - path: output/fastp/test_2.fastp.fastq.gz
+      contains:
+        - "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/2"
+        - "GTACAAAAATAGCCTAAGAAACAATAAACTAGCATTATACACTGAAGTGTATTACCAGTTATGAAGAAAATAGGGCAATACTCAACACACATAAAAACAATACCTCTGGCCAAAAACATGACAGTTGTAACTACACCTGAGTAGTTAGAAG"
+        - "AAAAAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEA/EAA</EEEEEEEEEE/AE//A/E<AE<AA<AEEE/AAEAAAEEAEEA<A6AEEA<EEAEEEEEEEAA//EE"
+        - "@ERR5069949.324865 NS500628:121:HK3MMAFX2:1:11102:17526:14721/2"
+        - "ATGAATCTGATGAATACATAGCTACTAATGGACCTCTTAAAGTGCGTGGTAGTTGTGATTAAAGCGGACACATACTTGCTAAACACTCTCTTCATGATGTC"
+        - "A/AAAEEEEA6AA6EE//EEA/EEEAE/EA/A////E</EEAA//EEA////EAE<///E/AEA</AAE/EA//E<EAAAE/AA//AEE//A/AE//</EE"
+    - path: output/fastp/test.merged.fastq.gz
+      contains:
+        - "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1 merged_150_37"
+        - "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGTGGTGCAGGTAATTGAGCAGGGTCGCCAATGTACACAT"
+        - "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAAEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEAAAAA"
+        - "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1 merged_77_0"
+        - "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
+        - "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
diff --git a/tests/modules/nf-core/fastqc/main.nf b/tests/modules/nf-core/fastqc/main.nf
new file mode 100644
index 00000000000..ebb3660f761
--- /dev/null
+++ b/tests/modules/nf-core/fastqc/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTQC } from '../../../../modules/nf-core/fastqc/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_fastqc_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    FASTQC ( input )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_fastqc_paired_end {
+    input = [ [id: 'test', single_end: false], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    FASTQC ( input )
+}
diff --git a/tests/modules/fastqc/nextflow.config b/tests/modules/nf-core/fastqc/nextflow.config
similarity index 100%
rename from tests/modules/fastqc/nextflow.config
rename to tests/modules/nf-core/fastqc/nextflow.config
diff --git a/tests/modules/nf-core/fastqc/test.yml b/tests/modules/nf-core/fastqc/test.yml
new file mode 100644
index 00000000000..920010db690
--- /dev/null
+++ b/tests/modules/nf-core/fastqc/test.yml
@@ -0,0 +1,17 @@
+- name: fastqc single-end
+  command: nextflow run ./tests/modules/nf-core/fastqc/ -entry test_fastqc_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqc/nextflow.config -c ./tests/modules/nf-core/fastqc/nextflow.config
+  tags:
+    - fastqc
+  files:
+    - path: ./output/fastqc/test_fastqc.html
+    - path: ./output/fastqc/test_fastqc.zip
+
+- name: fastqc paired-end
+  command: nextflow run ./tests/modules/nf-core/fastqc/ -entry test_fastqc_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqc/nextflow.config -c ./tests/modules/nf-core/fastqc/nextflow.config
+  tags:
+    - fastqc
+  files:
+    - path: ./output/fastqc/test_1_fastqc.html
+    - path: ./output/fastqc/test_2_fastqc.html
+    - path: ./output/fastqc/test_2_fastqc.zip
+    - path: ./output/fastqc/test_1_fastqc.zip
diff --git a/tests/modules/nf-core/fastqscan/main.nf b/tests/modules/nf-core/fastqscan/main.nf
new file mode 100644
index 00000000000..a51053efab6
--- /dev/null
+++ b/tests/modules/nf-core/fastqscan/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTQSCAN } from '../../../../modules/nf-core/fastqscan/main.nf'
+
+workflow test_fastqscan {
+    
+    input = [ [ id:'test', single_end:true ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+
+    FASTQSCAN ( input )
+}
diff --git a/tests/modules/fastqscan/nextflow.config b/tests/modules/nf-core/fastqscan/nextflow.config
similarity index 100%
rename from tests/modules/fastqscan/nextflow.config
rename to tests/modules/nf-core/fastqscan/nextflow.config
diff --git a/tests/modules/nf-core/fastqscan/test.yml b/tests/modules/nf-core/fastqscan/test.yml
new file mode 100644
index 00000000000..e6d2da77762
--- /dev/null
+++ b/tests/modules/nf-core/fastqscan/test.yml
@@ -0,0 +1,7 @@
+- name: fastqscan test_fastqscan
+  command: nextflow run ./tests/modules/nf-core/fastqscan -entry test_fastqscan -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqscan/nextflow.config
+  tags:
+    - fastqscan
+  files:
+    - path: output/fastqscan/test.json
+      md5sum: b9d59a36fe85e556b5a80573ea0b0266
diff --git a/tests/modules/nf-core/fasttree/main.nf b/tests/modules/nf-core/fasttree/main.nf
new file mode 100644
index 00000000000..a7ce7f0d214
--- /dev/null
+++ b/tests/modules/nf-core/fasttree/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTTREE } from '../../../../modules/nf-core/fasttree/main.nf'
+
+workflow test_fasttree {
+    
+    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
+
+    FASTTREE ( input )
+}
diff --git a/tests/modules/fasttree/nextflow.config b/tests/modules/nf-core/fasttree/nextflow.config
similarity index 100%
rename from tests/modules/fasttree/nextflow.config
rename to tests/modules/nf-core/fasttree/nextflow.config
diff --git a/tests/modules/nf-core/fasttree/test.yml b/tests/modules/nf-core/fasttree/test.yml
new file mode 100644
index 00000000000..e537a1e280f
--- /dev/null
+++ b/tests/modules/nf-core/fasttree/test.yml
@@ -0,0 +1,7 @@
+- name: fasttree
+  command: nextflow run ./tests/modules/nf-core/fasttree -entry test_fasttree -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fasttree/nextflow.config
+  tags:
+    - fasttree
+  files:
+    - path: output/fasttree/fasttree_phylogeny.tre
+      md5sum: 63a886117535847c1e66fa4487f3b7d2
diff --git a/tests/modules/nf-core/fcs/fcsadaptor/main.nf b/tests/modules/nf-core/fcs/fcsadaptor/main.nf
new file mode 100644
index 00000000000..b6f38e0d8d6
--- /dev/null
+++ b/tests/modules/nf-core/fcs/fcsadaptor/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FCS_FCSADAPTOR } from '../../../../../modules/nf-core/fcs/fcsadaptor/main.nf'
+
+workflow test_fcs_fcsadaptor {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+
+    FCS_FCSADAPTOR ( input )
+}
diff --git a/tests/modules/fcs/fcsadaptor/nextflow.config b/tests/modules/nf-core/fcs/fcsadaptor/nextflow.config
similarity index 100%
rename from tests/modules/fcs/fcsadaptor/nextflow.config
rename to tests/modules/nf-core/fcs/fcsadaptor/nextflow.config
diff --git a/tests/modules/nf-core/fcs/fcsadaptor/test.yml b/tests/modules/nf-core/fcs/fcsadaptor/test.yml
new file mode 100644
index 00000000000..d9e63dcd6aa
--- /dev/null
+++ b/tests/modules/nf-core/fcs/fcsadaptor/test.yml
@@ -0,0 +1,15 @@
+- name: fcs fcsadaptor test_fcs_fcsadaptor
+  command: nextflow run ./tests/modules/nf-core/fcs/fcsadaptor -entry test_fcs_fcsadaptor -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fcs/fcsadaptor/nextflow.config
+  tags:
+    - fcs/fcsadaptor
+    - fcs
+  files:
+    - path: output/fcs/test.cleaned_sequences.fa.gz
+      md5sum: 2f331e59b352418420a35236091bf93c
+    - path: output/fcs/test.fcs_adaptor.log
+      contains: ["Original command:", "Executing:", "INFO:cwltool:[workflow ] completed success"]
+    - path: output/fcs/test.fcs_adaptor_report.txt
+      md5sum: 27375be4671e01d2d2674ddd1d44414a
+    - path: output/fcs/test.pipeline_args.yaml
+      md5sum: 80effed2a75550a6a861c47f4c30449d
+    - path: output/fcs/test.skipped_trims.jsonl
diff --git a/tests/modules/nf-core/ffq/main.nf b/tests/modules/nf-core/ffq/main.nf
new file mode 100644
index 00000000000..1546fc97599
--- /dev/null
+++ b/tests/modules/nf-core/ffq/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FFQ } from '../../../../modules/nf-core/ffq/main.nf'
+
+workflow test_ffq_single_id {
+
+    FFQ ( [ 'SRR9990627' ] )
+}
+
+workflow test_ffq_multiple_ids {
+
+    FFQ ( [ 'SRR9990627', 'SRX7347523' ] )
+}
diff --git a/tests/modules/ffq/nextflow.config b/tests/modules/nf-core/ffq/nextflow.config
similarity index 100%
rename from tests/modules/ffq/nextflow.config
rename to tests/modules/nf-core/ffq/nextflow.config
diff --git a/tests/modules/nf-core/ffq/test.yml b/tests/modules/nf-core/ffq/test.yml
new file mode 100644
index 00000000000..bdbd9295e1d
--- /dev/null
+++ b/tests/modules/nf-core/ffq/test.yml
@@ -0,0 +1,15 @@
+- name: ffq test_ffq_single_id
+  command: nextflow run ./tests/modules/nf-core/ffq -entry test_ffq_single_id -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ffq/nextflow.config
+  tags:
+    - ffq
+  files:
+    - path: output/ffq/SRR9990627.json
+      md5sum: 68db6114ef348f721c139cd4c9534f73
+
+- name: ffq test_ffq_multiple_ids
+  command: nextflow run ./tests/modules/nf-core/ffq -entry test_ffq_multiple_ids -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ffq/nextflow.config
+  tags:
+    - ffq
+  files:
+    - path: output/ffq/metadata.json
+      md5sum: af253a5587b54520f01a0ff5715b0c0a
diff --git a/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf
new file mode 100644
index 00000000000..33364cc85e7
--- /dev/null
+++ b/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FGBIO_SORTBAM } from '../../../../../modules/nf-core/fgbio/sortbam/main.nf'
+include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../../modules/nf-core/fgbio/callmolecularconsensusreads/main.nf'
+
+workflow test_fgbio_callmolecularconsensusreads {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
+    FGBIO_SORTBAM ( input )
+    FGBIO_CALLMOLECULARCONSENSUSREADS ( FGBIO_SORTBAM.out.bam  )
+}
diff --git a/tests/modules/fgbio/callmolecularconsensusreads/nextflow.config b/tests/modules/nf-core/fgbio/callmolecularconsensusreads/nextflow.config
similarity index 100%
rename from tests/modules/fgbio/callmolecularconsensusreads/nextflow.config
rename to tests/modules/nf-core/fgbio/callmolecularconsensusreads/nextflow.config
diff --git a/tests/modules/nf-core/fgbio/callmolecularconsensusreads/test.yml b/tests/modules/nf-core/fgbio/callmolecularconsensusreads/test.yml
new file mode 100644
index 00000000000..22ae2ce2638
--- /dev/null
+++ b/tests/modules/nf-core/fgbio/callmolecularconsensusreads/test.yml
@@ -0,0 +1,10 @@
+- name: fgbio callmolecularconsensusreads
+  command: nextflow run ./tests/modules/nf-core/fgbio/callmolecularconsensusreads -entry test_fgbio_callmolecularconsensusreads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fgbio/callmolecularconsensusreads/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/callmolecularconsensusreads
+  files:
+    - path: output/fgbio/test_molreads.bam
+      md5sum: 6ae57429e3218f5eba9555d597b7c60f
+    - path: output/fgbio/test_out.bam
+      md5sum: d84e28fecc90c0752c543e934f10aa31
diff --git a/tests/modules/nf-core/fgbio/fastqtobam/main.nf b/tests/modules/nf-core/fgbio/fastqtobam/main.nf
new file mode 100644
index 00000000000..79d58ebad46
--- /dev/null
+++ b/tests/modules/nf-core/fgbio/fastqtobam/main.nf
@@ -0,0 +1,83 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FGBIO_FASTQTOBAM } from '../../../../../modules/nf-core/fgbio/fastqtobam/main.nf'
+
+workflow test_fgbio_fastqtobam_paired_default {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
+
+
+workflow test_fgbio_fastqtobam_paired_cram {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
+
+workflow test_fgbio_fastqtobam_paired_bam {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
+
+workflow test_fgbio_fastqtobam_single {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
+
+workflow test_fgbio_fastqtobam_paired_umi {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
+
+workflow test_fgbio_fastqtobam_paired_custom_samplename {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
diff --git a/tests/modules/fgbio/fastqtobam/nextflow.config b/tests/modules/nf-core/fgbio/fastqtobam/nextflow.config
similarity index 100%
rename from tests/modules/fgbio/fastqtobam/nextflow.config
rename to tests/modules/nf-core/fgbio/fastqtobam/nextflow.config
diff --git a/tests/modules/nf-core/fgbio/fastqtobam/test.yml b/tests/modules/nf-core/fgbio/fastqtobam/test.yml
new file mode 100644
index 00000000000..e8432ad7747
--- /dev/null
+++ b/tests/modules/nf-core/fgbio/fastqtobam/test.yml
@@ -0,0 +1,52 @@
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_default
+  command: nextflow run ./tests/modules/nf-core/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_default -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: 83cd60e01e5ab90ea3729431ce401add
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_cram
+  command: nextflow run ./tests/modules/nf-core/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.cram
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_bam
+  command: nextflow run ./tests/modules/nf-core/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_bam -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: 83f879e3a302ca8a50dc9675be7a9216
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_single
+  command: nextflow run ./tests/modules/nf-core/fgbio/fastqtobam -entry test_fgbio_fastqtobam_single -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: c08fe1b035b972808f05128e37e8e669
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_umi
+  command: nextflow run ./tests/modules/nf-core/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_umi -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: 9510735554e5eff29244077a72075fb6
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_custom_samplename
+  command: nextflow run ./tests/modules/nf-core/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_custom_samplename -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: ab8d7d2d9c1559b19a501d120296ebe0
diff --git a/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf
new file mode 100644
index 00000000000..8082f60168d
--- /dev/null
+++ b/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FGBIO_GROUPREADSBYUMI } from '../../../../../modules/nf-core/fgbio/groupreadsbyumi/main.nf'
+
+workflow test_fgbio_groupreadsbyumi {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_unsorted_tagged_bam'], checkIfExists: true)
+    ]
+
+    FGBIO_GROUPREADSBYUMI ( input, 'Adjacency' )
+}
diff --git a/tests/modules/fgbio/groupreadsbyumi/nextflow.config b/tests/modules/nf-core/fgbio/groupreadsbyumi/nextflow.config
similarity index 100%
rename from tests/modules/fgbio/groupreadsbyumi/nextflow.config
rename to tests/modules/nf-core/fgbio/groupreadsbyumi/nextflow.config
diff --git a/tests/modules/nf-core/fgbio/groupreadsbyumi/test.yml b/tests/modules/nf-core/fgbio/groupreadsbyumi/test.yml
new file mode 100644
index 00000000000..373a02cc321
--- /dev/null
+++ b/tests/modules/nf-core/fgbio/groupreadsbyumi/test.yml
@@ -0,0 +1,10 @@
+- name: fgbio groupreadsbyumi test_fgbio_groupreadsbyumi
+  command: nextflow run ./tests/modules/nf-core/fgbio/groupreadsbyumi -entry test_fgbio_groupreadsbyumi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fgbio/groupreadsbyumi/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/groupreadsbyumi
+  files:
+    - path: output/fgbio/test_umi-grouped.bam
+      md5sum: c7a9aee0b9b277c85d6a112d3021082d
+    - path: output/fgbio/test_umi_histogram.txt
+      md5sum: f2f29523bb7016e1a78fe634466cbfba
diff --git a/tests/modules/nf-core/fgbio/sortbam/main.nf b/tests/modules/nf-core/fgbio/sortbam/main.nf
new file mode 100644
index 00000000000..99d78230d7f
--- /dev/null
+++ b/tests/modules/nf-core/fgbio/sortbam/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FGBIO_SORTBAM } from '../../../../../modules/nf-core/fgbio/sortbam/main.nf'
+
+workflow test_fgbio_sortbam {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    FGBIO_SORTBAM ( input )
+}
diff --git a/tests/modules/fgbio/sortbam/nextflow.config b/tests/modules/nf-core/fgbio/sortbam/nextflow.config
similarity index 100%
rename from tests/modules/fgbio/sortbam/nextflow.config
rename to tests/modules/nf-core/fgbio/sortbam/nextflow.config
diff --git a/tests/modules/nf-core/fgbio/sortbam/test.yml b/tests/modules/nf-core/fgbio/sortbam/test.yml
new file mode 100644
index 00000000000..be7dc69b1e7
--- /dev/null
+++ b/tests/modules/nf-core/fgbio/sortbam/test.yml
@@ -0,0 +1,8 @@
+- name: fgbio sortbam
+  command: nextflow run ./tests/modules/nf-core/fgbio/sortbam -entry test_fgbio_sortbam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fgbio/sortbam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/sortbam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: 56987f74214cdc72ae840e0007ff4935
diff --git a/tests/modules/nf-core/filtlong/main.nf b/tests/modules/nf-core/filtlong/main.nf
new file mode 100644
index 00000000000..cf45097145b
--- /dev/null
+++ b/tests/modules/nf-core/filtlong/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FILTLONG } from '../../../../modules/nf-core/filtlong/main.nf'
+
+workflow test_filtlong {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [],
+              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    FILTLONG ( input )
+}
+
+workflow test_filtlong_illumina_se {
+    
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ],
+              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    FILTLONG ( input )
+}
+
+workflow test_filtlong_illumina_pe {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
+              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    FILTLONG ( input )
+}
diff --git a/tests/modules/filtlong/nextflow.config b/tests/modules/nf-core/filtlong/nextflow.config
similarity index 100%
rename from tests/modules/filtlong/nextflow.config
rename to tests/modules/nf-core/filtlong/nextflow.config
diff --git a/tests/modules/nf-core/filtlong/test.yml b/tests/modules/nf-core/filtlong/test.yml
new file mode 100644
index 00000000000..44b3660461a
--- /dev/null
+++ b/tests/modules/nf-core/filtlong/test.yml
@@ -0,0 +1,26 @@
+- name: filtlong test_filtlong
+  command: nextflow run ./tests/modules/nf-core/filtlong -entry test_filtlong -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/filtlong/nextflow.config
+  tags:
+    - filtlong
+  files:
+    - path: output/filtlong/test_lr.fastq.gz
+    - path: output/filtlong/test_lr.log
+      contains: ["Scoring long reads"]
+
+- name: filtlong test_filtlong_illumina_se
+  command: nextflow run ./tests/modules/nf-core/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/filtlong/nextflow.config
+  tags:
+    - filtlong
+  files:
+    - path: output/filtlong/test_lr.fastq.gz
+    - path: output/filtlong/test_lr.log
+      contains: ["Scoring long reads"]
+
+- name: filtlong test_filtlong_illumina_pe
+  command: nextflow run ./tests/modules/nf-core/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/filtlong/nextflow.config
+  tags:
+    - filtlong
+  files:
+    - path: output/filtlong/test_lr.fastq.gz
+    - path: output/filtlong/test_lr.log
+      contains: ["Scoring long reads"]
diff --git a/tests/modules/nf-core/flash/main.nf b/tests/modules/nf-core/flash/main.nf
new file mode 100644
index 00000000000..2e3bd94c858
--- /dev/null
+++ b/tests/modules/nf-core/flash/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FLASH } from '../../../../modules/nf-core/flash/main.nf'
+
+workflow test_flash {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    FLASH ( input )
+}
diff --git a/tests/modules/flash/nextflow.config b/tests/modules/nf-core/flash/nextflow.config
similarity index 100%
rename from tests/modules/flash/nextflow.config
rename to tests/modules/nf-core/flash/nextflow.config
diff --git a/tests/modules/nf-core/flash/test.yml b/tests/modules/nf-core/flash/test.yml
new file mode 100644
index 00000000000..042c94aa34b
--- /dev/null
+++ b/tests/modules/nf-core/flash/test.yml
@@ -0,0 +1,8 @@
+- name: flash test_flash
+  command: nextflow run ./tests/modules/nf-core/flash -entry test_flash -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/flash/nextflow.config
+  tags:
+    - flash
+  files:
+    - path: output/flash/test.notCombined_2.fastq.gz
+    - path: output/flash/test.extendedFrags.fastq.gz
+    - path: output/flash/test.notCombined_1.fastq.gz
diff --git a/tests/modules/nf-core/flye/main.nf b/tests/modules/nf-core/flye/main.nf
new file mode 100644
index 00000000000..aef37343ecf
--- /dev/null
+++ b/tests/modules/nf-core/flye/main.nf
@@ -0,0 +1,71 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FLYE } from '../../../../modules/nf-core/flye/main.nf'
+
+workflow test_flye_pacbio_raw {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
+    ]
+    mode = "--pacbio-raw"
+
+    FLYE ( input, mode )
+}
+
+workflow test_flye_pacbio_corr {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
+    ]
+    mode = "--pacbio-corr"
+
+    FLYE ( input, mode )
+}
+
+workflow test_flye_pacbio_hifi {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
+    ]
+    mode = "--pacbio-hifi"
+
+    FLYE ( input, mode )
+}
+
+workflow test_flye_nano_raw {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
+    ]
+    mode = "--nano-raw"
+
+    FLYE ( input, mode )
+}
+
+workflow test_flye_nano_corr {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
+    ]
+    mode = "--nano-corr"
+
+    FLYE ( input, mode )
+}
+
+workflow test_flye_nano_hq {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
+    ]
+    mode = "--nano-hq"
+
+    FLYE ( input, mode )
+}
diff --git a/tests/modules/flye/nextflow.config b/tests/modules/nf-core/flye/nextflow.config
similarity index 100%
rename from tests/modules/flye/nextflow.config
rename to tests/modules/nf-core/flye/nextflow.config
diff --git a/tests/modules/nf-core/flye/test.yml b/tests/modules/nf-core/flye/test.yml
new file mode 100644
index 00000000000..e12b02af913
--- /dev/null
+++ b/tests/modules/nf-core/flye/test.yml
@@ -0,0 +1,85 @@
+# According to the issue https://github.com/fenderglass/Flye/issues/164
+# Some fluctuations are expected because of the heuristics
+# Here we check the that test.assembly_info.txt contains at least one contig
+
+- name: flye test_flye_pacbio_raw
+  command: nextflow run ./tests/modules/nf-core/flye -entry test_flye_pacbio_raw -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/flye/nextflow.config -stub-run
+  tags:
+    - flye
+  files:
+    - path: output/flye/test.assembly.fasta.gz
+    - path: output/flye/test.assembly_graph.gfa.gz
+    - path: output/flye/test.assembly_graph.gv.gz
+    - path: output/flye/test.assembly_info.txt
+      contains: ["contig_1"]
+    - path: output/flye/test.flye.log
+    - path: output/flye/test.params.json
+
+- name: flye test_flye_pacbio_corr
+  command: nextflow run ./tests/modules/nf-core/flye -entry test_flye_pacbio_corr -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/flye/nextflow.config
+  tags:
+    - flye
+  files:
+    - path: output/flye/test.assembly.fasta.gz
+    - path: output/flye/test.assembly_graph.gfa.gz
+    - path: output/flye/test.assembly_graph.gv.gz
+    - path: output/flye/test.assembly_info.txt
+      contains: ["contig_1"]
+    - path: output/flye/test.flye.log
+    - path: output/flye/test.params.json
+      md5sum: 54b576cb6d4d27656878a7fd3657bde9
+
+- name: flye test_flye_pacbio_hifi
+  command: nextflow run ./tests/modules/nf-core/flye -entry test_flye_pacbio_hifi -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/flye/nextflow.config
+  tags:
+    - flye
+  files:
+    - path: output/flye/test.assembly.fasta.gz
+    - path: output/flye/test.assembly_graph.gfa.gz
+    - path: output/flye/test.assembly_graph.gv.gz
+    - path: output/flye/test.assembly_info.txt
+      contains: ["contig_1"]
+    - path: output/flye/test.flye.log
+    - path: output/flye/test.params.json
+      md5sum: 54b576cb6d4d27656878a7fd3657bde9
+
+- name: flye test_flye_nano_raw
+  command: nextflow run ./tests/modules/nf-core/flye -entry test_flye_nano_raw -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/flye/nextflow.config -stub-run
+  tags:
+    - flye
+  files:
+    - path: output/flye/test.assembly.fasta.gz
+    - path: output/flye/test.assembly_graph.gfa.gz
+    - path: output/flye/test.assembly_graph.gv.gz
+    - path: output/flye/test.assembly_info.txt
+      contains: ["contig_1"]
+    - path: output/flye/test.flye.log
+    - path: output/flye/test.params.json
+
+- name: flye test_flye_nano_corr
+  command: nextflow run ./tests/modules/nf-core/flye -entry test_flye_nano_corr -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/flye/nextflow.config
+  tags:
+    - flye
+  files:
+    - path: output/flye/test.assembly.fasta.gz
+    - path: output/flye/test.assembly_graph.gfa.gz
+    - path: output/flye/test.assembly_graph.gv.gz
+    - path: output/flye/test.assembly_info.txt
+      contains: ["contig_1"]
+    - path: output/flye/test.flye.log
+    - path: output/flye/test.params.json
+      md5sum: 54b576cb6d4d27656878a7fd3657bde9
+
+- name: flye test_flye_nano_hq
+  command: nextflow run ./tests/modules/nf-core/flye -entry test_flye_nano_hq -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/flye/nextflow.config
+  tags:
+    - flye
+  files:
+    - path: output/flye/test.assembly.fasta.gz
+    - path: output/flye/test.assembly_graph.gfa.gz
+    - path: output/flye/test.assembly_graph.gv.gz
+    - path: output/flye/test.assembly_info.txt
+      contains: ["contig_1"]
+    - path: output/flye/test.flye.log
+    - path: output/flye/test.params.json
+      md5sum: 54b576cb6d4d27656878a7fd3657bde9
diff --git a/tests/modules/nf-core/fq/lint/main.nf b/tests/modules/nf-core/fq/lint/main.nf
new file mode 100644
index 00000000000..97a18da7910
--- /dev/null
+++ b/tests/modules/nf-core/fq/lint/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FQ_LINT } from '../../../../../modules/nf-core/fq/lint/main.nf'
+
+workflow test_fq_lint_success {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FQ_LINT ( input )
+}
+
+workflow test_fq_lint_fail {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FQ_LINT ( input )
+}
diff --git a/tests/modules/fq/lint/nextflow.config b/tests/modules/nf-core/fq/lint/nextflow.config
similarity index 100%
rename from tests/modules/fq/lint/nextflow.config
rename to tests/modules/nf-core/fq/lint/nextflow.config
diff --git a/tests/modules/nf-core/fq/lint/test.yml b/tests/modules/nf-core/fq/lint/test.yml
new file mode 100644
index 00000000000..e0037cc680c
--- /dev/null
+++ b/tests/modules/nf-core/fq/lint/test.yml
@@ -0,0 +1,18 @@
+- name: fq lint test_fq_lint_success
+  command: nextflow run ./tests/modules/nf-core/fq/lint -entry test_fq_lint_success -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fq/lint/nextflow.config
+  tags:
+    - fq
+    - fq/lint
+  files:
+    - path: output/fq/test.fq_lint.txt
+      contains:
+        - "fq-lint start"
+        - "read 100 records"
+        - "fq-lint end"
+
+- name: fq lint test_fq_lint_fail
+  command: nextflow run ./tests/modules/nf-core/fq/lint -entry test_fq_lint_fail -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fq/lint/nextflow.config
+  tags:
+    - fq
+    - fq/lint
+  exit_code: 1
diff --git a/tests/modules/nf-core/freebayes/main.nf b/tests/modules/nf-core/freebayes/main.nf
new file mode 100644
index 00000000000..4c4a1031f34
--- /dev/null
+++ b/tests/modules/nf-core/freebayes/main.nf
@@ -0,0 +1,102 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FREEBAYES } from '../../../../modules/nf-core/freebayes/main.nf'
+
+workflow test_freebayes {
+    targets     = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+              [],
+              [],
+              targets
+            ]
+    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai         = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, samples, populations, cnv)
+}
+
+workflow test_freebayes_bed {
+
+    targets     = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+              [],
+              [],
+              targets
+            ]
+    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai         = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, samples, populations, cnv)
+}
+
+workflow test_freebayes_cram {
+
+    targets     = []
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+              [],
+              [],
+              targets
+            ]
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai         = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, samples, populations, cnv)
+}
+
+workflow test_freebayes_somatic {
+
+    targets     = []
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
+                targets
+            ]
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai         = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, samples, populations, cnv)
+}
+
+workflow test_freebayes_somatic_cram_intervals {
+
+    targets     = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),
+                targets
+            ]
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai         = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, samples, populations, cnv)
+}
diff --git a/tests/modules/freebayes/nextflow.config b/tests/modules/nf-core/freebayes/nextflow.config
similarity index 100%
rename from tests/modules/freebayes/nextflow.config
rename to tests/modules/nf-core/freebayes/nextflow.config
diff --git a/tests/modules/nf-core/freebayes/test.yml b/tests/modules/nf-core/freebayes/test.yml
new file mode 100644
index 00000000000..6148591bd82
--- /dev/null
+++ b/tests/modules/nf-core/freebayes/test.yml
@@ -0,0 +1,49 @@
+- name: freebayes test_freebayes
+  command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes -c ./tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: f28d0b8e2ccedeac0e590ca2ecaac83d
+    - path: output/freebayes/versions.yml
+      md5sum: 53651eb835af65df829241257584a7d2
+
+- name: freebayes test_freebayes_bed
+  command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_bed -c ./tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: 1927441d1b7a4c48cbb61821de300ad4
+    - path: output/freebayes/versions.yml
+      md5sum: becc93c8a0be580c09d55b955d60a5e1
+
+- name: freebayes test_freebayes_cram
+  command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_cram -c ./tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: 9b8d1d51d779bbea4086c7f7a2ece641
+    - path: output/freebayes/versions.yml
+      md5sum: 2e5b266edfc6cab81353cfc72c00f67c
+
+- name: freebayes test_freebayes_somatic
+  command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_somatic -c ./tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: dcaa639912174055c1380913d6102c01
+    - path: output/freebayes/versions.yml
+      md5sum: 8fbdb4c052fb3e42b5508a966125fa05
+
+- name: freebayes test_freebayes_somatic_cram_intervals
+  command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_somatic_cram_intervals -c ./tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: b0052a2b83c0ba1b9686d0c96e61712f
+    - path: output/freebayes/versions.yml
+      md5sum: af97e3dfdc086188739907c3460e49e0
diff --git a/tests/modules/nf-core/gamma/gamma/main.nf b/tests/modules/nf-core/gamma/gamma/main.nf
new file mode 100644
index 00000000000..f8158a5e81c
--- /dev/null
+++ b/tests/modules/nf-core/gamma/gamma/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAMMA_GAMMA } from '../../../../../modules/nf-core/gamma/gamma/main.nf'
+
+workflow test_unzip {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true),
+    ]
+
+    db = [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/ResGANNCBI_20210507_srst2.fasta", checkIfExists: true), ]
+
+    GAMMA_GAMMA ( input, db )
+}
+
+workflow test_gamma {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+
+    GAMMA_GAMMA ( input, db )
+}
diff --git a/tests/modules/gamma/gamma/nextflow.config b/tests/modules/nf-core/gamma/gamma/nextflow.config
similarity index 100%
rename from tests/modules/gamma/gamma/nextflow.config
rename to tests/modules/nf-core/gamma/gamma/nextflow.config
diff --git a/tests/modules/nf-core/gamma/gamma/test.yml b/tests/modules/nf-core/gamma/gamma/test.yml
new file mode 100644
index 00000000000..3b15296d9ac
--- /dev/null
+++ b/tests/modules/nf-core/gamma/gamma/test.yml
@@ -0,0 +1,29 @@
+- name: gamma gamma test_unzip
+  command: nextflow run ./tests/modules/nf-core/gamma/gamma -entry test_unzip -c ./tests/config/nextflow.config
+  tags:
+    - gamma/gamma
+    - gamma
+  files:
+    - path: output/gamma/test.fasta
+      md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce
+    - path: output/gamma/test.gamma
+      md5sum: 46165a89e10b7315d3a9b0aa6c561626
+    - path: output/gamma/test.psl
+      md5sum: f489ce4602ddbcb692d5781ee3fbf449
+    - path: output/gamma/versions.yml
+      md5sum: 8baafec7b3b87f788f69e30d317c9722
+
+- name: gamma gamma test_gamma
+  command: nextflow run ./tests/modules/nf-core/gamma/gamma -entry test_gamma -c ./tests/config/nextflow.config
+  tags:
+    - gamma/gamma
+    - gamma
+  files:
+    - path: output/gamma/test.fasta
+      md5sum: df37b48466181311e0a679f3c5878484
+    - path: output/gamma/test.gamma
+      md5sum: 3256708fa517a65ed01d99e0e3c762ae
+    - path: output/gamma/test.psl
+      md5sum: 162a2757ed3b167ae1e0cdb24213f940
+    - path: output/gamma/versions.yml
+      md5sum: b75c2871d8cac2f8ac67c0fbd22babd6
diff --git a/tests/modules/nf-core/gappa/examineassign/main.nf b/tests/modules/nf-core/gappa/examineassign/main.nf
new file mode 100644
index 00000000000..845393b5e49
--- /dev/null
+++ b/tests/modules/nf-core/gappa/examineassign/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAPPA_EXAMINEASSIGN } from '../../../../../modules/nf-core/gappa/examineassign/main.nf'
+
+workflow test_gappa_examineassign {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true)
+    ]
+    taxonomy = file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/gappa_taxonomy.tsv', checkIfExists: true)
+
+    GAPPA_EXAMINEASSIGN ( input, taxonomy )
+}
diff --git a/tests/modules/gappa/examineassign/nextflow.config b/tests/modules/nf-core/gappa/examineassign/nextflow.config
similarity index 100%
rename from tests/modules/gappa/examineassign/nextflow.config
rename to tests/modules/nf-core/gappa/examineassign/nextflow.config
diff --git a/tests/modules/nf-core/gappa/examineassign/test.yml b/tests/modules/nf-core/gappa/examineassign/test.yml
new file mode 100644
index 00000000000..e97ebb92213
--- /dev/null
+++ b/tests/modules/nf-core/gappa/examineassign/test.yml
@@ -0,0 +1,18 @@
+- name: gappa examineassign test_gappa_examineassign
+  command: nextflow run ./tests/modules/nf-core/gappa/examineassign -entry test_gappa_examineassign -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gappa/examineassign/nextflow.config
+  tags:
+    - gappa
+    - gappa/examineassign
+  files:
+    - path: output/gappa/test.labelled_tree.newick
+      md5sum: 39de8a46303ea757f6eb94478db1ffe0
+    - path: output/gappa/test.per_query.tsv
+      md5sum: 16e1fbcc5f79588a0ed21e495cdd91ee
+    - path: output/gappa/test.profile.tsv
+      md5sum: ce604fa03604462358b69cfbff7c1593
+    - path: output/gappa/test.krona.profile
+      md5sum: 19110ac998eaa7532f2a92772cd35aa6
+    - path: output/gappa/test.sativa.tsv
+      md5sum: 28020fc2f8440fabb5ae83b0c7114cdb
+    - path: output/gappa/versions.yml
+      md5sum: a6a80882e5a6b76a412ba2378bb40b51
diff --git a/tests/modules/nf-core/gappa/examinegraft/main.nf b/tests/modules/nf-core/gappa/examinegraft/main.nf
new file mode 100644
index 00000000000..af3f74f4541
--- /dev/null
+++ b/tests/modules/nf-core/gappa/examinegraft/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAPPA_EXAMINEGRAFT } from '../../../../../modules/nf-core/gappa/examinegraft/main.nf'
+
+workflow test_gappa_examinegraft {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true)
+    ]
+
+    GAPPA_EXAMINEGRAFT ( input )
+}
diff --git a/tests/modules/gappa/examinegraft/nextflow.config b/tests/modules/nf-core/gappa/examinegraft/nextflow.config
similarity index 100%
rename from tests/modules/gappa/examinegraft/nextflow.config
rename to tests/modules/nf-core/gappa/examinegraft/nextflow.config
diff --git a/tests/modules/nf-core/gappa/examinegraft/test.yml b/tests/modules/nf-core/gappa/examinegraft/test.yml
new file mode 100644
index 00000000000..9b8ea958d43
--- /dev/null
+++ b/tests/modules/nf-core/gappa/examinegraft/test.yml
@@ -0,0 +1,11 @@
+- name: gappa examinegraft test_gappa_examinegraft
+  command: nextflow run ./tests/modules/nf-core/gappa/examinegraft -entry test_gappa_examinegraft -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gappa/examinegraft/nextflow.config
+  tags:
+    - gappa
+    - gappa/examinegraft
+  files:
+    - path: output/gappa/test.epa_result.newick
+      md5sum: 97e54b6a9576a78b774fd63a050e5474
+    - path: output/gappa/versions.yml
+      contains:
+        - "0.8.0"
diff --git a/tests/modules/nf-core/gappa/examineheattree/main.nf b/tests/modules/nf-core/gappa/examineheattree/main.nf
new file mode 100644
index 00000000000..ce167497081
--- /dev/null
+++ b/tests/modules/nf-core/gappa/examineheattree/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAPPA_EXAMINEHEATTREE } from '../../../../../modules/nf-core/gappa/examineheattree/main.nf'
+
+workflow test_gappa_examineheattree {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true)
+    ]
+
+    GAPPA_EXAMINEHEATTREE ( input )
+}
diff --git a/tests/modules/gappa/examineheattree/nextflow.config b/tests/modules/nf-core/gappa/examineheattree/nextflow.config
similarity index 100%
rename from tests/modules/gappa/examineheattree/nextflow.config
rename to tests/modules/nf-core/gappa/examineheattree/nextflow.config
diff --git a/tests/modules/nf-core/gappa/examineheattree/test.yml b/tests/modules/nf-core/gappa/examineheattree/test.yml
new file mode 100644
index 00000000000..97748301102
--- /dev/null
+++ b/tests/modules/nf-core/gappa/examineheattree/test.yml
@@ -0,0 +1,18 @@
+- name: "gappa examineheattree"
+  command: nextflow run ./tests/modules/nf-core/gappa/examineheattree -entry test_gappa_examineheattree -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gappa/examineheattree/nextflow.config
+  tags:
+    - "gappa"
+    - "gappa/examineheattree"
+  files:
+    - path: output/gappa/test.tree.newick
+      md5sum: f055e11c9b44b6d3afb502aba99d9579
+    - path: output/gappa/test.tree.nexus
+      md5sum: e1cfdcb63f3a751677d0e78fb6b9230a
+    - path: output/gappa/test.tree.phyloxml
+      md5sum: ea35b07e4fd8d174fd6b2f204629cc4e
+    - path: output/gappa/test.tree.svg
+    - path: output/gappa/test.colours.txt
+      md5sum: 7704cd341c8693981253ba6d740c1061
+    - path: output/gappa/test.log
+    - path: output/gappa/versions.yml
+      md5sum: 1cfb752399307413b475438ab1997731
diff --git a/tests/modules/nf-core/gatk/indelrealigner/main.nf b/tests/modules/nf-core/gatk/indelrealigner/main.nf
new file mode 100644
index 00000000000..ece32ead2e7
--- /dev/null
+++ b/tests/modules/nf-core/gatk/indelrealigner/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK_REALIGNERTARGETCREATOR } from '../../../../../modules/nf-core/gatk/realignertargetcreator/main.nf'
+include { GATK_INDELREALIGNER } from '../../../../../modules/nf-core/gatk/indelrealigner/main.nf'
+
+
+workflow test_gatk_indelrealigner {
+
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    input_realignertargetcreator     = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                ]
+
+    GATK_REALIGNERTARGETCREATOR ( input_realignertargetcreator, fasta, fai, dict, [] )
+
+    ch_intervals = GATK_REALIGNERTARGETCREATOR.out.intervals
+
+    ch_bams_indelrealigner = Channel.of([ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+                ])
+
+    ch_input_indelrealigner = ch_bams_indelrealigner.mix(ch_intervals).groupTuple(by: 0).map{ [it[0], it[1][0], it[2], it[1][1] ] }.dump(tag: "input")
+
+    GATK_INDELREALIGNER ( ch_input_indelrealigner, fasta, fai, dict, [] )
+}
diff --git a/tests/modules/gatk/indelrealigner/nextflow.config b/tests/modules/nf-core/gatk/indelrealigner/nextflow.config
similarity index 100%
rename from tests/modules/gatk/indelrealigner/nextflow.config
rename to tests/modules/nf-core/gatk/indelrealigner/nextflow.config
diff --git a/tests/modules/nf-core/gatk/indelrealigner/test.yml b/tests/modules/nf-core/gatk/indelrealigner/test.yml
new file mode 100644
index 00000000000..fcf996c1bb0
--- /dev/null
+++ b/tests/modules/nf-core/gatk/indelrealigner/test.yml
@@ -0,0 +1,12 @@
+- name: gatk indelrealigner test_gatk_indelrealigner
+  command: nextflow run ./tests/modules/nf-core/gatk/indelrealigner -entry test_gatk_indelrealigner -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk/indelrealigner/nextflow.config
+  tags:
+    - gatk/indelrealigner
+    - gatk
+  files:
+    - path: output/gatk/test.realigned.bai
+      md5sum: 85a67df8827fe426e7f3a458134c0551
+    - path: output/gatk/test.realigned.bam
+      md5sum: ea1df6f7fcafc408fae4dc1574813d8a
+    - path: output/gatk/test.realigned.intervals
+      md5sum: 7aa7a1b235a510e6591e262382086bf8
diff --git a/tests/modules/nf-core/gatk/realignertargetcreator/main.nf b/tests/modules/nf-core/gatk/realignertargetcreator/main.nf
new file mode 100644
index 00000000000..9effbc9f80d
--- /dev/null
+++ b/tests/modules/nf-core/gatk/realignertargetcreator/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK_REALIGNERTARGETCREATOR } from '../../../../../modules/nf-core/gatk/realignertargetcreator/main.nf'
+
+workflow test_gatk_realignertargetcreator {
+
+    input     = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK_REALIGNERTARGETCREATOR ( input, fasta, fai, dict, [] )
+}
diff --git a/tests/modules/gatk/realignertargetcreator/nextflow.config b/tests/modules/nf-core/gatk/realignertargetcreator/nextflow.config
similarity index 100%
rename from tests/modules/gatk/realignertargetcreator/nextflow.config
rename to tests/modules/nf-core/gatk/realignertargetcreator/nextflow.config
diff --git a/tests/modules/nf-core/gatk/realignertargetcreator/test.yml b/tests/modules/nf-core/gatk/realignertargetcreator/test.yml
new file mode 100644
index 00000000000..217833bc16a
--- /dev/null
+++ b/tests/modules/nf-core/gatk/realignertargetcreator/test.yml
@@ -0,0 +1,8 @@
+- name: gatk realignertargetcreator test_gatk_realignertargetcreator
+  command: nextflow run ./tests/modules/nf-core/gatk/realignertargetcreator -entry test_gatk_realignertargetcreator -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk/realignertargetcreator/nextflow.config
+  tags:
+    - gatk
+    - gatk/realignertargetcreator
+  files:
+    - path: output/gatk/test.intervals
+      md5sum: 7aa7a1b235a510e6591e262382086bf8
diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf
new file mode 100644
index 00000000000..9d7fc80904f
--- /dev/null
+++ b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK_UNIFIEDGENOTYPER } from '../../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf'
+
+workflow test_gatk_unifiedgenotyper {
+
+    input     = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [], [], [], [])
+}
diff --git a/tests/modules/gatk/unifiedgenotyper/nextflow.config b/tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config
similarity index 100%
rename from tests/modules/gatk/unifiedgenotyper/nextflow.config
rename to tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config
diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml b/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml
new file mode 100644
index 00000000000..9350e5a6af6
--- /dev/null
+++ b/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml
@@ -0,0 +1,9 @@
+- name: gatk unifiedgenotyper test_gatk_unifiedgenotyper
+  command: nextflow run ./tests/modules/nf-core/gatk/unifiedgenotyper -entry test_gatk_unifiedgenotyper -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config
+  tags:
+    - gatk
+    - gatk/unifiedgenotyper
+  files:
+    - path: output/gatk/test.vcf.gz
+      contains:
+        - "#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	test"
diff --git a/tests/modules/nf-core/gatk4/applybqsr/main.nf b/tests/modules/nf-core/gatk4/applybqsr/main.nf
new file mode 100644
index 00000000000..78ca943e91d
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/applybqsr/main.nf
@@ -0,0 +1,47 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_APPLYBQSR } from '../../../../../modules/nf-core/gatk4/applybqsr/main.nf'
+
+workflow test_gatk4_applybqsr {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
+              []
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_APPLYBQSR ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_applybqsr_intervals {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
+                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+              ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+  GATK4_APPLYBQSR ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_applybqsr_cram {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+              ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+  GATK4_APPLYBQSR ( input, fasta, fai, dict )
+}
diff --git a/tests/modules/gatk4/applybqsr/nextflow.config b/tests/modules/nf-core/gatk4/applybqsr/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/applybqsr/nextflow.config
rename to tests/modules/nf-core/gatk4/applybqsr/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/applybqsr/test.yml b/tests/modules/nf-core/gatk4/applybqsr/test.yml
new file mode 100644
index 00000000000..9821c649384
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/applybqsr/test.yml
@@ -0,0 +1,29 @@
+- name: gatk4 applybqsr test_gatk4_applybqsr
+  command: nextflow run ./tests/modules/nf-core/gatk4/applybqsr -entry test_gatk4_applybqsr -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsr/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/applybqsr
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: e11b7eaf2034740a953626518e3c3d6e
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsr/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/applybqsr
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: e9e9aa753c106e43f936ad573e23d2e6
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 applybqsr test_gatk4_applybqsr_cram
+  command: nextflow run ./tests/modules/nf-core/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsr/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/applybqsr
+  files:
+    - path: output/gatk4/test.cram
+      md5sum: bca9d234a5d484ce2a6f4826ca2ea308
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/applybqsrspark/main.nf b/tests/modules/nf-core/gatk4/applybqsrspark/main.nf
new file mode 100644
index 00000000000..32660254840
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/applybqsrspark/main.nf
@@ -0,0 +1,47 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_APPLYBQSR_SPARK } from '../../../../../modules/nf-core/gatk4/applybqsrspark/main.nf'
+
+workflow test_gatk4_applybqsr_spark {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
+              []
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_APPLYBQSR_SPARK ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_applybqsr_spark_intervals {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
+                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+              ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+  GATK4_APPLYBQSR_SPARK ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_applybqsr_spark_cram {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+              ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+  GATK4_APPLYBQSR_SPARK ( input, fasta, fai, dict )
+}
diff --git a/tests/modules/gatk4/applybqsrspark/nextflow.config b/tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/applybqsrspark/nextflow.config
rename to tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/applybqsrspark/test.yml b/tests/modules/nf-core/gatk4/applybqsrspark/test.yml
new file mode 100644
index 00000000000..fdffc886608
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/applybqsrspark/test.yml
@@ -0,0 +1,28 @@
+- name: gatk4 applybqsr test_gatk4_applybqsr_spark
+  command: nextflow run ./tests/modules/nf-core/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/applybqsrspark
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: 1901c819fcba0fdd5e2482e6dc8285ef
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/applybqsrspark
+  files:
+    - path: output/gatk4/test.bam
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram
+  command: nextflow run ./tests/modules/nf-core/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/applybqsrspark
+  files:
+    - path: output/gatk4/test.cram
+      md5sum: 60f7c822a9f2833e11eb7bfd16e4421f
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/applyvqsr/main.nf b/tests/modules/nf-core/gatk4/applyvqsr/main.nf
new file mode 100644
index 00000000000..ea209478555
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/applyvqsr/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../../modules/nf-core/gatk4/applyvqsr/main.nf'
+include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../../modules/nf-core/gatk4/applyvqsr/main.nf'
+
+workflow test_gatk4_applyvqsr {
+    input = [ [ id:'test'], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test2_recal'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test2_recal_idx'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test2_tranches'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_APPLYVQSR_NO_ALLELSPECIFICITY ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_applyvqsr_allele_specific {
+    input = [ [ id:'test'], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal_idx'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_tranches'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY ( input, fasta, fai, dict)
+}
diff --git a/tests/modules/gatk4/applyvqsr/nextflow.config b/tests/modules/nf-core/gatk4/applyvqsr/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/applyvqsr/nextflow.config
rename to tests/modules/nf-core/gatk4/applyvqsr/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/applyvqsr/test.yml b/tests/modules/nf-core/gatk4/applyvqsr/test.yml
new file mode 100644
index 00000000000..63e5ceba396
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/applyvqsr/test.yml
@@ -0,0 +1,19 @@
+- name: gatk4 applyvqsr test_gatk4_applyvqsr
+  command: nextflow run ./tests/modules/nf-core/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applyvqsr/nextflow.config
+  tags:
+    - gatk4/applyvqsr
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific
+  command: nextflow run ./tests/modules/nf-core/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applyvqsr/nextflow.config
+  tags:
+    - gatk4/applyvqsr
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/baserecalibrator/main.nf b/tests/modules/nf-core/gatk4/baserecalibrator/main.nf
new file mode 100644
index 00000000000..e66f2c0e45d
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/baserecalibrator/main.nf
@@ -0,0 +1,69 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_BASERECALIBRATOR } from '../../../../../modules/nf-core/gatk4/baserecalibrator/main.nf'
+
+workflow test_gatk4_baserecalibrator {
+    input     = [ [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                    []
+                  ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+    sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
+    sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
+}
+
+workflow test_gatk4_baserecalibrator_cram {
+   input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                []
+              ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
+    sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
+}
+
+workflow test_gatk4_baserecalibrator_intervals {
+    input     = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+    sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
+    sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
+}
+
+workflow test_gatk4_baserecalibrator_multiple_sites {
+    input     = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                  []
+                ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+    sites =     [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)
+                ]
+    sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
+                ]
+
+  GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
+}
diff --git a/tests/modules/gatk4/baserecalibrator/nextflow.config b/tests/modules/nf-core/gatk4/baserecalibrator/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/baserecalibrator/nextflow.config
rename to tests/modules/nf-core/gatk4/baserecalibrator/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/baserecalibrator/test.yml b/tests/modules/nf-core/gatk4/baserecalibrator/test.yml
new file mode 100644
index 00000000000..0efa13593f2
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/baserecalibrator/test.yml
@@ -0,0 +1,39 @@
+- name: gatk4 baserecalibrator test_gatk4_baserecalibrator
+  command: nextflow run ./tests/modules/nf-core/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/baserecalibrator/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/baserecalibrator
+  files:
+    - path: output/gatk4/test.table
+      md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_cram
+  command: nextflow run ./tests/modules/nf-core/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/baserecalibrator/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/baserecalibrator
+  files:
+    - path: output/gatk4/test.table
+      md5sum: 35d89a3811aa31711fc9815b6b80e6ec
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/baserecalibrator/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/baserecalibrator
+  files:
+    - path: output/gatk4/test.table
+      md5sum: 9ecb5f00a2229291705addc09c0ec231
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_multiple_sites
+  command: nextflow run ./tests/modules/nf-core/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/baserecalibrator/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/baserecalibrator
+  files:
+    - path: output/gatk4/test.table
+      md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf b/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf
new file mode 100644
index 00000000000..8108332ef7e
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf
@@ -0,0 +1,69 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_BASERECALIBRATOR_SPARK } from '../../../../../modules/nf-core/gatk4/baserecalibratorspark/main.nf'
+
+workflow test_gatk4_baserecalibrator_spark {
+    input     = [ [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                    []
+                  ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+    sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
+    sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_BASERECALIBRATOR_SPARK ( input, fasta, fai, dict, sites, sites_tbi )
+}
+
+workflow test_gatk4_baserecalibrator_spark_cram {
+   input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                []
+              ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
+    sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_BASERECALIBRATOR_SPARK ( input, fasta, fai, dict, sites, sites_tbi )
+}
+
+workflow test_gatk4_baserecalibrator_spark_intervals {
+    input     = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+    sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
+    sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_BASERECALIBRATOR_SPARK ( input, fasta, fai, dict, sites, sites_tbi )
+}
+
+workflow test_gatk4_baserecalibrator_spark_multiple_sites {
+    input     = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                  []
+                ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+    sites =     [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)
+                ]
+    sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
+                ]
+
+  GATK4_BASERECALIBRATOR_SPARK ( input, fasta, fai, dict, sites, sites_tbi )
+}
diff --git a/tests/modules/gatk4/baserecalibratorspark/nextflow.config b/tests/modules/nf-core/gatk4/baserecalibratorspark/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/baserecalibratorspark/nextflow.config
rename to tests/modules/nf-core/gatk4/baserecalibratorspark/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/baserecalibratorspark/test.yml b/tests/modules/nf-core/gatk4/baserecalibratorspark/test.yml
new file mode 100644
index 00000000000..7bb1e1510e5
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/baserecalibratorspark/test.yml
@@ -0,0 +1,39 @@
+- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_spark
+  command: nextflow run ./tests/modules/nf-core/gatk4/baserecalibratorspark -entry test_gatk4_baserecalibrator_spark -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/baserecalibratorspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/baserecalibratorspark
+  files:
+    - path: output/gatk4/test.table
+      md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_spark_cram
+  command: nextflow run ./tests/modules/nf-core/gatk4/baserecalibratorspark -entry test_gatk4_baserecalibrator_spark_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/baserecalibratorspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/baserecalibratorspark
+  files:
+    - path: output/gatk4/test.table
+      md5sum: 35d89a3811aa31711fc9815b6b80e6ec
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_spark_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/baserecalibratorspark -entry test_gatk4_baserecalibrator_spark_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/baserecalibratorspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/baserecalibratorspark
+  files:
+    - path: output/gatk4/test.table
+      md5sum: 9ecb5f00a2229291705addc09c0ec231
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_spark_multiple_sites
+  command: nextflow run ./tests/modules/nf-core/gatk4/baserecalibratorspark -entry test_gatk4_baserecalibrator_spark_multiple_sites -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/baserecalibratorspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/baserecalibratorspark
+  files:
+    - path: output/gatk4/test.table
+      md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/bedtointervallist/main.nf b/tests/modules/nf-core/gatk4/bedtointervallist/main.nf
new file mode 100644
index 00000000000..3ee8478c870
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/bedtointervallist/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/gatk4/bedtointervallist/main.nf'
+
+workflow test_gatk4_bedtointervallist {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+            ]
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_BEDTOINTERVALLIST ( input, dict )
+}
diff --git a/tests/modules/gatk4/bedtointervallist/nextflow.config b/tests/modules/nf-core/gatk4/bedtointervallist/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/bedtointervallist/nextflow.config
rename to tests/modules/nf-core/gatk4/bedtointervallist/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/bedtointervallist/test.yml b/tests/modules/nf-core/gatk4/bedtointervallist/test.yml
new file mode 100644
index 00000000000..e07ee44eaec
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/bedtointervallist/test.yml
@@ -0,0 +1,9 @@
+- name: gatk4 bedtointervallist test_gatk4_bedtointervallist
+  command: nextflow run ./tests/modules/nf-core/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/bedtointervallist/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/bedtointervallist
+  files:
+    - path: output/gatk4/test.interval_list
+      md5sum: e51101c9357fb2d59fd30e370eefa39c
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/calculatecontamination/main.nf b/tests/modules/nf-core/gatk4/calculatecontamination/main.nf
new file mode 100644
index 00000000000..dd24f2e055b
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/calculatecontamination/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_CALCULATECONTAMINATION                                              } from '../../../../../modules/nf-core/gatk4/calculatecontamination/main.nf'
+include { GATK4_CALCULATECONTAMINATION as GATK4_CALCULATECONTAMINATION_SEGMENTATION } from '../../../../../modules/nf-core/gatk4/calculatecontamination/main.nf'
+
+workflow test_gatk4_calculatecontamination_tumor_only {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
+              [] ]
+
+    GATK4_CALCULATECONTAMINATION ( input )
+}
+
+workflow test_gatk4_calculatecontamination_matched_pair {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ]
+
+    GATK4_CALCULATECONTAMINATION ( input )
+}
+
+workflow test_gatk4_calculatecontamination_segmentation {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ]
+
+    GATK4_CALCULATECONTAMINATION_SEGMENTATION ( input )
+}
diff --git a/tests/modules/gatk4/calculatecontamination/nextflow.config b/tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/calculatecontamination/nextflow.config
rename to tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/calculatecontamination/test.yml b/tests/modules/nf-core/gatk4/calculatecontamination/test.yml
new file mode 100644
index 00000000000..a673dd68cf1
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/calculatecontamination/test.yml
@@ -0,0 +1,31 @@
+- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_tumor_only
+  command: nextflow run ./tests/modules/nf-core/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/calculatecontamination
+  files:
+    - path: output/gatk4/test.contamination.table
+      md5sum: 46c708c943b453da89a3da08acfdb2a7
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair
+  command: nextflow run ./tests/modules/nf-core/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/calculatecontamination
+  files:
+    - path: output/gatk4/test.contamination.table
+      md5sum: 46c708c943b453da89a3da08acfdb2a7
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation
+  command: nextflow run ./tests/modules/nf-core/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/calculatecontamination
+  files:
+    - path: output/gatk4/test.contamination.table
+      md5sum: 46c708c943b453da89a3da08acfdb2a7
+    - path: output/gatk4/test.segmentation.table
+      md5sum: f4643d9319bde4efbfbe516d6fb13052
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf
new file mode 100644
index 00000000000..de7307aae95
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf
@@ -0,0 +1,66 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../../modules/nf-core/gatk4/calibratedragstrmodel/main.nf'
+
+workflow test_gatk4_calibratedragstrmodel_bam {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
+
+    GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
+}
+
+workflow test_gatk4_calibratedragstrmodel_cram {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
+
+    GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
+}
+
+workflow test_gatk4_calibratedragstrmodel_beds {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
+
+    GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
+}
+
diff --git a/tests/modules/gatk4/calibratedragstrmodel/nextflow.config b/tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/calibratedragstrmodel/nextflow.config
rename to tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/calibratedragstrmodel/test.yml b/tests/modules/nf-core/gatk4/calibratedragstrmodel/test.yml
new file mode 100644
index 00000000000..1184fc2a615
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/calibratedragstrmodel/test.yml
@@ -0,0 +1,26 @@
+- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_bam
+  command: nextflow run ./tests/modules/nf-core/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_bam -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/calibratedragstrmodel
+  files:
+    - path: output/gatk4/test.txt
+      md5sum: e16fa32906c74bb18b93e98a86718ff1
+
+- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_cram
+  command: nextflow run ./tests/modules/nf-core/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/calibratedragstrmodel
+  files:
+    - path: output/gatk4/test.txt
+      md5sum: 81c7bf338886cb4d5c2cc07fc56afe44
+
+- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_beds
+  command: nextflow run ./tests/modules/nf-core/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_beds -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/calibratedragstrmodel
+  files:
+    - path: output/gatk4/test.txt
+      md5sum: cb6a9acdee042302b54fd1f59b5f54ee
diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf b/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf
new file mode 100644
index 00000000000..8a218e1b884
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_CNNSCOREVARIANTS } from '../../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf'
+
+workflow test_gatk4_cnnscorevariants {
+
+    input     = [ [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
+                    [],
+                    []
+                ]
+    fasta  = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai    = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict   = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    GATK4_CNNSCOREVARIANTS ( input, fasta, fai, dict, [], [] )
+}
diff --git a/tests/modules/gatk4/cnnscorevariants/nextflow.config b/tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/cnnscorevariants/nextflow.config
rename to tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/test.yml b/tests/modules/nf-core/gatk4/cnnscorevariants/test.yml
new file mode 100644
index 00000000000..9c8b2a839ea
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/cnnscorevariants/test.yml
@@ -0,0 +1,9 @@
+- name: gatk4 cnnscorevariants test_gatk4_cnnscorevariants
+  command: nextflow run ./tests/modules/nf-core/gatk4/cnnscorevariants -entry test_gatk4_cnnscorevariants -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config
+  tags:
+    - gatk4/cnnscorevariants
+    - gatk4
+  files:
+    - path: output/gatk4/test.cnn.vcf.gz
+      contains: ["##ALT=<ID=NON_REF,Description="]
+    - path: output/gatk4/test.cnn.vcf.gz.tbi
diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/main.nf b/tests/modules/nf-core/gatk4/collectreadcounts/main.nf
new file mode 100644
index 00000000000..8a056a24c43
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/collectreadcounts/main.nf
@@ -0,0 +1,54 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf'
+
+workflow test_gatk4_collectreadcounts_hdf5 {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
+    ]
+
+    fasta = []
+    fai = []
+    dict = []
+
+    GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_collectreadcounts_tsv {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
+    ]
+
+    fasta = []
+    fai = []
+    dict = []
+
+    GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_collectreadcounts_cram {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
+}
+
diff --git a/tests/modules/gatk4/collectreadcounts/nextflow.config b/tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/collectreadcounts/nextflow.config
rename to tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/test.yml b/tests/modules/nf-core/gatk4/collectreadcounts/test.yml
new file mode 100644
index 00000000000..dffbb8a9992
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/collectreadcounts/test.yml
@@ -0,0 +1,25 @@
+- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_hdf5
+  command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_hdf5 -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
+  tags:
+    - gatk4/collectreadcounts
+    - gatk4
+  files:
+    - path: output/gatk4/test.hdf5
+
+- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_tsv
+  command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_tsv -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
+  tags:
+    - gatk4/collectreadcounts
+    - gatk4
+  files:
+    - path: output/gatk4/test.tsv
+      md5sum: 8e45a6164916c303387f39f02ce45841
+
+- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_cram
+  command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
+  tags:
+    - gatk4/collectreadcounts
+    - gatk4
+  files:
+    - path: output/gatk4/test.tsv
+      md5sum: d9a32039b7a84f5bb74e8382e5427670
diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/main.nf b/tests/modules/nf-core/gatk4/collectsvevidence/main.nf
new file mode 100644
index 00000000000..68f406bd560
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/collectsvevidence/main.nf
@@ -0,0 +1,56 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_COLLECTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf'
+
+workflow test_gatk4_collectsvevidence_cram {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        [],
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
+}
+
+workflow test_gatk4_collectsvevidence_bam {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        [],
+        []
+    ]
+
+    fasta = []
+    fasta_fai = []
+    dict = []
+
+    GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
+}
+
+workflow test_gatk4_collectsvevidence_allele_count {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    fasta = []
+    fasta_fai = []
+    dict = []
+
+    GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
+}
diff --git a/tests/modules/gatk4/collectsvevidence/nextflow.config b/tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/collectsvevidence/nextflow.config
rename to tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/test.yml b/tests/modules/nf-core/gatk4/collectsvevidence/test.yml
new file mode 100644
index 00000000000..ad206584c41
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/collectsvevidence/test.yml
@@ -0,0 +1,48 @@
+- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_cram
+  command: nextflow run ./tests/modules/nf-core/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/collectsvevidence
+  files:
+    - path: output/gatk4/test.pe.txt.gz
+      md5sum: 19f13dd0408204590b40239d14acbdde
+    - path: output/gatk4/test.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/test.sr.txt.gz
+      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
+    - path: output/gatk4/test.sr.txt.gz.tbi
+      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
+
+- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_bam
+  command: nextflow run ./tests/modules/nf-core/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_bam -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/collectsvevidence
+  files:
+    - path: output/gatk4/test.pe.txt.gz
+      md5sum: 19f13dd0408204590b40239d14acbdde
+    - path: output/gatk4/test.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/test.sr.txt.gz
+      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
+    - path: output/gatk4/test.sr.txt.gz.tbi
+      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
+
+- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_allele_count
+  command: nextflow run ./tests/modules/nf-core/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_allele_count -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/collectsvevidence
+  files:
+    - path: output/gatk4/test.ld.txt.gz
+      md5sum: c07747510deb2c2c886ee4e34d0a9c97
+    - path: output/gatk4/test.ld.txt.gz.tbi
+      md5sum: d1479eeb2217c2b8b4a84cf7237aca45
+    - path: output/gatk4/test.pe.txt.gz
+      md5sum: 19f13dd0408204590b40239d14acbdde
+    - path: output/gatk4/test.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/test.sr.txt.gz
+      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
+    - path: output/gatk4/test.sr.txt.gz.tbi
+      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
diff --git a/tests/modules/nf-core/gatk4/combinegvcfs/main.nf b/tests/modules/nf-core/gatk4/combinegvcfs/main.nf
new file mode 100644
index 00000000000..42a92c9bef5
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/combinegvcfs/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_COMBINEGVCFS } from '../../../../../modules/nf-core/gatk4/combinegvcfs/main.nf'
+
+workflow test_gatk4_combinegvcfs {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf'], checkIfExists: true) ],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_idx'], checkIfExists: true) ]              
+           ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)       
+
+    GATK4_COMBINEGVCFS ( input, fasta, fasta_fai, fasta_dict )
+}
+
diff --git a/tests/modules/gatk4/combinegvcfs/nextflow.config b/tests/modules/nf-core/gatk4/combinegvcfs/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/combinegvcfs/nextflow.config
rename to tests/modules/nf-core/gatk4/combinegvcfs/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/combinegvcfs/test.yml b/tests/modules/nf-core/gatk4/combinegvcfs/test.yml
new file mode 100644
index 00000000000..7ad0610f2b7
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/combinegvcfs/test.yml
@@ -0,0 +1,9 @@
+- name: gatk4 combinegvcfs test_gatk4_combinegvcfs
+  command: nextflow run ./tests/modules/nf-core/gatk4/combinegvcfs -entry test_gatk4_combinegvcfs -c ./tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/combinegvcfs
+  files:
+    - path: output/gatk4/test.combined.g.vcf.gz
+      contains: ["VCFv4.2"]
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/composestrtablefile/main.nf b/tests/modules/nf-core/gatk4/composestrtablefile/main.nf
new file mode 100644
index 00000000000..4c62f05de88
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/composestrtablefile/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_COMPOSESTRTABLEFILE } from '../../../../../modules/nf-core/gatk4/composestrtablefile/main.nf'
+
+workflow test_gatk4_composestrtablefile {
+    
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_COMPOSESTRTABLEFILE ( fasta, fasta_fai, dict )
+}
diff --git a/tests/modules/gatk4/composestrtablefile/nextflow.config b/tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/composestrtablefile/nextflow.config
rename to tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/composestrtablefile/test.yml b/tests/modules/nf-core/gatk4/composestrtablefile/test.yml
new file mode 100644
index 00000000000..71dd4067c1c
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/composestrtablefile/test.yml
@@ -0,0 +1,7 @@
+- name: gatk4 composestrtablefile test_gatk4_composestrtablefile
+  command: nextflow run ./tests/modules/nf-core/gatk4/composestrtablefile -entry test_gatk4_composestrtablefile -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config
+  tags:
+    - gatk4/composestrtablefile
+    - gatk4
+  files:
+    - path: output/gatk4/genome.zip
diff --git a/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf b/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf
new file mode 100644
index 00000000000..c687c15ec48
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../../modules/nf-core/gatk4/createsequencedictionary/main.nf'
+
+workflow test_gatk4_createsequencedictionary {
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    GATK4_CREATESEQUENCEDICTIONARY ( fasta )
+}
diff --git a/tests/modules/gatk4/createsequencedictionary/nextflow.config b/tests/modules/nf-core/gatk4/createsequencedictionary/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/createsequencedictionary/nextflow.config
rename to tests/modules/nf-core/gatk4/createsequencedictionary/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/createsequencedictionary/test.yml b/tests/modules/nf-core/gatk4/createsequencedictionary/test.yml
new file mode 100644
index 00000000000..f62f59d775b
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/createsequencedictionary/test.yml
@@ -0,0 +1,9 @@
+- name: gatk4 createsequencedictionary test_gatk4_createsequencedictionary
+  command: nextflow run ./tests/modules/nf-core/gatk4/createsequencedictionary -entry test_gatk4_createsequencedictionary -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/createsequencedictionary/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/createsequencedictionary
+  files:
+    - path: output/gatk4/genome.dict
+      md5sum: 7362679f176e0f52add03c08f457f646
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf
new file mode 100644
index 00000000000..25a191d82ec
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR           } from '../../../../../modules/nf-core/untar/main.nf'
+include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../../modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf'
+
+workflow test_gatk4_createsomaticpanelofnormals {
+    db    = [[], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+
+    input = Channel.of([ id:'test'])
+              .combine(UNTAR.out.untar.map{ it[1] })
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_CREATESOMATICPANELOFNORMALS ( input, fasta, fastaidx, dict )
+}
diff --git a/tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config
rename to tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml
new file mode 100644
index 00000000000..5f8d73fb480
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml
@@ -0,0 +1,10 @@
+- name: gatk4 createsomaticpanelofnormals test_gatk4_createsomaticpanelofnormals
+  command: nextflow run ./tests/modules/nf-core/gatk4/createsomaticpanelofnormals -entry test_gatk4_createsomaticpanelofnormals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/createsomaticpanelofnormals
+  files:
+    - path: output/gatk4/test.pon.vcf.gz
+    - path: output/gatk4/test.pon.vcf.gz.tbi
+      md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf
new file mode 100644
index 00000000000..decc9114132
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf'
+
+workflow test_gatk4_estimatelibrarycomplexity {
+
+    input = [   [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_ESTIMATELIBRARYCOMPLEXITY ( input, fasta, fai, dict )
+}
diff --git a/tests/modules/gatk4/estimatelibrarycomplexity/nextflow.config b/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/estimatelibrarycomplexity/nextflow.config
rename to tests/modules/nf-core/gatk4/estimatelibrarycomplexity/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/test.yml b/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/test.yml
new file mode 100644
index 00000000000..b2288a6f67c
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/test.yml
@@ -0,0 +1,8 @@
+- name: gatk4 estimatelibrarycomplexity test_gatk4_estimatelibrarycomplexity
+  command: nextflow run ./tests/modules/nf-core/gatk4/estimatelibrarycomplexity -entry test_gatk4_estimatelibrarycomplexity -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/estimatelibrarycomplexity/nextflow.config
+  tags:
+    - gatk4/estimatelibrarycomplexity
+    - gatk4
+  files:
+    - path: output/gatk4/test.metrics
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/fastqtosam/main.nf b/tests/modules/nf-core/gatk4/fastqtosam/main.nf
new file mode 100644
index 00000000000..0a3aef644d4
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/fastqtosam/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_FASTQTOSAM } from '../../../../../modules/nf-core/gatk4/fastqtosam/main.nf'
+
+workflow test_gatk4_fastqtosam_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ]
+
+    GATK4_FASTQTOSAM ( input )
+}
+
+workflow test_gatk4_fastqtosam_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+            ]
+
+    GATK4_FASTQTOSAM ( input )
+}
diff --git a/tests/modules/gatk4/fastqtosam/nextflow.config b/tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/fastqtosam/nextflow.config
rename to tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/fastqtosam/test.yml b/tests/modules/nf-core/gatk4/fastqtosam/test.yml
new file mode 100644
index 00000000000..e4932ebf135
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/fastqtosam/test.yml
@@ -0,0 +1,17 @@
+- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
+  command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/fastqtosam
+  files:
+    - path: output/gatk4/test.bam
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
+  command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/fastqtosam
+  files:
+    - path: output/gatk4/test.bam
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf b/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf
new file mode 100644
index 00000000000..039a39853d0
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf
@@ -0,0 +1,85 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_FILTERMUTECTCALLS } from '../../../../../modules/nf-core/gatk4/filtermutectcalls/main.nf'
+
+workflow test_gatk4_filtermutectcalls_base {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
+        [],
+        [],
+        [],
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_filtermutectcalls_with_files {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_artifact_prior_tar_gz'], checkIfExists: true) ],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_segmentation_table'], checkIfExists: true) ],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_contamination_table'], checkIfExists: true) ],
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_filtermutectcalls_use_val {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_artifact_prior_tar_gz'], checkIfExists: true) ],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_segmentation_table'], checkIfExists: true) ],
+        [],
+        '20.0'
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_filtermutectcalls_base_stubs {
+
+    input = [
+         [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
+        [],
+        [],
+        [],
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
+}
diff --git a/tests/modules/gatk4/filtermutectcalls/nextflow.config b/tests/modules/nf-core/gatk4/filtermutectcalls/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/filtermutectcalls/nextflow.config
rename to tests/modules/nf-core/gatk4/filtermutectcalls/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/filtermutectcalls/test.yml b/tests/modules/nf-core/gatk4/filtermutectcalls/test.yml
new file mode 100644
index 00000000000..044772fb877
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/filtermutectcalls/test.yml
@@ -0,0 +1,46 @@
+- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_base
+  command: nextflow run ./tests/modules/nf-core/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_base -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filtermutectcalls/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/filtermutectcalls
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
+      md5sum: 55f228e5520c8b9fbac017d3a3a6c5fd
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_with_files
+  command: nextflow run ./tests/modules/nf-core/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_with_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filtermutectcalls/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/filtermutectcalls
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
+      md5sum: 9ae27fbd04af1a2ea574e2ff1c3a683b
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_use_val
+  command: nextflow run ./tests/modules/nf-core/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_use_val -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filtermutectcalls/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/filtermutectcalls
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
+      md5sum: 95cc3e37705bd3b97a292c5d46ab82f3
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_base_stubs
+  command: nextflow run ./tests/modules/nf-core/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_base_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filtermutectcalls/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/filtermutectcalls
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf b/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf
new file mode 100644
index 00000000000..5b2b0d484b3
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_FILTERVARIANTTRANCHES } from '../../../../../modules/nf-core/gatk4/filtervarianttranches/main.nf'
+include { GATK4_CNNSCOREVARIANTS } from '../../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf'
+include { GATK4_HAPLOTYPECALLER  } from '../../../../../modules/nf-core/gatk4/haplotypecaller/main.nf'
+workflow test_gatk4_filtervarianttranches {
+
+    resources = [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ]
+    resources_index  = [
+                    file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true),
+                ]
+
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true),
+                []
+            ]
+
+    fasta  = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai    = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict   = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_FILTERVARIANTTRANCHES (input , resources, resources_index, fasta, fai, dict)
+}
diff --git a/tests/modules/gatk4/filtervarianttranches/nextflow.config b/tests/modules/nf-core/gatk4/filtervarianttranches/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/filtervarianttranches/nextflow.config
rename to tests/modules/nf-core/gatk4/filtervarianttranches/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/test.yml b/tests/modules/nf-core/gatk4/filtervarianttranches/test.yml
new file mode 100644
index 00000000000..23a782d05ef
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/filtervarianttranches/test.yml
@@ -0,0 +1,9 @@
+- name: gatk4 filtervarianttranches test_gatk4_filtervarianttranches
+  command: nextflow run ./tests/modules/nf-core/gatk4/filtervarianttranches -entry test_gatk4_filtervarianttranches -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/filtervarianttranches/nextflow.config
+  tags:
+    - gatk4/filtervarianttranches
+    - gatk4
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf
new file mode 100644
index 00000000000..150c958c682
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf
@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_GATHERBQSRREPORTS } from '../../../../../modules/nf-core/gatk4/gatherbqsrreports/main.nf'
+
+workflow test_gatk4_gatherbqsrreports {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
+    ]
+
+    GATK4_GATHERBQSRREPORTS ( input )
+}
+
+workflow test_gatk4_gatherbqsrreports_multiple {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_baserecalibrator_table'], checkIfExists: true)
+        ]
+    ]
+
+    GATK4_GATHERBQSRREPORTS ( input )
+}
diff --git a/tests/modules/gatk4/gatherbqsrreports/nextflow.config b/tests/modules/nf-core/gatk4/gatherbqsrreports/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/gatherbqsrreports/nextflow.config
rename to tests/modules/nf-core/gatk4/gatherbqsrreports/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml b/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml
new file mode 100644
index 00000000000..e70c49eaa86
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml
@@ -0,0 +1,19 @@
+- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports
+  command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports -c ./tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/gatherbqsrreports
+  files:
+    - path: output/gatk4/test.table
+      md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple
+  command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c ./tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/gatherbqsrreports
+  files:
+    - path: output/gatk4/test.table
+      md5sum: 0c1257eececf95db8ca378272d0f21f9
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
new file mode 100644
index 00000000000..a30364439f5
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_GATHERPILEUPSUMMARIES } from '../../../../../modules/nf-core/gatk4/gatherpileupsummaries/main.nf'
+
+workflow test_gatk4_gatherpileupsummaries {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)]
+        //file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)]
+    ]
+
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_GATHERPILEUPSUMMARIES ( input, dict )
+}
diff --git a/tests/modules/gatk4/gatherpileupsummaries/nextflow.config b/tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/gatherpileupsummaries/nextflow.config
rename to tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/test.yml b/tests/modules/nf-core/gatk4/gatherpileupsummaries/test.yml
new file mode 100644
index 00000000000..6ad66fea6d0
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/gatherpileupsummaries/test.yml
@@ -0,0 +1,9 @@
+- name: gatk4 gatherpileupsummaries
+  command: nextflow run ./tests/modules/nf-core/gatk4/gatherpileupsummaries -entry test_gatk4_gatherpileupsummaries -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/gatherpileupsummaries
+  files:
+    - path: output/gatk4/test.pileupsummaries.table
+      md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf b/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf
new file mode 100644
index 00000000000..ca0b67241b9
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf
@@ -0,0 +1,61 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR           } from '../../../../../modules/nf-core/untar/main.nf'
+include { GATK4_GENOMICSDBIMPORT } from '../../../../../modules/nf-core/gatk4/genomicsdbimport/main.nf'
+
+workflow test_gatk4_genomicsdbimport_create_genomicsdb {
+
+    input = [ [ id:'test'], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) ,
+              file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ,
+              file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true) ,
+              [] ,
+              [] ]
+
+    run_intlist = false
+    run_updatewspace = false
+    input_map = false
+
+    GATK4_GENOMICSDBIMPORT ( input, run_intlist, run_updatewspace, input_map )
+}
+
+workflow test_gatk4_genomicsdbimport_get_intervalslist {
+    db    = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+
+    def input = Channel.of([ [ id:'test'], // meta map
+              [] ,
+              [] ,
+              [] ,
+              [] ])
+              .combine(UNTAR.out.untar.map{ it[1] })
+
+    run_intlist = true
+    run_updatewspace = false
+    input_map = false
+
+    GATK4_GENOMICSDBIMPORT ( input, run_intlist, run_updatewspace, input_map )
+}
+
+workflow test_gatk4_genomicsdbimport_update_genomicsdb {
+    db    = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+
+    def input = Channel.of([ [ id:'test'], // meta map
+              file( params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'] , checkIfExists: true) ,
+              file( params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz_tbi'] , checkIfExists: true) ,
+              [] ,
+              [] ])
+              .combine(UNTAR.out.untar.map{ it[1] })
+
+    run_intlist = false
+    run_updatewspace = true
+    input_map = false
+
+    GATK4_GENOMICSDBIMPORT ( input, run_intlist, run_updatewspace, input_map )
+
+}
diff --git a/tests/modules/gatk4/genomicsdbimport/nextflow.config b/tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/genomicsdbimport/nextflow.config
rename to tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/genomicsdbimport/test.yml b/tests/modules/nf-core/gatk4/genomicsdbimport/test.yml
new file mode 100644
index 00000000000..5a972c8bbe1
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/genomicsdbimport/test.yml
@@ -0,0 +1,51 @@
+- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_create_genomicsdb
+  command: nextflow run ./tests/modules/nf-core/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genomicsdbimport
+  files:
+    - path: output/gatk4/test/__tiledb_workspace.tdb
+    - path: output/gatk4/test/callset.json
+      md5sum: a7d07d1c86449bbb1091ff29368da07a
+    - path: output/gatk4/test/chr22$1$40001/.__consolidation_lock
+    - path: output/gatk4/test/chr22$1$40001/__array_schema.tdb
+    - path: output/gatk4/test/chr22$1$40001/genomicsdb_meta_dir/genomicsdb_column_bounds.json
+      md5sum: 2502f79658bc000578ebcfddfc1194c0
+    - path: output/gatk4/test/vcfheader.vcf
+      contains:
+        - "FORMAT=<ID=AD,Number=R,Type=Integer,Description="
+    - path: output/gatk4/test/vidmap.json
+      md5sum: 18d3f68bd2cb6f4474990507ff95017a
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist
+  command: nextflow run ./tests/modules/nf-core/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genomicsdbimport
+  files:
+    - path: output/gatk4/test.interval_list
+      md5sum: 4c85812ac15fc1cd29711a851d23c0bf
+    - path: output/gatk4/versions.yml
+    - path: output/untar/versions.yml
+
+- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_update_genomicsdb
+  command: nextflow run ./tests/modules/nf-core/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_update_genomicsdb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genomicsdbimport
+  files:
+    - path: output/gatk4/test_genomicsdb/__tiledb_workspace.tdb
+    - path: output/gatk4/test_genomicsdb/callset.json
+      md5sum: 1ea31b59b9a218dd5681164aff4a5e07
+    - path: output/gatk4/test_genomicsdb/chr22$1$40001/.__consolidation_lock
+    - path: output/gatk4/test_genomicsdb/chr22$1$40001/__array_schema.tdb
+      md5sum: 6709e67921ae840bf61fbfb192554eda
+    - path: output/gatk4/test_genomicsdb/chr22$1$40001/genomicsdb_meta_dir/genomicsdb_column_bounds.json
+      md5sum: 2502f79658bc000578ebcfddfc1194c0
+    - path: output/gatk4/test_genomicsdb/vcfheader.vcf
+      md5sum: 3717f34ad68ff491f40a138410b2667a
+    - path: output/gatk4/test_genomicsdb/vidmap.json
+      md5sum: 18d3f68bd2cb6f4474990507ff95017a
+    - path: output/gatk4/versions.yml
+    - path: output/untar/versions.yml
diff --git a/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf b/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf
new file mode 100644
index 00000000000..06423b29d1d
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf
@@ -0,0 +1,182 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_GENOTYPEGVCFS } from '../../../../../modules/nf-core/gatk4/genotypegvcfs/main.nf'
+include { UNTAR               } from '../../../../../modules/nf-core/untar/main.nf'
+
+// Basic parameters with uncompressed VCF input
+workflow test_gatk4_genotypegvcfs_vcf_input {
+
+    input = [ [ id:'test' ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true),
+            [],
+            []
+        ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
+}
+
+// Basic parameters with compressed VCF input
+workflow test_gatk4_genotypegvcfs_gz_input {
+
+    input = [ [ id:'test' ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
+            [],
+            []
+        ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
+}
+
+// Basic parameters + optional dbSNP
+workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
+
+    input = [ [ id:'test' ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
+            [],
+            []
+        ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi)
+}
+
+// Basic parameters + optional intervals
+workflow test_gatk4_genotypegvcfs_gz_input_intervals {
+
+    input = [ [ id:'test' ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ,
+            []
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
+}
+
+// Basic parameters + optional dbSNP + optional intervals
+workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
+
+    input = [ [ id:'test' ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
+            []
+        ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )
+}
+
+// Basic parameters with GenomicsDB input
+workflow test_gatk4_genotypegvcfs_gendb_input {
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( test_genomicsdb )
+    gendb = UNTAR.out.untar.map{ it[1] }.collect()
+    gendb.add([])
+    gendb.add([])
+    gendb.add([])
+
+    input = Channel.of([ id:'test' ]).combine(gendb)
+
+    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
+}
+
+// Basic parameters with GenomicsDB + optional dbSNP
+workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
+
+    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( test_genomicsdb )
+    gendb = UNTAR.out.untar.map{ it[1] }.collect()
+    gendb.add([])
+    gendb.add([])
+    gendb.add([])
+    input = Channel.of([ id:'test' ]).combine(gendb)
+
+    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi)
+}
+
+// Basic parameters with GenomicsDB + optional intervals
+workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( test_genomicsdb )
+    gendb = UNTAR.out.untar.map{ it[1] }.collect()
+    gendb.add([])
+    gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
+    gendb.add([])
+
+    input = Channel.of([ id:'test' ]).combine(gendb)
+
+    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [] )
+}
+
+// Basic parameters with GenomicsDB + optional dbSNP + optional intervals
+workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
+
+    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( test_genomicsdb )
+    gendb = UNTAR.out.untar.map{ it[1] }.collect()
+    gendb.add([])
+    gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
+    gendb.add([])
+
+    input = Channel.of([ id:'test' ]).combine(gendb)
+
+    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )
+}
diff --git a/tests/modules/gatk4/genotypegvcfs/nextflow.config b/tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/genotypegvcfs/nextflow.config
rename to tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/genotypegvcfs/test.yml b/tests/modules/nf-core/gatk4/genotypegvcfs/test.yml
new file mode 100644
index 00000000000..ac39ddfeaba
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/genotypegvcfs/test.yml
@@ -0,0 +1,119 @@
+- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_vcf_input
+  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genotypegvcfs
+  files:
+    - path: output/gatk4/test.genotyped.vcf.gz
+      contains:
+        [
+          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
+        ]
+    - path: output/gatk4/test.genotyped.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input
+  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genotypegvcfs
+  files:
+    - path: output/gatk4/test.genotyped.vcf.gz
+      contains:
+        [
+          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
+        ]
+    - path: output/gatk4/test.genotyped.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp
+  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genotypegvcfs
+  files:
+    - path: output/gatk4/test.genotyped.vcf.gz
+      contains:
+        [
+          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
+        ]
+    - path: output/gatk4/test.genotyped.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genotypegvcfs
+  files:
+    - path: output/gatk4/test.genotyped.vcf.gz
+      contains:
+        [
+          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
+        ]
+    - path: output/gatk4/test.genotyped.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genotypegvcfs
+  files:
+    - path: output/gatk4/test.genotyped.vcf.gz
+      contains: ["AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693"]
+    - path: output/gatk4/test.genotyped.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
+  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genotypegvcfs
+  files:
+    - path: output/gatk4/test.genotyped.vcf.gz
+      contains:
+        [
+          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
+        ]
+    - path: output/gatk4/test.genotyped.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp
+  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genotypegvcfs
+  files:
+    - path: output/gatk4/test.genotyped.vcf.gz
+      contains:
+        [
+          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
+        ]
+    - path: output/gatk4/test.genotyped.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genotypegvcfs
+  files:
+    - path: output/gatk4/test.genotyped.vcf.gz
+      contains:
+        [
+          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
+        ]
+    - path: output/gatk4/test.genotyped.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/genotypegvcfs
+  files:
+    - path: output/gatk4/test.genotyped.vcf.gz
+      contains: ["AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693"]
+    - path: output/gatk4/test.genotyped.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf b/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf
new file mode 100644
index 00000000000..45a7cc116b7
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf
@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_GETPILEUPSUMMARIES } from '../../../../../modules/nf-core/gatk4/getpileupsummaries/main.nf'
+
+
+workflow test_gatk4_getpileupsummaries_separate_sites {
+
+    input = [ [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) ]
+
+    variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
+    variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
+    fasta = []
+    fai = []
+    dict = []
+    GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi)
+}
+
+workflow test_gatk4_getpileupsummaries_separate_sites_cram {
+
+    input = [ [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) ,
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true)
+        ]
+
+    variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
+    variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+    GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi)
+}
diff --git a/tests/modules/gatk4/getpileupsummaries/nextflow.config b/tests/modules/nf-core/gatk4/getpileupsummaries/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/getpileupsummaries/nextflow.config
rename to tests/modules/nf-core/gatk4/getpileupsummaries/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/getpileupsummaries/test.yml b/tests/modules/nf-core/gatk4/getpileupsummaries/test.yml
new file mode 100644
index 00000000000..b727ff4d269
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/getpileupsummaries/test.yml
@@ -0,0 +1,19 @@
+- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites
+  command: nextflow run ./tests/modules/nf-core/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c ./tests/config/nextflow.config
+  tags:
+    - gatk4/getpileupsummaries
+    - gatk4
+  files:
+    - path: output/gatk4/test.pileups.table
+      md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram
+  command: nextflow run ./tests/modules/nf-core/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c ./tests/config/nextflow.config
+  tags:
+    - gatk4/getpileupsummaries
+    - gatk4
+  files:
+    - path: output/gatk4/test.pileups.table
+      md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/haplotypecaller/main.nf b/tests/modules/nf-core/gatk4/haplotypecaller/main.nf
new file mode 100644
index 00000000000..ada5013dda5
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/haplotypecaller/main.nf
@@ -0,0 +1,67 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_HAPLOTYPECALLER } from '../../../../../modules/nf-core/gatk4/haplotypecaller/main.nf'
+
+workflow test_gatk4_haplotypecaller {
+    input     = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                  [],
+                  []
+                ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [])
+}
+
+workflow test_gatk4_haplotypecaller_cram {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                [],
+                []
+              ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [])
+}
+
+workflow test_gatk4_haplotypecaller_intervals_dbsnp {
+   input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
+                []
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
+    sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
+}
+
+workflow test_gatk4_haplotypecaller_dragstr_model {
+   input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                [],
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true)
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    sites = []
+    sites_tbi = []
+
+    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
+}
diff --git a/tests/modules/gatk4/haplotypecaller/nextflow.config b/tests/modules/nf-core/gatk4/haplotypecaller/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/haplotypecaller/nextflow.config
rename to tests/modules/nf-core/gatk4/haplotypecaller/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/haplotypecaller/test.yml b/tests/modules/nf-core/gatk4/haplotypecaller/test.yml
new file mode 100644
index 00000000000..a88b984149e
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/haplotypecaller/test.yml
@@ -0,0 +1,35 @@
+- name: gatk4 haplotypecaller test_gatk4_haplotypecaller
+  command: nextflow run ./tests/modules/nf-core/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/haplotypecaller/nextflow.config
+  tags:
+    - gatk4/haplotypecaller
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.tbi
+
+- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
+  command: nextflow run ./tests/modules/nf-core/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/haplotypecaller/nextflow.config
+  tags:
+    - gatk4/haplotypecaller
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.tbi
+
+- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
+  command: nextflow run ./tests/modules/nf-core/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/haplotypecaller/nextflow.config
+  tags:
+    - gatk4/haplotypecaller
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.tbi
+
+- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_dragstr_model
+  command: nextflow run ./tests/modules/nf-core/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_dragstr_model -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/haplotypecaller/nextflow.config
+  tags:
+    - gatk4/haplotypecaller
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.tbi
diff --git a/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf b/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf
new file mode 100644
index 00000000000..15c88cb38bb
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf
@@ -0,0 +1,45 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_INDEXFEATUREFILE } from '../../../../../modules/nf-core/gatk4/indexfeaturefile/main.nf'
+
+workflow test_gatk4_indexfeaturefile_bed {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) 
+    ]
+
+    GATK4_INDEXFEATUREFILE ( input )
+}
+
+workflow test_gatk4_indexfeaturefile_bed_gz {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
+    ]
+
+    GATK4_INDEXFEATUREFILE ( input )
+}
+
+workflow test_gatk4_indexfeaturefile_vcf {
+    
+    input = [ 
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) 
+    ]
+
+    GATK4_INDEXFEATUREFILE ( input )
+}
+
+workflow test_gatk4_indexfeaturefile_vcf_gz {
+    
+    input = [ 
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) 
+    ]
+
+    GATK4_INDEXFEATUREFILE ( input )
+}
diff --git a/tests/modules/gatk4/indexfeaturefile/nextflow.config b/tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/indexfeaturefile/nextflow.config
rename to tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/indexfeaturefile/test.yml b/tests/modules/nf-core/gatk4/indexfeaturefile/test.yml
new file mode 100644
index 00000000000..3e7483a2e6d
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/indexfeaturefile/test.yml
@@ -0,0 +1,37 @@
+- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed
+  command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/indexfeaturefile
+  files:
+    - path: output/gatk4/genome.bed.idx
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed_gz
+  command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/indexfeaturefile
+  files:
+    - path: output/gatk4/genome.bed.gz.tbi
+      md5sum: 4bc51e2351a6e83f20e13be75861f941
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf
+  command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/indexfeaturefile
+  files:
+    - path: output/gatk4/test.genome.vcf.idx
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz
+  command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c ./tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/indexfeaturefile
+  files:
+    - path: output/gatk4/test.genome.vcf.gz.tbi
+      md5sum: fedd68eaddf8d31257853d9da8325bd3
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/main.nf b/tests/modules/nf-core/gatk4/intervallisttobed/main.nf
new file mode 100644
index 00000000000..c8a5b819098
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/intervallisttobed/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_INTERVALLISTTOBED } from '../../../../../modules/nf-core/gatk4/intervallisttobed/main.nf'
+
+workflow test_gatk4_intervallisttobed {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true)
+    ]
+
+    GATK4_INTERVALLISTTOBED ( input )
+}
diff --git a/tests/modules/gatk4/intervallisttobed/nextflow.config b/tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/intervallisttobed/nextflow.config
rename to tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/test.yml b/tests/modules/nf-core/gatk4/intervallisttobed/test.yml
new file mode 100644
index 00000000000..461d484c855
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/intervallisttobed/test.yml
@@ -0,0 +1,9 @@
+- name: gatk4 intervallisttobed
+  command: nextflow run ./tests/modules/nf-core/gatk4/intervallisttobed -entry test_gatk4_intervallisttobed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/intervallisttobed
+  files:
+    - path: output/gatk4/test.bed
+      md5sum: 9046675d01199fbbee79f2bc1c5dce52
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/intervallisttools/main.nf b/tests/modules/nf-core/gatk4/intervallisttools/main.nf
new file mode 100644
index 00000000000..0845c7d017d
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/intervallisttools/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/gatk4/bedtointervallist/main.nf'
+include { GATK4_INTERVALLISTTOOLS } from '../../../../../modules/nf-core/gatk4/intervallisttools/main.nf'
+
+workflow test_gatk4_intervallisttools {
+
+    input = [
+        [ id:'test' ],
+        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    ]
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_BEDTOINTERVALLIST ( input, dict )
+    GATK4_INTERVALLISTTOOLS ( GATK4_BEDTOINTERVALLIST.out.interval_list )
+}
diff --git a/tests/modules/gatk4/intervallisttools/nextflow.config b/tests/modules/nf-core/gatk4/intervallisttools/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/intervallisttools/nextflow.config
rename to tests/modules/nf-core/gatk4/intervallisttools/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/intervallisttools/test.yml b/tests/modules/nf-core/gatk4/intervallisttools/test.yml
new file mode 100644
index 00000000000..d98116eff97
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/intervallisttools/test.yml
@@ -0,0 +1,17 @@
+- name: gatk4 intervallisttools test_gatk4_intervallisttools
+  command: nextflow run ./tests/modules/nf-core/gatk4/intervallisttools -entry test_gatk4_intervallisttools -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/intervallisttools/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/intervallisttools
+  files:
+    - path: output/gatk4/test.interval_list
+      md5sum: e51101c9357fb2d59fd30e370eefa39c
+    - path: output/gatk4/test_split/temp_0001_of_6/1scattered.interval_list
+      md5sum: 39385d38ac6cb7c05190026fc3b81411
+    - path: output/gatk4/test_split/temp_0002_of_6/2scattered.interval_list
+      md5sum: 59f1978c5f4ef3fce3b110816283d9f5
+    - path: output/gatk4/test_split/temp_0003_of_6/3scattered.interval_list
+      md5sum: 709fe81bfcf700bd80d96c62a71629fd
+    - path: output/gatk4/test_split/temp_0004_of_6/4scattered.interval_list
+      md5sum: c24044490cfedbcba61dbc646d3aa570
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf
new file mode 100644
index 00000000000..5960a568964
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../../modules/nf-core/gatk4/learnreadorientationmodel/main.nf'
+
+workflow test_gatk4_learnreadorientationmodel {
+
+    input = [ [ id:'test' ], // meta map
+              [file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_f1r2_tar_gz'], checkIfExists: true)] ]
+
+    GATK4_LEARNREADORIENTATIONMODEL ( input )
+}
diff --git a/tests/modules/gatk4/learnreadorientationmodel/nextflow.config b/tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/learnreadorientationmodel/nextflow.config
rename to tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/test.yml b/tests/modules/nf-core/gatk4/learnreadorientationmodel/test.yml
new file mode 100644
index 00000000000..fff1b387ac4
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/learnreadorientationmodel/test.yml
@@ -0,0 +1,8 @@
+- name: gatk4 learnreadorientationmodel test_gatk4_learnreadorientationmodel
+  command: nextflow run ./tests/modules/nf-core/gatk4/learnreadorientationmodel -entry test_gatk4_learnreadorientationmodel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/learnreadorientationmodel
+  files:
+    - path: output/gatk4/test.artifact-prior.tar.gz
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf
new file mode 100644
index 00000000000..8028168f366
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf
@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../../modules/nf-core/gatk4/leftalignandtrimvariants/main.nf'
+
+workflow test_gatk4_leftalignandtrimvariants_interval {
+
+    input = [ [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_leftalignandtrimvariants_no_interval {
+
+    input = [ [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+        []
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
+}
diff --git a/tests/modules/gatk4/leftalignandtrimvariants/nextflow.config b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/leftalignandtrimvariants/nextflow.config
rename to tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/test.yml b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/test.yml
new file mode 100644
index 00000000000..16712cfb023
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/test.yml
@@ -0,0 +1,22 @@
+- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_interval
+  command: nextflow run ./tests/modules/nf-core/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_interval -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/leftalignandtrimvariants
+  files:
+    - path: output/gatk4/test.normalised.vcf.gz
+      contains:
+        - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
+    - path: output/gatk4/test.normalised.vcf.gz.tbi
+
+- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_no_interval
+  command: nextflow run ./tests/modules/nf-core/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_no_interval -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/leftalignandtrimvariants
+  files:
+    - path: output/gatk4/test.normalised.vcf.gz
+      contains:
+        - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
+        - "MT192765.1\t10502\t.\tTAGATTATGACTGTGTCTCTTTTTGTTACATGCACCA\tTAGAT"
+    - path: output/gatk4/test.normalised.vcf.gz.tbi
diff --git a/tests/modules/nf-core/gatk4/markduplicates/main.nf b/tests/modules/nf-core/gatk4/markduplicates/main.nf
new file mode 100644
index 00000000000..90d7402684f
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/markduplicates/main.nf
@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_MARKDUPLICATES } from '../../../../../modules/nf-core/gatk4/markduplicates/main.nf'
+include { GATK4_MARKDUPLICATES as GATK4_MARKDUPLICATES_CRAM } from '../../../../../modules/nf-core/gatk4/markduplicates/main.nf'
+
+workflow test_gatk4_markduplicates {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    GATK4_MARKDUPLICATES ( input, [], [] )
+}
+
+workflow test_gatk4_markduplicates_multiple_bams {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+            ] ]
+
+    GATK4_MARKDUPLICATES ( input, [], [] )
+}
+
+workflow test_gatk4_markduplicates_multiple_cram_output {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+            ] ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    GATK4_MARKDUPLICATES_CRAM ( input, fasta, fai )
+}
diff --git a/tests/modules/gatk4/markduplicates/nextflow.config b/tests/modules/nf-core/gatk4/markduplicates/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/markduplicates/nextflow.config
rename to tests/modules/nf-core/gatk4/markduplicates/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/markduplicates/test.yml b/tests/modules/nf-core/gatk4/markduplicates/test.yml
new file mode 100644
index 00000000000..3ac215597e2
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/markduplicates/test.yml
@@ -0,0 +1,40 @@
+- name: gatk4 markduplicates test_gatk4_markduplicates
+  command: nextflow run ./tests/modules/nf-core/gatk4/markduplicates -entry test_gatk4_markduplicates -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/markduplicates/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/markduplicates
+  files:
+    - path: output/gatk4/test.bai
+      md5sum: 4ac375b5288501c832bc3e4773f06d39
+    - path: output/gatk4/test.bam
+      md5sum: c1a0d25c5f65514e72aa490326557a88
+    - path: output/gatk4/test.bam.metrics
+
+- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
+  command: nextflow run ./tests/modules/nf-core/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/markduplicates/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/markduplicates
+  files:
+    - path: output/gatk4/test.bai
+      md5sum: 832fbc6b3c3266d024fc7131ffd1b45d
+    - path: output/gatk4/test.bam
+      md5sum: 36909e80bde1aa547fae6382fd35764d
+    - path: output/gatk4/test.bam.metrics
+      contains:
+        - "testN"
+        - "2820"
+
+- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_cram_output
+  command: nextflow run ./tests/modules/nf-core/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_cram_output -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/markduplicates/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/markduplicates
+  files:
+    - path: output/gatk4/test.cram
+    - path: output/gatk4/test.cram.crai
+      md5sum: 53a329f0828210e317ad81b0e6ca4bc5
+    - path: output/gatk4/test.cram.metrics
+      contains:
+        - "testN"
+        - "2820"
diff --git a/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf b/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf
new file mode 100644
index 00000000000..e2fe9f7f8fa
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf
@@ -0,0 +1,57 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_MARKDUPLICATES_SPARK } from '../../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf'
+include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf'
+include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf'
+
+workflow test_gatk4_markduplicates_spark {
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
+}
+
+// chr 22
+workflow test_gatk4_markduplicates_spark_multiple_bams {
+    input = [ [ id:'test', single_end:false ], // meta map
+            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
+            ] ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
+}
+
+// chr 22
+workflow test_gatk4_markduplicates_spark_multiple_bams_cram_out {
+    input = [ [ id:'test', single_end:false ], // meta map
+            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
+            ] ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MARKDUPLICATES_SPARK_CRAM ( input, fasta, fai, dict )
+}
+
+// chr 22
+workflow test_gatk4_markduplicates_spark_multiple_bams_metrics {
+    input = [ [ id:'test', single_end:false ], // meta map
+            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
+            ] ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MARKDUPLICATES_SPARK_METRICS ( input, fasta, fai, dict )
+}
diff --git a/tests/modules/gatk4/markduplicatesspark/nextflow.config b/tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config
similarity index 91%
rename from tests/modules/gatk4/markduplicatesspark/nextflow.config
rename to tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config
index e0455b4be19..1b948a6aa39 100644
--- a/tests/modules/gatk4/markduplicatesspark/nextflow.config
+++ b/tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config
@@ -14,6 +14,6 @@ process {
     }
 
 }
-// override tests/config/nextflow.config
+// override ./tests/config/nextflow.config
 docker.userEmulation = false
 
diff --git a/tests/modules/nf-core/gatk4/markduplicatesspark/test.yml b/tests/modules/nf-core/gatk4/markduplicatesspark/test.yml
new file mode 100644
index 00000000000..b6ac329f835
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/markduplicatesspark/test.yml
@@ -0,0 +1,41 @@
+- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark
+  command: nextflow run ./tests/modules/nf-core/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/markduplicatesspark
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: dc1a09ac6371aab7c50d1a554baa06d3
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams
+  command: nextflow run ./tests/modules/nf-core/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/markduplicatesspark
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: 898cb0a6616897d8ada90bab53bf0837
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_cram_out
+  command: nextflow run ./tests/modules/nf-core/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_cram_out -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/markduplicatesspark
+  files:
+    - path: output/gatk4/test.cram
+      md5sum: 2271016de5e4199736598f39d12d7587
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_metrics
+  command: nextflow run ./tests/modules/nf-core/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_metrics -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/markduplicatesspark
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: 898cb0a6616897d8ada90bab53bf0837
+    - path: output/gatk4/test.metrics
+      contains: ["## METRICS CLASS", "org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics"]
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/mergebamalignment/main.nf b/tests/modules/nf-core/gatk4/mergebamalignment/main.nf
new file mode 100644
index 00000000000..6c5d463534f
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/mergebamalignment/main.nf
@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_MERGEBAMALIGNMENT } from '../../../../../modules/nf-core/gatk4/mergebamalignment/main.nf'
+
+workflow test_gatk4_mergebamalignment {
+    input    = [ [ id:'test' ], // meta map
+                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
+               ]
+    fasta    = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    dict     = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
+}
+
+workflow test_gatk4_mergebamalignment_stubs {
+     input    = [ [ id:'test' ], // meta map
+                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
+               ]
+    fasta    = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    dict     = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
+}
diff --git a/tests/modules/gatk4/mergebamalignment/nextflow.config b/tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/mergebamalignment/nextflow.config
rename to tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/mergebamalignment/test.yml b/tests/modules/nf-core/gatk4/mergebamalignment/test.yml
new file mode 100644
index 00000000000..c918d6297c1
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/mergebamalignment/test.yml
@@ -0,0 +1,18 @@
+- name: gatk4 mergebamalignment test_gatk4_mergebamalignment
+  command: nextflow run ./tests/modules/nf-core/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/mergebamalignment
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: e6f1b343700b7ccb94e81ae127433988
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
+  command: nextflow run ./tests/modules/nf-core/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/mergebamalignment
+  files:
+    - path: output/gatk4/test.bam
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/mergemutectstats/main.nf b/tests/modules/nf-core/gatk4/mergemutectstats/main.nf
new file mode 100644
index 00000000000..672706ad3cf
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/mergemutectstats/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_MERGEMUTECTSTATS } from '../../../../../modules/nf-core/gatk4/mergemutectstats/main.nf'
+
+workflow test_gatk4_mergemutectstats {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+         file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true)
+        ]
+
+    GATK4_MERGEMUTECTSTATS ( input )
+}
diff --git a/tests/modules/gatk4/mergemutectstats/nextflow.config b/tests/modules/nf-core/gatk4/mergemutectstats/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/mergemutectstats/nextflow.config
rename to tests/modules/nf-core/gatk4/mergemutectstats/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/mergemutectstats/test.yml b/tests/modules/nf-core/gatk4/mergemutectstats/test.yml
new file mode 100644
index 00000000000..09053a4a50a
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/mergemutectstats/test.yml
@@ -0,0 +1,9 @@
+- name: gatk4 mergemutectstats
+  command: nextflow run ./tests/modules/nf-core/gatk4/mergemutectstats -entry test_gatk4_mergemutectstats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergemutectstats/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/mergemutectstats
+  files:
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: 17d2091015d04cbd4a26b7a67dc659e6
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/mergevcfs/main.nf b/tests/modules/nf-core/gatk4/mergevcfs/main.nf
new file mode 100644
index 00000000000..0316fc441eb
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/mergevcfs/main.nf
@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_MERGEVCFS } from '../../../../../modules/nf-core/gatk4/mergevcfs/main.nf'
+
+workflow test_gatk4_mergevcfs {
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MERGEVCFS ( input, dict )
+}
+
+workflow test_gatk4_mergevcfs_no_dict {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+
+    GATK4_MERGEVCFS ( input, [] )
+}
+
+workflow test_gatk4_mergevcfs_no_dict_stubs {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+
+    GATK4_MERGEVCFS ( input, [] )
+}
diff --git a/tests/modules/gatk4/mergevcfs/nextflow.config b/tests/modules/nf-core/gatk4/mergevcfs/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/mergevcfs/nextflow.config
rename to tests/modules/nf-core/gatk4/mergevcfs/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/mergevcfs/test.yml b/tests/modules/nf-core/gatk4/mergevcfs/test.yml
new file mode 100644
index 00000000000..24fbddf21bc
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/mergevcfs/test.yml
@@ -0,0 +1,30 @@
+- name: gatk4 mergevcfs test_gatk4_mergevcfs
+  command: nextflow run ./tests/modules/nf-core/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergevcfs/nextflow.config
+  tags:
+    - gatk4/mergevcfs
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+      md5sum: 5b289bda88d3a3504f2e19ee8cff177c
+    - path: output/gatk4/test.vcf.gz.tbi
+      md5sum: a81673763b13086cfce9a23e72a35a16
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 mergevcfs test_gatk4_mergevcfs_no_dict
+  command: nextflow run ./tests/modules/nf-core/gatk4/mergevcfs -entry test_gatk4_mergevcfs_no_dict -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergevcfs/nextflow.config
+  tags:
+    - gatk4/mergevcfs
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+      md5sum: 5b289bda88d3a3504f2e19ee8cff177c
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 mergevcfs test_gatk4_mergevcfs_no_dict_stubs
+  command: nextflow run ./tests/modules/nf-core/gatk4/mergevcfs -entry test_gatk4_mergevcfs_no_dict_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergevcfs/nextflow.config -stub-run
+  tags:
+    - gatk4/mergevcfs
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/mutect2/main.nf b/tests/modules/nf-core/gatk4/mutect2/main.nf
new file mode 100644
index 00000000000..7567f7cebc8
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/mutect2/main.nf
@@ -0,0 +1,142 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_MUTECT2                       } from '../../../../../modules/nf-core/gatk4/mutect2/main.nf'
+include { GATK4_MUTECT2 as GATK4_MUTECT2_PAIR } from '../../../../../modules/nf-core/gatk4/mutect2/main.nf'
+include { GATK4_MUTECT2 as GATK4_MUTECT2_MITO } from '../../../../../modules/nf-core/gatk4/mutect2/main.nf'
+include { GATK4_MUTECT2 as GATK4_MUTECT2_F1R2 } from '../../../../../modules/nf-core/gatk4/mutect2/main.nf'
+
+workflow test_gatk4_mutect2_tumor_normal_pair {
+    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
+                ],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
+                ],
+              []
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_MUTECT2_PAIR ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
+}
+
+workflow test_gatk4_mutect2_tumor_normal_pair_f1r2 {
+    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
+                ],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
+                ],
+              []
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
+}
+
+workflow test_gatk4_mutect2_tumor_single {
+    input = [ [ id:'test'], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
+              []
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
+}
+
+workflow test_gatk4_mutect2_cram_input {
+    input = [ [ id:'test'], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)],
+              []
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
+}
+
+workflow test_gatk4_mutect2_generate_pon {
+    input = [ [ id:'test'], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
+              []
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_MUTECT2 ( input, fasta, fai, dict, [], [], [], [] )
+}
+
+// mitochondria mode would ideally have some mitochondria test data
+// but since the mitochondria settings only increase detection sensitivity
+// we can use the chr22 data as a stand in as it is already a small dataset
+// the extra variants detected compared to generate_pon shows the mode is working
+workflow test_gatk4_mutect2_mitochondria {
+    input = [ [ id:'test'], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam_bai'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] )
+}
+
+workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
+     input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
+                ],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
+                ],
+              []
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
+}
diff --git a/tests/modules/gatk4/mutect2/nextflow.config b/tests/modules/nf-core/gatk4/mutect2/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/mutect2/nextflow.config
rename to tests/modules/nf-core/gatk4/mutect2/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/mutect2/test.yml b/tests/modules/nf-core/gatk4/mutect2/test.yml
new file mode 100644
index 00000000000..0908ebc0e74
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/mutect2/test.yml
@@ -0,0 +1,83 @@
+- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair
+  command: nextflow run ./tests/modules/nf-core/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mutect2/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/mutect2
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: 17d2091015d04cbd4a26b7a67dc659e6
+    - path: output/gatk4/test.vcf.gz.tbi
+
+- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2
+  command: nextflow run ./tests/modules/nf-core/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mutect2/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/mutect2
+  files:
+    - path: output/gatk4/test.f1r2.tar.gz
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: 17d2091015d04cbd4a26b7a67dc659e6
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
+  command: nextflow run ./tests/modules/nf-core/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mutect2/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/mutect2
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: 55ed641e16089afb33cdbc478e202d3d
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 mutect2 test_gatk4_mutect2_cram_input
+  command: nextflow run ./tests/modules/nf-core/gatk4/mutect2 -entry test_gatk4_mutect2_cram_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mutect2/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/mutect2
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: 55ed641e16089afb33cdbc478e202d3d
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
+  command: nextflow run ./tests/modules/nf-core/gatk4/mutect2 -entry test_gatk4_mutect2_generate_pon -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mutect2/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/mutect2
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: b569ce66bbffe9588b3d221e821023ee
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 mutect2 test_gatk4_mutect2_mitochondria
+  command: nextflow run ./tests/modules/nf-core/gatk4/mutect2 -entry test_gatk4_mutect2_mitochondria -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mutect2/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/mutect2
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: fc6ea14ca2da346babe78161beea28c9
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
+  command: nextflow run ./tests/modules/nf-core/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mutect2/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/mutect2
+  files:
+    - path: output/gatk4/test.f1r2.tar.gz
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/printsvevidence/main.nf b/tests/modules/nf-core/gatk4/printsvevidence/main.nf
new file mode 100644
index 00000000000..78bf31cdaf4
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/printsvevidence/main.nf
@@ -0,0 +1,116 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_PE } from '../../../../../modules/nf-core/gatk4/printsvevidence/main.nf'
+include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_SR } from '../../../../../modules/nf-core/gatk4/printsvevidence/main.nf'
+include { GATK4_COLLECTSVEVIDENCE                           } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf'
+
+workflow test_gatk4_printsvevidence {
+    
+    input = Channel.of(
+        [
+            [ id:'normal', single_end:false ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+            [],
+            []
+        ],
+        [
+            [ id:'tumour', single_end:false ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
+            [],
+            []
+        ]
+    )
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+
+    GATK4_COLLECTSVEVIDENCE(
+        input, 
+        fasta, 
+        fasta_fai, 
+        dict
+    )
+
+    pe_files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence
+                    .combine(GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index, by:0)
+    sr_files = GATK4_COLLECTSVEVIDENCE.out.split_read_evidence
+                    .combine(GATK4_COLLECTSVEVIDENCE.out.split_read_evidence_index, by:0)
+
+    GATK4_PRINTSVEVIDENCE_PE( 
+        pe_files,
+        [],
+        fasta,
+        fasta_fai,
+        dict
+    )
+
+    GATK4_PRINTSVEVIDENCE_SR( 
+        sr_files,
+        [],
+        fasta,
+        fasta_fai,
+        dict
+    )
+
+}
+
+workflow test_gatk4_printsvevidence_bed_no_fasta {
+    
+    input = Channel.of(
+        [
+            [ id:'normal', single_end:false ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+            [],
+            []
+        ],
+        [
+            [ id:'tumour', single_end:false ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
+            [],
+            []
+        ]
+    )
+
+    fasta = []
+    fasta_fai = []
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    GATK4_COLLECTSVEVIDENCE(
+        input, 
+        fasta, 
+        fasta_fai, 
+        dict
+    )
+
+    pe_files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence
+                    .combine(GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index, by:0)
+    sr_files = GATK4_COLLECTSVEVIDENCE.out.split_read_evidence
+                    .combine(GATK4_COLLECTSVEVIDENCE.out.split_read_evidence_index, by:0)
+
+    GATK4_PRINTSVEVIDENCE_PE( 
+        pe_files,
+        bed,
+        fasta,
+        fasta_fai,
+        dict
+    )
+
+    GATK4_PRINTSVEVIDENCE_SR( 
+        sr_files,
+        bed,
+        fasta,
+        fasta_fai,
+        dict
+    )
+
+}
diff --git a/tests/modules/gatk4/printsvevidence/nextflow.config b/tests/modules/nf-core/gatk4/printsvevidence/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/printsvevidence/nextflow.config
rename to tests/modules/nf-core/gatk4/printsvevidence/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/printsvevidence/test.yml b/tests/modules/nf-core/gatk4/printsvevidence/test.yml
new file mode 100644
index 00000000000..040ee64728c
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/printsvevidence/test.yml
@@ -0,0 +1,77 @@
+- name: gatk4 printsvevidence test_gatk4_printsvevidence
+  command: nextflow run ./tests/modules/nf-core/gatk4/printsvevidence -entry test_gatk4_printsvevidence -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/printsvevidence/nextflow.config
+  tags:
+    - gatk4/printsvevidence
+    - gatk4
+  files:
+    - path: output/gatk4/normal.pe.txt.gz
+      md5sum: 19f13dd0408204590b40239d14acbdde
+    - path: output/gatk4/normal.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/normal.sr.txt.gz
+      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
+    - path: output/gatk4/normal.sr.txt.gz.tbi
+      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
+    - path: output/gatk4/normal_print.pe.txt.gz
+      md5sum: 19f13dd0408204590b40239d14acbdde
+    - path: output/gatk4/normal_print.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/normal_print.sr.txt.gz
+      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
+    - path: output/gatk4/normal_print.sr.txt.gz.tbi
+      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
+    - path: output/gatk4/tumour.pe.txt.gz
+      md5sum: 11fb8aeeea29370d9d1b49448456da81
+    - path: output/gatk4/tumour.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/tumour.sr.txt.gz
+      md5sum: 3ce47a0e0abac1c2b291e73a2b57cba0
+    - path: output/gatk4/tumour.sr.txt.gz.tbi
+      md5sum: f2105270ba79ed645bac9842be79f411
+    - path: output/gatk4/tumour_print.pe.txt.gz
+      md5sum: 11fb8aeeea29370d9d1b49448456da81
+    - path: output/gatk4/tumour_print.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/tumour_print.sr.txt.gz
+      md5sum: 3ce47a0e0abac1c2b291e73a2b57cba0
+    - path: output/gatk4/tumour_print.sr.txt.gz.tbi
+      md5sum: f2105270ba79ed645bac9842be79f411
+
+- name: gatk4 printsvevidence test_gatk4_printsvevidence_bed_no_fasta
+  command: nextflow run ./tests/modules/nf-core/gatk4/printsvevidence -entry test_gatk4_printsvevidence_bed_no_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/printsvevidence/nextflow.config
+  tags:
+    - gatk4/printsvevidence
+    - gatk4
+  files:
+    - path: output/gatk4/normal.pe.txt.gz
+      md5sum: 19f13dd0408204590b40239d14acbdde
+    - path: output/gatk4/normal.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/normal.sr.txt.gz
+      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
+    - path: output/gatk4/normal.sr.txt.gz.tbi
+      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
+    - path: output/gatk4/normal_print.pe.txt.gz
+      md5sum: 19f13dd0408204590b40239d14acbdde
+    - path: output/gatk4/normal_print.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/normal_print.sr.txt.gz
+      md5sum: fb9ce52193a0db3a084890bd6bbf6a64
+    - path: output/gatk4/normal_print.sr.txt.gz.tbi
+      md5sum: 3e7b04492c53765e3c84d76b59e1f2c5
+    - path: output/gatk4/tumour.pe.txt.gz
+      md5sum: 11fb8aeeea29370d9d1b49448456da81
+    - path: output/gatk4/tumour.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/tumour.sr.txt.gz
+      md5sum: 3ce47a0e0abac1c2b291e73a2b57cba0
+    - path: output/gatk4/tumour.sr.txt.gz.tbi
+      md5sum: f2105270ba79ed645bac9842be79f411
+    - path: output/gatk4/tumour_print.pe.txt.gz
+      md5sum: 11fb8aeeea29370d9d1b49448456da81
+    - path: output/gatk4/tumour_print.pe.txt.gz.tbi
+      md5sum: 876170d2727a467263cbacecbd9979ee
+    - path: output/gatk4/tumour_print.sr.txt.gz
+      md5sum: 3ce47a0e0abac1c2b291e73a2b57cba0
+    - path: output/gatk4/tumour_print.sr.txt.gz.tbi
+      md5sum: f2105270ba79ed645bac9842be79f411
diff --git a/tests/modules/nf-core/gatk4/reblockgvcf/main.nf b/tests/modules/nf-core/gatk4/reblockgvcf/main.nf
new file mode 100644
index 00000000000..d379e8fd828
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/reblockgvcf/main.nf
@@ -0,0 +1,55 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_REBLOCKGVCF } from '../../../../../modules/nf-core/gatk4/reblockgvcf/main.nf'
+
+workflow test_gatk4_reblockgvcf {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+        []
+    ]
+
+    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_index = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict        = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, [], [] )
+}
+
+workflow test_gatk4_reblockgvcf_intervals {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    ]
+
+    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_index = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict        = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, [], [] )
+}
+
+workflow test_gatk4_reblockgvcf_dbsnp {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true),
+        []
+    ]
+
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict        = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    dbsnp       = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi   = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, dbsnp, dbsnp_tbi )
+}
\ No newline at end of file
diff --git a/tests/modules/gatk4/reblockgvcf/nextflow.config b/tests/modules/nf-core/gatk4/reblockgvcf/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/reblockgvcf/nextflow.config
rename to tests/modules/nf-core/gatk4/reblockgvcf/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/reblockgvcf/test.yml b/tests/modules/nf-core/gatk4/reblockgvcf/test.yml
new file mode 100644
index 00000000000..2ea4ce196bc
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/reblockgvcf/test.yml
@@ -0,0 +1,26 @@
+- name: gatk4 reblockgvcf test_gatk4_reblockgvcf
+  command: nextflow run ./tests/modules/nf-core/gatk4/reblockgvcf -entry test_gatk4_reblockgvcf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/reblockgvcf/nextflow.config
+  tags:
+    - gatk4/reblockgvcf
+    - gatk4
+  files:
+    - path: output/gatk4/test.rb.g.vcf.gz
+    - path: output/gatk4/test.rb.g.vcf.gz.tbi
+
+- name: gatk4 reblockgvcf test_gatk4_reblockgvcf_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/reblockgvcf -entry test_gatk4_reblockgvcf_intervals -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/reblockgvcf/nextflow.config
+  tags:
+    - gatk4/reblockgvcf
+    - gatk4
+  files:
+    - path: output/gatk4/test.rb.g.vcf.gz
+    - path: output/gatk4/test.rb.g.vcf.gz.tbi
+
+- name: gatk4 reblockgvcf test_gatk4_reblockgvcf_dbsnp
+  command: nextflow run ./tests/modules/nf-core/gatk4/reblockgvcf -entry test_gatk4_reblockgvcf_dbsnp -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/reblockgvcf/nextflow.config
+  tags:
+    - gatk4/reblockgvcf
+    - gatk4
+  files:
+    - path: output/gatk4/test.rb.g.vcf.gz
+    - path: output/gatk4/test.rb.g.vcf.gz.tbi
diff --git a/tests/modules/nf-core/gatk4/revertsam/main.nf b/tests/modules/nf-core/gatk4/revertsam/main.nf
new file mode 100644
index 00000000000..2f4c153be69
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/revertsam/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_REVERTSAM } from '../../../../../modules/nf-core/gatk4/revertsam/main.nf'
+
+workflow test_gatk4_revertsam {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+            ]
+
+    GATK4_REVERTSAM ( input )
+}
+
+workflow test_gatk4_revertsam_stubs {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+            ]
+
+    GATK4_REVERTSAM ( input )
+}
diff --git a/tests/modules/gatk4/revertsam/nextflow.config b/tests/modules/nf-core/gatk4/revertsam/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/revertsam/nextflow.config
rename to tests/modules/nf-core/gatk4/revertsam/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/revertsam/test.yml b/tests/modules/nf-core/gatk4/revertsam/test.yml
new file mode 100644
index 00000000000..9666fd19a40
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/revertsam/test.yml
@@ -0,0 +1,18 @@
+- name: gatk4 revertsam test_gatk4_revertsam
+  command: nextflow run ./tests/modules/nf-core/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/revertsam/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/revertsam
+  files:
+    - path: output/gatk4/test.reverted.bam
+      md5sum: f783a88deb45c3a2c20ca12cbe1c5652
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 revertsam test_gatk4_revertsam_stubs
+  command: nextflow run ./tests/modules/nf-core/gatk4/revertsam -entry test_gatk4_revertsam_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/revertsam/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/revertsam
+  files:
+    - path: output/gatk4/test.reverted.bam
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/samtofastq/main.nf b/tests/modules/nf-core/gatk4/samtofastq/main.nf
new file mode 100644
index 00000000000..35f1f9d36c9
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/samtofastq/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_SAMTOFASTQ } from '../../../../../modules/nf-core/gatk4/samtofastq/main.nf'
+
+workflow test_gatk4_samtofastq_single_end {
+    input = [ [ id:'test', single_end: true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
+            ]
+
+    GATK4_SAMTOFASTQ ( input )
+}
+
+workflow test_gatk4_samtofastq_paired_end {
+    input = [ [ id:'test', single_end: false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+            ]
+
+    GATK4_SAMTOFASTQ ( input )
+}
+
+workflow test_gatk4_samtofastq_paired_end_stubs {
+    input = [ [ id:'test', single_end: true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
+            ]
+
+    GATK4_SAMTOFASTQ ( input )
+}
diff --git a/tests/modules/gatk4/samtofastq/nextflow.config b/tests/modules/nf-core/gatk4/samtofastq/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/samtofastq/nextflow.config
rename to tests/modules/nf-core/gatk4/samtofastq/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/samtofastq/test.yml b/tests/modules/nf-core/gatk4/samtofastq/test.yml
new file mode 100644
index 00000000000..41b8504e142
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/samtofastq/test.yml
@@ -0,0 +1,31 @@
+- name: gatk4 samtofastq test_gatk4_samtofastq_single_end
+  command: nextflow run ./tests/modules/nf-core/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/samtofastq/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/samtofastq
+  files:
+    - path: output/gatk4/test.fastq.gz
+      md5sum: 50ace41d4c24467f24f8b929540a7797
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end
+  command: nextflow run ./tests/modules/nf-core/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/samtofastq/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/samtofastq
+  files:
+    - path: output/gatk4/test_1.fastq.gz
+      md5sum: cfea607c9d75fd9ea9704780ad3a499c
+    - path: output/gatk4/test_2.fastq.gz
+      md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
+  command: nextflow run ./tests/modules/nf-core/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/samtofastq/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/samtofastq
+  files:
+    - path: output/gatk4/test_1.fastq.gz
+    - path: output/gatk4/test_2.fastq.gz
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/selectvariants/main.nf b/tests/modules/nf-core/gatk4/selectvariants/main.nf
new file mode 100644
index 00000000000..5ded13562a7
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/selectvariants/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_SELECTVARIANTS } from '../../../../../modules/nf-core/gatk4/selectvariants/main.nf'
+
+// Basic parameters with uncompressed VCF input
+workflow test_gatk4_selectvariants_vcf_input {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true)
+    ]
+
+    GATK4_SELECTVARIANTS ( input)
+}
+
+// Basic parameters with compressed VCF input
+workflow test_gatk4_selectvariants_gz_input {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    GATK4_SELECTVARIANTS ( input )
+}
diff --git a/tests/modules/gatk4/selectvariants/nextflow.config b/tests/modules/nf-core/gatk4/selectvariants/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/selectvariants/nextflow.config
rename to tests/modules/nf-core/gatk4/selectvariants/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/selectvariants/test.yml b/tests/modules/nf-core/gatk4/selectvariants/test.yml
new file mode 100644
index 00000000000..ad6568ddf60
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/selectvariants/test.yml
@@ -0,0 +1,19 @@
+- name: gatk4 selectvariants test_gatk4_selectvariants_vcf_input
+  command: nextflow run ./tests/modules/nf-core/gatk4/selectvariants -entry test_gatk4_selectvariants_vcf_input -c ./tests/config/nextflow.config
+  tags:
+    - gatk4/selectvariants
+    - gatk4
+  files:
+    - path: output/gatk4/test.selectvariants.vcf.gz
+    - path: output/gatk4/test.selectvariants.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 selectvariants test_gatk4_selectvariants_gz_input
+  command: nextflow run ./tests/modules/nf-core/gatk4/selectvariants -entry test_gatk4_selectvariants_gz_input -c ./tests/config/nextflow.config
+  tags:
+    - gatk4/selectvariants
+    - gatk4
+  files:
+    - path: output/gatk4/test.selectvariants.vcf.gz
+    - path: output/gatk4/test.selectvariants.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/splitintervals/main.nf b/tests/modules/nf-core/gatk4/splitintervals/main.nf
new file mode 100644
index 00000000000..5c744e351ce
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/splitintervals/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_SPLITINTERVALS } from '../../../../../modules/nf-core/gatk4/splitintervals/main.nf'
+
+workflow test_gatk4_splitintervals_bed {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_SPLITINTERVALS ( input, fasta, fasta_fai, fasta_dict)
+}
+
+workflow test_gatk4_splitintervals_intervals {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_SPLITINTERVALS ( input, fasta, fasta_fai, fasta_dict)
+}
\ No newline at end of file
diff --git a/tests/modules/gatk4/splitintervals/nextflow.config b/tests/modules/nf-core/gatk4/splitintervals/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/splitintervals/nextflow.config
rename to tests/modules/nf-core/gatk4/splitintervals/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/splitintervals/test.yml b/tests/modules/nf-core/gatk4/splitintervals/test.yml
new file mode 100644
index 00000000000..1230731471f
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/splitintervals/test.yml
@@ -0,0 +1,23 @@
+- name: gatk4 splitintervals test_gatk4_splitintervals_bed
+  command: nextflow run ./tests/modules/nf-core/gatk4/splitintervals -entry test_gatk4_splitintervals_bed -c ./tests/config/nextflow.config
+  tags:
+    - gatk4/splitintervals
+    - gatk4
+  files:
+    - path: output/gatk4/test/0000-scattered.interval_list
+      md5sum: c8d6b19e7a92535b6ce9608eae558faa
+    - path: output/gatk4/test/0001-scattered.interval_list
+      md5sum: b1877ad96aec308906594c50ebbe3ded
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 splitintervals test_gatk4_splitintervals_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/splitintervals -entry test_gatk4_splitintervals_intervals -c ./tests/config/nextflow.config
+  tags:
+    - gatk4/splitintervals
+    - gatk4
+  files:
+    - path: output/gatk4/test/0000-scattered.interval_list
+      md5sum: ebd6b34a335efc6732ff541936c6d2d5
+    - path: output/gatk4/test/0001-scattered.interval_list
+      md5sum: 9459b0e124fa84ec1e64ac4615bc9af7
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/splitncigarreads/main.nf b/tests/modules/nf-core/gatk4/splitncigarreads/main.nf
new file mode 100644
index 00000000000..979cf8b9a90
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/splitncigarreads/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_SPLITNCIGARREADS } from '../../../../../modules/nf-core/gatk4/splitncigarreads/main.nf'
+
+workflow test_gatk4_splitncigarreads {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+                [],
+                []
+            ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_splitncigarreads_intervals {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
+}
diff --git a/tests/modules/gatk4/splitncigarreads/nextflow.config b/tests/modules/nf-core/gatk4/splitncigarreads/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/splitncigarreads/nextflow.config
rename to tests/modules/nf-core/gatk4/splitncigarreads/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/splitncigarreads/test.yml b/tests/modules/nf-core/gatk4/splitncigarreads/test.yml
new file mode 100644
index 00000000000..1fcf4de65bd
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/splitncigarreads/test.yml
@@ -0,0 +1,18 @@
+- name: gatk4 splitncigarreads test_gatk4_splitncigarreads
+  command: nextflow run ./tests/modules/nf-core/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c ./tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/splitncigarreads
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: 37e5dbce8692b54c3292b539c91dfbd7
+    - path: output/gatk4/versions.yml
+- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
+  command: nextflow run ./tests/modules/nf-core/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c ./tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/splitncigarreads
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: e5cd2fd1822298a9bf7bc8b8d42146af
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/variantfiltration/main.nf b/tests/modules/nf-core/gatk4/variantfiltration/main.nf
new file mode 100644
index 00000000000..0b90440740a
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/variantfiltration/main.nf
@@ -0,0 +1,39 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_VARIANTFILTRATION } from '../../../../../modules/nf-core/gatk4/variantfiltration/main.nf'
+
+// Basic parameters with uncompressed VCF input
+workflow test_gatk4_variantfiltration_vcf_input {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true)
+    ]
+
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fasta_dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_VARIANTFILTRATION ( input, fasta, fasta_index, fasta_dict )
+}
+
+// Basic parameters with compressed VCF input
+workflow test_gatk4_variantfiltration_gz_input {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    fasta_dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_VARIANTFILTRATION ( input, fasta, fasta_index, fasta_dict )
+}
+
+
diff --git a/tests/modules/gatk4/variantfiltration/nextflow.config b/tests/modules/nf-core/gatk4/variantfiltration/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/variantfiltration/nextflow.config
rename to tests/modules/nf-core/gatk4/variantfiltration/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/variantfiltration/test.yml b/tests/modules/nf-core/gatk4/variantfiltration/test.yml
new file mode 100644
index 00000000000..84a63bc462f
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/variantfiltration/test.yml
@@ -0,0 +1,27 @@
+- name: gatk4 variantfiltration test_gatk4_variantfiltration_vcf_input
+  command: nextflow run ./tests/modules/nf-core/gatk4/variantfiltration -entry test_gatk4_variantfiltration_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantfiltration/nextflow.config
+  tags:
+    - gatk4/variantfiltration
+    - gatk4
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+      contains:
+        [
+          "BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365",
+        ]
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 variantfiltration test_gatk4_variantfiltration_gz_input
+  command: nextflow run ./tests/modules/nf-core/gatk4/variantfiltration -entry test_gatk4_variantfiltration_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantfiltration/nextflow.config
+  tags:
+    - gatk4/variantfiltration
+    - gatk4
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+      contains:
+        [
+          "BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365",
+        ]
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf b/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf
new file mode 100644
index 00000000000..f8680f9dec1
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf
@@ -0,0 +1,72 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY   } from '../../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf'
+include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf'
+
+workflow test_gatk4_variantrecalibrator {
+
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
+            ]
+
+    resources_vcf = [
+                    file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+                ]
+    resources_tbi = [
+                    file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+                ]
+    labels = [
+                '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz',
+                '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz',
+                '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz',
+                '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz'
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY(input, resources_vcf, resources_tbi, labels, fasta, fai, dict)
+}
+
+workflow test_gatk4_variantrecalibrator_allele_specific {
+
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
+            ]
+
+    resources_vcf = [
+                    file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+                ]
+    resources_tbi = [
+                    file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+                ]
+    labels = [
+                '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz',
+                '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz',
+                '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz',
+                '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz'
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY(input, resources_vcf, resources_tbi, labels, fasta, fai, dict)
+}
diff --git a/tests/modules/gatk4/variantrecalibrator/nextflow.config b/tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config
similarity index 100%
rename from tests/modules/gatk4/variantrecalibrator/nextflow.config
rename to tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml b/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml
new file mode 100644
index 00000000000..b24b45cbe13
--- /dev/null
+++ b/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml
@@ -0,0 +1,27 @@
+- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator
+  command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/variantrecalibrator
+  files:
+    - path: output/gatk4/test.recal
+      contains:
+        - "#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"
+    - path: output/gatk4/test.recal.idx
+    - path: output/gatk4/test.tranches
+      md5sum: c029e52fd63a893e1154cc9144a19eeb
+    - path: output/gatk4/versions.yml
+
+- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific
+  command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator_allele_specific -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/variantrecalibrator
+  files:
+    - path: output/gatk4/test.recal
+      contains:
+        - "#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"
+    - path: output/gatk4/test.recal.idx
+    - path: output/gatk4/test.tranches
+      md5sum: ad52fa69325c758f458a30ee5b43d6b5
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gecco/run/main.nf b/tests/modules/nf-core/gecco/run/main.nf
new file mode 100644
index 00000000000..76b971e2ffa
--- /dev/null
+++ b/tests/modules/nf-core/gecco/run/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GECCO_RUN } from '../../../../../modules/nf-core/gecco/run/main.nf'
+
+workflow test_gecco_run {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true),
+        []
+    ]
+    model_dir = []
+
+    GECCO_RUN ( input, model_dir )
+}
diff --git a/tests/modules/gecco/run/nextflow.config b/tests/modules/nf-core/gecco/run/nextflow.config
similarity index 100%
rename from tests/modules/gecco/run/nextflow.config
rename to tests/modules/nf-core/gecco/run/nextflow.config
diff --git a/tests/modules/nf-core/gecco/run/test.yml b/tests/modules/nf-core/gecco/run/test.yml
new file mode 100644
index 00000000000..847364f7da5
--- /dev/null
+++ b/tests/modules/nf-core/gecco/run/test.yml
@@ -0,0 +1,13 @@
+- name: gecco run test_gecco_run
+  command: nextflow run ./tests/modules/nf-core/gecco/run -entry test_gecco_run -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gecco/run/nextflow.config
+  tags:
+    - gecco/run
+    - gecco
+  files:
+    - path: output/gecco/NC_018507.1_cluster_1.gbk
+    - path: output/gecco/genome.clusters.tsv
+      md5sum: 6560ec765f6bbae50645896fd93b35cd
+    - path: output/gecco/genome.features.tsv
+      md5sum: 07492cf186003311ba9829056c65787f
+    - path: output/gecco/genome.genes.tsv
+      md5sum: 031a37dc603f8a5296f462608fd7bcc3
diff --git a/tests/modules/nf-core/genescopefk/main.nf b/tests/modules/nf-core/genescopefk/main.nf
new file mode 100644
index 00000000000..fcd2fc491a5
--- /dev/null
+++ b/tests/modules/nf-core/genescopefk/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTK_FASTK  } from '../../../../modules/nf-core/fastk/fastk/main.nf'
+include { FASTK_HISTEX } from '../../../../modules/nf-core/fastk/histex/main.nf'
+include { GENESCOPEFK  } from '../../../../modules/nf-core/genescopefk/main.nf'
+
+workflow test_genescopefk {
+
+    input = [
+        [ id:'test' , single_end: true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    FASTK_FASTK ( input )
+    FASTK_HISTEX ( FASTK_FASTK.out.hist )
+    GENESCOPEFK ( FASTK_HISTEX.out.hist )
+}
diff --git a/tests/modules/genescopefk/nextflow.config b/tests/modules/nf-core/genescopefk/nextflow.config
similarity index 100%
rename from tests/modules/genescopefk/nextflow.config
rename to tests/modules/nf-core/genescopefk/nextflow.config
diff --git a/tests/modules/nf-core/genescopefk/test.yml b/tests/modules/nf-core/genescopefk/test.yml
new file mode 100644
index 00000000000..056fc41190c
--- /dev/null
+++ b/tests/modules/nf-core/genescopefk/test.yml
@@ -0,0 +1,17 @@
+- name: genescopefk test_genescopefk
+  command: nextflow run ./tests/modules/nf-core/genescopefk -entry test_genescopefk -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/genescopefk/nextflow.config
+  tags:
+    - genescopefk
+  files:
+    - path: output/genescopefk/test_linear_plot.png
+      md5sum: bb221e2e21a6c0d04dcb6ec8f1bf1cd7
+    - path: output/genescopefk/test_log_plot.png
+      md5sum: d71ad0c963775992043c8f3c55d27fc4
+    - path: output/genescopefk/test_model.txt
+      md5sum: 49e5a66cf02b53a3b20880bfabef2ee8
+    - path: output/genescopefk/test_summary.txt
+      md5sum: 34540dcc2ba4ab9530f8878bbdc0921c
+    - path: output/genescopefk/test_transformed_linear_plot.png
+      md5sum: 3c8e3ad315e6c15cdf51c87de277ec1f
+    - path: output/genescopefk/test_transformed_log_plot.png
+      md5sum: 90d983c6faa9b8a02a1d26b777feefc6
diff --git a/tests/modules/nf-core/genmap/index/main.nf b/tests/modules/nf-core/genmap/index/main.nf
new file mode 100644
index 00000000000..1135eb977c6
--- /dev/null
+++ b/tests/modules/nf-core/genmap/index/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GENMAP_INDEX } from '../../../../../modules/nf-core/genmap/index/main.nf'
+
+workflow test_genmap_index {
+
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    GENMAP_INDEX ( input )
+}
diff --git a/tests/modules/genmap/index/nextflow.config b/tests/modules/nf-core/genmap/index/nextflow.config
similarity index 100%
rename from tests/modules/genmap/index/nextflow.config
rename to tests/modules/nf-core/genmap/index/nextflow.config
diff --git a/tests/modules/nf-core/genmap/index/test.yml b/tests/modules/nf-core/genmap/index/test.yml
new file mode 100644
index 00000000000..146049d0ee2
--- /dev/null
+++ b/tests/modules/nf-core/genmap/index/test.yml
@@ -0,0 +1,48 @@
+- name: genmap index test_genmap_index
+  command: nextflow run ./tests/modules/nf-core/genmap/index -entry test_genmap_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmap/index/nextflow.config
+  tags:
+    - genmap
+    - genmap/index
+  files:
+    - path: output/genmap/genmap/index.ids.concat
+      md5sum: da6caa25f62c5407ccdfbcce1fa92408
+    - path: output/genmap/genmap/index.ids.limits
+      md5sum: f82636c5da188aec131d3a809473eff1
+    - path: output/genmap/genmap/index.info.concat
+      md5sum: 8ba5273aa9e58722bf45b9cc39fc6bfe
+    - path: output/genmap/genmap/index.info.limits
+      md5sum: 3522f2811f4ddf04598809fc84a1459e
+    - path: output/genmap/genmap/index.lf.drp
+      md5sum: dd85d6a23af2c7adf2695658e3056c08
+    - path: output/genmap/genmap/index.lf.drp.sbl
+      md5sum: f1d3ff8443297732862df21dc4e57262
+    - path: output/genmap/genmap/index.lf.drs
+      md5sum: 93b885adfe0da089cdf634904fd59f71
+    - path: output/genmap/genmap/index.lf.drv
+      md5sum: e06b605496bd91b32afa3c4f56d934ac
+    - path: output/genmap/genmap/index.lf.drv.sbl
+      md5sum: 8dd6bb7329a71449b0a1b292b5999164
+    - path: output/genmap/genmap/index.lf.pst
+      md5sum: e8daba34298e99e42942435286f9b3f0
+    - path: output/genmap/genmap/index.rev.lf.drp
+      md5sum: 5d9107e3aeec0721553dd661d4365fef
+    - path: output/genmap/genmap/index.rev.lf.drp.sbl
+      md5sum: f1d3ff8443297732862df21dc4e57262
+    - path: output/genmap/genmap/index.rev.lf.drs
+      md5sum: 93b885adfe0da089cdf634904fd59f71
+    - path: output/genmap/genmap/index.rev.lf.drv
+      md5sum: df7e795edc0a034577a9d2599fe8cfeb
+    - path: output/genmap/genmap/index.rev.lf.drv.sbl
+      md5sum: 8dd6bb7329a71449b0a1b292b5999164
+    - path: output/genmap/genmap/index.rev.lf.pst
+      md5sum: e8daba34298e99e42942435286f9b3f0
+    - path: output/genmap/genmap/index.sa.ind
+      md5sum: e21e5c7ce887cc8e3d0fa44ab1019cab
+    - path: output/genmap/genmap/index.sa.len
+      md5sum: 5dfc20cfe8ed9892451461a8d402f51c
+    - path: output/genmap/genmap/index.sa.val
+      md5sum: 400ee7f2fe93b2000ae3a5da5e509730
+    - path: output/genmap/genmap/index.txt.concat
+      md5sum: b4303962e0c176107945f3405370e6ae
+    - path: output/genmap/genmap/index.txt.limits
+      md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
diff --git a/tests/modules/nf-core/genmap/mappability/main.nf b/tests/modules/nf-core/genmap/mappability/main.nf
new file mode 100644
index 00000000000..ba2e996e93b
--- /dev/null
+++ b/tests/modules/nf-core/genmap/mappability/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GENMAP_INDEX       } from '../../../../../modules/nf-core/genmap/index/main.nf'
+include { GENMAP_MAPPABILITY } from '../../../../../modules/nf-core/genmap/mappability/main.nf'
+
+workflow test_genmap_map {
+
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    GENMAP_INDEX ( input )
+    GENMAP_MAPPABILITY ( GENMAP_INDEX.out.index )
+}
diff --git a/tests/modules/genmap/mappability/nextflow.config b/tests/modules/nf-core/genmap/mappability/nextflow.config
similarity index 100%
rename from tests/modules/genmap/mappability/nextflow.config
rename to tests/modules/nf-core/genmap/mappability/nextflow.config
diff --git a/tests/modules/nf-core/genmap/mappability/test.yml b/tests/modules/nf-core/genmap/mappability/test.yml
new file mode 100644
index 00000000000..96926dfc833
--- /dev/null
+++ b/tests/modules/nf-core/genmap/mappability/test.yml
@@ -0,0 +1,12 @@
+- name: genmap mappability test_genmap_map
+  command: nextflow run ./tests/modules/nf-core/genmap/mappability -entry test_genmap_map -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmap/mappability/nextflow.config
+  tags:
+    - genmap
+    - genmap/mappability
+  files:
+    - path: output/genmap/mappability.bedgraph
+      md5sum: c4203b84a84331282ef8660279f80b26
+    - path: output/genmap/mappability.txt
+      md5sum: 602d409493457f92b2e5f075f62ebe30
+    - path: output/genmap/mappability.wig
+      md5sum: fd2afb6512ab9e86f9a3b62f8b9d9088
diff --git a/tests/modules/nf-core/genmod/annotate/main.nf b/tests/modules/nf-core/genmod/annotate/main.nf
new file mode 100644
index 00000000000..5152245453f
--- /dev/null
+++ b/tests/modules/nf-core/genmod/annotate/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GENMOD_ANNOTATE } from '../../../../../modules/nf-core/genmod/annotate/main.nf'
+
+input = [
+    [ id:'test', single_end:false ], // meta map
+    file(params.test_data['homo_sapiens']['illumina']['genmod_vcf_gz'], checkIfExists: true)
+]
+
+workflow test_genmod_annotate {
+
+    GENMOD_ANNOTATE ( input )
+}
+
+workflow test_genmod_annotate_stub {
+
+    GENMOD_ANNOTATE ( input )
+}
diff --git a/tests/modules/genmod/annotate/nextflow.config b/tests/modules/nf-core/genmod/annotate/nextflow.config
similarity index 100%
rename from tests/modules/genmod/annotate/nextflow.config
rename to tests/modules/nf-core/genmod/annotate/nextflow.config
diff --git a/tests/modules/nf-core/genmod/annotate/test.yml b/tests/modules/nf-core/genmod/annotate/test.yml
new file mode 100644
index 00000000000..60ffa3d4355
--- /dev/null
+++ b/tests/modules/nf-core/genmod/annotate/test.yml
@@ -0,0 +1,17 @@
+- name: "genmod annotate"
+  command: nextflow run ./tests/modules/nf-core/genmod/annotate -entry test_genmod_annotate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmod/annotate/nextflow.config
+  tags:
+    - "genmod"
+    - "genmod/annotate"
+  files:
+    - path: "output/genmod/test_annotate.vcf"
+    - path: output/genmod/versions.yml
+
+- name: "genmod annotate stub"
+  command: nextflow run ./tests/modules/nf-core/genmod/annotate -entry test_genmod_annotate_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmod/annotate/nextflow.config -stub-run
+  tags:
+    - "genmod"
+    - "genmod/annotate"
+  files:
+    - path: "output/genmod/test_annotate.vcf"
+    - path: output/genmod/versions.yml
diff --git a/tests/modules/nf-core/genmod/compound/main.nf b/tests/modules/nf-core/genmod/compound/main.nf
new file mode 100644
index 00000000000..ce0bb4779d2
--- /dev/null
+++ b/tests/modules/nf-core/genmod/compound/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GENMOD_COMPOUND } from '../../../../../modules/nf-core/genmod/compound/main.nf'
+
+input = [
+    [ id:'test', single_end:false ], // meta map
+    file(params.test_data['homo_sapiens']['illumina']['genmod_score_vcf_gz'], checkIfExists: true)
+]
+fam = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+config = file(params.test_data['homo_sapiens']['illumina']['rank_model'], checkIfExists: true)
+
+workflow test_genmod_compound {
+
+    GENMOD_COMPOUND ( input )
+}
+
+workflow test_genmod_compound_stub {
+
+    GENMOD_COMPOUND ( input )
+}
diff --git a/tests/modules/genmod/compound/nextflow.config b/tests/modules/nf-core/genmod/compound/nextflow.config
similarity index 100%
rename from tests/modules/genmod/compound/nextflow.config
rename to tests/modules/nf-core/genmod/compound/nextflow.config
diff --git a/tests/modules/nf-core/genmod/compound/test.yml b/tests/modules/nf-core/genmod/compound/test.yml
new file mode 100644
index 00000000000..04f469e5b5b
--- /dev/null
+++ b/tests/modules/nf-core/genmod/compound/test.yml
@@ -0,0 +1,17 @@
+- name: "genmod compound"
+  command: nextflow run ./tests/modules/nf-core/genmod/compound -entry test_genmod_compound -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmod/compound/nextflow.config
+  tags:
+    - "genmod"
+    - "genmod/compound"
+  files:
+    - path: output/genmod/test_compound.vcf
+    - path: output/genmod/versions.yml
+
+- name: "genmod compound stub"
+  command: nextflow run ./tests/modules/nf-core/genmod/compound -entry test_genmod_compound_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmod/compound/nextflow.config -stub-run
+  tags:
+    - "genmod"
+    - "genmod/compound"
+  files:
+    - path: output/genmod/test_compound.vcf
+    - path: output/genmod/versions.yml
diff --git a/tests/modules/nf-core/genmod/models/main.nf b/tests/modules/nf-core/genmod/models/main.nf
new file mode 100644
index 00000000000..ef983c48dc9
--- /dev/null
+++ b/tests/modules/nf-core/genmod/models/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GENMOD_MODELS   } from '../../../../../modules/nf-core/genmod/models/main.nf'
+
+input = [
+    [ id:'test', single_end:false ], // meta map
+    file(params.test_data['homo_sapiens']['illumina']['genmod_annotate_vcf_gz'], checkIfExists: true)
+]
+fam = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+
+workflow test_genmod_models {
+
+    GENMOD_MODELS ( input, fam, [] )
+}
+
+workflow test_genmod_models_stub {
+
+    GENMOD_MODELS ( input, fam, [] )
+}
diff --git a/tests/modules/genmod/models/nextflow.config b/tests/modules/nf-core/genmod/models/nextflow.config
similarity index 100%
rename from tests/modules/genmod/models/nextflow.config
rename to tests/modules/nf-core/genmod/models/nextflow.config
diff --git a/tests/modules/nf-core/genmod/models/test.yml b/tests/modules/nf-core/genmod/models/test.yml
new file mode 100644
index 00000000000..d985c433615
--- /dev/null
+++ b/tests/modules/nf-core/genmod/models/test.yml
@@ -0,0 +1,17 @@
+- name: "genmod models"
+  command: nextflow run ./tests/modules/nf-core/genmod/models -entry test_genmod_models -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmod/models/nextflow.config
+  tags:
+    - "genmod"
+    - "genmod/models"
+  files:
+    - path: output/genmod/test_models.vcf
+    - path: output/genmod/versions.yml
+
+- name: "genmod models stub"
+  command: nextflow run ./tests/modules/nf-core/genmod/models -entry test_genmod_models_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmod/models/nextflow.config -stub-run
+  tags:
+    - "genmod"
+    - "genmod/models"
+  files:
+    - path: output/genmod/test_models.vcf
+    - path: output/genmod/versions.yml
diff --git a/tests/modules/nf-core/genmod/score/main.nf b/tests/modules/nf-core/genmod/score/main.nf
new file mode 100644
index 00000000000..d7c8c5c1a08
--- /dev/null
+++ b/tests/modules/nf-core/genmod/score/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GENMOD_SCORE    } from '../../../../../modules/nf-core/genmod/score/main.nf'
+
+input = [
+    [ id:'test', single_end:false ], // meta map
+    file(params.test_data['homo_sapiens']['illumina']['genmod_models_vcf_gz'], checkIfExists: true)
+]
+fam = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+config = file(params.test_data['homo_sapiens']['illumina']['rank_model'], checkIfExists: true)
+
+workflow test_genmod_score {
+
+    GENMOD_SCORE    ( input, fam, config)
+}
+
+workflow test_genmod_score_stub {
+
+    GENMOD_SCORE    ( input, fam, config)
+}
diff --git a/tests/modules/genmod/score/nextflow.config b/tests/modules/nf-core/genmod/score/nextflow.config
similarity index 100%
rename from tests/modules/genmod/score/nextflow.config
rename to tests/modules/nf-core/genmod/score/nextflow.config
diff --git a/tests/modules/nf-core/genmod/score/test.yml b/tests/modules/nf-core/genmod/score/test.yml
new file mode 100644
index 00000000000..942492c2334
--- /dev/null
+++ b/tests/modules/nf-core/genmod/score/test.yml
@@ -0,0 +1,17 @@
+- name: "genmod score"
+  command: nextflow run ./tests/modules/nf-core/genmod/score -entry test_genmod_score -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmod/score/nextflow.config
+  tags:
+    - "genmod"
+    - "genmod/score"
+  files:
+    - path: output/genmod/test_score.vcf
+    - path: output/genmod/versions.yml
+
+- name: "genmod score stub"
+  command: nextflow run ./tests/modules/nf-core/genmod/score -entry test_genmod_score_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genmod/score/nextflow.config -stub-run
+  tags:
+    - "genmod"
+    - "genmod/score"
+  files:
+    - path: output/genmod/test_score.vcf
+    - path: output/genmod/versions.yml
diff --git a/tests/modules/nf-core/genomescope2/main.nf b/tests/modules/nf-core/genomescope2/main.nf
new file mode 100644
index 00000000000..1cb7c1b2229
--- /dev/null
+++ b/tests/modules/nf-core/genomescope2/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERYL_COUNT     } from '../../../../modules/nf-core/meryl/count/main.nf'
+include { MERYL_HISTOGRAM } from '../../../../modules/nf-core/meryl/histogram/main.nf'
+include { GENOMESCOPE2    } from '../../../../modules/nf-core/genomescope2/main.nf'
+
+workflow test_genomescope2 {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MERYL_COUNT ( input )
+    MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
+    GENOMESCOPE2 ( MERYL_HISTOGRAM.out.hist )
+}
diff --git a/tests/modules/genomescope2/nextflow.config b/tests/modules/nf-core/genomescope2/nextflow.config
similarity index 100%
rename from tests/modules/genomescope2/nextflow.config
rename to tests/modules/nf-core/genomescope2/nextflow.config
diff --git a/tests/modules/nf-core/genomescope2/test.yml b/tests/modules/nf-core/genomescope2/test.yml
new file mode 100644
index 00000000000..cb6a1fb6fcc
--- /dev/null
+++ b/tests/modules/nf-core/genomescope2/test.yml
@@ -0,0 +1,22 @@
+- name: genomescope2 test_genomescope2
+  command: nextflow run ./tests/modules/nf-core/genomescope2 -entry test_genomescope2 -c ./tests/config/nextflow.config
+  tags:
+    - genomescope2
+  files:
+    - path: output/genomescope2/test_linear_plot.png
+      md5sum: 94c165c5028156299a1d4d05766cac51
+    - path: output/genomescope2/test_log_plot.png
+      md5sum: 9d25ca463d92a0c73a893da7fd3979ba
+    - path: output/genomescope2/test_model.txt
+      md5sum: 3caf62f715f64a2f2b8fdff5d079cb84
+    - path: output/genomescope2/test_summary.txt
+      md5sum: 7452860e2cea99b85f3ff60daeac77f5
+    - path: output/genomescope2/test_transformed_linear_plot.png
+      md5sum: 99a64c1c18d8670f64cb863d4334abbb
+    - path: output/genomescope2/test_transformed_log_plot.png
+      md5sum: b4e029c9fb9987ca33b17392a691c1b4
+    - path: output/genomescope2/versions.yml
+      md5sum: 18afeb26f62a47f680b2bb3e27da9cbc
+    - path: output/meryl/test.hist
+      md5sum: f75362ab9cd70d96621b3690e952085f
+    - path: output/meryl/versions.yml
diff --git a/tests/modules/nf-core/genotyphi/parse/main.nf b/tests/modules/nf-core/genotyphi/parse/main.nf
new file mode 100644
index 00000000000..6e5f633ec1b
--- /dev/null
+++ b/tests/modules/nf-core/genotyphi/parse/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MYKROBE_PREDICT } from '../../../../../modules/nf-core/mykrobe/predict/main.nf'
+include { GENOTYPHI_PARSE } from '../../../../../modules/nf-core/genotyphi/parse/main.nf'
+
+workflow test_mykrobe_predict {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    MYKROBE_PREDICT ( input, "typhi" )
+    GENOTYPHI_PARSE ( MYKROBE_PREDICT.out.json )
+}
diff --git a/tests/modules/genotyphi/parse/nextflow.config b/tests/modules/nf-core/genotyphi/parse/nextflow.config
similarity index 100%
rename from tests/modules/genotyphi/parse/nextflow.config
rename to tests/modules/nf-core/genotyphi/parse/nextflow.config
diff --git a/tests/modules/nf-core/genotyphi/parse/test.yml b/tests/modules/nf-core/genotyphi/parse/test.yml
new file mode 100644
index 00000000000..925b9963d9c
--- /dev/null
+++ b/tests/modules/nf-core/genotyphi/parse/test.yml
@@ -0,0 +1,12 @@
+- name: genotyphi parse test_mykrobe_predict
+  command: nextflow run ./tests/modules/nf-core/genotyphi/parse -entry test_mykrobe_predict -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/genotyphi/parse/nextflow.config
+  tags:
+    - genotyphi/parse
+    - genotyphi
+  files:
+    - path: output/genotyphi/test_predictResults.tsv
+      contains: ["genome", "confidence", "supported", "test", "NA"]
+    - path: output/mykrobe/test.csv
+      contains: ["susceptibility", "genotype_model", "variants", "test.paired_end.bam"]
+    - path: output/mykrobe/test.json
+      contains: ["susceptibility", "kmer_count", "files", "test.paired_end.bam"]
diff --git a/tests/modules/nf-core/genrich/main.nf b/tests/modules/nf-core/genrich/main.nf
new file mode 100644
index 00000000000..71f9b21ccbe
--- /dev/null
+++ b/tests/modules/nf-core/genrich/main.nf
@@ -0,0 +1,79 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GENRICH } from '../../../../modules/nf-core/genrich/main.nf'
+include { GENRICH as GENRICH_CTRL    } from '../../../../modules/nf-core/genrich/main.nf'
+include { GENRICH as GENRICH_ALL     } from '../../../../modules/nf-core/genrich/main.nf'
+include { GENRICH as GENRICH_ATACSEQ } from '../../../../modules/nf-core/genrich/main.nf'
+
+workflow test_genrich {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
+    control   = [ ]
+    blacklist = [ ]
+
+    save_pvalues    = false
+    save_pileup     = false
+    save_bed        = false
+    save_duplicates = false
+
+    GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+}
+
+workflow test_genrich_ctrl {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
+    control   = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
+    blacklist = [ ]
+
+    save_pvalues    = false
+    save_pileup     = false
+    save_bed        = false
+    save_duplicates = false
+
+    GENRICH_CTRL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+}
+
+workflow test_genrich_all_outputs {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
+    control   = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
+    blacklist = [ ]
+
+    save_pvalues    = true
+    save_pileup     = true
+    save_bed        = true
+    save_duplicates = true
+
+    GENRICH_ALL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+}
+
+workflow test_genrich_blacklist {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
+    control   = [ ]
+    blacklist = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
+
+    save_pvalues    = false
+    save_pileup     = false
+    save_bed        = false
+    save_duplicates = false
+
+    GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+}
+
+workflow test_genrich_atacseq {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
+    control   = [ ]
+    blacklist = [ ]
+
+    save_pvalues    = false
+    save_pileup     = false
+    save_bed        = false
+    save_duplicates = false
+
+    GENRICH_ATACSEQ ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+}
+
diff --git a/tests/modules/genrich/nextflow.config b/tests/modules/nf-core/genrich/nextflow.config
similarity index 100%
rename from tests/modules/genrich/nextflow.config
rename to tests/modules/nf-core/genrich/nextflow.config
diff --git a/tests/modules/nf-core/genrich/test.yml b/tests/modules/nf-core/genrich/test.yml
new file mode 100644
index 00000000000..6d9f2139444
--- /dev/null
+++ b/tests/modules/nf-core/genrich/test.yml
@@ -0,0 +1,47 @@
+- name: genrich test_genrich
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  tags:
+    - genrich
+  files:
+    - path: output/genrich/test.narrowPeak
+      md5sum: 6afabdd3f691c7c84c66ff8a23984681
+
+- name: genrich test_genrich_ctrl
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_ctrl -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  tags:
+    - genrich
+  files:
+    - path: output/genrich/test.narrowPeak
+      md5sum: 2fcc392360b317f5ebee88cdbc149e05
+
+- name: genrich test_genrich_all_outputs
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_all_outputs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  tags:
+    - genrich
+  files:
+    - path: output/genrich/test.duplicates.txt
+      md5sum: 159d557af7c23bc3cfb802d87fa96c34
+    - path: output/genrich/test.intervals.bed
+      md5sum: 4bea65caa3f4043d703af4b57161112e
+    - path: output/genrich/test.narrowPeak
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/genrich/test.pileup.bedGraph
+      md5sum: 03e53848de695b5794f32f15b2709203
+    - path: output/genrich/test.pvalues.bedGraph
+      md5sum: b14feef34b6d2379a173a734ca963cde
+
+- name: genrich test_genrich_blacklist
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_blacklist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  tags:
+    - genrich
+  files:
+    - path: output/genrich/test.narrowPeak
+      md5sum: 6afabdd3f691c7c84c66ff8a23984681
+
+- name: genrich test_genrich_atacseq
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_atacseq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  tags:
+    - genrich
+  files:
+    - path: output/genrich/test.narrowPeak
+      md5sum: ddea556b820f8be3695ffdf6c6f70aff
diff --git a/tests/modules/nf-core/gfaffix/main.nf b/tests/modules/nf-core/gfaffix/main.nf
new file mode 100644
index 00000000000..712f7dca3e1
--- /dev/null
+++ b/tests/modules/nf-core/gfaffix/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GFAFFIX } from '../../../../modules/nf-core/gfaffix/main.nf'
+
+workflow test_gfaffix {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)]
+            ]
+
+    GFAFFIX ( input )
+}
diff --git a/tests/modules/gfaffix/nextflow.config b/tests/modules/nf-core/gfaffix/nextflow.config
similarity index 100%
rename from tests/modules/gfaffix/nextflow.config
rename to tests/modules/nf-core/gfaffix/nextflow.config
diff --git a/tests/modules/nf-core/gfaffix/test.yml b/tests/modules/nf-core/gfaffix/test.yml
new file mode 100644
index 00000000000..6937808d0c3
--- /dev/null
+++ b/tests/modules/nf-core/gfaffix/test.yml
@@ -0,0 +1,9 @@
+- name: gfaffix
+  command: nextflow run ./tests/modules/nf-core/gfaffix -entry test_gfaffix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gfaffix/nextflow.config
+  tags:
+    - gfaffix
+  files:
+    - path: output/gfaffix/test.gfaffix.gfa
+      md5sum: 7b51abeeab7706393957fcb66d31704a
+    - path: output/gfaffix/test.affixes.txt
+      md5sum: c3540baa386462552d7ebe4e4b7eda6a
diff --git a/tests/modules/nf-core/gffread/main.nf b/tests/modules/nf-core/gffread/main.nf
new file mode 100644
index 00000000000..014f938a518
--- /dev/null
+++ b/tests/modules/nf-core/gffread/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GFFREAD } from '../../../../modules/nf-core/gffread/main.nf'
+
+workflow test_gffread {
+    input = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+
+    GFFREAD ( input )
+}
diff --git a/tests/modules/gffread/nextflow.config b/tests/modules/nf-core/gffread/nextflow.config
similarity index 100%
rename from tests/modules/gffread/nextflow.config
rename to tests/modules/nf-core/gffread/nextflow.config
diff --git a/tests/modules/nf-core/gffread/test.yml b/tests/modules/nf-core/gffread/test.yml
new file mode 100644
index 00000000000..b6bba7cd609
--- /dev/null
+++ b/tests/modules/nf-core/gffread/test.yml
@@ -0,0 +1,7 @@
+- name: gffread
+  command: nextflow run ./tests/modules/nf-core/gffread/ -entry test_gffread -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gffread/nextflow.config
+  tags:
+    - gffread
+  files:
+    - path: ./output/gffread/genome.out.gtf
+      md5sum: fcbf5744ed806e47768bc456fa043263
diff --git a/tests/modules/nf-core/glimpse/chunk/main.nf b/tests/modules/nf-core/glimpse/chunk/main.nf
new file mode 100644
index 00000000000..594d3e0d7b6
--- /dev/null
+++ b/tests/modules/nf-core/glimpse/chunk/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GLIMPSE_CHUNK } from '../../../../../modules/nf-core/glimpse/chunk/main.nf'
+
+workflow test_glimpse_chunk {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)]
+    ]
+    GLIMPSE_CHUNK (input,"chr21")
+}
diff --git a/tests/modules/glimpse/chunk/nextflow.config b/tests/modules/nf-core/glimpse/chunk/nextflow.config
similarity index 100%
rename from tests/modules/glimpse/chunk/nextflow.config
rename to tests/modules/nf-core/glimpse/chunk/nextflow.config
diff --git a/tests/modules/nf-core/glimpse/chunk/test.yml b/tests/modules/nf-core/glimpse/chunk/test.yml
new file mode 100644
index 00000000000..5fd2ba9e2d6
--- /dev/null
+++ b/tests/modules/nf-core/glimpse/chunk/test.yml
@@ -0,0 +1,8 @@
+- name: glimpse chunk test_glimpse_chunk
+  command: nextflow run ./tests/modules/nf-core/glimpse/chunk -entry test_glimpse_chunk -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/glimpse/chunk/nextflow.config
+  tags:
+    - glimpse
+    - glimpse/chunk
+  files:
+    - path: output/glimpse/test.txt
+      md5sum: c690cdcc7aa086bb85431bb2b193176f
diff --git a/tests/modules/nf-core/glnexus/main.nf b/tests/modules/nf-core/glnexus/main.nf
new file mode 100644
index 00000000000..86debecc4ab
--- /dev/null
+++ b/tests/modules/nf-core/glnexus/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GLNEXUS } from '../../../../modules/nf-core/glnexus/main.nf'
+
+workflow test_glnexus {
+    input = [
+        [ id:'test' ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true)
+        ]
+    ]
+
+    GLNEXUS ( input )
+}
diff --git a/tests/modules/glnexus/nextflow.config b/tests/modules/nf-core/glnexus/nextflow.config
similarity index 100%
rename from tests/modules/glnexus/nextflow.config
rename to tests/modules/nf-core/glnexus/nextflow.config
diff --git a/tests/modules/nf-core/glnexus/test.yml b/tests/modules/nf-core/glnexus/test.yml
new file mode 100644
index 00000000000..b8ed6751541
--- /dev/null
+++ b/tests/modules/nf-core/glnexus/test.yml
@@ -0,0 +1,7 @@
+- name: glnexus test_glnexus
+  command: nextflow run ./tests/modules/nf-core/glnexus -entry test_glnexus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/glnexus/nextflow.config
+  tags:
+    - glnexus
+  files:
+    - path: output/glnexus/test.bcf
+      md5sum: 62b2cea9c1b92ac63645cb031eea46fc
diff --git a/tests/modules/nf-core/goat/taxonsearch/main.nf b/tests/modules/nf-core/goat/taxonsearch/main.nf
new file mode 100644
index 00000000000..cc8db9235d6
--- /dev/null
+++ b/tests/modules/nf-core/goat/taxonsearch/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GOAT_TAXONSEARCH } from '../../../../../modules/nf-core/goat/taxonsearch/main.nf'
+
+//
+// Test with genus name (Canis)
+//
+workflow test_goat_taxonsearch_single_species {
+
+    input = [
+      [ id:'test_single_species' ], // meta map
+      taxon = 'Meles meles',
+      []
+  ]
+    GOAT_TAXONSEARCH ( input )
+}
+
+//
+// Test with genus (Drosophila, fruit flies) using NCBI taxonomy ID
+//
+workflow test_goat_taxonsearch_genus_id {
+
+    input = [
+      [ id:'test_genus_id' ], // meta map
+      taxon = '7215',
+      []
+  ]
+    GOAT_TAXONSEARCH ( input )
+}
+
+//
+// Test with multiple species from a taxa file
+//
+workflow test_goat_taxonsearch_species {
+
+    input = [
+      [ id:'test_species' ], // meta map
+      taxon = '',
+      file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/goat_taxonsearch/taxonomy_ids.txt', checkIfExists: true)
+  ]
+    GOAT_TAXONSEARCH ( input )
+}
diff --git a/tests/modules/goat/taxonsearch/nextflow.config b/tests/modules/nf-core/goat/taxonsearch/nextflow.config
similarity index 100%
rename from tests/modules/goat/taxonsearch/nextflow.config
rename to tests/modules/nf-core/goat/taxonsearch/nextflow.config
diff --git a/tests/modules/nf-core/goat/taxonsearch/test.yml b/tests/modules/nf-core/goat/taxonsearch/test.yml
new file mode 100644
index 00000000000..427a5aae7bd
--- /dev/null
+++ b/tests/modules/nf-core/goat/taxonsearch/test.yml
@@ -0,0 +1,26 @@
+- name: goat taxonsearch test_goat_taxonsearch_single_species
+  command: nextflow run ./tests/modules/nf-core/goat/taxonsearch -entry test_goat_taxonsearch_single_species -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/goat/taxonsearch/nextflow.config
+  tags:
+    - goat/taxonsearch
+    - goat
+  files:
+    - path: output/goat/test_single_species.tsv
+      md5sum: ed5b0afc7a6cf2f4b558882c10b35ef7
+
+- name: goat taxonsearch test_goat_taxonsearch_genus_id
+  command: nextflow run ./tests/modules/nf-core/goat/taxonsearch -entry test_goat_taxonsearch_genus_id -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/goat/taxonsearch/nextflow.config
+  tags:
+    - goat/taxonsearch
+    - goat
+  files:
+    - path: output/goat/test_genus_id.tsv
+      md5sum: 2cc41abbbc21b4b66f4d5126cfbba2bc
+
+- name: goat taxonsearch test_goat_taxonsearch_species
+  command: nextflow run ./tests/modules/nf-core/goat/taxonsearch -entry test_goat_taxonsearch_species -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/goat/taxonsearch/nextflow.config
+  tags:
+    - goat/taxonsearch
+    - goat
+  files:
+    - path: output/goat/test_species.tsv
+      md5sum: 7f5b36414820bd3ce2bfda06d98e479c
diff --git a/tests/modules/nf-core/graphmap2/align/main.nf b/tests/modules/nf-core/graphmap2/align/main.nf
new file mode 100644
index 00000000000..d4dc83d9d39
--- /dev/null
+++ b/tests/modules/nf-core/graphmap2/align/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GRAPHMAP2_INDEX } from '../../../../../modules/nf-core/graphmap2/index/main.nf'
+include { GRAPHMAP2_ALIGN } from '../../../../../modules/nf-core/graphmap2/align/main.nf'
+
+workflow test_graphmap2_align {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    GRAPHMAP2_INDEX ( fasta )
+    GRAPHMAP2_ALIGN ( input, fasta, GRAPHMAP2_INDEX.out.index )
+}
diff --git a/tests/modules/graphmap2/align/nextflow.config b/tests/modules/nf-core/graphmap2/align/nextflow.config
similarity index 100%
rename from tests/modules/graphmap2/align/nextflow.config
rename to tests/modules/nf-core/graphmap2/align/nextflow.config
diff --git a/tests/modules/nf-core/graphmap2/align/test.yml b/tests/modules/nf-core/graphmap2/align/test.yml
new file mode 100644
index 00000000000..dc4f241870d
--- /dev/null
+++ b/tests/modules/nf-core/graphmap2/align/test.yml
@@ -0,0 +1,7 @@
+- name: graphmap2 align
+  command: nextflow run ./tests/modules/nf-core/graphmap2/align -entry test_graphmap2_align -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/graphmap2/align/nextflow.config
+  tags:
+    - graphmap2
+    - graphmap2/align
+  files:
+    - path: ./output/graphmap2/test.sam
diff --git a/tests/modules/nf-core/graphmap2/index/main.nf b/tests/modules/nf-core/graphmap2/index/main.nf
new file mode 100644
index 00000000000..cb71cd9918a
--- /dev/null
+++ b/tests/modules/nf-core/graphmap2/index/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GRAPHMAP2_INDEX } from '../../../../../modules/nf-core/graphmap2/index/main.nf'
+
+workflow test_graphmap2_index {
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    GRAPHMAP2_INDEX ( fasta )
+}
diff --git a/tests/modules/graphmap2/index/nextflow.config b/tests/modules/nf-core/graphmap2/index/nextflow.config
similarity index 100%
rename from tests/modules/graphmap2/index/nextflow.config
rename to tests/modules/nf-core/graphmap2/index/nextflow.config
diff --git a/tests/modules/nf-core/graphmap2/index/test.yml b/tests/modules/nf-core/graphmap2/index/test.yml
new file mode 100644
index 00000000000..674c043956b
--- /dev/null
+++ b/tests/modules/nf-core/graphmap2/index/test.yml
@@ -0,0 +1,8 @@
+- name: graphmap2 index
+  command: nextflow run ./tests/modules/nf-core/graphmap2/index -entry test_graphmap2_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/graphmap2/index/nextflow.config
+  tags:
+    - graphmap2
+    - graphmap2/index
+  files:
+    - path: ./output/graphmap2/genome.fasta.gmidx
+      md5sum: 2973f9b7fa52c78899c73908f8afc6be
diff --git a/tests/modules/nf-core/gstama/collapse/main.nf b/tests/modules/nf-core/gstama/collapse/main.nf
new file mode 100644
index 00000000000..20c3ff74ccf
--- /dev/null
+++ b/tests/modules/nf-core/gstama/collapse/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GSTAMA_COLLAPSE } from '../../../../../modules/nf-core/gstama/collapse/main.nf'
+
+workflow test_gstama_collapse {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['aligned'], checkIfExists: true)
+    ]
+    genome = file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true)
+
+    GSTAMA_COLLAPSE ( input, genome )
+}
diff --git a/tests/modules/gstama/collapse/nextflow.config b/tests/modules/nf-core/gstama/collapse/nextflow.config
similarity index 100%
rename from tests/modules/gstama/collapse/nextflow.config
rename to tests/modules/nf-core/gstama/collapse/nextflow.config
diff --git a/tests/modules/nf-core/gstama/collapse/test.yml b/tests/modules/nf-core/gstama/collapse/test.yml
new file mode 100644
index 00000000000..484fe1db4d9
--- /dev/null
+++ b/tests/modules/nf-core/gstama/collapse/test.yml
@@ -0,0 +1,24 @@
+- name: gstama collapse test_gstama_collapse
+  command: nextflow run ./tests/modules/nf-core/gstama/collapse -entry test_gstama_collapse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gstama/collapse/nextflow.config
+  tags:
+    - gstama
+    - gstama/collapse
+  files:
+    - path: output/gstama/test_tc_collapsed.bed
+      md5sum: e5105198ed970a33ae0ecaa7bff421d9
+    - path: output/gstama/test_tc_local_density_error.txt
+      md5sum: b917ac1f14eccd590b6881a686f324d5
+    - path: output/gstama/test_tc_polya.txt
+      md5sum: 628ea62b918fc4f31e109f724d714a66
+    - path: output/gstama/test_tc_read.txt
+      md5sum: d2685d7f24cd1611e0770a5ce25422fe
+    - path: output/gstama/test_tc_strand_check.txt
+      md5sum: 42cc52b2660b1e0b84e1c9ab37a965ec
+    - path: output/gstama/test_tc_trans_read.bed
+      md5sum: 0ca1a32f33ef05242d897d913802554b
+    - path: output/gstama/test_tc_trans_report.txt
+      md5sum: 33a86c15ca2acce36b2a5962f4c1adc4
+    - path: output/gstama/test_tc_varcov.txt
+      md5sum: 587fd899ff658eb66b1770a35283bfcb
+    - path: output/gstama/test_tc_variants.txt
+      md5sum: 5b1165e9f33faba4f7207013fc27257e
diff --git a/tests/modules/nf-core/gstama/merge/main.nf b/tests/modules/nf-core/gstama/merge/main.nf
new file mode 100644
index 00000000000..dad081f557b
--- /dev/null
+++ b/tests/modules/nf-core/gstama/merge/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GSTAMA_MERGE } from '../../../../../modules/nf-core/gstama/merge/main'
+
+workflow test_gstama_merge {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['pacbio']['genemodel1'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['pacbio']['genemodel2'], checkIfExists: true)
+        ]
+    ]
+    filelist = file(params.test_data['homo_sapiens']['pacbio']['filelist'], checkIfExists: true)
+
+    GSTAMA_MERGE ( input, filelist )
+}
diff --git a/tests/modules/gstama/merge/nextflow.config b/tests/modules/nf-core/gstama/merge/nextflow.config
similarity index 100%
rename from tests/modules/gstama/merge/nextflow.config
rename to tests/modules/nf-core/gstama/merge/nextflow.config
diff --git a/tests/modules/nf-core/gstama/merge/test.yml b/tests/modules/nf-core/gstama/merge/test.yml
new file mode 100644
index 00000000000..b0a81a3f1bc
--- /dev/null
+++ b/tests/modules/nf-core/gstama/merge/test.yml
@@ -0,0 +1,14 @@
+- name: gstama merge test_gstama_merge
+  command: nextflow run ./tests/modules/nf-core/gstama/merge -entry test_gstama_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gstama/merge/nextflow.config
+  tags:
+    - gstama
+    - gstama/merge
+  files:
+    - path: output/gstama/test_merged.bed
+      md5sum: 60ec34e1ff9655d4ce2e83d3f4bbf448
+    - path: output/gstama/test_merged_gene_report.txt
+      md5sum: 7029fd183dfd905a233403cfbe44722a
+    - path: output/gstama/test_merged_merge.txt
+      md5sum: 4279e59ed5739ce4f2f811568962893f
+    - path: output/gstama/test_merged_trans_report.txt
+      md5sum: 97d8346d9eb9da140941656c3a3325cd
diff --git a/tests/modules/nf-core/gstama/polyacleanup/main.nf b/tests/modules/nf-core/gstama/polyacleanup/main.nf
new file mode 100644
index 00000000000..e1ed59663f9
--- /dev/null
+++ b/tests/modules/nf-core/gstama/polyacleanup/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GSTAMA_POLYACLEANUP } from '../../../../../modules/nf-core/gstama/polyacleanup/main.nf'
+
+workflow test_gstama_polyacleanup {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
+    ]
+
+    GSTAMA_POLYACLEANUP ( input )
+}
diff --git a/tests/modules/gstama/polyacleanup/nextflow.config b/tests/modules/nf-core/gstama/polyacleanup/nextflow.config
similarity index 100%
rename from tests/modules/gstama/polyacleanup/nextflow.config
rename to tests/modules/nf-core/gstama/polyacleanup/nextflow.config
diff --git a/tests/modules/nf-core/gstama/polyacleanup/test.yml b/tests/modules/nf-core/gstama/polyacleanup/test.yml
new file mode 100644
index 00000000000..6a1ed064c0e
--- /dev/null
+++ b/tests/modules/nf-core/gstama/polyacleanup/test.yml
@@ -0,0 +1,14 @@
+- name: gstama polyacleanup test_gstama_polyacleanup
+  command: nextflow run ./tests/modules/nf-core/gstama/polyacleanup -entry test_gstama_polyacleanup -c ./tests/config/nextflow.config
+  tags:
+    - gstama
+    - gstama/polyacleanup
+  files:
+    - path: output/gstama/test_tama.fa.gz
+      md5sum: 9c768387478e5f966a42c369c0270b09
+    - path: output/gstama/test_tama_polya_flnc_report.txt.gz
+      md5sum: fe3606979ed11538aacd83159f4cff03
+    - path: output/gstama/test_tama_tails.fa.gz
+      md5sum: ba21256c0afe0bda71b3ee66b4c761bf
+    - path: output/gstama/versions.yml
+      md5sum: 07ebb812ae13a350d955fab7600b2542
diff --git a/tests/modules/nf-core/gtdbtk/classifywf/main.nf b/tests/modules/nf-core/gtdbtk/classifywf/main.nf
new file mode 100644
index 00000000000..a3373a1e9b9
--- /dev/null
+++ b/tests/modules/nf-core/gtdbtk/classifywf/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GTDBTK_CLASSIFYWF } from '../../../../../modules/nf-core/gtdbtk/classifywf/main.nf'
+
+process STUB_GTDBTK_DATABASE {
+    output:
+    tuple val("gtdbtk_r202_data"), path("database/*"), emit: database
+
+    stub:
+    """
+    mkdir database
+    touch database/gtdbtk_r202_data
+    """
+}
+
+workflow test_gtdbtk_classifywf {
+
+    STUB_GTDBTK_DATABASE()
+
+    input = [ 
+        [ id:'test', single_end:false, assembler:'SPADES' ],
+        [ 
+            file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
+        ]
+    ]
+	
+    GTDBTK_CLASSIFYWF ( input, STUB_GTDBTK_DATABASE.out.database )
+}
diff --git a/tests/modules/gtdbtk/classifywf/nextflow.config b/tests/modules/nf-core/gtdbtk/classifywf/nextflow.config
similarity index 100%
rename from tests/modules/gtdbtk/classifywf/nextflow.config
rename to tests/modules/nf-core/gtdbtk/classifywf/nextflow.config
diff --git a/tests/modules/nf-core/gtdbtk/classifywf/test.yml b/tests/modules/nf-core/gtdbtk/classifywf/test.yml
new file mode 100644
index 00000000000..0afccaae727
--- /dev/null
+++ b/tests/modules/nf-core/gtdbtk/classifywf/test.yml
@@ -0,0 +1,8 @@
+- name: gtdbtk classifywf
+  command: nextflow run ./tests/modules/nf-core/gtdbtk/classifywf -entry test_gtdbtk_classifywf -c ./tests/config/nextflow.config -stub-run -c ./tests/modules/nf-core/gtdbtk/classifywf/nextflow.config
+  tags:
+    - gtdbtk
+    - gtdbtk/classifywf
+  files:
+    - path: output/gtdbtk/gtdbtk.SPADES-test.stub.summary.tsv
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/nf-core/gubbins/main.nf b/tests/modules/nf-core/gubbins/main.nf
new file mode 100644
index 00000000000..f65460d821e
--- /dev/null
+++ b/tests/modules/nf-core/gubbins/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUBBINS } from '../../../../modules/nf-core/gubbins/main.nf'
+
+workflow test_gubbins { 
+    input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
+
+    GUBBINS ( input )
+}
diff --git a/tests/modules/gubbins/nextflow.config b/tests/modules/nf-core/gubbins/nextflow.config
similarity index 100%
rename from tests/modules/gubbins/nextflow.config
rename to tests/modules/nf-core/gubbins/nextflow.config
diff --git a/tests/modules/nf-core/gubbins/test.yml b/tests/modules/nf-core/gubbins/test.yml
new file mode 100644
index 00000000000..39b9d738cf2
--- /dev/null
+++ b/tests/modules/nf-core/gubbins/test.yml
@@ -0,0 +1,23 @@
+- name: gubbins
+  command: nextflow run ./tests/modules/nf-core/gubbins -entry test_gubbins -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gubbins/nextflow.config
+  tags:
+    - gubbins
+  files:
+    - path: output/gubbins/all_sites.filtered_polymorphic_sites.fasta
+      md5sum: 4cbfd93868d8ed7d4d8b099eba137134
+    - path: output/gubbins/all_sites.recombination_predictions.embl
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/gubbins/all_sites.recombination_predictions.gff
+      md5sum: f95871e79968340cb82532e2c9b0c92b
+    - path: output/gubbins/all_sites.branch_base_reconstruction.embl
+      md5sum: 9e051646d630f528fff58f1f73286006
+    - path: output/gubbins/all_sites.summary_of_snp_distribution.vcf
+      md5sum: 276e62e888ea811577c8ffb2da0b3aff
+    - path: output/gubbins/all_sites.per_branch_statistics.csv
+      md5sum: 25e4fdb6681c3709a9add1d5632bbf3e
+    - path: output/gubbins/all_sites.filtered_polymorphic_sites.phylip
+      md5sum: 0a77f397a7797c5c3386832745b0c97a
+    - path: output/gubbins/all_sites.final_tree.tre
+      md5sum: 6cb251b58307aab11cb4b48792d6cda1
+    - path: output/gubbins/all_sites.node_labelled.final_tree.tre
+      md5sum: e01f965a15924b4f97603b8011c8d3f7
diff --git a/tests/modules/nf-core/gunc/downloaddb/main.nf b/tests/modules/nf-core/gunc/downloaddb/main.nf
new file mode 100644
index 00000000000..a708f54e6ff
--- /dev/null
+++ b/tests/modules/nf-core/gunc/downloaddb/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNC_DOWNLOADDB } from '../../../../../modules/nf-core/gunc/downloaddb/main.nf'
+
+workflow test_gunc_downloaddb {
+
+    input = 'progenomes'
+
+    GUNC_DOWNLOADDB ( input )
+}
diff --git a/tests/modules/gunc/downloaddb/nextflow.config b/tests/modules/nf-core/gunc/downloaddb/nextflow.config
similarity index 100%
rename from tests/modules/gunc/downloaddb/nextflow.config
rename to tests/modules/nf-core/gunc/downloaddb/nextflow.config
diff --git a/tests/modules/nf-core/gunc/downloaddb/test.yml b/tests/modules/nf-core/gunc/downloaddb/test.yml
new file mode 100644
index 00000000000..9f0e52b55b6
--- /dev/null
+++ b/tests/modules/nf-core/gunc/downloaddb/test.yml
@@ -0,0 +1,8 @@
+- name: gunc downloaddb
+  command: nextflow run ./tests/modules/nf-core/gunc/downloaddb -entry test_gunc_downloaddb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gunc/downloaddb/nextflow.config
+  tags:
+    - gunc
+    - gunc/downloaddb
+  files:
+    - path: output/gunc/gunc_db_progenomes2.1.dmnd
+      md5sum: 447c9330056b02f29f30fe81fe4af4eb
diff --git a/tests/modules/nf-core/gunc/run/main.nf b/tests/modules/nf-core/gunc/run/main.nf
new file mode 100644
index 00000000000..b676599ec38
--- /dev/null
+++ b/tests/modules/nf-core/gunc/run/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNC_RUN        } from '../../../../../modules/nf-core/gunc/run/main.nf'
+include { GUNC_DOWNLOADDB } from '../../../../../modules/nf-core/gunc/downloaddb/main.nf'
+
+workflow test_gunc_run {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+    ]
+
+    GUNC_DOWNLOADDB ( 'progenomes' )
+    GUNC_RUN ( input, GUNC_DOWNLOADDB.out.db )
+}
diff --git a/tests/modules/gunc/run/nextflow.config b/tests/modules/nf-core/gunc/run/nextflow.config
similarity index 100%
rename from tests/modules/gunc/run/nextflow.config
rename to tests/modules/nf-core/gunc/run/nextflow.config
diff --git a/tests/modules/nf-core/gunc/run/test.yml b/tests/modules/nf-core/gunc/run/test.yml
new file mode 100644
index 00000000000..b42a20f77e3
--- /dev/null
+++ b/tests/modules/nf-core/gunc/run/test.yml
@@ -0,0 +1,8 @@
+- name: gunc run
+  command: nextflow run ./tests/modules/nf-core/gunc/run -entry test_gunc_run -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gunc/run/nextflow.config
+  tags:
+    - gunc
+    - gunc/run
+  files:
+    - path: output/gunc/GUNC.progenomes_2.1.maxCSS_level.tsv
+      md5sum: 0420c1a9f2c50fefaee9fab5d80a551a
diff --git a/tests/modules/nf-core/gunzip/main.nf b/tests/modules/nf-core/gunzip/main.nf
new file mode 100644
index 00000000000..b106b1e6ac1
--- /dev/null
+++ b/tests/modules/nf-core/gunzip/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf'
+
+workflow test_gunzip {
+    input = [ [],
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ]
+
+    GUNZIP ( input )
+}
diff --git a/tests/modules/gunzip/nextflow.config b/tests/modules/nf-core/gunzip/nextflow.config
similarity index 100%
rename from tests/modules/gunzip/nextflow.config
rename to tests/modules/nf-core/gunzip/nextflow.config
diff --git a/tests/modules/nf-core/gunzip/test.yml b/tests/modules/nf-core/gunzip/test.yml
new file mode 100644
index 00000000000..5ea0d8d2df8
--- /dev/null
+++ b/tests/modules/nf-core/gunzip/test.yml
@@ -0,0 +1,7 @@
+- name: gunzip
+  command: nextflow run ./tests/modules/nf-core/gunzip -entry test_gunzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gunzip/nextflow.config
+  tags:
+    - gunzip
+  files:
+    - path: ./output/gunzip/test_1.fastq
+      md5sum: 4161df271f9bfcd25d5845a1e220dbec
diff --git a/tests/modules/nf-core/gvcftools/extractvariants/main.nf b/tests/modules/nf-core/gvcftools/extractvariants/main.nf
new file mode 100644
index 00000000000..0d26f24e5f5
--- /dev/null
+++ b/tests/modules/nf-core/gvcftools/extractvariants/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GVCFTOOLS_EXTRACTVARIANTS } from '../../../../../modules/nf-core/gvcftools/extractvariants/main.nf'
+
+workflow test_gvcftools_extractvariants {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true)
+    ]
+
+    GVCFTOOLS_EXTRACTVARIANTS ( input )
+}
+
+workflow test_gvcftools_extractvariants_uncompressed {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
+    ]
+
+    GVCFTOOLS_EXTRACTVARIANTS ( input )
+}
diff --git a/tests/modules/gvcftools/extractvariants/nextflow.config b/tests/modules/nf-core/gvcftools/extractvariants/nextflow.config
similarity index 100%
rename from tests/modules/gvcftools/extractvariants/nextflow.config
rename to tests/modules/nf-core/gvcftools/extractvariants/nextflow.config
diff --git a/tests/modules/nf-core/gvcftools/extractvariants/test.yml b/tests/modules/nf-core/gvcftools/extractvariants/test.yml
new file mode 100644
index 00000000000..a02d29e7655
--- /dev/null
+++ b/tests/modules/nf-core/gvcftools/extractvariants/test.yml
@@ -0,0 +1,15 @@
+- name: gvcftools extractvariants test_gvcftools_extractvariants
+  command: nextflow run ./tests/modules/nf-core/gvcftools/extractvariants -entry test_gvcftools_extractvariants -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gvcftools/extractvariants/nextflow.config
+  tags:
+    - gvcftools
+    - gvcftools/extractvariants
+  files:
+    - path: output/gvcftools/test.vcf.gz
+
+- name: gvcftools extractvariants test_gvcftools_extractvariants_uncompressed
+  command: nextflow run ./tests/modules/nf-core/gvcftools/extractvariants -entry test_gvcftools_extractvariants_uncompressed -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gvcftools/extractvariants/nextflow.config
+  tags:
+    - gvcftools
+    - gvcftools/extractvariants
+  files:
+    - path: output/gvcftools/test.vcf.gz
diff --git a/tests/modules/nf-core/hamronization/abricate/main.nf b/tests/modules/nf-core/hamronization/abricate/main.nf
new file mode 100644
index 00000000000..51fbf61ad5a
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/abricate/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAMRONIZATION_ABRICATE } from '../../../../../modules/nf-core/hamronization/abricate/main.nf'
+
+workflow test_hamronization_abricate {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true),
+    ]
+
+    HAMRONIZATION_ABRICATE ( input, 'tsv', '1.0.1', '2021-Mar-27' )
+}
diff --git a/tests/modules/hamronization/abricate/nextflow.config b/tests/modules/nf-core/hamronization/abricate/nextflow.config
similarity index 100%
rename from tests/modules/hamronization/abricate/nextflow.config
rename to tests/modules/nf-core/hamronization/abricate/nextflow.config
diff --git a/tests/modules/nf-core/hamronization/abricate/test.yml b/tests/modules/nf-core/hamronization/abricate/test.yml
new file mode 100644
index 00000000000..b2c4047d0c3
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/abricate/test.yml
@@ -0,0 +1,9 @@
+- name: hamronization abricate test_hamronization_abricate
+  command: nextflow run ./tests/modules/nf-core/hamronization/abricate -entry test_hamronization_abricate -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hamronization/abricate/nextflow.config
+  tags:
+    - hamronization/abricate
+    - hamronization
+  files:
+    - path: output/hamronization/test.tsv
+      contains:
+        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"
diff --git a/tests/modules/nf-core/hamronization/amrfinderplus/main.nf b/tests/modules/nf-core/hamronization/amrfinderplus/main.nf
new file mode 100644
index 00000000000..2410104ce3d
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/amrfinderplus/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+include { HAMRONIZATION_AMRFINDERPLUS } from '../../../../../modules/nf-core/hamronization/amrfinderplus/main.nf'
+
+workflow test_hamronization_amrfinderplus {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true)
+    ]
+
+    HAMRONIZATION_AMRFINDERPLUS ( input, 'tsv', '3.10.30', '2022-05-26.1' )
+}
diff --git a/tests/modules/hamronization/amrfinderplus/nextflow.config b/tests/modules/nf-core/hamronization/amrfinderplus/nextflow.config
similarity index 100%
rename from tests/modules/hamronization/amrfinderplus/nextflow.config
rename to tests/modules/nf-core/hamronization/amrfinderplus/nextflow.config
diff --git a/tests/modules/nf-core/hamronization/amrfinderplus/test.yml b/tests/modules/nf-core/hamronization/amrfinderplus/test.yml
new file mode 100644
index 00000000000..8cd42a902a3
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/amrfinderplus/test.yml
@@ -0,0 +1,9 @@
+- name: hamronization amrfinderplus test_hamronization_amrfinderplus
+  command: nextflow run ./tests/modules/nf-core/hamronization/amrfinderplus -entry test_hamronization_amrfinderplus -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hamronization/amrfinderplus/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/amrfinderplus
+  files:
+    - path: output/hamronization/test.tsv
+      contains:
+        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"
diff --git a/tests/modules/nf-core/hamronization/deeparg/main.nf b/tests/modules/nf-core/hamronization/deeparg/main.nf
new file mode 100644
index 00000000000..ad452e0d415
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/deeparg/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAMRONIZATION_DEEPARG } from '../../../../../modules/nf-core/hamronization/deeparg/main.nf'
+
+workflow test_hamronization_deeparg {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
+    ]
+
+    HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2'  )
+}
diff --git a/tests/modules/hamronization/deeparg/nextflow.config b/tests/modules/nf-core/hamronization/deeparg/nextflow.config
similarity index 100%
rename from tests/modules/hamronization/deeparg/nextflow.config
rename to tests/modules/nf-core/hamronization/deeparg/nextflow.config
diff --git a/tests/modules/nf-core/hamronization/deeparg/test.yml b/tests/modules/nf-core/hamronization/deeparg/test.yml
new file mode 100644
index 00000000000..f5a2ce83b24
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/deeparg/test.yml
@@ -0,0 +1,9 @@
+- name: hamronization deeparg test_hamronization_deeparg
+  command: nextflow run ./tests/modules/nf-core/hamronization/deeparg -entry test_hamronization_deeparg -c ./tests/config/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/deeparg
+  files:
+    - path: output/hamronization/test.tsv
+      contains:
+        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"
diff --git a/tests/modules/nf-core/hamronization/fargene/main.nf b/tests/modules/nf-core/hamronization/fargene/main.nf
new file mode 100644
index 00000000000..6ded7b2ac34
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/fargene/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP                } from '../../../../modules/nf-core/gunzip/main.nf'
+include { FARGENE               } from '../../../../modules/nf-core/fargene/main.nf'
+include { HAMRONIZATION_FARGENE } from '../../../../../modules/nf-core/hamronization/fargene/main.nf'
+
+workflow test_hamronization_fargene {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) ]
+    hmm_model = 'class_a'
+
+    GUNZIP ( input )
+    FARGENE ( GUNZIP.out.gunzip, hmm_model )
+
+    HAMRONIZATION_FARGENE ( FARGENE.out.hmm, 'tsv', '0.1', '0.1' )
+}
diff --git a/tests/modules/hamronization/fargene/nextflow.config b/tests/modules/nf-core/hamronization/fargene/nextflow.config
similarity index 100%
rename from tests/modules/hamronization/fargene/nextflow.config
rename to tests/modules/nf-core/hamronization/fargene/nextflow.config
diff --git a/tests/modules/nf-core/hamronization/fargene/test.yml b/tests/modules/nf-core/hamronization/fargene/test.yml
new file mode 100644
index 00000000000..ebde50d6f53
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/fargene/test.yml
@@ -0,0 +1,7 @@
+- name: hamronization fargene test_hamronization_fargene
+  command: nextflow run ./tests/modules/nf-core/hamronization/fargene -entry test_hamronization_fargene -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hamronization/fargene/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/fargene
+  files:
+    - path: output/hamronization/test.tsv
diff --git a/tests/modules/nf-core/hamronization/rgi/main.nf b/tests/modules/nf-core/hamronization/rgi/main.nf
new file mode 100644
index 00000000000..ef9c5a9fd89
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/rgi/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+include { RGI_MAIN } from '../../../../../modules/nf-core/rgi/main/main.nf'
+include { HAMRONIZATION_RGI } from '../../../../../modules/nf-core/hamronization/rgi/main.nf'
+
+workflow test_hamronization_rgi {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+
+    RGI_MAIN ( input )
+    HAMRONIZATION_RGI ( RGI_MAIN.out.tsv, 'tsv', '1.0.2', '3.2.3' )
+}
diff --git a/tests/modules/hamronization/rgi/nextflow.config b/tests/modules/nf-core/hamronization/rgi/nextflow.config
similarity index 100%
rename from tests/modules/hamronization/rgi/nextflow.config
rename to tests/modules/nf-core/hamronization/rgi/nextflow.config
diff --git a/tests/modules/nf-core/hamronization/rgi/test.yml b/tests/modules/nf-core/hamronization/rgi/test.yml
new file mode 100644
index 00000000000..cd8e2c6bd72
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/rgi/test.yml
@@ -0,0 +1,9 @@
+- name: hamronization rgi
+  command: nextflow run ./tests/modules/nf-core/hamronization/rgi -entry test_hamronization_rgi -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hamronization/rgi/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/rgi
+  files:
+    - path: output/hamronization/test.tsv
+      contains:
+        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"
diff --git a/tests/modules/nf-core/hamronization/summarize/main.nf b/tests/modules/nf-core/hamronization/summarize/main.nf
new file mode 100644
index 00000000000..b5f096c0b13
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/summarize/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAMRONIZATION_DEEPARG                                 } from '../../../../../modules/nf-core/hamronization/deeparg/main.nf'
+include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../../modules/nf-core/hamronization/deeparg/main.nf'
+include { HAMRONIZATION_SUMMARIZE                               } from '../../../../../modules/nf-core/hamronization/summarize/main.nf'
+
+workflow test_hamronization_summarize {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
+    ]
+
+    input2 = [
+        [ id:'test2', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
+    ]
+
+    HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2'  )
+    HAMRONIZATION_DEEPARG_SECOND ( input2, 'tsv', '1.0.2', '2' )
+
+    ch_deeparg_run_one = HAMRONIZATION_DEEPARG.out.tsv
+    ch_deeparg_run_two = HAMRONIZATION_DEEPARG_SECOND.out.tsv
+
+    ch_deeparg_run_one
+        .mix( ch_deeparg_run_two )
+        .map{
+            [ it[1] ]
+        }
+        .collect()
+        .set { ch_input_for_summarize }
+
+    HAMRONIZATION_SUMMARIZE ( ch_input_for_summarize , 'json' )
+}
diff --git a/tests/modules/hamronization/summarize/nextflow.config b/tests/modules/nf-core/hamronization/summarize/nextflow.config
similarity index 100%
rename from tests/modules/hamronization/summarize/nextflow.config
rename to tests/modules/nf-core/hamronization/summarize/nextflow.config
diff --git a/tests/modules/nf-core/hamronization/summarize/test.yml b/tests/modules/nf-core/hamronization/summarize/test.yml
new file mode 100644
index 00000000000..17be8f273b9
--- /dev/null
+++ b/tests/modules/nf-core/hamronization/summarize/test.yml
@@ -0,0 +1,12 @@
+- name: hamronization summarize test_hamronization_summarize
+  command: nextflow run ./tests/modules/nf-core/hamronization/summarize -entry test_hamronization_summarize -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hamronization/summarize/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/summarize
+  files:
+    - path: output/hamronization/hamronization_combined_report.json
+      md5sum: ab0c899664398193a25a699b92f960b9
+    - path: output/hamronization/test.tsv
+      md5sum: e886d665bf9fc266be8193859863d2f4
+    - path: output/hamronization/test2.tsv
+      md5sum: 2d94ecb8be8d9036877e47a81ae92a41
diff --git a/tests/modules/nf-core/haplocheck/main.nf b/tests/modules/nf-core/haplocheck/main.nf
new file mode 100644
index 00000000000..b00de96ff49
--- /dev/null
+++ b/tests/modules/nf-core/haplocheck/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAPLOCHECK } from '../../../../modules/nf-core/haplocheck/main.nf'
+
+workflow test_haplocheck {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mito_vcf'], checkIfExists: true)
+    ]
+
+    HAPLOCHECK ( input )
+}
diff --git a/tests/modules/haplocheck/nextflow.config b/tests/modules/nf-core/haplocheck/nextflow.config
similarity index 100%
rename from tests/modules/haplocheck/nextflow.config
rename to tests/modules/nf-core/haplocheck/nextflow.config
diff --git a/tests/modules/nf-core/haplocheck/test.yml b/tests/modules/nf-core/haplocheck/test.yml
new file mode 100644
index 00000000000..9768231151f
--- /dev/null
+++ b/tests/modules/nf-core/haplocheck/test.yml
@@ -0,0 +1,20 @@
+- name: haplocheck test_haplocheck
+  command: nextflow run ./tests/modules/nf-core/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/haplocheck/nextflow.config
+  tags:
+    - haplocheck
+  files:
+    - path: output/haplocheck/test.html
+      md5sum: 59d69052c86edff0301816956eaf4d5f
+    - path: output/haplocheck/test.raw.txt
+      md5sum: 69f4e5b28a59b97fc19eb8e8b650d9d5
+    - path: output/haplocheck/versions.yml
+      md5sum: 94e2fa3ceb3946487319f92cea08c942
+
+- name: haplocheck test_haplocheck using stubs
+  command: nextflow run ./tests/modules/nf-core/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/haplocheck/nextflow.config -stub-run
+  tags:
+    - haplocheck
+  files:
+    - path: output/haplocheck/test.html
+    - path: output/haplocheck/test.raw.txt
+    - path: output/haplocheck/versions.yml
diff --git a/tests/modules/nf-core/haplogrep2/classify/main.nf b/tests/modules/nf-core/haplogrep2/classify/main.nf
new file mode 100644
index 00000000000..6385aed5de7
--- /dev/null
+++ b/tests/modules/nf-core/haplogrep2/classify/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAPLOGREP2_CLASSIFY } from '../../../../../modules/nf-core/haplogrep2/classify/main.nf'
+
+workflow test_haplogrep2_classify {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mito_vcf'], checkIfExists: true)
+    ]
+    format = 'vcf'
+
+    HAPLOGREP2_CLASSIFY ( input,format )
+}
diff --git a/tests/modules/haplogrep2/classify/nextflow.config b/tests/modules/nf-core/haplogrep2/classify/nextflow.config
similarity index 100%
rename from tests/modules/haplogrep2/classify/nextflow.config
rename to tests/modules/nf-core/haplogrep2/classify/nextflow.config
diff --git a/tests/modules/nf-core/haplogrep2/classify/test.yml b/tests/modules/nf-core/haplogrep2/classify/test.yml
new file mode 100644
index 00000000000..a182a080e01
--- /dev/null
+++ b/tests/modules/nf-core/haplogrep2/classify/test.yml
@@ -0,0 +1,17 @@
+- name: haplogrep2 classify
+  command: nextflow run ./tests/modules/nf-core/haplogrep2/classify -entry test_haplogrep2_classify -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/haplogrep2/classify/nextflow.config
+  tags:
+    - haplogrep2
+    - haplogrep2/classify
+  files:
+    - path: output/haplogrep2/test.txt
+    - path: output/haplogrep2/versions.yml
+
+- name: haplogrep2 classify stubs
+  command: nextflow run ./tests/modules/nf-core/haplogrep2/classify -stub-run -entry test_haplogrep2_classify -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/haplogrep2/classify/nextflow.config
+  tags:
+    - haplogrep2
+    - haplogrep2/classify
+  files:
+    - path: output/haplogrep2/test.txt
+    - path: output/haplogrep2/versions.yml
diff --git a/tests/modules/nf-core/happy/happy/main.nf b/tests/modules/nf-core/happy/happy/main.nf
new file mode 100644
index 00000000000..0b6f898fc7a
--- /dev/null
+++ b/tests/modules/nf-core/happy/happy/main.nf
@@ -0,0 +1,39 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAPPY_HAPPY } from '../../../../../modules/nf-core/happy/happy/main.nf'
+
+workflow test_happy_vcf {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
+    ]
+
+    fasta = Channel.value([
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ])
+
+    HAPPY_HAPPY ( input, fasta )
+}
+
+workflow test_happy_gvcf {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
+    ]
+
+    fasta = Channel.value([
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ])
+
+    HAPPY_HAPPY ( input, fasta )
+}
diff --git a/tests/modules/happy/happy/nextflow.config b/tests/modules/nf-core/happy/happy/nextflow.config
similarity index 100%
rename from tests/modules/happy/happy/nextflow.config
rename to tests/modules/nf-core/happy/happy/nextflow.config
diff --git a/tests/modules/nf-core/happy/happy/test.yml b/tests/modules/nf-core/happy/happy/test.yml
new file mode 100644
index 00000000000..f0bcc1cf66d
--- /dev/null
+++ b/tests/modules/nf-core/happy/happy/test.yml
@@ -0,0 +1,27 @@
+- name: happy happy test_happy_vcf
+  command: nextflow run ./tests/modules/nf-core/happy/happy -entry test_happy_vcf -c ./tests/config/nextflow.config
+  tags:
+    - happy
+    - happy/happy
+  files:
+    - path: output/happy/test.extended.csv
+      md5sum: ef79c7c789ef4f146ca2e50dafaf22b3
+    - path: output/happy/test.runinfo.json
+    - path: output/happy/test.summary.csv
+      md5sum: f8aa5d36d3c48dede2f607fd565894ad
+    - path: output/happy/versions.yml
+      md5sum: 82243bf6dbdc71aa63211ee2a89f47f2
+
+- name: happy happy test_happy_gvcf
+  command: nextflow run ./tests/modules/nf-core/happy/happy -entry test_happy_gvcf -c ./tests/config/nextflow.config
+  tags:
+    - happy
+    - happy/happy
+  files:
+    - path: output/happy/test.extended.csv
+      md5sum: 3d5c21b67a259a3f6dcb088d55b86cd3
+    - path: output/happy/test.runinfo.json
+    - path: output/happy/test.summary.csv
+      md5sum: 03044e9bb5a0c6f0947b7e910fc8a558
+    - path: output/happy/versions.yml
+      md5sum: 551fa216952d6f5de78e6e453b92aaab
diff --git a/tests/modules/nf-core/happy/prepy/main.nf b/tests/modules/nf-core/happy/prepy/main.nf
new file mode 100644
index 00000000000..2991b1d1220
--- /dev/null
+++ b/tests/modules/nf-core/happy/prepy/main.nf
@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAPPY_PREPY } from '../../../../../modules/nf-core/happy/prepy/main.nf'
+
+workflow test_happy_prepy_vcf {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
+    ]
+
+    fasta = Channel.value([
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ])
+
+    HAPPY_PREPY ( input, fasta )
+}
+
+workflow test_happy_prepy_gvcf {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
+    ]
+
+    fasta = Channel.value([
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ])
+
+    HAPPY_PREPY ( input, fasta )
+}
diff --git a/tests/modules/happy/prepy/nextflow.config b/tests/modules/nf-core/happy/prepy/nextflow.config
similarity index 100%
rename from tests/modules/happy/prepy/nextflow.config
rename to tests/modules/nf-core/happy/prepy/nextflow.config
diff --git a/tests/modules/nf-core/happy/prepy/test.yml b/tests/modules/nf-core/happy/prepy/test.yml
new file mode 100644
index 00000000000..fd929d83277
--- /dev/null
+++ b/tests/modules/nf-core/happy/prepy/test.yml
@@ -0,0 +1,19 @@
+- name: happy prepy test_happy_prepy_vcf
+  command: nextflow run ./tests/modules/nf-core/happy/prepy -entry test_happy_prepy_vcf -c ./tests/config/nextflow.config
+  tags:
+    - happy/prepy
+    - happy
+  files:
+    - path: output/happy/test.vcf.gz
+    - path: output/happy/versions.yml
+      md5sum: 814d20f1f29f23a3d21012748a5d6393
+
+- name: happy prepy test_happy_prepy_gvcf
+  command: nextflow run ./tests/modules/nf-core/happy/prepy -entry test_happy_prepy_gvcf -c ./tests/config/nextflow.config
+  tags:
+    - happy/prepy
+    - happy
+  files:
+    - path: output/happy/test.vcf.gz
+    - path: output/happy/versions.yml
+      md5sum: 970a54de46e68ef6d5228a26eaa4c8e7
diff --git a/tests/modules/nf-core/hicap/main.nf b/tests/modules/nf-core/hicap/main.nf
new file mode 100644
index 00000000000..b74a9656015
--- /dev/null
+++ b/tests/modules/nf-core/hicap/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HICAP } from '../../../../modules/nf-core/hicap/main.nf'
+
+workflow test_hicap {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+    database_dir = []
+    model_fp = []
+
+    HICAP ( input, database_dir, model_fp )
+}
diff --git a/tests/modules/hicap/nextflow.config b/tests/modules/nf-core/hicap/nextflow.config
similarity index 100%
rename from tests/modules/hicap/nextflow.config
rename to tests/modules/nf-core/hicap/nextflow.config
diff --git a/tests/modules/nf-core/hicap/test.yml b/tests/modules/nf-core/hicap/test.yml
new file mode 100644
index 00000000000..cede173abea
--- /dev/null
+++ b/tests/modules/nf-core/hicap/test.yml
@@ -0,0 +1,10 @@
+- name: hicap test_hicap
+  command: nextflow run ./tests/modules/nf-core/hicap -entry test_hicap -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hicap/nextflow.config
+  tags:
+    - hicap
+  files:
+    - path: output/hicap/genome.gbk
+      md5sum: 562d026956903354ac80721f501335d4
+    - path: output/hicap/genome.svg
+      md5sum: 4fb94871dd0fdd8b4496049668176631
+    - path: output/hicap/genome.tsv
diff --git a/tests/modules/nf-core/hifiasm/main.nf b/tests/modules/nf-core/hifiasm/main.nf
new file mode 100644
index 00000000000..e52e91e99de
--- /dev/null
+++ b/tests/modules/nf-core/hifiasm/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HIFIASM } from '../../../../modules/nf-core/hifiasm/main.nf'
+
+/*
+ * Test with long reads only
+ */
+workflow test_hifiasm_hifi_only {
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
+    ]
+
+    HIFIASM ( input, [], [], false )
+}
+
+/*
+ * Test with parental reads for phasing
+ */
+workflow test_hifiasm_with_parental_reads {
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
+    ]
+    paternal_kmer_dump = file(params.test_data['homo_sapiens']['illumina']['test_yak'], checkIfExists: true)
+    maternal_kmer_dump = file(params.test_data['homo_sapiens']['illumina']['test2_yak'], checkIfExists: true)
+
+    HIFIASM ( input, paternal_kmer_dump, maternal_kmer_dump, true )
+}
diff --git a/tests/modules/hifiasm/nextflow.config b/tests/modules/nf-core/hifiasm/nextflow.config
similarity index 100%
rename from tests/modules/hifiasm/nextflow.config
rename to tests/modules/nf-core/hifiasm/nextflow.config
diff --git a/tests/modules/nf-core/hifiasm/test.yml b/tests/modules/nf-core/hifiasm/test.yml
new file mode 100644
index 00000000000..c55a85f3079
--- /dev/null
+++ b/tests/modules/nf-core/hifiasm/test.yml
@@ -0,0 +1,33 @@
+- name: hifiasm test_hifiasm_hifi_only
+  command: nextflow run ./tests/modules/nf-core/hifiasm -entry test_hifiasm_hifi_only -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hifiasm/nextflow.config
+  tags:
+    - hifiasm
+  files:
+    - path: output/hifiasm/test.asm.bp.hap1.p_ctg.gfa
+      md5sum: 73b0c1b01d445db91c269034b8660501
+    - path: output/hifiasm/test.asm.bp.hap2.p_ctg.gfa
+      md5sum: 76847b7835185ab92611a820467c0066
+    - path: output/hifiasm/test.asm.bp.p_utg.gfa
+      md5sum: 97446fb95de214835c36b10a90838486
+    - path: output/hifiasm/test.asm.bp.r_utg.gfa
+      md5sum: 97446fb95de214835c36b10a90838486
+    - path: output/hifiasm/test.asm.ec.bin
+    - path: output/hifiasm/test.asm.ovlp.reverse.bin
+    - path: output/hifiasm/test.asm.ovlp.source.bin
+
+- name: hifiasm test_hifiasm_with_parental_reads
+  command: nextflow run ./tests/modules/nf-core/hifiasm -entry test_hifiasm_with_parental_reads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hifiasm/nextflow.config
+  tags:
+    - hifiasm
+  files:
+    - path: output/hifiasm/test.asm.dip.hap1.p_ctg.gfa
+      md5sum: 16907b1aea2081884deb9d039dd14038
+    - path: output/hifiasm/test.asm.dip.hap2.p_ctg.gfa
+      md5sum: d283479bf72a31d0cc34f880535d0bd4
+    - path: output/hifiasm/test.asm.dip.p_utg.gfa
+      md5sum: 97446fb95de214835c36b10a90838486
+    - path: output/hifiasm/test.asm.dip.r_utg.gfa
+      md5sum: 97446fb95de214835c36b10a90838486
+    - path: output/hifiasm/test.asm.ec.bin
+    - path: output/hifiasm/test.asm.ovlp.reverse.bin
+    - path: output/hifiasm/test.asm.ovlp.source.bin
diff --git a/tests/modules/nf-core/hisat2/align/main.nf b/tests/modules/nf-core/hisat2/align/main.nf
new file mode 100644
index 00000000000..2c0590842e4
--- /dev/null
+++ b/tests/modules/nf-core/hisat2/align/main.nf
@@ -0,0 +1,38 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HISAT2_EXTRACTSPLICESITES } from '../../../../../modules/nf-core/hisat2/extractsplicesites/main.nf'
+include { HISAT2_BUILD              } from '../../../../../modules/nf-core/hisat2/build/main.nf'
+include { HISAT2_ALIGN              } from '../../../../../modules/nf-core/hisat2/align/main.nf'
+
+workflow test_hisat2_align_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    HISAT2_EXTRACTSPLICESITES ( gtf )
+    HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
+    HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
+}
+
+workflow test_hisat2_align_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    HISAT2_EXTRACTSPLICESITES ( gtf )
+    HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
+    HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
+}
diff --git a/tests/modules/hisat2/align/nextflow.config b/tests/modules/nf-core/hisat2/align/nextflow.config
similarity index 100%
rename from tests/modules/hisat2/align/nextflow.config
rename to tests/modules/nf-core/hisat2/align/nextflow.config
diff --git a/tests/modules/nf-core/hisat2/align/test.yml b/tests/modules/nf-core/hisat2/align/test.yml
new file mode 100644
index 00000000000..80bff97fc6b
--- /dev/null
+++ b/tests/modules/nf-core/hisat2/align/test.yml
@@ -0,0 +1,53 @@
+- name: hisat2 align test_hisat2_align_single_end
+  command: nextflow run ./tests/modules/nf-core/hisat2/align -entry test_hisat2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hisat2/align/nextflow.config
+  tags:
+    - hisat2
+    - hisat2/align
+  files:
+    - path: output/hisat2/test.hisat2.summary.log
+      md5sum: 7b8a9e61b7646da1089b041333c41a87
+    - path: output/hisat2/genome.splice_sites.txt
+    - path: output/hisat2/test.bam
+    - path: output/hisat2/hisat2/genome.5.ht2
+      md5sum: 91198831aaba993acac1734138c5f173
+    - path: output/hisat2/hisat2/genome.7.ht2
+      md5sum: 9013eccd91ad614d7893c739275a394f
+    - path: output/hisat2/hisat2/genome.1.ht2
+      md5sum: 057cfa8a22b97ee9cff4c8d342498803
+    - path: output/hisat2/hisat2/genome.2.ht2
+      md5sum: 47b153cd1319abc88dda532462651fcf
+    - path: output/hisat2/hisat2/genome.6.ht2
+      md5sum: 265e1284ce85686516fae5d35540994a
+    - path: output/hisat2/hisat2/genome.3.ht2
+      md5sum: 4ed93abba181d8dfab2e303e33114777
+    - path: output/hisat2/hisat2/genome.8.ht2
+      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
+    - path: output/hisat2/hisat2/genome.4.ht2
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
+
+- name: hisat2 align test_hisat2_align_paired_end
+  command: nextflow run ./tests/modules/nf-core/hisat2/align -entry test_hisat2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hisat2/align/nextflow.config
+  tags:
+    - hisat2
+    - hisat2/align
+  files:
+    - path: output/hisat2/test.hisat2.summary.log
+      md5sum: 9839b31db795958cc4b70711a3414e9c
+    - path: output/hisat2/genome.splice_sites.txt
+    - path: output/hisat2/test.bam
+    - path: output/hisat2/hisat2/genome.5.ht2
+      md5sum: 91198831aaba993acac1734138c5f173
+    - path: output/hisat2/hisat2/genome.7.ht2
+      md5sum: 9013eccd91ad614d7893c739275a394f
+    - path: output/hisat2/hisat2/genome.1.ht2
+      md5sum: 057cfa8a22b97ee9cff4c8d342498803
+    - path: output/hisat2/hisat2/genome.2.ht2
+      md5sum: 47b153cd1319abc88dda532462651fcf
+    - path: output/hisat2/hisat2/genome.6.ht2
+      md5sum: 265e1284ce85686516fae5d35540994a
+    - path: output/hisat2/hisat2/genome.3.ht2
+      md5sum: 4ed93abba181d8dfab2e303e33114777
+    - path: output/hisat2/hisat2/genome.8.ht2
+      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
+    - path: output/hisat2/hisat2/genome.4.ht2
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
diff --git a/tests/modules/hisat2/build b/tests/modules/nf-core/hisat2/build
similarity index 100%
rename from tests/modules/hisat2/build
rename to tests/modules/nf-core/hisat2/build
diff --git a/tests/modules/nf-core/hisat2/build_test/main.nf b/tests/modules/nf-core/hisat2/build_test/main.nf
new file mode 100644
index 00000000000..8029d10e2ff
--- /dev/null
+++ b/tests/modules/nf-core/hisat2/build_test/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HISAT2_EXTRACTSPLICESITES } from '../../../../../modules/nf-core/hisat2/extractsplicesites/main.nf'
+include { HISAT2_BUILD              } from '../../../../../modules/nf-core/hisat2/build/main.nf'
+
+workflow test_hisat2_build {
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    HISAT2_EXTRACTSPLICESITES ( gtf )
+    HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
+}
diff --git a/tests/modules/hisat2/build_test/nextflow.config b/tests/modules/nf-core/hisat2/build_test/nextflow.config
similarity index 100%
rename from tests/modules/hisat2/build_test/nextflow.config
rename to tests/modules/nf-core/hisat2/build_test/nextflow.config
diff --git a/tests/modules/nf-core/hisat2/build_test/test.yml b/tests/modules/nf-core/hisat2/build_test/test.yml
new file mode 100644
index 00000000000..ba6702aeead
--- /dev/null
+++ b/tests/modules/nf-core/hisat2/build_test/test.yml
@@ -0,0 +1,23 @@
+- name: hisat2 build test_hisat2_build
+  command: nextflow run ./tests/modules/nf-core/hisat2/build_test -entry test_hisat2_build -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hisat2/build/nextflow.config
+  tags:
+    - hisat2
+    - hisat2/build
+  files:
+    - path: output/hisat2/genome.splice_sites.txt
+    - path: output/hisat2/hisat2/genome.5.ht2
+      md5sum: 91198831aaba993acac1734138c5f173
+    - path: output/hisat2/hisat2/genome.7.ht2
+      md5sum: 9013eccd91ad614d7893c739275a394f
+    - path: output/hisat2/hisat2/genome.1.ht2
+      md5sum: 057cfa8a22b97ee9cff4c8d342498803
+    - path: output/hisat2/hisat2/genome.2.ht2
+      md5sum: 47b153cd1319abc88dda532462651fcf
+    - path: output/hisat2/hisat2/genome.6.ht2
+      md5sum: 265e1284ce85686516fae5d35540994a
+    - path: output/hisat2/hisat2/genome.3.ht2
+      md5sum: 4ed93abba181d8dfab2e303e33114777
+    - path: output/hisat2/hisat2/genome.8.ht2
+      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
+    - path: output/hisat2/hisat2/genome.4.ht2
+      md5sum: c25be5f8b0378abf7a58c8a880b87626
diff --git a/tests/modules/nf-core/hisat2/extractsplicesites/main.nf b/tests/modules/nf-core/hisat2/extractsplicesites/main.nf
new file mode 100644
index 00000000000..0a05990af00
--- /dev/null
+++ b/tests/modules/nf-core/hisat2/extractsplicesites/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HISAT2_EXTRACTSPLICESITES } from '../../../../../modules/nf-core/hisat2/extractsplicesites/main.nf'
+
+workflow test_hisat2_extractsplicesites {
+    gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    HISAT2_EXTRACTSPLICESITES ( gtf )
+}
diff --git a/tests/modules/hisat2/extractsplicesites/nextflow.config b/tests/modules/nf-core/hisat2/extractsplicesites/nextflow.config
similarity index 100%
rename from tests/modules/hisat2/extractsplicesites/nextflow.config
rename to tests/modules/nf-core/hisat2/extractsplicesites/nextflow.config
diff --git a/tests/modules/nf-core/hisat2/extractsplicesites/test.yml b/tests/modules/nf-core/hisat2/extractsplicesites/test.yml
new file mode 100644
index 00000000000..3368f5dc79a
--- /dev/null
+++ b/tests/modules/nf-core/hisat2/extractsplicesites/test.yml
@@ -0,0 +1,7 @@
+- name: hisat2 extractsplicesites test_hisat2_extractsplicesites
+  command: nextflow run ./tests/modules/nf-core/hisat2/extractsplicesites -entry test_hisat2_extractsplicesites -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hisat2/extractsplicesites/nextflow.config
+  tags:
+    - hisat2
+    - hisat2/extractsplicesites
+  files:
+    - path: output/hisat2/genome.splice_sites.txt
diff --git a/tests/modules/nf-core/hmmcopy/gccounter/main.nf b/tests/modules/nf-core/hmmcopy/gccounter/main.nf
new file mode 100644
index 00000000000..8ef200a92e3
--- /dev/null
+++ b/tests/modules/nf-core/hmmcopy/gccounter/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMCOPY_GCCOUNTER } from '../../../../../modules/nf-core/hmmcopy/gccounter/main.nf'
+
+workflow test_hmmcopy_gccounter {
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HMMCOPY_GCCOUNTER (fasta)
+}
diff --git a/tests/modules/hmmcopy/gccounter/nextflow.config b/tests/modules/nf-core/hmmcopy/gccounter/nextflow.config
similarity index 100%
rename from tests/modules/hmmcopy/gccounter/nextflow.config
rename to tests/modules/nf-core/hmmcopy/gccounter/nextflow.config
diff --git a/tests/modules/nf-core/hmmcopy/gccounter/test.yml b/tests/modules/nf-core/hmmcopy/gccounter/test.yml
new file mode 100644
index 00000000000..b6073c100cf
--- /dev/null
+++ b/tests/modules/nf-core/hmmcopy/gccounter/test.yml
@@ -0,0 +1,8 @@
+- name: hmmcopy gccounter test_hmmcopy_gccounter
+  command: nextflow run ./tests/modules/nf-core/hmmcopy/gccounter -entry test_hmmcopy_gccounter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hmmcopy/gccounter/nextflow.config
+  tags:
+    - hmmcopy
+    - hmmcopy/gccounter
+  files:
+    - path: output/hmmcopy/genome.gc.wig
+      md5sum: 59ad14bc5aaa903187d7b248c9490deb
diff --git a/tests/modules/nf-core/hmmcopy/generatemap/main.nf b/tests/modules/nf-core/hmmcopy/generatemap/main.nf
new file mode 100644
index 00000000000..e89f152571b
--- /dev/null
+++ b/tests/modules/nf-core/hmmcopy/generatemap/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMCOPY_GENERATEMAP } from '../../../../../modules/nf-core/hmmcopy/generatemap/main.nf'
+
+workflow test_hmmcopy_generatemap {
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HMMCOPY_GENERATEMAP ( fasta )
+}
diff --git a/tests/modules/hmmcopy/generatemap/nextflow.config b/tests/modules/nf-core/hmmcopy/generatemap/nextflow.config
similarity index 100%
rename from tests/modules/hmmcopy/generatemap/nextflow.config
rename to tests/modules/nf-core/hmmcopy/generatemap/nextflow.config
diff --git a/tests/modules/nf-core/hmmcopy/generatemap/test.yml b/tests/modules/nf-core/hmmcopy/generatemap/test.yml
new file mode 100644
index 00000000000..ef45a71782c
--- /dev/null
+++ b/tests/modules/nf-core/hmmcopy/generatemap/test.yml
@@ -0,0 +1,10 @@
+- name: hmmcopy generatemap test_hmmcopy_generatemap
+  command: nextflow run ./tests/modules/nf-core/hmmcopy/generatemap -entry test_hmmcopy_generatemap -c ./tests/config/nextflow.config
+  tags:
+    - hmmcopy
+    - hmmcopy/generatemap
+  files:
+    - path: output/hmmcopy/genome.fasta.map.bw
+      md5sum: 7ad68224a1e40287978284c387e8eb70
+    - path: output/hmmcopy/versions.yml
+      md5sum: f950580f94d8a2d88332c477972cb9f0
diff --git a/tests/modules/nf-core/hmmcopy/mapcounter/main.nf b/tests/modules/nf-core/hmmcopy/mapcounter/main.nf
new file mode 100644
index 00000000000..afc3cee2370
--- /dev/null
+++ b/tests/modules/nf-core/hmmcopy/mapcounter/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMCOPY_MAPCOUNTER } from '../../../../../modules/nf-core/hmmcopy/mapcounter/main.nf'
+include { HMMCOPY_GENERATEMAP } from '../../../../../modules/nf-core/hmmcopy/generatemap/main.nf'
+workflow test_hmmcopy_mapcounter {
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HMMCOPY_GENERATEMAP( fasta )
+
+    HMMCOPY_MAPCOUNTER ( HMMCOPY_GENERATEMAP.out.bigwig )
+}
diff --git a/tests/modules/hmmcopy/mapcounter/nextflow.config b/tests/modules/nf-core/hmmcopy/mapcounter/nextflow.config
similarity index 100%
rename from tests/modules/hmmcopy/mapcounter/nextflow.config
rename to tests/modules/nf-core/hmmcopy/mapcounter/nextflow.config
diff --git a/tests/modules/nf-core/hmmcopy/mapcounter/test.yml b/tests/modules/nf-core/hmmcopy/mapcounter/test.yml
new file mode 100644
index 00000000000..dd8d1336b54
--- /dev/null
+++ b/tests/modules/nf-core/hmmcopy/mapcounter/test.yml
@@ -0,0 +1,12 @@
+- name: hmmcopy mapcounter test_hmmcopy_mapcounter
+  command: nextflow run ./tests/modules/nf-core/hmmcopy/mapcounter -entry test_hmmcopy_mapcounter -c ./tests/config/nextflow.config
+  tags:
+    - hmmcopy/mapcounter
+    - hmmcopy
+  files:
+    - path: output/hmmcopy/genome.fasta.map.bw
+      md5sum: 7ad68224a1e40287978284c387e8eb70
+    - path: output/hmmcopy/genome.fasta.map.map.wig
+      md5sum: e2d39dc204ed31c1ce372d633a42560f
+    - path: output/hmmcopy/versions.yml
+      md5sum: 8361e3c0f8b96cf84834678cf988a209
diff --git a/tests/modules/nf-core/hmmcopy/readcounter/main.nf b/tests/modules/nf-core/hmmcopy/readcounter/main.nf
new file mode 100644
index 00000000000..03cda463d5b
--- /dev/null
+++ b/tests/modules/nf-core/hmmcopy/readcounter/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMCOPY_READCOUNTER } from '../../../../../modules/nf-core/hmmcopy/readcounter/main.nf'
+
+workflow test_hmmcopy_readcounter {
+
+    input = [ [ id:'test'], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)]
+            ]
+    HMMCOPY_READCOUNTER ( input )
+}
diff --git a/tests/modules/hmmcopy/readcounter/nextflow.config b/tests/modules/nf-core/hmmcopy/readcounter/nextflow.config
similarity index 100%
rename from tests/modules/hmmcopy/readcounter/nextflow.config
rename to tests/modules/nf-core/hmmcopy/readcounter/nextflow.config
diff --git a/tests/modules/nf-core/hmmcopy/readcounter/test.yml b/tests/modules/nf-core/hmmcopy/readcounter/test.yml
new file mode 100644
index 00000000000..8184e7c1552
--- /dev/null
+++ b/tests/modules/nf-core/hmmcopy/readcounter/test.yml
@@ -0,0 +1,10 @@
+- name: hmmcopy readcounter test_hmmcopy_readcounter
+  command: nextflow run ./tests/modules/nf-core/hmmcopy/readcounter -entry test_hmmcopy_readcounter -c ./tests/config/nextflow.config
+  tags:
+    - hmmcopy
+    - hmmcopy/readcounter
+  files:
+    - path: output/hmmcopy/test.wig
+      md5sum: 4682778422b9a2510a3cb70bd13ccd08
+    - path: output/hmmcopy/versions.yml
+      md5sum: 624a85e6a1bc61abc33cac03aea33a1e
diff --git a/tests/modules/nf-core/hmmer/eslalimask/main.nf b/tests/modules/nf-core/hmmer/eslalimask/main.nf
new file mode 100644
index 00000000000..c1a92a9ece8
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/eslalimask/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMER_HMMALIGN             } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf'
+include { HMMER_ESLALIMASK as RFMASK } from '../../../../../modules/nf-core/hmmer/eslalimask/main.nf'
+
+workflow test_hmmer_rfmask {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
+    ]
+
+    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
+
+    HMMER_HMMALIGN ( input, hmm )
+
+    RFMASK ( HMMER_HMMALIGN.out.sthlm, [] )
+}
diff --git a/tests/modules/hmmer/eslalimask/nextflow.config b/tests/modules/nf-core/hmmer/eslalimask/nextflow.config
similarity index 100%
rename from tests/modules/hmmer/eslalimask/nextflow.config
rename to tests/modules/nf-core/hmmer/eslalimask/nextflow.config
diff --git a/tests/modules/nf-core/hmmer/eslalimask/test.yml b/tests/modules/nf-core/hmmer/eslalimask/test.yml
new file mode 100644
index 00000000000..dd887ef9db4
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/eslalimask/test.yml
@@ -0,0 +1,13 @@
+- name: hmmer eslalimask test_hmmer_rfmask
+  command: nextflow run ./tests/modules/nf-core/hmmer/eslalimask -entry test_hmmer_rfmask -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hmmer/eslalimask/nextflow.config
+  tags:
+    - hmmer
+    - hmmer/eslalimask
+  files:
+    - path: output/rfmask/test.masked.sthlm.gz
+      contains:
+        - "GS CP025268.1:223601-225154 DE Escherichia coli"
+        - "=GC RF"
+    - path: output/rfmask/versions.yml
+      contains:
+        - "easel:"
diff --git a/tests/modules/nf-core/hmmer/eslreformat/main.nf b/tests/modules/nf-core/hmmer/eslreformat/main.nf
new file mode 100644
index 00000000000..92f23eafa12
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/eslreformat/main.nf
@@ -0,0 +1,50 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMER_HMMALIGN                                 } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf'
+include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_AFA     } from '../../../../../modules/nf-core/hmmer/eslreformat/main.nf'
+include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_PHYLIP  } from '../../../../../modules/nf-core/hmmer/eslreformat/main.nf'
+include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_UNALIGN } from '../../../../../modules/nf-core/hmmer/eslreformat/main.nf'
+
+workflow test_hmmer_eslreformat_afa {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
+    ]
+
+    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
+
+    HMMER_HMMALIGN ( input, hmm )
+
+    HMMER_ESLREFORMAT_AFA ( HMMER_HMMALIGN.out.sthlm )
+}
+
+workflow test_hmmer_eslreformat_phylip {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
+    ]
+
+    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
+
+    HMMER_HMMALIGN ( input, hmm )
+
+    HMMER_ESLREFORMAT_PHYLIP ( HMMER_HMMALIGN.out.sthlm )
+}
+
+workflow test_hmmer_eslreformat_unalign {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
+    ]
+
+    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
+
+    HMMER_HMMALIGN ( input, hmm )
+
+    HMMER_ESLREFORMAT_UNALIGN ( HMMER_HMMALIGN.out.sthlm )
+}
diff --git a/tests/modules/hmmer/eslreformat/nextflow.config b/tests/modules/nf-core/hmmer/eslreformat/nextflow.config
similarity index 100%
rename from tests/modules/hmmer/eslreformat/nextflow.config
rename to tests/modules/nf-core/hmmer/eslreformat/nextflow.config
diff --git a/tests/modules/nf-core/hmmer/eslreformat/test.yml b/tests/modules/nf-core/hmmer/eslreformat/test.yml
new file mode 100644
index 00000000000..56ff24a8e5a
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/eslreformat/test.yml
@@ -0,0 +1,38 @@
+- name: hmmer eslreformat test_hmmer_eslreformat_afa
+  command: nextflow run ./tests/modules/nf-core/hmmer/eslreformat -entry test_hmmer_eslreformat_afa -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hmmer/eslreformat/nextflow.config
+  tags:
+    - hmmer/eslreformat
+    - hmmer
+  files:
+    - path: output/hmmer/test.afa.gz
+      contains:
+        - ">CP025268.1"
+        - "aaa---UUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUG"
+    - path: output/hmmer/versions.yml
+      contains:
+        - "easel:"
+- name: hmmer eslreformat test_hmmer_eslreformat_phylip
+  command: nextflow run ./tests/modules/nf-core/hmmer/eslreformat -entry test_hmmer_eslreformat_phylip -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hmmer/eslreformat/nextflow.config
+  tags:
+    - hmmer/eslreformat
+    - hmmer
+  files:
+    - path: output/hmmer/test.phylip.gz
+      contains:
+        - "CP025268.1 AAA---UUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUG"
+    - path: output/hmmer/versions.yml
+      contains:
+        - "easel:"
+- name: hmmer eslreformat test_hmmer_eslreformat_unalign
+  command: nextflow run ./tests/modules/nf-core/hmmer/eslreformat -entry test_hmmer_eslreformat_unalign -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hmmer/eslreformat/nextflow.config
+  tags:
+    - hmmer/eslreformat
+    - hmmer
+  files:
+    - path: output/hmmer/test.afa.gz
+      contains:
+        - ">CP025268.1"
+        - "aaaUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUG"
+    - path: output/hmmer/versions.yml
+      contains:
+        - "easel:"
diff --git a/tests/modules/nf-core/hmmer/hmmalign/main.nf b/tests/modules/nf-core/hmmer/hmmalign/main.nf
new file mode 100644
index 00000000000..64814641c3d
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/hmmalign/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMER_HMMALIGN as HMMER_HMMALIGN        } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf'
+include { HMMER_HMMALIGN as HMMER_HMMALIGN_PREFIX } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf'
+
+workflow test_hmmer_hmmalign {
+
+    input = [
+        [ id:'test' ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
+    ]
+
+    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
+
+    HMMER_HMMALIGN ( input, hmm )
+}
+
+workflow test_hmmer_hmmalign_prefix {
+
+    input = [
+        [ id:'test' ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
+    ]
+
+    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
+
+    HMMER_HMMALIGN_PREFIX ( input, hmm )
+}
diff --git a/tests/modules/hmmer/hmmalign/nextflow.config b/tests/modules/nf-core/hmmer/hmmalign/nextflow.config
similarity index 100%
rename from tests/modules/hmmer/hmmalign/nextflow.config
rename to tests/modules/nf-core/hmmer/hmmalign/nextflow.config
diff --git a/tests/modules/nf-core/hmmer/hmmalign/test.yml b/tests/modules/nf-core/hmmer/hmmalign/test.yml
new file mode 100644
index 00000000000..2f483956c98
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/hmmalign/test.yml
@@ -0,0 +1,16 @@
+- name: hmmer hmmalign test_hmmer_hmmalign
+  command: nextflow run ./tests/modules/nf-core/hmmer/hmmalign -entry test_hmmer_hmmalign -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hmmer/hmmalign/nextflow.config
+  tags:
+    - hmmer
+    - hmmer/hmmalign
+  files:
+    - path: output/hmmer/test.sthlm.gz
+      md5sum: ddaa8b96291edf4e1a929a224329161b
+- name: hmmer hmmalign test_hmmer_hmmalign_prefix
+  command: nextflow run ./tests/modules/nf-core/hmmer/hmmalign -entry test_hmmer_hmmalign_prefix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hmmer/hmmalign/nextflow.config
+  tags:
+    - hmmer
+    - hmmer/hmmalign
+  files:
+    - path: output/hmmer/test.prefix.sthlm.gz
+      md5sum: ddaa8b96291edf4e1a929a224329161b
diff --git a/tests/modules/nf-core/hmmer/hmmbuild/main.nf b/tests/modules/nf-core/hmmer/hmmbuild/main.nf
new file mode 100644
index 00000000000..7bd3a4b3a5f
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/hmmbuild/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMER_HMMBUILD } from '../../../../../modules/nf-core/hmmer/hmmbuild/main.nf'
+
+workflow test_hmmer_hmmbuild {
+    
+    input = [
+        [ id: 'PF14720' ],      // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true)
+    ]
+
+    HMMER_HMMBUILD ( input, [] )
+}
diff --git a/tests/modules/hmmer/hmmbuild/nextflow.config b/tests/modules/nf-core/hmmer/hmmbuild/nextflow.config
similarity index 100%
rename from tests/modules/hmmer/hmmbuild/nextflow.config
rename to tests/modules/nf-core/hmmer/hmmbuild/nextflow.config
diff --git a/tests/modules/nf-core/hmmer/hmmbuild/test.yml b/tests/modules/nf-core/hmmer/hmmbuild/test.yml
new file mode 100644
index 00000000000..be321bf489a
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/hmmbuild/test.yml
@@ -0,0 +1,12 @@
+- name: hmmer hmmbuild test_hmmer_hmmbuild
+  command: nextflow run ./tests/modules/nf-core/hmmer/hmmbuild -entry test_hmmer_hmmbuild -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/hmmer/hmmbuild/nextflow.config
+  tags:
+    - hmmer
+    - hmmer/hmmbuild
+  files:
+    - path: output/hmmer/PF14720.hmm.gz
+      contains:
+        - "LENG  80"
+    - path: output/hmmer/versions.yml
+      contains:
+        - "hmmer:"
diff --git a/tests/modules/nf-core/hmmer/hmmsearch/main.nf b/tests/modules/nf-core/hmmer/hmmsearch/main.nf
new file mode 100644
index 00000000000..f32df1ecba1
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/hmmsearch/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMER_HMMSEARCH } from '../../../../../modules/nf-core/hmmer/hmmsearch/main.nf'
+
+workflow test_hmmer_hmmsearch {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true),
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz', checkIfExists: true),
+        false,
+        false,
+        false
+    ]
+
+    HMMER_HMMSEARCH ( input )
+}
+
+workflow test_hmmer_hmmsearch_optional {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true),
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz', checkIfExists: true),
+        true,
+        true,
+        true
+    ]
+
+    HMMER_HMMSEARCH ( input )
+}
diff --git a/tests/modules/hmmer/hmmsearch/nextflow.config b/tests/modules/nf-core/hmmer/hmmsearch/nextflow.config
similarity index 100%
rename from tests/modules/hmmer/hmmsearch/nextflow.config
rename to tests/modules/nf-core/hmmer/hmmsearch/nextflow.config
diff --git a/tests/modules/nf-core/hmmer/hmmsearch/test.yml b/tests/modules/nf-core/hmmer/hmmsearch/test.yml
new file mode 100644
index 00000000000..8e6ddcd7ae1
--- /dev/null
+++ b/tests/modules/nf-core/hmmer/hmmsearch/test.yml
@@ -0,0 +1,31 @@
+- name: hmmer hmmsearch test_hmmer_hmmsearch
+  command: nextflow run ./tests/modules/nf-core/hmmer/hmmsearch -entry test_hmmer_hmmsearch -c ./tests/config/nextflow.config
+  tags:
+    - hmmer/hmmsearch
+    - hmmer
+  files:
+    - path: output/hmmer/test.txt.gz
+      contains:
+        - "[ok]"
+    - path: output/hmmer/versions.yml
+      md5sum: ed0808c10abd205c6bd0fb01f45259bb
+
+- name: hmmer hmmsearch test_hmmer_hmmsearch_optional
+  command: nextflow run ./tests/modules/nf-core/hmmer/hmmsearch -entry test_hmmer_hmmsearch_optional -c ./tests/config/nextflow.config
+  tags:
+    - hmmer/hmmsearch
+    - hmmer
+  files:
+    - path: output/hmmer/test.sto.gz
+      md5sum: d3121aa33455074c566fb7f8fdcda7b0
+    - path: output/hmmer/test.domtbl.gz
+      contains:
+        - "# [ok]"
+    - path: output/hmmer/test.tbl.gz
+      contains:
+        - "# [ok]"
+    - path: output/hmmer/test.txt.gz
+      contains:
+        - "[ok]"
+    - path: output/hmmer/versions.yml
+      md5sum: ebdcb08ae540e840f7b5c4c75a3a2993
diff --git a/tests/modules/nf-core/hmtnote/main.nf b/tests/modules/nf-core/hmtnote/main.nf
new file mode 100644
index 00000000000..efaee619f38
--- /dev/null
+++ b/tests/modules/nf-core/hmtnote/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMTNOTE } from '../../../../modules/nf-core/hmtnote/main.nf'
+
+workflow test_hmtnote {
+    
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+            ]
+
+    HMTNOTE ( input)
+}
diff --git a/tests/modules/hmtnote/nextflow.config b/tests/modules/nf-core/hmtnote/nextflow.config
similarity index 100%
rename from tests/modules/hmtnote/nextflow.config
rename to tests/modules/nf-core/hmtnote/nextflow.config
diff --git a/tests/modules/nf-core/hmtnote/test.yml b/tests/modules/nf-core/hmtnote/test.yml
new file mode 100644
index 00000000000..5b036829413
--- /dev/null
+++ b/tests/modules/nf-core/hmtnote/test.yml
@@ -0,0 +1,6 @@
+- name: hmtnote test_hmtnote
+  command: nextflow run ./tests/modules/nf-core/hmtnote -entry test_hmtnote -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hmtnote/nextflow.config
+  tags:
+    - hmtnote
+  files:
+    - path: output/hmtnote/test_annotated.vcf
diff --git a/tests/modules/nf-core/homer/annotatepeaks/main.nf b/tests/modules/nf-core/homer/annotatepeaks/main.nf
new file mode 100644
index 00000000000..cfd52c1ba49
--- /dev/null
+++ b/tests/modules/nf-core/homer/annotatepeaks/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_ANNOTATEPEAKS } from '../../../../../modules/nf-core/homer/annotatepeaks/main.nf'
+
+workflow test_homer_annotatepeaks {
+    input = [ [ id:'test'],
+              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gtf   = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+    HOMER_ANNOTATEPEAKS ( input, fasta, gtf )
+}
diff --git a/tests/modules/homer/annotatepeaks/nextflow.config b/tests/modules/nf-core/homer/annotatepeaks/nextflow.config
similarity index 100%
rename from tests/modules/homer/annotatepeaks/nextflow.config
rename to tests/modules/nf-core/homer/annotatepeaks/nextflow.config
diff --git a/tests/modules/nf-core/homer/annotatepeaks/test.yml b/tests/modules/nf-core/homer/annotatepeaks/test.yml
new file mode 100644
index 00000000000..9bb1256e684
--- /dev/null
+++ b/tests/modules/nf-core/homer/annotatepeaks/test.yml
@@ -0,0 +1,7 @@
+- name: homer annotatepeaks test_homer_annotatepeaks
+  command: nextflow run ./tests/modules/nf-core/homer/annotatepeaks -entry test_homer_annotatepeaks -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/homer/annotatepeaks/nextflow.config
+  tags:
+    - homer
+    - homer/annotatepeaks
+  files:
+    - path: output/homer/test.annotatePeaks.txt
diff --git a/tests/modules/nf-core/homer/findpeaks/main.nf b/tests/modules/nf-core/homer/findpeaks/main.nf
new file mode 100644
index 00000000000..2e9002bd6c7
--- /dev/null
+++ b/tests/modules/nf-core/homer/findpeaks/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_MAKETAGDIRECTORY } from '../../../../../modules/nf-core/homer/maketagdirectory/main.nf'
+include { HOMER_FINDPEAKS } from '../../../../../modules/nf-core/homer/findpeaks/main.nf'
+
+workflow test_homer_findpeaks {
+    input = [[id:'test'],
+             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HOMER_MAKETAGDIRECTORY (input, fasta)
+    HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
+}
+
diff --git a/tests/modules/homer/findpeaks/nextflow.config b/tests/modules/nf-core/homer/findpeaks/nextflow.config
similarity index 100%
rename from tests/modules/homer/findpeaks/nextflow.config
rename to tests/modules/nf-core/homer/findpeaks/nextflow.config
diff --git a/tests/modules/nf-core/homer/findpeaks/test.yml b/tests/modules/nf-core/homer/findpeaks/test.yml
new file mode 100644
index 00000000000..efd55b38289
--- /dev/null
+++ b/tests/modules/nf-core/homer/findpeaks/test.yml
@@ -0,0 +1,8 @@
+- name: homer findpeaks
+  command: nextflow run ./tests/modules/nf-core/homer/findpeaks -entry test_homer_findpeaks -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/homer/findpeaks/nextflow.config
+  tags:
+    - homer
+    - homer/findpeaks
+  files:
+    - path: output/homer/test.peaks.txt
+      md5sum: 86e15beaa4b439585786478e58418c0c
diff --git a/tests/modules/nf-core/homer/maketagdirectory/main.nf b/tests/modules/nf-core/homer/maketagdirectory/main.nf
new file mode 100644
index 00000000000..1359fa5430c
--- /dev/null
+++ b/tests/modules/nf-core/homer/maketagdirectory/main.nf
@@ -0,0 +1,41 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include {
+    HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BED
+    HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BAM
+} from '../../../../../modules/nf-core/homer/maketagdirectory/main.nf'
+
+workflow test_homer_maketagdirectory_bed {
+    input = [[id:'test'],
+             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HOMER_MAKETAGDIRECTORY_BED (input, fasta)
+}
+
+
+workflow test_homer_maketagdirectory_meta {
+    input =
+        [[[ id:'test1'],
+          [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]],
+         [[ id:'test2'],
+          [file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    meta_input = [[id: 'meta_test']] + [ input.collect{it[1]}.flatten() ]
+
+    HOMER_MAKETAGDIRECTORY_BED (meta_input, fasta)
+}
+
+workflow test_homer_maketagdirectory_bam {
+    input = [[id:'test'],
+             [file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HOMER_MAKETAGDIRECTORY_BAM (input, fasta)
+}
diff --git a/tests/modules/homer/maketagdirectory/nextflow.config b/tests/modules/nf-core/homer/maketagdirectory/nextflow.config
similarity index 100%
rename from tests/modules/homer/maketagdirectory/nextflow.config
rename to tests/modules/nf-core/homer/maketagdirectory/nextflow.config
diff --git a/tests/modules/nf-core/homer/maketagdirectory/test.yml b/tests/modules/nf-core/homer/maketagdirectory/test.yml
new file mode 100644
index 00000000000..f4b40bdfe93
--- /dev/null
+++ b/tests/modules/nf-core/homer/maketagdirectory/test.yml
@@ -0,0 +1,50 @@
+- name: homer maketagdirectory bed
+  command: nextflow run ./tests/modules/nf-core/homer/maketagdirectory -entry test_homer_maketagdirectory_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/homer/maketagdirectory/nextflow.config
+  tags:
+    - homer
+    - homer/maketagdirectory
+  files:
+    - path: output/homer/test_tagdir/MT192765.1.tags.tsv
+      md5sum: e29522171ca2169b57396495f8b97485
+    - path: output/homer/test_tagdir/tagAutocorrelation.txt
+      md5sum: 62b107c4971b94126fb89a0bc2800455
+    - path: output/homer/test_tagdir/tagCountDistribution.txt
+      md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
+    - path: output/homer/test_tagdir/tagInfo.txt
+      md5sum: c9bb2ca53bb101d74c1ec92d2b0ad26e
+    - path: output/homer/test_tagdir/tagLengthDistribution.txt
+      md5sum: e5aa2b9843ca9c04ace297280aed6af4
+
+- name: homer maketagdirectory meta
+  command: nextflow run ./tests/modules/nf-core/homer/maketagdirectory -entry test_homer_maketagdirectory_meta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/homer/maketagdirectory/nextflow.config
+  tags:
+    - homer
+    - homer/maketagdirectory
+  files:
+    - path: output/homer/meta_test_tagdir/MT192765.1.tags.tsv
+      md5sum: e29522171ca2169b57396495f8b97485
+    - path: output/homer/meta_test_tagdir/tagAutocorrelation.txt
+      md5sum: 62b107c4971b94126fb89a0bc2800455
+    - path: output/homer/meta_test_tagdir/tagCountDistribution.txt
+      md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
+    - path: output/homer/meta_test_tagdir/tagInfo.txt
+      md5sum: cb907ebf9afc042bb61196d624e793c8
+    - path: output/homer/meta_test_tagdir/tagLengthDistribution.txt
+      md5sum: e5aa2b9843ca9c04ace297280aed6af4
+
+- name: homer maketagdirectory bam
+  command: nextflow run ./tests/modules/nf-core/homer/maketagdirectory -entry test_homer_maketagdirectory_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/homer/maketagdirectory/nextflow.config
+  tags:
+    - homer
+    - homer/maketagdirectory
+  files:
+    - path: output/homer/test_tagdir/MT192765.1.tags.tsv
+      md5sum: 365808c4751ef6dd7085ac52037a22bc
+    - path: output/homer/test_tagdir/tagAutocorrelation.txt
+      md5sum: 8b396f2aef1cdd3af4fab57b142d3250
+    - path: output/homer/test_tagdir/tagCountDistribution.txt
+      md5sum: afc6d007096c3872bbe84c9dc8edb832
+    - path: output/homer/test_tagdir/tagInfo.txt
+      md5sum: aebf6ff15fd0a238ee6a94d623c578ca
+    - path: output/homer/test_tagdir/tagLengthDistribution.txt
+      md5sum: 44f231adb2a705ae81950808c55cf248
diff --git a/tests/modules/nf-core/homer/makeucscfile/main.nf b/tests/modules/nf-core/homer/makeucscfile/main.nf
new file mode 100644
index 00000000000..f4649462e8a
--- /dev/null
+++ b/tests/modules/nf-core/homer/makeucscfile/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_MAKETAGDIRECTORY } from '../../../../../modules/nf-core/homer/maketagdirectory/main.nf'
+include { HOMER_MAKEUCSCFILE } from '../../../../../modules/nf-core/homer/makeucscfile/main.nf'
+
+workflow test_homer_makeucscfile {
+    input = [[id:'test'],
+             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HOMER_MAKETAGDIRECTORY (input, fasta)
+    HOMER_MAKEUCSCFILE ( HOMER_MAKETAGDIRECTORY.out.tagdir )
+}
+
diff --git a/tests/modules/homer/makeucscfile/nextflow.config b/tests/modules/nf-core/homer/makeucscfile/nextflow.config
similarity index 100%
rename from tests/modules/homer/makeucscfile/nextflow.config
rename to tests/modules/nf-core/homer/makeucscfile/nextflow.config
diff --git a/tests/modules/nf-core/homer/makeucscfile/test.yml b/tests/modules/nf-core/homer/makeucscfile/test.yml
new file mode 100644
index 00000000000..a79732d7338
--- /dev/null
+++ b/tests/modules/nf-core/homer/makeucscfile/test.yml
@@ -0,0 +1,7 @@
+- name: homer makeucscfile
+  command: nextflow run ./tests/modules/nf-core/homer/makeucscfile -entry test_homer_makeucscfile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/homer/makeucscfile/nextflow.config
+  tags:
+    - homer
+    - homer/makeucscfile
+  files:
+    - path: output/homer/test.bedGraph.gz
diff --git a/tests/modules/nf-core/homer/pos2bed/main.nf b/tests/modules/nf-core/homer/pos2bed/main.nf
new file mode 100644
index 00000000000..4eb9269541d
--- /dev/null
+++ b/tests/modules/nf-core/homer/pos2bed/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_MAKETAGDIRECTORY } from '../../../../../modules/nf-core/homer/maketagdirectory/main.nf'
+include { HOMER_FINDPEAKS } from '../../../../../modules/nf-core/homer/findpeaks/main.nf'
+include { HOMER_POS2BED } from '../../../../../modules/nf-core/homer/pos2bed/main.nf'
+
+workflow test_homer_pos2bed {
+    input = [[id:'test'],
+             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HOMER_MAKETAGDIRECTORY (input, fasta)
+    HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
+
+    HOMER_POS2BED ( HOMER_FINDPEAKS.out.txt )
+}
diff --git a/tests/modules/homer/pos2bed/nextflow.config b/tests/modules/nf-core/homer/pos2bed/nextflow.config
similarity index 100%
rename from tests/modules/homer/pos2bed/nextflow.config
rename to tests/modules/nf-core/homer/pos2bed/nextflow.config
diff --git a/tests/modules/nf-core/homer/pos2bed/test.yml b/tests/modules/nf-core/homer/pos2bed/test.yml
new file mode 100644
index 00000000000..68ee9192cee
--- /dev/null
+++ b/tests/modules/nf-core/homer/pos2bed/test.yml
@@ -0,0 +1,10 @@
+- name: "homer pos2bed"
+  command: nextflow run ./tests/modules/nf-core/homer/pos2bed -entry test_homer_pos2bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/homer/pos2bed/nextflow.config
+  tags:
+    - "homer"
+    - "homer/pos2bed"
+  files:
+    - path: output/homer/test.bed
+      md5sum: 5d6ddd9c7e621a66f6f045b9b5abecb4
+    - path: output/homer/versions.yml
+      md5sum: 1485f4b2d76484e8fe3310e2505de2fd
diff --git a/tests/modules/nf-core/hpsuissero/main.nf b/tests/modules/nf-core/hpsuissero/main.nf
new file mode 100644
index 00000000000..4bda9843fe9
--- /dev/null
+++ b/tests/modules/nf-core/hpsuissero/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HPSUISSERO } from '../../../../modules/nf-core/hpsuissero/main.nf'
+
+workflow test_hpsuissero {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    HPSUISSERO ( input )
+}
diff --git a/tests/modules/hpsuissero/nextflow.config b/tests/modules/nf-core/hpsuissero/nextflow.config
similarity index 100%
rename from tests/modules/hpsuissero/nextflow.config
rename to tests/modules/nf-core/hpsuissero/nextflow.config
diff --git a/tests/modules/nf-core/hpsuissero/test.yml b/tests/modules/nf-core/hpsuissero/test.yml
new file mode 100644
index 00000000000..f4a88f76abf
--- /dev/null
+++ b/tests/modules/nf-core/hpsuissero/test.yml
@@ -0,0 +1,9 @@
+- name: hpsuissero test_hpsuissero
+  command: nextflow run ./tests/modules/nf-core/hpsuissero -entry test_hpsuissero -c ./tests/config/nextflow.config
+  tags:
+    - hpsuissero
+  files:
+    - path: output/hpsuissero/test_serotyping_res.tsv
+      md5sum: 559dd2ca386eeb58f3975e3204ce9d43
+    - path: output/hpsuissero/versions.yml
+      md5sum: f65438e63a74ac6ee365bfdbbd3f996a
diff --git a/tests/modules/nf-core/ichorcna/createpon/main.nf b/tests/modules/nf-core/ichorcna/createpon/main.nf
new file mode 100644
index 00000000000..9d9a291abb3
--- /dev/null
+++ b/tests/modules/nf-core/ichorcna/createpon/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ICHORCNA_CREATEPON } from '../../../../../modules/nf-core/ichorcna/createpon/main.nf'
+
+workflow test_ichorcna_createpon {
+
+    input = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
+
+    gcwig   = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
+    mapwig  = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
+
+    centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
+
+    ICHORCNA_CREATEPON ( input, gcwig, mapwig, centromere )
+}
+
+workflow test_ichorcna_createpon2 {
+
+    input = [file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true),
+             file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315_T2.ctDNA.reads.wig", checkIfExists: true)]
+
+    gcwig   = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
+    mapwig  = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
+
+    centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
+
+    ICHORCNA_CREATEPON ( input, gcwig, mapwig, centromere )
+}
diff --git a/tests/modules/ichorcna/createpon/nextflow.config b/tests/modules/nf-core/ichorcna/createpon/nextflow.config
similarity index 100%
rename from tests/modules/ichorcna/createpon/nextflow.config
rename to tests/modules/nf-core/ichorcna/createpon/nextflow.config
diff --git a/tests/modules/nf-core/ichorcna/createpon/test.yml b/tests/modules/nf-core/ichorcna/createpon/test.yml
new file mode 100644
index 00000000000..a4352ad5c09
--- /dev/null
+++ b/tests/modules/nf-core/ichorcna/createpon/test.yml
@@ -0,0 +1,21 @@
+- name: ichorcna createpon test_ichorcna_createpon
+  command: nextflow run ./tests/modules/nf-core/ichorcna/createpon -entry test_ichorcna_createpon -c ./tests/config/nextflow.config
+  tags:
+    - ichorcna/createpon
+    - ichorcna
+  files:
+    - path: output/ichorcna/PoN_median.txt
+      contains: ["seqnames"]
+    - path: output/ichorcna/versions.yml
+      md5sum: 59a2121301113cc013bfae65935e07f1
+
+- name: ichorcna createpon test_ichorcna_createpon2
+  command: nextflow run ./tests/modules/nf-core/ichorcna/createpon -entry test_ichorcna_createpon2 -c ./tests/config/nextflow.config
+  tags:
+    - ichorcna/createpon
+    - ichorcna
+  files:
+    - path: output/ichorcna/PoN_median.txt
+      contains: ["seqnames"]
+    - path: output/ichorcna/versions.yml
+      md5sum: 31a5fcc0075dbe747f7736efbdb99644
diff --git a/tests/modules/nf-core/ichorcna/run/main.nf b/tests/modules/nf-core/ichorcna/run/main.nf
new file mode 100644
index 00000000000..ed57cccc46c
--- /dev/null
+++ b/tests/modules/nf-core/ichorcna/run/main.nf
@@ -0,0 +1,40 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ICHORCNA_RUN } from '../../../../../modules/nf-core/ichorcna/run/main.nf'
+include { HMMCOPY_READCOUNTER } from '../../../../../modules/nf-core/hmmcopy/readcounter/main.nf'
+include { HMMCOPY_GCCOUNTER } from '../../../../../modules/nf-core/hmmcopy/gccounter/main.nf'
+include { HMMCOPY_MAPCOUNTER } from '../../../../../modules/nf-core/hmmcopy/mapcounter/main.nf'
+include { HMMCOPY_GENERATEMAP } from '../../../../../modules/nf-core/hmmcopy/generatemap/main.nf'
+
+workflow test_ichorcna_run_no_panel {
+
+    input = [ [ id:'test'], // meta map
+              file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
+            ]
+
+    gcwig   = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
+    mapwig  = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
+
+    panel_of_normals = []
+    centromere = []
+
+    ICHORCNA_RUN ( input, gcwig, mapwig, panel_of_normals, centromere)
+}
+
+workflow test_ichorcna_run_inc_panel {
+
+    input = [ [ id:'test'], // meta map
+              file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
+            ]
+
+    gcwig   = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
+    mapwig  = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
+
+    panel_of_normals = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds", checkIfExists: true)
+
+    centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
+
+    ICHORCNA_RUN ( input, gcwig, mapwig, panel_of_normals, centromere)
+}
diff --git a/tests/modules/ichorcna/run/nextflow.config b/tests/modules/nf-core/ichorcna/run/nextflow.config
similarity index 100%
rename from tests/modules/ichorcna/run/nextflow.config
rename to tests/modules/nf-core/ichorcna/run/nextflow.config
diff --git a/tests/modules/nf-core/ichorcna/run/test.yml b/tests/modules/nf-core/ichorcna/run/test.yml
new file mode 100644
index 00000000000..963cae64906
--- /dev/null
+++ b/tests/modules/nf-core/ichorcna/run/test.yml
@@ -0,0 +1,25 @@
+- name: ichorcna run test_ichorcna_run_no_panel
+  command: nextflow run ./tests/modules/nf-core/ichorcna/run -entry test_ichorcna_run_no_panel -c ./tests/config/nextflow.config
+  tags:
+    - ichorcna
+    - ichorcna/run
+  files:
+    - path: output/ichorcna/test.cna.seg
+      contains: ["Corrected_Copy_Number"]
+    - path: output/ichorcna/test.params.txt
+      md5sum: e39a579cdcc9576679f06dc5c22605a7
+    - path: output/ichorcna/versions.yml
+      md5sum: effb37e19bec3609417aaccad4b6a294
+
+- name: ichorcna run test_ichorcna_run_inc_panel
+  command: nextflow run ./tests/modules/nf-core/ichorcna/run -entry test_ichorcna_run_inc_panel -c ./tests/config/nextflow.config
+  tags:
+    - ichorcna
+    - ichorcna/run
+  files:
+    - path: output/ichorcna/test.cna.seg
+      contains: ["Corrected_Copy_Number"]
+    - path: output/ichorcna/test.params.txt
+      md5sum: 0b97e0269cd0b571f5a85890f6ddb181
+    - path: output/ichorcna/versions.yml
+      md5sum: fc9d96de0a1c15cea59208305b14e535
diff --git a/tests/modules/nf-core/idr/main.nf b/tests/modules/nf-core/idr/main.nf
new file mode 100644
index 00000000000..f532e8f5994
--- /dev/null
+++ b/tests/modules/nf-core/idr/main.nf
@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IDR } from '../../../../modules/nf-core/idr/main.nf'
+
+workflow test_idr_narrowpeak {
+
+    input = [
+        file(params.test_data['homo_sapiens']['illumina']['test_narrowpeak'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_narrowpeak'], checkIfExists: true)
+    ]
+
+    IDR ( input, 'narrowPeak', 'test' )
+}
+
+workflow test_idr_broadpeak {
+
+    input = [
+        file(params.test_data['homo_sapiens']['illumina']['test_broadpeak'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_broadpeak'], checkIfExists: true)
+    ]
+
+    IDR ( input, 'broadPeak', 'test' )
+}
+
+workflow test_idr_noprefix {
+
+    input = [
+        file(params.test_data['homo_sapiens']['illumina']['test_narrowpeak'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_narrowpeak'], checkIfExists: true)
+    ]
+
+    IDR ( input, 'narrowPeak', '' )
+}
diff --git a/tests/modules/idr/nextflow.config b/tests/modules/nf-core/idr/nextflow.config
similarity index 100%
rename from tests/modules/idr/nextflow.config
rename to tests/modules/nf-core/idr/nextflow.config
diff --git a/tests/modules/nf-core/idr/test.yml b/tests/modules/nf-core/idr/test.yml
new file mode 100644
index 00000000000..42a4b1bda5a
--- /dev/null
+++ b/tests/modules/nf-core/idr/test.yml
@@ -0,0 +1,35 @@
+- name: idr test_idr_narrowpeak
+  command: nextflow run ./tests/modules/nf-core/idr -entry test_idr_narrowpeak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/idr/nextflow.config
+  tags:
+    - idr
+  files:
+    - path: output/idr/test.idrValues.txt
+      md5sum: 09be837cc6abbc3eb5958b74802eea55
+    - path: output/idr/test.idrValues.txt.png
+      md5sum: 4a7143ccc0ccadb37c2317bf626e6d96
+    - path: output/idr/test.log.txt
+      md5sum: 6443507ac66b9d3b64bc56b78328083e
+
+- name: idr test_idr_broadpeak
+  command: nextflow run ./tests/modules/nf-core/idr -entry test_idr_broadpeak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/idr/nextflow.config
+  tags:
+    - idr
+  files:
+    - path: output/idr/test.idrValues.txt
+      md5sum: 387441c716815e4caec3e70a2cc11a4a
+    - path: output/idr/test.idrValues.txt.png
+      md5sum: 7204083ca5b920b4215a5991c12cb4e7
+    - path: output/idr/test.log.txt
+      md5sum: e6917133112b5cec135c182ffac19237
+
+- name: idr test_idr_noprefix
+  command: nextflow run ./tests/modules/nf-core/idr -entry test_idr_noprefix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/idr/nextflow.config
+  tags:
+    - idr
+  files:
+    - path: output/idr/idrValues.txt
+      md5sum: 09be837cc6abbc3eb5958b74802eea55
+    - path: output/idr/idrValues.txt.png
+      md5sum: 4a7143ccc0ccadb37c2317bf626e6d96
+    - path: output/idr/log.txt
+      md5sum: 6443507ac66b9d3b64bc56b78328083e
diff --git a/tests/modules/nf-core/imputeme/vcftoprs/main.nf b/tests/modules/nf-core/imputeme/vcftoprs/main.nf
new file mode 100644
index 00000000000..fad879a2bb3
--- /dev/null
+++ b/tests/modules/nf-core/imputeme/vcftoprs/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IMPUTEME_VCFTOPRS } from '../../../../../modules/nf-core/imputeme/vcftoprs/main.nf'
+
+workflow test_imputeme_vcftoprs {
+    
+    input = [ 
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
+    ]
+
+    IMPUTEME_VCFTOPRS ( input )
+}
diff --git a/tests/modules/imputeme/vcftoprs/nextflow.config b/tests/modules/nf-core/imputeme/vcftoprs/nextflow.config
similarity index 100%
rename from tests/modules/imputeme/vcftoprs/nextflow.config
rename to tests/modules/nf-core/imputeme/vcftoprs/nextflow.config
diff --git a/tests/modules/nf-core/imputeme/vcftoprs/test.yml b/tests/modules/nf-core/imputeme/vcftoprs/test.yml
new file mode 100644
index 00000000000..239e37c6a8c
--- /dev/null
+++ b/tests/modules/nf-core/imputeme/vcftoprs/test.yml
@@ -0,0 +1,8 @@
+- name: imputeme vcftoprs test_imputeme_vcftoprs
+  command: nextflow run ./tests/modules/nf-core/imputeme/vcftoprs -entry test_imputeme_vcftoprs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/imputeme/vcftoprs/nextflow.config
+  tags:
+    - imputeme
+    - imputeme/vcftoprs
+  files:
+    - path: output/imputeme/output.json
+      contains: ['type_2_diabetes_32541925":{"GRS":[24.01]']
diff --git a/tests/modules/nf-core/instrain/profile/main.nf b/tests/modules/nf-core/instrain/profile/main.nf
new file mode 100644
index 00000000000..83239d6085d
--- /dev/null
+++ b/tests/modules/nf-core/instrain/profile/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { INSTRAIN_PROFILE } from '../../../../../modules/nf-core/instrain/profile/main.nf'
+
+workflow test_instrain_profile {
+    
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+        ]
+    ]
+    genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    INSTRAIN_PROFILE ( input , genome_fasta , [] , [] )
+}
diff --git a/tests/modules/instrain/profile/nextflow.config b/tests/modules/nf-core/instrain/profile/nextflow.config
similarity index 100%
rename from tests/modules/instrain/profile/nextflow.config
rename to tests/modules/nf-core/instrain/profile/nextflow.config
diff --git a/tests/modules/nf-core/instrain/profile/test.yml b/tests/modules/nf-core/instrain/profile/test.yml
new file mode 100644
index 00000000000..67a42ecb7ef
--- /dev/null
+++ b/tests/modules/nf-core/instrain/profile/test.yml
@@ -0,0 +1,9 @@
+- name: "instrain"
+  command: nextflow run ./tests/modules/nf-core/instrain/profile -entry test_instrain_profile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/instrain/profile/nextflow.config
+  tags:
+    - instrain
+    - instrain/profile
+  files:
+    - path: output/instrain/versions.yml
+    - path: output/instrain/test.IS/output/test.IS_SNVs.tsv
+      md5sum: 1d753903af5a25be540dcff255e25a1f
diff --git a/tests/modules/nf-core/iqtree/main.nf b/tests/modules/nf-core/iqtree/main.nf
new file mode 100644
index 00000000000..abf2e8cbb93
--- /dev/null
+++ b/tests/modules/nf-core/iqtree/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IQTREE } from '../../../../modules/nf-core/iqtree/main.nf'
+
+workflow test_iqtree {
+    
+    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
+
+    IQTREE ( input, '' )
+}
diff --git a/tests/modules/iqtree/nextflow.config b/tests/modules/nf-core/iqtree/nextflow.config
similarity index 100%
rename from tests/modules/iqtree/nextflow.config
rename to tests/modules/nf-core/iqtree/nextflow.config
diff --git a/tests/modules/nf-core/iqtree/test.yml b/tests/modules/nf-core/iqtree/test.yml
new file mode 100644
index 00000000000..86a6e5bc615
--- /dev/null
+++ b/tests/modules/nf-core/iqtree/test.yml
@@ -0,0 +1,11 @@
+- name: iqtree test workflow
+  command: nextflow run ./tests/modules/nf-core/iqtree -entry test_iqtree -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/iqtree/nextflow.config
+  tags:
+    - iqtree
+  files:
+    - path: output/iqtree/informative_sites.fas.treefile
+      contains:
+        - "(sample1:0.002"
+        - "(sample2:0.005"
+        - "sample3:0.0005"
+        - "sample4:0.001"
diff --git a/tests/modules/nf-core/ismapper/main.nf b/tests/modules/nf-core/ismapper/main.nf
new file mode 100644
index 00000000000..01e0b384829
--- /dev/null
+++ b/tests/modules/nf-core/ismapper/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ISMAPPER } from '../../../../modules/nf-core/ismapper/main.nf'
+
+workflow test_ismapper {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
+        file("https://github.com/jhawkey/IS_mapper/raw/master/test/inputs/S_suis_P17.gbk", checkIfExists: true),
+        file("https://github.com/jhawkey/IS_mapper/raw/master/test/inputs/ISSsu3.fasta", checkIfExists: true)
+    ]
+
+    ISMAPPER ( input )
+}
diff --git a/tests/modules/ismapper/nextflow.config b/tests/modules/nf-core/ismapper/nextflow.config
similarity index 100%
rename from tests/modules/ismapper/nextflow.config
rename to tests/modules/nf-core/ismapper/nextflow.config
diff --git a/tests/modules/nf-core/ismapper/test.yml b/tests/modules/nf-core/ismapper/test.yml
new file mode 100644
index 00000000000..86e6664fd75
--- /dev/null
+++ b/tests/modules/nf-core/ismapper/test.yml
@@ -0,0 +1,27 @@
+- name: ismapper test_ismapper
+  command: nextflow run ./tests/modules/nf-core/ismapper -entry test_ismapper -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ismapper/nextflow.config
+  tags:
+    - ismapper
+  files:
+    - path: output/ismapper/results/test/ISSsu3/test_ISSsu3_left_final.fastq
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/ismapper/results/test/ISSsu3/test_ISSsu3_right_final.fastq
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/ismapper/results/test/ISSsu3/test__AM946016.1_closest.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/ismapper/results/test/ISSsu3/test__AM946016.1_intersect.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/ismapper/results/test/ISSsu3/test__AM946016.1_table.txt
+      md5sum: 9e05cda3990cb841db2bfb6e6e04a1f5
+    - path: output/ismapper/results/test/ISSsu3/test_left_AM946016.1_finalcov.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/ismapper/results/test/ISSsu3/test_left_AM946016.1_merged.sorted.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/ismapper/results/test/ISSsu3/test_left_AM946016.1_unpaired.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/ismapper/results/test/ISSsu3/test_right_AM946016.1_finalcov.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/ismapper/results/test/ISSsu3/test_right_AM946016.1_merged.sorted.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/ismapper/results/test/ISSsu3/test_right_AM946016.1_unpaired.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/nf-core/isoseq3/cluster/main.nf b/tests/modules/nf-core/isoseq3/cluster/main.nf
new file mode 100644
index 00000000000..3f586d9a5f5
--- /dev/null
+++ b/tests/modules/nf-core/isoseq3/cluster/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ISOSEQ3_CLUSTER } from '../../../../../modules/nf-core/isoseq3/cluster/main.nf'
+
+workflow test_isoseq3_cluster {
+
+    input = [
+            [ id:'test' ], // meta map
+            file(params.test_data['homo_sapiens']['pacbio']['refine'], checkIfExists: true),
+        ]
+
+    ISOSEQ3_CLUSTER ( input )
+}
diff --git a/tests/modules/isoseq3/cluster/nextflow.config b/tests/modules/nf-core/isoseq3/cluster/nextflow.config
similarity index 100%
rename from tests/modules/isoseq3/cluster/nextflow.config
rename to tests/modules/nf-core/isoseq3/cluster/nextflow.config
diff --git a/tests/modules/nf-core/isoseq3/cluster/test.yml b/tests/modules/nf-core/isoseq3/cluster/test.yml
new file mode 100644
index 00000000000..0f275b93d9c
--- /dev/null
+++ b/tests/modules/nf-core/isoseq3/cluster/test.yml
@@ -0,0 +1,28 @@
+- name: isoseq3 cluster test_isoseq3_cluster
+  command: nextflow run ./tests/modules/nf-core/isoseq3/cluster -entry test_isoseq3_cluster -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/isoseq3/cluster/nextflow.config
+  tags:
+    - isoseq3
+    - isoseq3/cluster
+  files:
+    - path: output/isoseq3/test.transcripts.bam
+      md5sum: eb36697688099c757ef4196f54ad7d7a
+    - path: output/isoseq3/test.transcripts.bam.pbi
+      md5sum: db70cee03421822e9b8f9fb6b228f461
+    - path: output/isoseq3/test.transcripts.cluster
+      md5sum: d5059d856763fc5591332980bfc0d57b
+    - path: output/isoseq3/test.transcripts.cluster_report.csv
+      md5sum: 342d97dc10aedf80a45977edcb491c62
+    - path: output/isoseq3/test.transcripts.hq.bam
+      md5sum: 4c5f4ffb429107c9c9578419e07d6987
+    - path: output/isoseq3/test.transcripts.hq.bam.pbi
+      md5sum: 39ac3e957c8d55b0ce3f425d63baa154
+    - path: output/isoseq3/test.transcripts.lq.bam
+      md5sum: 710ca4bc58ac039d76775460e1c822a0
+    - path: output/isoseq3/test.transcripts.lq.bam.pbi
+      md5sum: 9b32036553bf3dced3065e6d0f36aef9
+    - path: output/isoseq3/test.transcripts.singletons.bam
+      md5sum: 0288577406b9d1e7356de9b4d7c2bb7c
+    - path: output/isoseq3/test.transcripts.singletons.bam.pbi
+      md5sum: 8e0e0681179c0c36209b49fa60783841
+    - path: output/isoseq3/test.transcripts.transcriptset.xml
+      contains: ["PacBio.DataSet.TranscriptSet"]
diff --git a/tests/modules/nf-core/isoseq3/refine/main.nf b/tests/modules/nf-core/isoseq3/refine/main.nf
new file mode 100644
index 00000000000..1ebafad4af2
--- /dev/null
+++ b/tests/modules/nf-core/isoseq3/refine/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ISOSEQ3_REFINE } from '../../../../../modules/nf-core/isoseq3/refine/main'
+
+workflow test_isoseq3_refine {
+
+    input = [
+            [ id:'test' ], // meta map
+            file(params.test_data['homo_sapiens']['pacbio']['lima'], checkIfExists: true),
+    ]
+    primers = file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true)
+
+    ISOSEQ3_REFINE ( input, primers )
+}
diff --git a/tests/modules/isoseq3/refine/nextflow.config b/tests/modules/nf-core/isoseq3/refine/nextflow.config
similarity index 100%
rename from tests/modules/isoseq3/refine/nextflow.config
rename to tests/modules/nf-core/isoseq3/refine/nextflow.config
diff --git a/tests/modules/nf-core/isoseq3/refine/test.yml b/tests/modules/nf-core/isoseq3/refine/test.yml
new file mode 100644
index 00000000000..99b6d511bac
--- /dev/null
+++ b/tests/modules/nf-core/isoseq3/refine/test.yml
@@ -0,0 +1,16 @@
+- name: isoseq3 refine test_isoseq3_refine
+  command: nextflow run ./tests/modules/nf-core/isoseq3/refine -entry test_isoseq3_refine -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/isoseq3/refine/nextflow.config
+  tags:
+    - isoseq3
+    - isoseq3/refine
+  files:
+    - path: output/isoseq3/test.refine.bam
+      md5sum: e8387afd5f66a7f6a89f90a0dcf3b823
+    - path: output/isoseq3/test.refine.bam.pbi
+      md5sum: 8097cad9e472f2f79de6de5fe3dcc822
+    - path: output/isoseq3/test.refine.consensusreadset.xml
+      contains: ["pbds:ConsensusReadSet"]
+    - path: output/isoseq3/test.refine.filter_summary.json
+      md5sum: 87f8bdd5c60741f47b8a991e002f7ef3
+    - path: output/isoseq3/test.refine.report.csv
+      md5sum: d42a139e5d9b08396bdb087c01243ea9
diff --git a/tests/modules/nf-core/ivar/consensus/main.nf b/tests/modules/nf-core/ivar/consensus/main.nf
new file mode 100644
index 00000000000..37ce0f8f17e
--- /dev/null
+++ b/tests/modules/nf-core/ivar/consensus/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IVAR_CONSENSUS } from '../../../../../modules/nf-core/ivar/consensus/main.nf'
+
+workflow test_ivar_consensus {
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = false
+
+    IVAR_CONSENSUS ( input, fasta, save_mpileup)
+}
+
+workflow test_ivar_consensus_mpileup {
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = true
+
+    IVAR_CONSENSUS ( input, fasta, save_mpileup)
+}
diff --git a/tests/modules/ivar/consensus/nextflow.config b/tests/modules/nf-core/ivar/consensus/nextflow.config
similarity index 100%
rename from tests/modules/ivar/consensus/nextflow.config
rename to tests/modules/nf-core/ivar/consensus/nextflow.config
diff --git a/tests/modules/nf-core/ivar/consensus/test.yml b/tests/modules/nf-core/ivar/consensus/test.yml
new file mode 100644
index 00000000000..a403b46487d
--- /dev/null
+++ b/tests/modules/nf-core/ivar/consensus/test.yml
@@ -0,0 +1,23 @@
+- name: ivar consensus test_ivar_consensus
+  command: nextflow run ./tests/modules/nf-core/ivar/consensus -entry test_ivar_consensus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/consensus/nextflow.config
+  tags:
+    - ivar
+    - ivar/consensus
+  files:
+    - path: output/ivar/test.fa
+      md5sum: 9e21a64818f4302b4dece5480fa5e8b8
+    - path: output/ivar/test.qual.txt
+      md5sum: 68b329da9893e34099c7d8ad5cb9c940
+
+- name: ivar consensus test_ivar_consensus_mpileup
+  command: nextflow run ./tests/modules/nf-core/ivar/consensus -entry test_ivar_consensus_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/consensus/nextflow.config
+  tags:
+    - ivar
+    - ivar/consensus
+  files:
+    - path: output/ivar/test.fa
+      md5sum: 9e21a64818f4302b4dece5480fa5e8b8
+    - path: output/ivar/test.qual.txt
+      md5sum: 68b329da9893e34099c7d8ad5cb9c940
+    - path: output/ivar/test.mpileup
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/nf-core/ivar/trim/main.nf b/tests/modules/nf-core/ivar/trim/main.nf
new file mode 100644
index 00000000000..550ce62c25e
--- /dev/null
+++ b/tests/modules/nf-core/ivar/trim/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IVAR_TRIM } from '../../../../../modules/nf-core/ivar/trim/main.nf'
+
+workflow test_ivar_trim {
+    input = [ [ id:'test'],
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) 
+            ]
+    bed_file   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+
+    IVAR_TRIM ( input, bed_file )
+}
diff --git a/tests/modules/ivar/trim/nextflow.config b/tests/modules/nf-core/ivar/trim/nextflow.config
similarity index 100%
rename from tests/modules/ivar/trim/nextflow.config
rename to tests/modules/nf-core/ivar/trim/nextflow.config
diff --git a/tests/modules/nf-core/ivar/trim/test.yml b/tests/modules/nf-core/ivar/trim/test.yml
new file mode 100644
index 00000000000..2cc949d075f
--- /dev/null
+++ b/tests/modules/nf-core/ivar/trim/test.yml
@@ -0,0 +1,8 @@
+- name: ivar trim
+  command: nextflow run ./tests/modules/nf-core/ivar/trim -entry test_ivar_trim -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/trim/nextflow.config
+  tags:
+    - ivar
+    - ivar/trim
+  files:
+    - path: output/ivar/test.bam
+      md5sum: 12cff17d43b1efdba8120a6bff5311e3
diff --git a/tests/modules/nf-core/ivar/variants/main.nf b/tests/modules/nf-core/ivar/variants/main.nf
new file mode 100644
index 00000000000..b8dd56b5ba3
--- /dev/null
+++ b/tests/modules/nf-core/ivar/variants/main.nf
@@ -0,0 +1,47 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IVAR_VARIANTS } from '../../../../../modules/nf-core/ivar/variants/main.nf'
+
+workflow test_ivar_variants_no_gff_no_mpileup {
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gff   = []
+    save_mpileup = false
+
+    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
+}
+
+workflow test_ivar_variants_no_gff_with_mpileup {
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gff   = []
+    save_mpileup = true
+
+    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
+}
+
+workflow test_ivar_variants_with_gff_with_mpileup {
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gff   = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+    save_mpileup = true
+
+    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
+}
diff --git a/tests/modules/ivar/variants/nextflow.config b/tests/modules/nf-core/ivar/variants/nextflow.config
similarity index 100%
rename from tests/modules/ivar/variants/nextflow.config
rename to tests/modules/nf-core/ivar/variants/nextflow.config
diff --git a/tests/modules/nf-core/ivar/variants/test.yml b/tests/modules/nf-core/ivar/variants/test.yml
new file mode 100644
index 00000000000..fbc4c080dcd
--- /dev/null
+++ b/tests/modules/nf-core/ivar/variants/test.yml
@@ -0,0 +1,30 @@
+- name: ivar variants no gff no mpileup
+  command: nextflow run ./tests/modules/nf-core/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/variants/nextflow.config
+  tags:
+    - ivar
+    - ivar/variants
+  files:
+    - path: output/ivar/test.tsv
+      md5sum: 728f1430f2402861396d9953465ac706
+
+- name: ivar variants no gff with mpileup
+  command: nextflow run ./tests/modules/nf-core/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c ./tests/config/nextflow.config --save_mpileup -c ./tests/modules/nf-core/ivar/variants/nextflow.config
+  tags:
+    - ivar
+    - ivar/variants
+  files:
+    - path: output/ivar/test.tsv
+      md5sum: 728f1430f2402861396d9953465ac706
+    - path: output/ivar/test.mpileup
+      md5sum: 56c4cd5a4ecb7d6364878818f46ae256
+
+- name: ivar variants with gff with mpileup
+  command: nextflow run ./tests/modules/nf-core/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c ./tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup -c ./tests/modules/nf-core/ivar/variants/nextflow.config
+  tags:
+    - ivar
+    - ivar/variants
+  files:
+    - path: output/ivar/test.tsv
+      md5sum: 7b59146132a60da58444bebffc3c2577
+    - path: output/ivar/test.mpileup
+      md5sum: 56c4cd5a4ecb7d6364878818f46ae256
diff --git a/tests/modules/nf-core/jupyternotebook/main.nf b/tests/modules/nf-core/jupyternotebook/main.nf
new file mode 100644
index 00000000000..80c3a568321
--- /dev/null
+++ b/tests/modules/nf-core/jupyternotebook/main.nf
@@ -0,0 +1,43 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { JUPYTERNOTEBOOK } from '../../../../modules/nf-core/jupyternotebook/main.nf'
+include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../../modules/nf-core/jupyternotebook/main.nf'
+include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../../modules/nf-core/jupyternotebook/main.nf'
+
+workflow test_jupyternotebook {
+
+    input = [ [ id:'test_jupyter' ], // meta map
+              file(params.test_data['generic']['notebooks']['ipython_md'], checkIfExists: true) ]
+
+    JUPYTERNOTEBOOK ( input, [:], [])
+
+}
+
+workflow test_jupyternotebook_parametrize {
+
+    input = [ [ id:'test_jupyter' ], // meta map
+              file(params.test_data['generic']['notebooks']['ipython_md'], checkIfExists: true) ]
+
+    JUPYTERNOTEBOOK_PARAMETRIZE(
+        input,
+        [input_filename: "hello.txt", n_iter: 12],
+        file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
+    )
+
+}
+
+workflow test_jupyternotebook_parametrize_ipynb {
+
+    input = [ [ id:'test_jupyter' ], // meta map
+              file(params.test_data['generic']['notebooks']['ipython_ipynb'], checkIfExists: true) ]
+
+    JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB(
+        input,
+        [input_filename: "hello.txt", n_iter: 12],
+        file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
+    )
+
+}
+
diff --git a/tests/modules/jupyternotebook/nextflow.config b/tests/modules/nf-core/jupyternotebook/nextflow.config
similarity index 100%
rename from tests/modules/jupyternotebook/nextflow.config
rename to tests/modules/nf-core/jupyternotebook/nextflow.config
diff --git a/tests/modules/nf-core/jupyternotebook/test.yml b/tests/modules/nf-core/jupyternotebook/test.yml
new file mode 100644
index 00000000000..dc5c1879c7a
--- /dev/null
+++ b/tests/modules/nf-core/jupyternotebook/test.yml
@@ -0,0 +1,30 @@
+- name: jupyternotebook test_jupyternotebook
+  command: nextflow run ./tests/modules/nf-core/jupyternotebook -entry test_jupyternotebook -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/jupyternotebook/nextflow.config
+  tags:
+    - jupyternotebook
+  files:
+    - path: output/jupyternotebook/test_jupyter.html
+      contains:
+        - "n_iter = 10"
+
+- name: jupyternotebook test_jupyternotebook_parametrize
+  command: nextflow run ./tests/modules/nf-core/jupyternotebook -entry test_jupyternotebook_parametrize -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/jupyternotebook/nextflow.config
+  tags:
+    - jupyternotebook
+  files:
+    - path: output/jupyternotebook/artifacts/artifact.txt
+      md5sum: 8ddd8be4b179a529afa5f2ffae4b9858
+    - path: output/jupyternotebook/test_jupyter.html
+      contains:
+        - "n_iter = 12"
+
+- name: jupyternotebook test_jupyternotebook_parametrize_ipynb
+  command: nextflow run ./tests/modules/nf-core/jupyternotebook -entry test_jupyternotebook_parametrize_ipynb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/jupyternotebook/nextflow.config
+  tags:
+    - jupyternotebook
+  files:
+    - path: output/jupyternotebook/artifacts/artifact.txt
+      md5sum: 8ddd8be4b179a529afa5f2ffae4b9858
+    - path: output/jupyternotebook/test_jupyter.html
+      contains:
+        - "n_iter = 12"
diff --git a/tests/modules/nf-core/kaiju/kaiju/main.nf b/tests/modules/nf-core/kaiju/kaiju/main.nf
new file mode 100644
index 00000000000..c2b1d60e712
--- /dev/null
+++ b/tests/modules/nf-core/kaiju/kaiju/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR       } from '../../../../../modules/nf-core/untar/main.nf'
+include { KAIJU_KAIJU } from '../../../../../modules/nf-core/kaiju/kaiju/main.nf'
+
+workflow test_kaiju_kaiju_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
+}
+
+workflow test_kaiju_kaiju_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+    ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
+
+}
diff --git a/tests/modules/kaiju/kaiju/nextflow.config b/tests/modules/nf-core/kaiju/kaiju/nextflow.config
similarity index 100%
rename from tests/modules/kaiju/kaiju/nextflow.config
rename to tests/modules/nf-core/kaiju/kaiju/nextflow.config
diff --git a/tests/modules/nf-core/kaiju/kaiju/test.yml b/tests/modules/nf-core/kaiju/kaiju/test.yml
new file mode 100644
index 00000000000..9e495ede0b0
--- /dev/null
+++ b/tests/modules/nf-core/kaiju/kaiju/test.yml
@@ -0,0 +1,21 @@
+- name: kaiju kaiju test_kaiju_kaiju_single_end
+  command: nextflow run ./tests/modules/nf-core/kaiju/kaiju -entry test_kaiju_kaiju_single_end -c ./tests/config/nextflow.config
+  tags:
+    - kaiju/kaiju
+    - kaiju
+  files:
+    - path: output/kaiju/test.tsv
+      contains: ["C\tERR5069949.2257580\t2697049"]
+    - path: output/kaiju/versions.yml
+      md5sum: 7e218c0ea00a71dd3a5ec5aaf28804f4
+
+- name: kaiju kaiju test_kaiju_kaiju_paired_end
+  command: nextflow run ./tests/modules/nf-core/kaiju/kaiju -entry test_kaiju_kaiju_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - kaiju/kaiju
+    - kaiju
+  files:
+    - path: output/kaiju/test.tsv
+      contains: ["C\tERR5069949.2257580\t2697049"]
+    - path: output/kaiju/versions.yml
+      md5sum: a74215f6f69979ae046fb1d65c56ac67
diff --git a/tests/modules/nf-core/kaiju/kaiju2krona/main.nf b/tests/modules/nf-core/kaiju/kaiju2krona/main.nf
new file mode 100644
index 00000000000..62adf390caf
--- /dev/null
+++ b/tests/modules/nf-core/kaiju/kaiju2krona/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf'
+include { KAIJU_KAIJU } from '../../../../../modules/nf-core/kaiju/kaiju/main.nf'
+include { KAIJU_KAIJU2KRONA } from '../../../../../modules/nf-core/kaiju/kaiju2krona/main.nf'
+
+workflow test_kaiju_kaiju2krona {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
+    KAIJU_KAIJU2KRONA ( KAIJU_KAIJU.out.results , UNTAR.out.untar.map{ it[1] } )
+}
diff --git a/tests/modules/kaiju/kaiju2krona/nextflow.config b/tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config
similarity index 100%
rename from tests/modules/kaiju/kaiju2krona/nextflow.config
rename to tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config
diff --git a/tests/modules/nf-core/kaiju/kaiju2krona/test.yml b/tests/modules/nf-core/kaiju/kaiju2krona/test.yml
new file mode 100644
index 00000000000..1dcf0565645
--- /dev/null
+++ b/tests/modules/nf-core/kaiju/kaiju2krona/test.yml
@@ -0,0 +1,8 @@
+- name: kaiju kaiju2krona test_kaiju_kaiju2krona
+  command: nextflow run ./tests/modules/nf-core/kaiju/kaiju2krona -entry test_kaiju_kaiju2krona -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config
+  tags:
+    - kaiju/kaiju2krona
+    - kaiju
+  files:
+    - path: output/kaiju/test.txt
+      md5sum: 68b2309d37767e444193fa6cea7c0494
diff --git a/tests/modules/nf-core/kaiju/kaiju2table/main.nf b/tests/modules/nf-core/kaiju/kaiju2table/main.nf
new file mode 100644
index 00000000000..413a7b39a93
--- /dev/null
+++ b/tests/modules/nf-core/kaiju/kaiju2table/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR             } from '../../../../../modules/nf-core/untar/main.nf'
+include { KAIJU_KAIJU       } from '../../../../../modules/nf-core/kaiju/kaiju/main.nf'
+include { KAIJU_KAIJU2TABLE } from '../../../../../modules/nf-core/kaiju/kaiju2table/main.nf'
+
+workflow test_kaiju_kaiju_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
+    taxon_rank = "species"
+
+    ch_db = UNTAR ( db )
+    KAIJU_KAIJU ( input, ch_db.untar.map{ it[1] } )
+    KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_db.untar.map{ it[1] }, taxon_rank )
+}
diff --git a/tests/modules/kaiju/kaiju2table/nextflow.config b/tests/modules/nf-core/kaiju/kaiju2table/nextflow.config
similarity index 100%
rename from tests/modules/kaiju/kaiju2table/nextflow.config
rename to tests/modules/nf-core/kaiju/kaiju2table/nextflow.config
diff --git a/tests/modules/nf-core/kaiju/kaiju2table/test.yml b/tests/modules/nf-core/kaiju/kaiju2table/test.yml
new file mode 100644
index 00000000000..aeb1fd57d75
--- /dev/null
+++ b/tests/modules/nf-core/kaiju/kaiju2table/test.yml
@@ -0,0 +1,9 @@
+- name: kaiju kaiju2table test_kaiju_kaiju_single_end
+  command: nextflow run ./tests/modules/nf-core/kaiju/kaiju2table -entry test_kaiju_kaiju_single_end -c ./tests/config/nextflow.config
+  tags:
+    - kaiju
+    - kaiju/kaiju2table
+  files:
+    - path: output/kaiju/test.txt
+      md5sum: 0d9f8fd36fcf2888296ae12632c5f0a8
+    - path: output/kaiju/versions.yml
diff --git a/tests/modules/nf-core/kallisto/index/main.nf b/tests/modules/nf-core/kallisto/index/main.nf
new file mode 100644
index 00000000000..3fe04ca9ecb
--- /dev/null
+++ b/tests/modules/nf-core/kallisto/index/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KALLISTO_INDEX } from '../../../../../modules/nf-core/kallisto/index/main.nf'
+
+workflow test_kallisto_index {
+
+    def input = []
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    KALLISTO_INDEX ( input )
+}
diff --git a/tests/modules/kallisto/index/nextflow.config b/tests/modules/nf-core/kallisto/index/nextflow.config
similarity index 100%
rename from tests/modules/kallisto/index/nextflow.config
rename to tests/modules/nf-core/kallisto/index/nextflow.config
diff --git a/tests/modules/nf-core/kallisto/index/test.yml b/tests/modules/nf-core/kallisto/index/test.yml
new file mode 100644
index 00000000000..c1ae1d61641
--- /dev/null
+++ b/tests/modules/nf-core/kallisto/index/test.yml
@@ -0,0 +1,16 @@
+- name: kallisto index test_kallisto_index
+  command: nextflow run ./tests/modules/nf-core/kallisto/index -entry test_kallisto_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallisto/index/nextflow.config
+  tags:
+    - kallisto
+    - kallisto/index
+  files:
+    - path: output/kallisto/kallisto
+      md5sum: bf8a58d329dddc96f0c32f7823bc0310
+
+- name: kallisto index test_kallisto_index stub
+  command: nextflow run ./tests/modules/nf-core/kallisto/index -entry test_kallisto_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallisto/index/nextflow.config -stub-run
+  tags:
+    - kallisto
+    - kallisto/index
+  files:
+    - path: output/kallisto/kallisto
diff --git a/tests/modules/nf-core/kallistobustools/count/main.nf b/tests/modules/nf-core/kallistobustools/count/main.nf
new file mode 100644
index 00000000000..ff7671ec5af
--- /dev/null
+++ b/tests/modules/nf-core/kallistobustools/count/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KALLISTOBUSTOOLS_REF   } from '../../../../../modules/nf-core/kallistobustools/ref/main.nf'
+include { KALLISTOBUSTOOLS_COUNT } from '../../../../../modules/nf-core/kallistobustools/count/main.nf'
+
+workflow test_kallistobustools_count {
+
+    input   = [
+        [id:'test'], // meta map
+        [ 
+          file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    sc_workflow = "standard"
+    technology  = "10XV3"
+
+    KALLISTOBUSTOOLS_REF(fasta, gtf, sc_workflow)
+    KALLISTOBUSTOOLS_COUNT ( 
+      input, 
+      KALLISTOBUSTOOLS_REF.out.index, 
+      KALLISTOBUSTOOLS_REF.out.t2g, 
+      KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] },   // when empty the module doesn't run unless something is passed. 
+      KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] }, // when empty the module doesn't run unless something is passed.
+      technology 
+    )
+}
diff --git a/tests/modules/kallistobustools/count/nextflow.config b/tests/modules/nf-core/kallistobustools/count/nextflow.config
similarity index 100%
rename from tests/modules/kallistobustools/count/nextflow.config
rename to tests/modules/nf-core/kallistobustools/count/nextflow.config
diff --git a/tests/modules/nf-core/kallistobustools/count/test.yml b/tests/modules/nf-core/kallistobustools/count/test.yml
new file mode 100644
index 00000000000..698bfcdd779
--- /dev/null
+++ b/tests/modules/nf-core/kallistobustools/count/test.yml
@@ -0,0 +1,33 @@
+- name: kallistobustools count test_kallistobustools_count
+  command: nextflow run ./tests/modules/nf-core/kallistobustools/count -entry test_kallistobustools_count -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/kallistobustools/count/nextflow.config
+  tags:
+    - kallistobustools/count
+    - kallistobustools
+  files:
+    - path: output/kallistobustools/cdna.fa
+    - path: output/kallistobustools/kb_ref_out.idx
+    - path: output/kallistobustools/t2g.txt
+    - path: output/kallistobustools/test.count/10x_version3_whitelist.txt
+      md5sum: 3d36d0a4021fd292b265e2b5e72aaaf3
+    - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/barcodes.tsv
+      md5sum: 8a41142de30df61fbb9551b29dd05a83
+    - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/genes.tsv
+      md5sum: 1b31f05f9b20a4c0ac3e07b9e3ff3a14
+    - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/matrix.mtx
+      md5sum: 5b7bff2d19fc90168733f4ac812c7d7b
+    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.barcodes.txt
+      md5sum: 8d7ef602416818a598f5680a707756a7
+    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.genes.txt
+      md5sum: fe6d5501923867b514a0447aa4b4995f
+    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.mtx
+      md5sum: 0a84dc5a7570b5821da4eef6b5769a0c
+    - path: output/kallistobustools/test.count/inspect.json
+      md5sum: b853330f160e06fc8af170a837384ef5
+    - path: output/kallistobustools/test.count/kb_info.json
+    - path: output/kallistobustools/test.count/matrix.ec
+    - path: output/kallistobustools/test.count/output.bus
+      md5sum: f5d8efa83f107826824292cbbdb4e37b
+    - path: output/kallistobustools/test.count/output.unfiltered.bus
+      md5sum: dcbc651dc64eb38ae14e0b90795b30d2
+    - path: output/kallistobustools/test.count/run_info.json
+    - path: output/kallistobustools/test.count/transcripts.txt
diff --git a/tests/modules/nf-core/kallistobustools/ref/main.nf b/tests/modules/nf-core/kallistobustools/ref/main.nf
new file mode 100644
index 00000000000..72bcd2d632a
--- /dev/null
+++ b/tests/modules/nf-core/kallistobustools/ref/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KALLISTOBUSTOOLS_REF } from '../../../../../modules/nf-core/kallistobustools/ref/main.nf'
+
+workflow test_kallistobustools_ref_standard {
+
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    workflow    = "standard"
+
+    KALLISTOBUSTOOLS_REF(fasta, gtf, workflow)
+}
+
+workflow test_kallistobustools_ref_lamanno {
+
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    workflow    = "lamanno"
+
+    KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
+}
+
+workflow test_kallistobustools_ref_nucleus {
+
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    workflow    = "nucleus"
+
+    KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
+}
+
diff --git a/tests/modules/kallistobustools/ref/nextflow.config b/tests/modules/nf-core/kallistobustools/ref/nextflow.config
similarity index 100%
rename from tests/modules/kallistobustools/ref/nextflow.config
rename to tests/modules/nf-core/kallistobustools/ref/nextflow.config
diff --git a/tests/modules/nf-core/kallistobustools/ref/test.yml b/tests/modules/nf-core/kallistobustools/ref/test.yml
new file mode 100644
index 00000000000..979c5c32037
--- /dev/null
+++ b/tests/modules/nf-core/kallistobustools/ref/test.yml
@@ -0,0 +1,35 @@
+- name: kallistobustools ref test_kallistobustools_ref_standard
+  command: nextflow run ./tests/modules/nf-core/kallistobustools/ref -entry test_kallistobustools_ref_standard -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallistobustools/ref/nextflow.config
+  tags:
+    - kallistobustools/ref
+    - kallistobustools
+  files:
+    - path: output/kallistobustools/cdna.fa
+    - path: output/kallistobustools/kb_ref_out.idx
+    - path: output/kallistobustools/t2g.txt
+
+- name: kallistobustools ref test_kallistobustools_ref_lamanno
+  command: nextflow run ./tests/modules/nf-core/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallistobustools/ref/nextflow.config
+  tags:
+    - kallistobustools/ref
+    - kallistobustools
+  files:
+    - path: output/kallistobustools/cdna.fa
+    - path: output/kallistobustools/cdna_t2c.txt
+    - path: output/kallistobustools/intron.fa
+    - path: output/kallistobustools/intron_t2c.txt
+    - path: output/kallistobustools/kb_ref_out.idx
+    - path: output/kallistobustools/t2g.txt
+
+- name: kallistobustools ref test_kallistobustools_ref_nucleus
+  command: nextflow run ./tests/modules/nf-core/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallistobustools/ref/nextflow.config
+  tags:
+    - kallistobustools/ref
+    - kallistobustools
+  files:
+    - path: output/kallistobustools/cdna.fa
+    - path: output/kallistobustools/cdna_t2c.txt
+    - path: output/kallistobustools/intron.fa
+    - path: output/kallistobustools/intron_t2c.txt
+    - path: output/kallistobustools/kb_ref_out.idx
+    - path: output/kallistobustools/t2g.txt
diff --git a/tests/modules/nf-core/kat/hist/main.nf b/tests/modules/nf-core/kat/hist/main.nf
new file mode 100644
index 00000000000..093674accdf
--- /dev/null
+++ b/tests/modules/nf-core/kat/hist/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KAT_HIST } from '../../../../../modules/nf-core/kat/hist/main.nf'
+
+workflow test_kat_hist_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    KAT_HIST ( input )
+}
+
+workflow test_kat_hist_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_2_fastq_gz'], checkIfExists: true),
+        ]
+    ]
+
+    KAT_HIST ( input )
+}
diff --git a/tests/modules/kat/hist/nextflow.config b/tests/modules/nf-core/kat/hist/nextflow.config
similarity index 100%
rename from tests/modules/kat/hist/nextflow.config
rename to tests/modules/nf-core/kat/hist/nextflow.config
diff --git a/tests/modules/nf-core/kat/hist/test.yml b/tests/modules/nf-core/kat/hist/test.yml
new file mode 100644
index 00000000000..640716e56a2
--- /dev/null
+++ b/tests/modules/nf-core/kat/hist/test.yml
@@ -0,0 +1,42 @@
+- name: kat hist test_kat_hist_single_end
+  command: nextflow run ./tests/modules/nf-core/kat/hist -entry test_kat_hist_single_end -c ./tests/config/nextflow.config
+  tags:
+    - kat/hist
+    - kat
+  files:
+    - path: output/kat/test.hist
+      md5sum: c6eba52b3a2653a684577a8ae20b74c1
+    - path: output/kat/test.hist-hash.jf27
+    - path: output/kat/test.hist.dist_analysis.json
+      # md5sum: 52a5a2d91c71b940f36f1f0a7fd5ef10 # This is variable for an unknown reason
+      contains:
+        - "nb_peaks"
+        - "global_minima"
+        - "global_maxima"
+        - "mean_freq"
+        - "est_genome_size"
+        - "est_het_rate"
+    - path: output/kat/test.hist.png
+      md5sum: 49861ef1a265e0edde3550b39c64a274
+    - path: output/kat/versions.yml
+
+- name: kat hist test_kat_hist_paired_end
+  command: nextflow run ./tests/modules/nf-core/kat/hist -entry test_kat_hist_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - kat/hist
+    - kat
+  files:
+    - path: output/kat/test.hist
+      md5sum: 91429091e74b1718051591d83a1ccb5d
+    - path: output/kat/test.hist.dist_analysis.json
+      # md5sum: 8b0dabeaff4ba706b33aa8964d687e13  # This is variable for an unknown reason
+      contains:
+        - "nb_peaks"
+        - "global_minima"
+        - "global_maxima"
+        - "mean_freq"
+        - "est_genome_size"
+        - "est_het_rate"
+    - path: output/kat/test.hist.png
+      md5sum: e20774d0d2b979cb6ead7b7fb5ad36d9
+    - path: output/kat/versions.yml
diff --git a/tests/modules/nf-core/khmer/normalizebymedian/main.nf b/tests/modules/nf-core/khmer/normalizebymedian/main.nf
new file mode 100644
index 00000000000..26727165f04
--- /dev/null
+++ b/tests/modules/nf-core/khmer/normalizebymedian/main.nf
@@ -0,0 +1,85 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQTK_MERGEPE                                           } from '../../../../../modules/nf-core/seqtk/mergepe/main.nf'
+include { KHMER_NORMALIZEBYMEDIAN                                 } from '../../../../../modules/nf-core/khmer/normalizebymedian/main.nf'
+include { KHMER_NORMALIZEBYMEDIAN as KHMER_NORMALIZEBYMEDIAN_ARGS } from '../../../../../modules/nf-core/khmer/normalizebymedian/main.nf'
+
+workflow test_khmer_normalizebymedian_only_pe {
+    
+    pe_reads = [
+        [ id:'khmer_test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+        ]
+    ]
+
+    SEQTK_MERGEPE(pe_reads)
+
+    KHMER_NORMALIZEBYMEDIAN ( SEQTK_MERGEPE.out.reads.collect { it[1] }, [], 'only_pe' )
+}
+
+workflow test_khmer_normalizebymedian_only_se {
+    
+    se_reads = [
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+    ]
+
+    KHMER_NORMALIZEBYMEDIAN ( [], se_reads, 'only_se' )
+}
+
+workflow test_khmer_normalizebymedian_mixed {
+    
+    pe_reads = [
+        [ id:'khmer_test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+        ]
+    ]
+    se_reads = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+
+    SEQTK_MERGEPE(pe_reads)
+
+    KHMER_NORMALIZEBYMEDIAN ( SEQTK_MERGEPE.out.reads.map { it[1] }, se_reads, 'mixed' )
+}
+
+workflow test_khmer_normalizebymedian_multiple_pe {
+    
+    pe_reads = [
+        [ id:'khmer_test0', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+        ],
+        [ id:'khmer_test1', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+        ]
+    ]
+    se_reads = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+
+    SEQTK_MERGEPE(pe_reads)
+
+    KHMER_NORMALIZEBYMEDIAN ( SEQTK_MERGEPE.out.reads.collect { it[1] }, se_reads, 'multiple_pe' )
+}
+
+workflow test_khmer_normalizebymedian_args {
+    
+    pe_reads = [
+        [ id:'khmer_test0', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+        ]
+    ]
+    se_reads = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+
+    SEQTK_MERGEPE(pe_reads)
+
+    KHMER_NORMALIZEBYMEDIAN_ARGS ( SEQTK_MERGEPE.out.reads.collect { it[1] }, se_reads, 'args' )
+}
diff --git a/tests/modules/khmer/normalizebymedian/nextflow.config b/tests/modules/nf-core/khmer/normalizebymedian/nextflow.config
similarity index 100%
rename from tests/modules/khmer/normalizebymedian/nextflow.config
rename to tests/modules/nf-core/khmer/normalizebymedian/nextflow.config
diff --git a/tests/modules/nf-core/khmer/normalizebymedian/test.yml b/tests/modules/nf-core/khmer/normalizebymedian/test.yml
new file mode 100644
index 00000000000..395eca646e2
--- /dev/null
+++ b/tests/modules/nf-core/khmer/normalizebymedian/test.yml
@@ -0,0 +1,42 @@
+#                nf-core modules create-test-yml khmer/normalizebymedian
+- name: khmer normalizebymedian only pe reads
+  command: nextflow run ./tests/modules/nf-core/khmer/normalizebymedian -entry test_khmer_normalizebymedian_only_pe -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/khmer/normalizebymedian/nextflow.config
+  tags:
+    - khmer
+    - khmer/normalizebymedian
+  files:
+    - path: output/khmer/only_pe.fastq.gz
+    # md5sum not stable even locally with docker (gzip done by tool)
+    # md5sum: 75e05f2e80cf4bd0b534d4b73f7c059c
+
+- name: khmer normalizebymedian only se reads
+  command: nextflow run ./tests/modules/nf-core/khmer/normalizebymedian -entry test_khmer_normalizebymedian_only_se -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/khmer/normalizebymedian/nextflow.config
+  tags:
+    - khmer
+    - khmer/normalizebymedian
+  files:
+    - path: output/khmer/only_se.fastq.gz
+
+- name: khmer normalizebymedian mixed reads
+  command: nextflow run ./tests/modules/nf-core/khmer/normalizebymedian -entry test_khmer_normalizebymedian_mixed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/khmer/normalizebymedian/nextflow.config
+  tags:
+    - khmer
+    - khmer/normalizebymedian
+  files:
+    - path: output/khmer/mixed.fastq.gz
+
+- name: khmer normalizebymedian multiple pe reads
+  command: nextflow run ./tests/modules/nf-core/khmer/normalizebymedian -entry test_khmer_normalizebymedian_multiple_pe -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/khmer/normalizebymedian/nextflow.config
+  tags:
+    - khmer
+    - khmer/normalizebymedian
+  files:
+    - path: output/khmer/multiple_pe.fastq.gz
+
+- name: khmer normalizebymedian args
+  command: nextflow run ./tests/modules/nf-core/khmer/normalizebymedian -entry test_khmer_normalizebymedian_args -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/khmer/normalizebymedian/nextflow.config
+  tags:
+    - khmer
+    - khmer/normalizebymedian
+  files:
+    - path: output/khmer/args.fastq.gz
diff --git a/tests/modules/nf-core/khmer/uniquekmers/main.nf b/tests/modules/nf-core/khmer/uniquekmers/main.nf
new file mode 100644
index 00000000000..4dae054890e
--- /dev/null
+++ b/tests/modules/nf-core/khmer/uniquekmers/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KHMER_UNIQUEKMERS } from '../../../../../modules/nf-core/khmer/uniquekmers/main.nf'
+
+workflow test_khmer_uniquekmers {
+
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    KHMER_UNIQUEKMERS ( input, 50 )
+}
diff --git a/tests/modules/khmer/uniquekmers/nextflow.config b/tests/modules/nf-core/khmer/uniquekmers/nextflow.config
similarity index 100%
rename from tests/modules/khmer/uniquekmers/nextflow.config
rename to tests/modules/nf-core/khmer/uniquekmers/nextflow.config
diff --git a/tests/modules/nf-core/khmer/uniquekmers/test.yml b/tests/modules/nf-core/khmer/uniquekmers/test.yml
new file mode 100644
index 00000000000..ff5b12c3e64
--- /dev/null
+++ b/tests/modules/nf-core/khmer/uniquekmers/test.yml
@@ -0,0 +1,10 @@
+- name: khmer uniquekmers test_khmer_uniquekmers
+  command: nextflow run ./tests/modules/nf-core/khmer/uniquekmers -entry test_khmer_uniquekmers -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/khmer/uniquekmers/nextflow.config
+  tags:
+    - khmer
+    - khmer/uniquekmers
+  files:
+    - path: output/khmer/kmers.txt
+      md5sum: 496ebf23653a01c7a42d743e47c19f65
+    - path: output/khmer/report.txt
+      md5sum: ee489abd3b244dea3640649e1790d55e
diff --git a/tests/modules/nf-core/kleborate/main.nf b/tests/modules/nf-core/kleborate/main.nf
new file mode 100644
index 00000000000..93c765c74f9
--- /dev/null
+++ b/tests/modules/nf-core/kleborate/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KLEBORATE } from '../../../../modules/nf-core/kleborate/main.nf'
+
+workflow test_kleborate {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
+        ]
+    ]
+
+    KLEBORATE ( input )
+}
diff --git a/tests/modules/kleborate/nextflow.config b/tests/modules/nf-core/kleborate/nextflow.config
similarity index 100%
rename from tests/modules/kleborate/nextflow.config
rename to tests/modules/nf-core/kleborate/nextflow.config
diff --git a/tests/modules/nf-core/kleborate/test.yml b/tests/modules/nf-core/kleborate/test.yml
new file mode 100644
index 00000000000..053d9caf5c0
--- /dev/null
+++ b/tests/modules/nf-core/kleborate/test.yml
@@ -0,0 +1,7 @@
+- name: kleborate
+  command: nextflow run ./tests/modules/nf-core/kleborate -entry test_kleborate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kleborate/nextflow.config
+  tags:
+    - kleborate
+  files:
+    - path: output/kleborate/test.results.txt
+      contains: ["strain", "genome", "scaffolds"]
diff --git a/tests/modules/nf-core/kraken2/kraken2/main.nf b/tests/modules/nf-core/kraken2/kraken2/main.nf
new file mode 100644
index 00000000000..ac27253c8ee
--- /dev/null
+++ b/tests/modules/nf-core/kraken2/kraken2/main.nf
@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR           } from '../../../../../modules/nf-core/untar/main.nf'
+include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main.nf'
+
+workflow test_kraken2_kraken2_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
+}
+
+workflow test_kraken2_kraken2_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
+}
+
+workflow test_kraken2_kraken2_classifyreads {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, true )
+}
diff --git a/tests/modules/kraken2/kraken2/nextflow.config b/tests/modules/nf-core/kraken2/kraken2/nextflow.config
similarity index 100%
rename from tests/modules/kraken2/kraken2/nextflow.config
rename to tests/modules/nf-core/kraken2/kraken2/nextflow.config
diff --git a/tests/modules/nf-core/kraken2/kraken2/test.yml b/tests/modules/nf-core/kraken2/kraken2/test.yml
new file mode 100644
index 00000000000..595647ba379
--- /dev/null
+++ b/tests/modules/nf-core/kraken2/kraken2/test.yml
@@ -0,0 +1,43 @@
+- name: kraken2 kraken2 test_kraken2_kraken2_single_end
+  command: nextflow run ./tests/modules/nf-core/kraken2/kraken2 -entry test_kraken2_kraken2_single_end -c ./tests/config/nextflow.config
+  tags:
+    - kraken2
+    - kraken2/kraken2
+  files:
+    - path: output/kraken2/test.classified.fastq.gz
+    - path: output/kraken2/test.kraken2.report.txt
+      md5sum: 4227755fe40478b8d7dc8634b489761e
+    - path: output/kraken2/test.unclassified.fastq.gz
+    - path: output/kraken2/versions.yml
+      md5sum: 6e3ad947ac8dee841a89216071c181cc
+    - path: output/untar/versions.yml
+
+- name: kraken2 kraken2 test_kraken2_kraken2_paired_end
+  command: nextflow run ./tests/modules/nf-core/kraken2/kraken2 -entry test_kraken2_kraken2_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - kraken2
+    - kraken2/kraken2
+  files:
+    - path: output/kraken2/test.classified_1.fastq.gz
+    - path: output/kraken2/test.classified_2.fastq.gz
+    - path: output/kraken2/test.kraken2.report.txt
+      md5sum: 4227755fe40478b8d7dc8634b489761e
+    - path: output/kraken2/test.unclassified_1.fastq.gz
+    - path: output/kraken2/test.unclassified_2.fastq.gz
+    - path: output/kraken2/versions.yml
+      md5sum: 604482fe7a4519f890fae9c8beb1bd6e
+    - path: output/untar/versions.yml
+
+- name: kraken2 kraken2 test_kraken2_kraken2_classifyreads
+  command: nextflow run ./tests/modules/nf-core/kraken2/kraken2 -entry test_kraken2_kraken2_classifyreads -c ./tests/config/nextflow.config
+  tags:
+    - kraken2
+    - kraken2/kraken2
+  files:
+    - path: output/kraken2/test.kraken2.classifiedreads.txt
+      md5sum: e7a90531f0d8d777316515c36fe4cae0
+    - path: output/kraken2/test.kraken2.report.txt
+      md5sum: 4227755fe40478b8d7dc8634b489761e
+    - path: output/kraken2/versions.yml
+      md5sum: 3488c304259e83c5bea573403293fce9
+    - path: output/untar/versions.yml
diff --git a/tests/modules/nf-core/krakentools/combinekreports/main.nf b/tests/modules/nf-core/krakentools/combinekreports/main.nf
new file mode 100644
index 00000000000..27f453f4cab
--- /dev/null
+++ b/tests/modules/nf-core/krakentools/combinekreports/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR } from '../../../../../modules/nf-core/untar/main'
+include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main'
+include { KRAKENTOOLS_COMBINEKREPORTS } from '../../../../../modules/nf-core/krakentools/combinekreports/main.nf'
+
+workflow test_krakentools_combinekreports {
+
+    input = Channel.of(
+        [[ id:'test', single_end:false ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
+        [[ id:'test2', single_end:false ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
+    )
+
+
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, false )
+
+    KRAKENTOOLS_COMBINEKREPORTS ( KRAKEN2_KRAKEN2.out.report.map{ [[id:"test"], it[1]] }.groupTuple().dump())
+}
diff --git a/tests/modules/krakentools/combinekreports/nextflow.config b/tests/modules/nf-core/krakentools/combinekreports/nextflow.config
similarity index 100%
rename from tests/modules/krakentools/combinekreports/nextflow.config
rename to tests/modules/nf-core/krakentools/combinekreports/nextflow.config
diff --git a/tests/modules/nf-core/krakentools/combinekreports/test.yml b/tests/modules/nf-core/krakentools/combinekreports/test.yml
new file mode 100644
index 00000000000..30f09ef8f95
--- /dev/null
+++ b/tests/modules/nf-core/krakentools/combinekreports/test.yml
@@ -0,0 +1,9 @@
+- name: krakentools combinekreports test_krakentools_combinekreports
+  command: nextflow run ./tests/modules/nf-core/krakentools/combinekreports -entry test_krakentools_combinekreports -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/krakentools/combinekreports/nextflow.config
+  tags:
+    - krakentools
+    - krakentools/combinekreports
+  files:
+    - path: output/krakentools/test.txt
+      contains:
+        - "#Number of Samples: 2"
diff --git a/tests/modules/nf-core/krakentools/kreport2krona/main.nf b/tests/modules/nf-core/krakentools/kreport2krona/main.nf
new file mode 100644
index 00000000000..5951acc070d
--- /dev/null
+++ b/tests/modules/nf-core/krakentools/kreport2krona/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR } from '../../../../../modules/nf-core/untar/main'
+include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main'
+include { KRAKENTOOLS_KREPORT2KRONA } from '../../../../../modules/nf-core/krakentools/kreport2krona/main'
+
+workflow test_krakentools_kreport2krona {
+
+    input = Channel.of([ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ])
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, false )
+    KRAKENTOOLS_KREPORT2KRONA ( KRAKEN2_KRAKEN2.out.report )
+}
diff --git a/tests/modules/krakentools/kreport2krona/nextflow.config b/tests/modules/nf-core/krakentools/kreport2krona/nextflow.config
similarity index 100%
rename from tests/modules/krakentools/kreport2krona/nextflow.config
rename to tests/modules/nf-core/krakentools/kreport2krona/nextflow.config
diff --git a/tests/modules/nf-core/krakentools/kreport2krona/test.yml b/tests/modules/nf-core/krakentools/kreport2krona/test.yml
new file mode 100644
index 00000000000..87c609cbb56
--- /dev/null
+++ b/tests/modules/nf-core/krakentools/kreport2krona/test.yml
@@ -0,0 +1,8 @@
+- name: krakentools kreport2krona test_krakentools_kreport2krona
+  command: nextflow run ./tests/modules/nf-core/krakentools/kreport2krona -entry test_krakentools_kreport2krona -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/krakentools/kreport2krona/nextflow.config
+  tags:
+    - krakentools/kreport2krona
+    - krakentools
+  files:
+    - path: output/krakentools/test.txt
+      md5sum: c89a9db7acbdba9dea0fe246bcaa85c1
diff --git a/tests/modules/nf-core/krona/kronadb/main.nf b/tests/modules/nf-core/krona/kronadb/main.nf
new file mode 100644
index 00000000000..b35b06a430b
--- /dev/null
+++ b/tests/modules/nf-core/krona/kronadb/main.nf
@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KRONADB } from '../../../../../modules/nf-core/krona/kronadb/main.nf'
+
+workflow test_krona_kronadb {
+    KRONA_KRONADB ( )
+}
diff --git a/tests/modules/krona/kronadb/nextflow.config b/tests/modules/nf-core/krona/kronadb/nextflow.config
similarity index 100%
rename from tests/modules/krona/kronadb/nextflow.config
rename to tests/modules/nf-core/krona/kronadb/nextflow.config
diff --git a/tests/modules/nf-core/krona/kronadb/test.yml b/tests/modules/nf-core/krona/kronadb/test.yml
new file mode 100644
index 00000000000..5691064da72
--- /dev/null
+++ b/tests/modules/nf-core/krona/kronadb/test.yml
@@ -0,0 +1,7 @@
+- name: krona kronadb test_krona_kronadb
+  command: nextflow run ./tests/modules/nf-core/krona/kronadb -entry test_krona_kronadb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/krona/kronadb/nextflow.config
+  tags:
+    - krona
+    - krona/kronadb
+  files:
+    - path: output/krona/taxonomy/taxonomy.tab
diff --git a/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf b/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf
new file mode 100644
index 00000000000..a267df50b2a
--- /dev/null
+++ b/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_READS  } from '../../../../../modules/nf-core/krona/ktimporttaxonomy/main.nf'
+include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../../modules/nf-core/krona/ktimporttaxonomy/main.nf'
+
+workflow test_krona_ktimporttaxonomy_reads {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['metagenome']['classified_reads_assignment'], checkIfExists: true)
+    ]
+    taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
+
+    KRONA_KTIMPORTTAXONOMY_READS ( input, taxonomy )
+}
+
+workflow test_krona_ktimporttaxonomy_report {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true)
+    ]
+    taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
+
+    KRONA_KTIMPORTTAXONOMY_REPORT ( input, taxonomy )
+}
diff --git a/tests/modules/krona/ktimporttaxonomy/nextflow.config b/tests/modules/nf-core/krona/ktimporttaxonomy/nextflow.config
similarity index 100%
rename from tests/modules/krona/ktimporttaxonomy/nextflow.config
rename to tests/modules/nf-core/krona/ktimporttaxonomy/nextflow.config
diff --git a/tests/modules/nf-core/krona/ktimporttaxonomy/test.yml b/tests/modules/nf-core/krona/ktimporttaxonomy/test.yml
new file mode 100644
index 00000000000..d61a68fbb82
--- /dev/null
+++ b/tests/modules/nf-core/krona/ktimporttaxonomy/test.yml
@@ -0,0 +1,17 @@
+- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_reads
+  command: nextflow run ./tests/modules/nf-core/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_reads -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/krona/ktimporttaxonomy/nextflow.config
+  tags:
+    - krona/ktimporttaxonomy
+    - krona
+  files:
+    - path: output/krona/test.html
+      contains: ["Krona is a flexible tool for exploring the relative proportions of"]
+
+- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_report
+  command: nextflow run ./tests/modules/nf-core/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_report -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/krona/ktimporttaxonomy/nextflow.config
+  tags:
+    - krona/ktimporttaxonomy
+    - krona
+  files:
+    - path: output/krona/test.html
+      contains: ["Krona is a flexible tool for exploring the relative proportions of"]
diff --git a/tests/modules/nf-core/krona/ktimporttext/main.nf b/tests/modules/nf-core/krona/ktimporttext/main.nf
new file mode 100644
index 00000000000..ee51b769fea
--- /dev/null
+++ b/tests/modules/nf-core/krona/ktimporttext/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KTIMPORTTEXT } from '../../../../../modules/nf-core/krona/ktimporttext/main.nf'
+
+workflow test_krona_ktimporttext_multi {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/ktimporttext.txt', checkIfExists: true), // krona default test file
+            file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true), //Kraken2 report file
+            file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/kaiju_out4krona.txt', checkIfExists: true) // Kaiju output 4 krona
+        ]
+    ]
+
+    KRONA_KTIMPORTTEXT ( input )
+}
+
+workflow test_krona_ktimporttext_single {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file('http://krona.sourceforge.net/examples/text.txt', checkIfExists: true) // krona default test file
+        ]
+    ]
+
+    KRONA_KTIMPORTTEXT ( input )
+}
diff --git a/tests/modules/krona/ktimporttext/nextflow.config b/tests/modules/nf-core/krona/ktimporttext/nextflow.config
similarity index 100%
rename from tests/modules/krona/ktimporttext/nextflow.config
rename to tests/modules/nf-core/krona/ktimporttext/nextflow.config
diff --git a/tests/modules/nf-core/krona/ktimporttext/test.yml b/tests/modules/nf-core/krona/ktimporttext/test.yml
new file mode 100644
index 00000000000..ff93014974c
--- /dev/null
+++ b/tests/modules/nf-core/krona/ktimporttext/test.yml
@@ -0,0 +1,19 @@
+- name: krona ktimporttext test_krona_ktimporttext_multi
+  command: nextflow run ./tests/modules/nf-core/krona/ktimporttext -entry test_krona_ktimporttext_multi -c ./tests/config/nextflow.config
+  tags:
+    - krona
+    - krona/ktimporttext
+  files:
+    - path: output/krona/test.html
+      contains:
+        - "DOCTYPE html PUBLIC"
+
+- name: krona ktimporttext test_krona_ktimporttext_single
+  command: nextflow run ./tests/modules/nf-core/krona/ktimporttext -entry test_krona_ktimporttext_single -c ./tests/config/nextflow.config
+  tags:
+    - krona
+    - krona/ktimporttext
+  files:
+    - path: output/krona/test.html
+      contains:
+        - "DOCTYPE html PUBLIC"
diff --git a/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf
new file mode 100644
index 00000000000..2323ba7d811
--- /dev/null
+++ b/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf
@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KTUPDATETAXONOMY } from '../../../../../modules/nf-core/krona/ktupdatetaxonomy/main.nf'
+
+workflow test_krona_ktupdatetaxonomy {
+    KRONA_KTUPDATETAXONOMY ( )
+}
diff --git a/tests/modules/krona/ktupdatetaxonomy/nextflow.config b/tests/modules/nf-core/krona/ktupdatetaxonomy/nextflow.config
similarity index 100%
rename from tests/modules/krona/ktupdatetaxonomy/nextflow.config
rename to tests/modules/nf-core/krona/ktupdatetaxonomy/nextflow.config
diff --git a/tests/modules/nf-core/krona/ktupdatetaxonomy/test.yml b/tests/modules/nf-core/krona/ktupdatetaxonomy/test.yml
new file mode 100644
index 00000000000..ae94a2ad3ea
--- /dev/null
+++ b/tests/modules/nf-core/krona/ktupdatetaxonomy/test.yml
@@ -0,0 +1,7 @@
+- name: krona ktupdatetaxonomy test_krona_ktupdatetaxonomy
+  command: nextflow run ./tests/modules/nf-core/krona/ktupdatetaxonomy -entry test_krona_ktupdatetaxonomy -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/krona/ktupdatetaxonomy/nextflow.config
+  tags:
+    - krona
+    - krona/ktupdatetaxonomy
+  files:
+    - path: output/krona/taxonomy/taxonomy.tab
diff --git a/tests/modules/nf-core/last/dotplot/main.nf b/tests/modules/nf-core/last/dotplot/main.nf
new file mode 100644
index 00000000000..1004535c6f6
--- /dev/null
+++ b/tests/modules/nf-core/last/dotplot/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LAST_DOTPLOT } from '../../../../../modules/nf-core/last/dotplot/main.nf'
+
+workflow test_last_dotplot {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
+
+    LAST_DOTPLOT ( input, "png" )
+}
diff --git a/tests/modules/last/dotplot/nextflow.config b/tests/modules/nf-core/last/dotplot/nextflow.config
similarity index 100%
rename from tests/modules/last/dotplot/nextflow.config
rename to tests/modules/nf-core/last/dotplot/nextflow.config
diff --git a/tests/modules/nf-core/last/dotplot/test.yml b/tests/modules/nf-core/last/dotplot/test.yml
new file mode 100644
index 00000000000..ceda8111257
--- /dev/null
+++ b/tests/modules/nf-core/last/dotplot/test.yml
@@ -0,0 +1,8 @@
+- name: last dotplot test_last_dotplot
+  command: nextflow run ./tests/modules/nf-core/last/dotplot -entry test_last_dotplot -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/dotplot/nextflow.config
+  tags:
+    - last/dotplot
+    - last
+  files:
+    - path: output/last/test.png
+      md5sum: 6189aaf96f522cdb664869724997bbcd
diff --git a/tests/modules/nf-core/last/lastal/main.nf b/tests/modules/nf-core/last/lastal/main.nf
new file mode 100644
index 00000000000..64162a944b3
--- /dev/null
+++ b/tests/modules/nf-core/last/lastal/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR       } from '../../../../../modules/nf-core/untar/main.nf'
+include { LAST_LASTAL } from '../../../../../modules/nf-core/last/lastal/main.nf'
+
+workflow test_last_lastal_with_dummy_param_file {
+
+    input = [ [ id:'contigs', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+              [] ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    LAST_LASTAL ( input, UNTAR.out.untar.map{ it[1] })
+}
+
+workflow test_last_lastal_with_real_param_file {
+
+    input      = [ [ id:'contigs', single_end:false ], // meta map
+                   file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                   file(params.test_data['sarscov2']['genome']['contigs_genome_par'], checkIfExists: true) ]
+    db         = [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    LAST_LASTAL ( input, UNTAR.out.untar.map{ it[1] })
+}
diff --git a/tests/modules/last/lastal/nextflow.config b/tests/modules/nf-core/last/lastal/nextflow.config
similarity index 100%
rename from tests/modules/last/lastal/nextflow.config
rename to tests/modules/nf-core/last/lastal/nextflow.config
diff --git a/tests/modules/nf-core/last/lastal/test.yml b/tests/modules/nf-core/last/lastal/test.yml
new file mode 100644
index 00000000000..d39cba0a340
--- /dev/null
+++ b/tests/modules/nf-core/last/lastal/test.yml
@@ -0,0 +1,45 @@
+- name: last lastal test_last_lastal_with_dummy_param_file
+  command: nextflow run ./tests/modules/nf-core/last/lastal -entry test_last_lastal_with_dummy_param_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/lastal/nextflow.config
+  tags:
+    - last
+    - last/lastal
+  files:
+    - path: output/last/contigs.genome.maf.gz
+      md5sum: 670f4fa1a94b23690cdb6fc603813c75
+    - path: output/untar/lastdb/genome.bck
+      md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
+    - path: output/untar/lastdb/genome.des
+      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
+    - path: output/untar/lastdb/genome.prj
+      md5sum: 489715f14b0fea6273822696e72357f9
+    - path: output/untar/lastdb/genome.sds
+      md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
+    - path: output/untar/lastdb/genome.ssp
+      md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
+    - path: output/untar/lastdb/genome.suf
+      md5sum: 1895efa8653e8e9bd3605cff0408ed33
+    - path: output/untar/lastdb/genome.tis
+      md5sum: b7c40f06b1309dc6f37849eeb86dfd22
+
+- name: last lastal test_last_lastal_with_real_param_file
+  command: nextflow run ./tests/modules/nf-core/last/lastal -entry test_last_lastal_with_real_param_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/lastal/nextflow.config
+  tags:
+    - last
+    - last/lastal
+  files:
+    - path: output/last/contigs.genome.maf.gz
+      md5sum: b0202b013e1caa9163516cd4ff4fbdbc
+    - path: output/untar/lastdb/genome.bck
+      md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
+    - path: output/untar/lastdb/genome.des
+      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
+    - path: output/untar/lastdb/genome.prj
+      md5sum: 489715f14b0fea6273822696e72357f9
+    - path: output/untar/lastdb/genome.sds
+      md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
+    - path: output/untar/lastdb/genome.ssp
+      md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
+    - path: output/untar/lastdb/genome.suf
+      md5sum: 1895efa8653e8e9bd3605cff0408ed33
+    - path: output/untar/lastdb/genome.tis
+      md5sum: b7c40f06b1309dc6f37849eeb86dfd22
diff --git a/tests/modules/nf-core/last/lastdb/main.nf b/tests/modules/nf-core/last/lastdb/main.nf
new file mode 100644
index 00000000000..56087905045
--- /dev/null
+++ b/tests/modules/nf-core/last/lastdb/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LAST_LASTDB } from '../../../../../modules/nf-core/last/lastdb/main.nf'
+
+workflow test_last_lastdb {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            ]
+
+    LAST_LASTDB ( input )
+}
+
+workflow test_last_lastdb_gzipped_input {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ]
+
+    LAST_LASTDB ( input )
+}
diff --git a/tests/modules/last/lastdb/nextflow.config b/tests/modules/nf-core/last/lastdb/nextflow.config
similarity index 100%
rename from tests/modules/last/lastdb/nextflow.config
rename to tests/modules/nf-core/last/lastdb/nextflow.config
diff --git a/tests/modules/nf-core/last/lastdb/test.yml b/tests/modules/nf-core/last/lastdb/test.yml
new file mode 100644
index 00000000000..d75e510d89d
--- /dev/null
+++ b/tests/modules/nf-core/last/lastdb/test.yml
@@ -0,0 +1,41 @@
+- name: last lastdb test_last_lastdb
+  command: nextflow run ./tests/modules/nf-core/last/lastdb -entry test_last_lastdb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/lastdb/nextflow.config
+  tags:
+    - last/lastdb
+    - last
+  files:
+    - path: output/last/lastdb/test.bck
+      md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
+    - path: output/last/lastdb/test.des
+      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
+    - path: output/last/lastdb/test.prj
+      md5sum: 6948d17d2a10e470ea545f659930a543
+    - path: output/last/lastdb/test.sds
+      md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
+    - path: output/last/lastdb/test.ssp
+      md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
+    - path: output/last/lastdb/test.suf
+      md5sum: 1895efa8653e8e9bd3605cff0408ed33
+    - path: output/last/lastdb/test.tis
+      md5sum: b7c40f06b1309dc6f37849eeb86dfd22
+
+- name: last lastdb test_last_lastdb_gzipped_input
+  command: nextflow run ./tests/modules/nf-core/last/lastdb -entry test_last_lastdb_gzipped_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/lastdb/nextflow.config
+  tags:
+    - last/lastdb
+    - last
+  files:
+    - path: output/last/lastdb/test.bck
+      md5sum: 8692b1229b1fff1c2d39c4c610ff842b
+    - path: output/last/lastdb/test.des
+      md5sum: 26ab49015cc572172b9efa50fc5190bc
+    - path: output/last/lastdb/test.prj
+      md5sum: d253fc4320d9b4d7fcfc43b2734412ee
+    - path: output/last/lastdb/test.sds
+      md5sum: cad9927d4bd161257e98165ad755d8e4
+    - path: output/last/lastdb/test.ssp
+      md5sum: 574c8a080247c2af9b5c46ff70936186
+    - path: output/last/lastdb/test.suf
+      md5sum: 8c406111b398631e51ca79d99b0ee897
+    - path: output/last/lastdb/test.tis
+      md5sum: d57a3a5f7e3e036807356c15bd3aad97
diff --git a/tests/modules/nf-core/last/mafconvert/main.nf b/tests/modules/nf-core/last/mafconvert/main.nf
new file mode 100644
index 00000000000..d04591be1b1
--- /dev/null
+++ b/tests/modules/nf-core/last/mafconvert/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LAST_MAFCONVERT } from '../../../../../modules/nf-core/last/mafconvert/main.nf'
+
+workflow test_last_mafconvert {
+    
+    input = [ [ id:'contigs.genome' ], // meta map
+              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
+
+    LAST_MAFCONVERT ( input, "psl" )
+}
diff --git a/tests/modules/last/mafconvert/nextflow.config b/tests/modules/nf-core/last/mafconvert/nextflow.config
similarity index 100%
rename from tests/modules/last/mafconvert/nextflow.config
rename to tests/modules/nf-core/last/mafconvert/nextflow.config
diff --git a/tests/modules/nf-core/last/mafconvert/test.yml b/tests/modules/nf-core/last/mafconvert/test.yml
new file mode 100644
index 00000000000..1f134c5fa35
--- /dev/null
+++ b/tests/modules/nf-core/last/mafconvert/test.yml
@@ -0,0 +1,8 @@
+- name: last mafconvert test_last_mafconvert
+  command: nextflow run ./tests/modules/nf-core/last/mafconvert -entry test_last_mafconvert -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/mafconvert/nextflow.config
+  tags:
+    - last/mafconvert
+    - last
+  files:
+    - path: output/last/contigs.genome.psl.gz
+      md5sum: 807889fbc4129884ae74c4ecf8804dde
diff --git a/tests/modules/nf-core/last/mafswap/main.nf b/tests/modules/nf-core/last/mafswap/main.nf
new file mode 100644
index 00000000000..49eef17c378
--- /dev/null
+++ b/tests/modules/nf-core/last/mafswap/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LAST_MAFSWAP } from '../../../../../modules/nf-core/last/mafswap/main.nf'
+
+workflow test_last_mafswap {
+
+    input = [ [ id:'contigs.genome' ], // meta map
+              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
+
+    LAST_MAFSWAP ( input )
+}
diff --git a/tests/modules/last/mafswap/nextflow.config b/tests/modules/nf-core/last/mafswap/nextflow.config
similarity index 100%
rename from tests/modules/last/mafswap/nextflow.config
rename to tests/modules/nf-core/last/mafswap/nextflow.config
diff --git a/tests/modules/nf-core/last/mafswap/test.yml b/tests/modules/nf-core/last/mafswap/test.yml
new file mode 100644
index 00000000000..8d435051927
--- /dev/null
+++ b/tests/modules/nf-core/last/mafswap/test.yml
@@ -0,0 +1,8 @@
+- name: last mafswap test_last_mafswap
+  command: nextflow run ./tests/modules/nf-core/last/mafswap -entry test_last_mafswap -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/mafswap/nextflow.config
+  tags:
+    - last
+    - last/mafswap
+  files:
+    - path: output/last/contigs.genome.swapped.maf.gz
+      md5sum: b98c5ff297878a19f1ab4f1a5e354678
diff --git a/tests/modules/nf-core/last/postmask/main.nf b/tests/modules/nf-core/last/postmask/main.nf
new file mode 100644
index 00000000000..697a431e8a8
--- /dev/null
+++ b/tests/modules/nf-core/last/postmask/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LAST_POSTMASK } from '../../../../../modules/nf-core/last/postmask/main.nf'
+
+workflow test_last_postmask {
+
+    input = [ [ id:'contigs.genome' ], // meta map
+              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
+
+    LAST_POSTMASK ( input )
+}
diff --git a/tests/modules/last/postmask/nextflow.config b/tests/modules/nf-core/last/postmask/nextflow.config
similarity index 100%
rename from tests/modules/last/postmask/nextflow.config
rename to tests/modules/nf-core/last/postmask/nextflow.config
diff --git a/tests/modules/nf-core/last/postmask/test.yml b/tests/modules/nf-core/last/postmask/test.yml
new file mode 100644
index 00000000000..109ceb3dfcc
--- /dev/null
+++ b/tests/modules/nf-core/last/postmask/test.yml
@@ -0,0 +1,8 @@
+- name: last postmask test_last_postmask
+  command: nextflow run ./tests/modules/nf-core/last/postmask -entry test_last_postmask -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/postmask/nextflow.config
+  tags:
+    - last
+    - last/postmask
+  files:
+    - path: output/last/contigs.genome.postmask.maf.gz
+      md5sum: 3a0f42e76da9549748983ac4d7ff7473
diff --git a/tests/modules/nf-core/last/split/main.nf b/tests/modules/nf-core/last/split/main.nf
new file mode 100644
index 00000000000..df8f20cfc36
--- /dev/null
+++ b/tests/modules/nf-core/last/split/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LAST_SPLIT } from '../../../../../modules/nf-core/last/split/main.nf'
+
+workflow test_last_split {
+    
+    input = [ [ id:'contigs.genome' ], // meta map
+              file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
+
+    LAST_SPLIT ( input )
+}
diff --git a/tests/modules/last/split/nextflow.config b/tests/modules/nf-core/last/split/nextflow.config
similarity index 100%
rename from tests/modules/last/split/nextflow.config
rename to tests/modules/nf-core/last/split/nextflow.config
diff --git a/tests/modules/nf-core/last/split/test.yml b/tests/modules/nf-core/last/split/test.yml
new file mode 100644
index 00000000000..eba99a19439
--- /dev/null
+++ b/tests/modules/nf-core/last/split/test.yml
@@ -0,0 +1,8 @@
+- name: last split test_last_split
+  command: nextflow run ./tests/modules/nf-core/last/split -entry test_last_split -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/split/nextflow.config
+  tags:
+    - last
+    - last/split
+  files:
+    - path: output/last/contigs.genome.split.maf.gz
+      md5sum: 2a177444f63c9294767a67a0247f0f05
diff --git a/tests/modules/nf-core/last/train/main.nf b/tests/modules/nf-core/last/train/main.nf
new file mode 100644
index 00000000000..a166fea8887
--- /dev/null
+++ b/tests/modules/nf-core/last/train/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR      } from '../../../../../modules/nf-core/untar/main.nf'
+include { LAST_TRAIN } from '../../../../../modules/nf-core/last/train/main.nf'
+
+workflow test_last_train {
+
+    db =         [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
+    input =      [ [ id:'contigs' ], // meta map
+                   file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
+    UNTAR ( db )
+    LAST_TRAIN ( input, UNTAR.out.untar.map{ it[1] } )
+}
diff --git a/tests/modules/last/train/nextflow.config b/tests/modules/nf-core/last/train/nextflow.config
similarity index 100%
rename from tests/modules/last/train/nextflow.config
rename to tests/modules/nf-core/last/train/nextflow.config
diff --git a/tests/modules/nf-core/last/train/test.yml b/tests/modules/nf-core/last/train/test.yml
new file mode 100644
index 00000000000..20b6cb7ca60
--- /dev/null
+++ b/tests/modules/nf-core/last/train/test.yml
@@ -0,0 +1,23 @@
+- name: last train test_last_train
+  command: nextflow run ./tests/modules/nf-core/last/train -entry test_last_train -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/train/nextflow.config
+  tags:
+    - last/train
+    - last
+  files:
+    - path: output/last/contigs.genome.par
+      contains:
+        - "score matrix"
+    - path: output/untar/lastdb/genome.bck
+      md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
+    - path: output/untar/lastdb/genome.des
+      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
+    - path: output/untar/lastdb/genome.prj
+      md5sum: 489715f14b0fea6273822696e72357f9
+    - path: output/untar/lastdb/genome.sds
+      md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
+    - path: output/untar/lastdb/genome.ssp
+      md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
+    - path: output/untar/lastdb/genome.suf
+      md5sum: 1895efa8653e8e9bd3605cff0408ed33
+    - path: output/untar/lastdb/genome.tis
+      md5sum: b7c40f06b1309dc6f37849eeb86dfd22
diff --git a/tests/modules/nf-core/leehom/main.nf b/tests/modules/nf-core/leehom/main.nf
new file mode 100644
index 00000000000..e91653319b5
--- /dev/null
+++ b/tests/modules/nf-core/leehom/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LEEHOM } from '../../../../modules/nf-core/leehom/main.nf'
+include { SAMTOOLS_VIEW } from '../../../../modules/nf-core/samtools/view/main.nf'
+
+workflow test_leehom_bam {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+
+    fasta = []
+
+    SAMTOOLS_VIEW ( input, fasta )
+    LEEHOM ( SAMTOOLS_VIEW.out.bam )
+}
+
+workflow test_leehom_se_fq {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+
+    LEEHOM ( input )
+}
+
+workflow test_leehom_pe_fq {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              [
+                  file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+              ] ]
+
+    LEEHOM ( input )
+}
diff --git a/tests/modules/leehom/nextflow.config b/tests/modules/nf-core/leehom/nextflow.config
similarity index 100%
rename from tests/modules/leehom/nextflow.config
rename to tests/modules/nf-core/leehom/nextflow.config
diff --git a/tests/modules/nf-core/leehom/test.yml b/tests/modules/nf-core/leehom/test.yml
new file mode 100644
index 00000000000..5ddbaaeb731
--- /dev/null
+++ b/tests/modules/nf-core/leehom/test.yml
@@ -0,0 +1,41 @@
+- name: leehom test_leehom_bam
+  command: nextflow run ./tests/modules/nf-core/leehom -entry test_leehom_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/leehom/nextflow.config
+  tags:
+    - leehom
+  files:
+    - path: output/leehom/test.bam
+    - path: output/samtools/test.bam
+    - path: output/leehom/test.log
+      md5sum: d1f5da273eb69f41babda510797c7671
+
+- name: leehom test_leehom_se_fq
+  command: nextflow run ./tests/modules/nf-core/leehom -entry test_leehom_se_fq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/leehom/nextflow.config
+  tags:
+    - leehom
+  files:
+    - path: output/leehom/test.fail.fq.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/leehom/test.fq.gz
+      md5sum: ed10c4bbf5c3082ca68823535b91e1e2
+    - path: output/leehom/test.log
+      md5sum: 59aa280cb72dfbea05ba913cb89db143
+
+- name: leehom test_leehom_pe_fq
+  command: nextflow run ./tests/modules/nf-core/leehom -entry test_leehom_pe_fq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/leehom/nextflow.config
+  tags:
+    - leehom
+  files:
+    - path: output/leehom/test.fail.fq.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/leehom/test.fq.gz
+      md5sum: 84929b78e3f89371ecd3b4c915b9ec33
+    - path: output/leehom/test.log
+      md5sum: 800b5a88dc0822886bfbb271029e2a4a
+    - path: output/leehom/test_r1.fail.fq.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/leehom/test_r1.fq.gz
+      md5sum: e9258420fa712e8536106995a7d1d97a
+    - path: output/leehom/test_r2.fail.fq.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/leehom/test_r2.fq.gz
+      md5sum: 27230bcc5eae81ec5c1701798d39c1af
diff --git a/tests/modules/nf-core/legsta/main.nf b/tests/modules/nf-core/legsta/main.nf
new file mode 100644
index 00000000000..b74a9cf278a
--- /dev/null
+++ b/tests/modules/nf-core/legsta/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LEGSTA } from '../../../../modules/nf-core/legsta/main.nf'
+
+workflow test_legsta {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
+    ]
+
+    LEGSTA ( input )
+}
diff --git a/tests/modules/legsta/nextflow.config b/tests/modules/nf-core/legsta/nextflow.config
similarity index 100%
rename from tests/modules/legsta/nextflow.config
rename to tests/modules/nf-core/legsta/nextflow.config
diff --git a/tests/modules/nf-core/legsta/test.yml b/tests/modules/nf-core/legsta/test.yml
new file mode 100644
index 00000000000..6d193422d34
--- /dev/null
+++ b/tests/modules/nf-core/legsta/test.yml
@@ -0,0 +1,9 @@
+- name: legsta test_legsta
+  command: nextflow run ./tests/modules/nf-core/legsta -entry test_legsta -c ./tests/config/nextflow.config
+  tags:
+    - legsta
+  files:
+    - path: output/legsta/test.tsv
+      md5sum: c493bdd19335de4828aa8b4e3ce7e1f8
+    - path: output/legsta/versions.yml
+      md5sum: d16c5f6fd68d2bcc2c71954e3342aabe
diff --git a/tests/modules/nf-core/lima/main.nf b/tests/modules/nf-core/lima/main.nf
new file mode 100644
index 00000000000..921b8dcba78
--- /dev/null
+++ b/tests/modules/nf-core/lima/main.nf
@@ -0,0 +1,60 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LIMA } from '../../../../modules/nf-core/lima/main.nf'
+
+workflow test_lima_bam {
+
+    input = [
+                [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['pacbio']['ccs'],     checkIfExists: true),
+            ]
+    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+
+    LIMA ( input, primers )
+}
+
+workflow test_lima_fa {
+
+    input = [
+                [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'],  checkIfExists: true),
+            ]
+    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+
+    LIMA ( input, primers )
+}
+
+workflow test_lima_fa_gz {
+
+    input = [
+                [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], checkIfExists: true),
+            ]
+    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'],   checkIfExists: true) ]
+
+    LIMA ( input, primers )
+}
+
+workflow test_lima_fq {
+
+    input = [
+                [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'],  checkIfExists: true),
+            ]
+    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+
+    LIMA ( input, primers )
+}
+
+workflow test_lima_fq_gz {
+
+    input = [
+                [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true),
+            ]
+    primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'],   checkIfExists: true) ]
+
+    LIMA ( input, primers )
+}
diff --git a/tests/modules/lima/nextflow.config b/tests/modules/nf-core/lima/nextflow.config
similarity index 100%
rename from tests/modules/lima/nextflow.config
rename to tests/modules/nf-core/lima/nextflow.config
diff --git a/tests/modules/nf-core/lima/test.yml b/tests/modules/nf-core/lima/test.yml
new file mode 100644
index 00000000000..75661ab9164
--- /dev/null
+++ b/tests/modules/nf-core/lima/test.yml
@@ -0,0 +1,91 @@
+- name: lima test_lima_bam
+  command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config
+  tags:
+    - lima
+  files:
+    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam
+      md5sum: 14b51d7f44e30c05a5b14e431a992097
+    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi
+      md5sum: 6ae7f057304ad17dd9d5f565d72d3f7b
+    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.consensusreadset.xml
+      contains: ["ConsensusReadSet"]
+    - path: output/lima/test.fl.json
+      contains: ["ConsensusReadSet"]
+    - path: output/lima/test.fl.lima.clips
+      md5sum: fa03bc75bd78b2648a139fd67c69208f
+    - path: output/lima/test.fl.lima.counts
+      md5sum: 842c6a23ca2de504ced4538ad5111da1
+    - path: output/lima/test.fl.lima.guess
+      md5sum: d3675af3ca8a908ee9e3c231668392d3
+    - path: output/lima/test.fl.lima.report
+      md5sum: dc073985322ae0a003ccc7e0fa4db5e6
+    - path: output/lima/test.fl.lima.summary
+      md5sum: bcbcaaaca418bdeb91141c81715ca420
+
+- name: lima test_lima_fa
+  command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_fa -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config
+  tags:
+    - lima
+  files:
+    - path: output/lima/test.fl.lima.clips
+      md5sum: 1012bc8874a14836f291bac48e8482a4
+    - path: output/lima/test.fl.lima.counts
+      md5sum: a4ceaa408be334eaa711577e95f8730e
+    - path: output/lima/test.fl.lima.guess
+      md5sum: 651e5f2b438b8ceadb3e06a2177e1818
+    - path: output/lima/test.fl.lima.report
+      md5sum: bd4a8bde17471563cf91aab4c787911d
+    - path: output/lima/test.fl.lima.summary
+      md5sum: 03be2311ba4afb878d8e547ab38c11eb
+
+- name: lima test_lima_fa_gz
+  command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_fa_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config
+  tags:
+    - lima
+  files:
+    - path: output/lima/test.fl.lima.clips
+      md5sum: 1012bc8874a14836f291bac48e8482a4
+    - path: output/lima/test.fl.lima.counts
+      md5sum: a4ceaa408be334eaa711577e95f8730e
+    - path: output/lima/test.fl.lima.guess
+      md5sum: 651e5f2b438b8ceadb3e06a2177e1818
+    - path: output/lima/test.fl.lima.report
+      md5sum: bd4a8bde17471563cf91aab4c787911d
+    - path: output/lima/test.fl.lima.summary
+      md5sum: 03be2311ba4afb878d8e547ab38c11eb
+
+- name: lima test_lima_fq
+  command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_fq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config
+  tags:
+    - lima
+  files:
+    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq
+      md5sum: ef395f689c5566f501e300bb83d7a5f2
+    - path: output/lima/test.fl.lima.clips
+      md5sum: 5c16ef8122f6f1798acc30eb8a30828c
+    - path: output/lima/test.fl.lima.counts
+      md5sum: 767b687e6eda7b24cd0e577f527eb2f0
+    - path: output/lima/test.fl.lima.guess
+      md5sum: 31b988aab6bda84867e704b9edd8a763
+    - path: output/lima/test.fl.lima.report
+      md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd
+    - path: output/lima/test.fl.lima.summary
+      md5sum: e91d3c386aaf4effa63f33ee2eb7da2a
+
+- name: lima test_lima_fq_gz
+  command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_fq_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config
+  tags:
+    - lima
+  files:
+    - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq.gz
+      md5sum: 32c11db85f69a1b4454b6bbd794b6df2
+    - path: output/lima/test.fl.lima.clips
+      md5sum: 5c16ef8122f6f1798acc30eb8a30828c
+    - path: output/lima/test.fl.lima.counts
+      md5sum: 767b687e6eda7b24cd0e577f527eb2f0
+    - path: output/lima/test.fl.lima.guess
+      md5sum: 31b988aab6bda84867e704b9edd8a763
+    - path: output/lima/test.fl.lima.report
+      md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd
+    - path: output/lima/test.fl.lima.summary
+      md5sum: e91d3c386aaf4effa63f33ee2eb7da2a
diff --git a/tests/modules/nf-core/lissero/main.nf b/tests/modules/nf-core/lissero/main.nf
new file mode 100644
index 00000000000..3387251d6f7
--- /dev/null
+++ b/tests/modules/nf-core/lissero/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LISSERO } from '../../../../modules/nf-core/lissero/main.nf'
+
+workflow test_lissero {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://github.com/MDU-PHL/LisSero/raw/master/tests/test_seq/NC_002973.fna", checkIfExists: true) ]
+
+    LISSERO ( input )
+}
diff --git a/tests/modules/lissero/nextflow.config b/tests/modules/nf-core/lissero/nextflow.config
similarity index 100%
rename from tests/modules/lissero/nextflow.config
rename to tests/modules/nf-core/lissero/nextflow.config
diff --git a/tests/modules/nf-core/lissero/test.yml b/tests/modules/nf-core/lissero/test.yml
new file mode 100644
index 00000000000..1e9c1bc482c
--- /dev/null
+++ b/tests/modules/nf-core/lissero/test.yml
@@ -0,0 +1,7 @@
+- name: lissero test_lissero
+  command: nextflow run ./tests/modules/nf-core/lissero -entry test_lissero -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lissero/nextflow.config
+  tags:
+    - lissero
+  files:
+    - path: output/lissero/test.tsv
+      contains: ["ID", "SEROTYPE", "FULL"]
diff --git a/tests/modules/nf-core/lofreq/call/main.nf b/tests/modules/nf-core/lofreq/call/main.nf
new file mode 100644
index 00000000000..0492da377e5
--- /dev/null
+++ b/tests/modules/nf-core/lofreq/call/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LOFREQ_CALL } from '../../../../../modules/nf-core/lofreq/call/main.nf'
+
+workflow test_lofreq_call {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    LOFREQ_CALL ( input, fasta )
+}
diff --git a/tests/modules/lofreq/call/nextflow.config b/tests/modules/nf-core/lofreq/call/nextflow.config
similarity index 100%
rename from tests/modules/lofreq/call/nextflow.config
rename to tests/modules/nf-core/lofreq/call/nextflow.config
diff --git a/tests/modules/nf-core/lofreq/call/test.yml b/tests/modules/nf-core/lofreq/call/test.yml
new file mode 100644
index 00000000000..dfff0370648
--- /dev/null
+++ b/tests/modules/nf-core/lofreq/call/test.yml
@@ -0,0 +1,11 @@
+- name: lofreq call test_lofreq_call
+  command: nextflow run ./tests/modules/nf-core/lofreq/call -entry test_lofreq_call -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lofreq/call/nextflow.config
+  tags:
+    - lofreq
+    - lofreq/call
+  files:
+    - path: output/lofreq/test.vcf.gz
+      contains:
+        [
+          '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
+        ]
diff --git a/tests/modules/nf-core/lofreq/callparallel/main.nf b/tests/modules/nf-core/lofreq/callparallel/main.nf
new file mode 100644
index 00000000000..dacc323854b
--- /dev/null
+++ b/tests/modules/nf-core/lofreq/callparallel/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LOFREQ_CALLPARALLEL } from '../../../../../modules/nf-core/lofreq/callparallel/main.nf'
+
+workflow test_lofreq_callparallel {
+    
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    LOFREQ_CALLPARALLEL ( input, fasta, fai )
+}
diff --git a/tests/modules/lofreq/callparallel/nextflow.config b/tests/modules/nf-core/lofreq/callparallel/nextflow.config
similarity index 100%
rename from tests/modules/lofreq/callparallel/nextflow.config
rename to tests/modules/nf-core/lofreq/callparallel/nextflow.config
diff --git a/tests/modules/nf-core/lofreq/callparallel/test.yml b/tests/modules/nf-core/lofreq/callparallel/test.yml
new file mode 100644
index 00000000000..525a7d8564a
--- /dev/null
+++ b/tests/modules/nf-core/lofreq/callparallel/test.yml
@@ -0,0 +1,11 @@
+- name: lofreq callparallel test_lofreq_callparallel
+  command: nextflow run ./tests/modules/nf-core/lofreq/callparallel -entry test_lofreq_callparallel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lofreq/callparallel/nextflow.config
+  tags:
+    - lofreq/callparallel
+    - lofreq
+  files:
+    - path: output/lofreq/test.vcf.gz
+      contains:
+        [
+          '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
+        ]
diff --git a/tests/modules/nf-core/lofreq/filter/main.nf b/tests/modules/nf-core/lofreq/filter/main.nf
new file mode 100644
index 00000000000..d775ffb4d2f
--- /dev/null
+++ b/tests/modules/nf-core/lofreq/filter/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LOFREQ_FILTER } from '../../../../../modules/nf-core/lofreq/filter/main.nf'
+
+workflow test_lofreq_filter {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+
+    LOFREQ_FILTER ( input )
+}
diff --git a/tests/modules/lofreq/filter/nextflow.config b/tests/modules/nf-core/lofreq/filter/nextflow.config
similarity index 100%
rename from tests/modules/lofreq/filter/nextflow.config
rename to tests/modules/nf-core/lofreq/filter/nextflow.config
diff --git a/tests/modules/nf-core/lofreq/filter/test.yml b/tests/modules/nf-core/lofreq/filter/test.yml
new file mode 100644
index 00000000000..8c62f479792
--- /dev/null
+++ b/tests/modules/nf-core/lofreq/filter/test.yml
@@ -0,0 +1,8 @@
+- name: lofreq filter test_lofreq_filter
+  command: nextflow run ./tests/modules/nf-core/lofreq/filter -entry test_lofreq_filter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lofreq/filter/nextflow.config
+  tags:
+    - lofreq
+    - lofreq/filter
+  files:
+    - path: output/lofreq/test.vcf.gz
+      md5sum: 1914d9bc5d855ff11fe89da7d795e57a
diff --git a/tests/modules/nf-core/lofreq/indelqual/main.nf b/tests/modules/nf-core/lofreq/indelqual/main.nf
new file mode 100644
index 00000000000..8fe400bb857
--- /dev/null
+++ b/tests/modules/nf-core/lofreq/indelqual/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+
+include { LOFREQ_INDELQUAL } from '../../../../../modules/nf-core/lofreq/indelqual/main.nf'
+
+workflow test_lofreq_indelqual {
+    
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    LOFREQ_INDELQUAL ( input, fasta )
+}
diff --git a/tests/modules/lofreq/indelqual/nextflow.config b/tests/modules/nf-core/lofreq/indelqual/nextflow.config
similarity index 100%
rename from tests/modules/lofreq/indelqual/nextflow.config
rename to tests/modules/nf-core/lofreq/indelqual/nextflow.config
diff --git a/tests/modules/nf-core/lofreq/indelqual/test.yml b/tests/modules/nf-core/lofreq/indelqual/test.yml
new file mode 100644
index 00000000000..7c91fee063e
--- /dev/null
+++ b/tests/modules/nf-core/lofreq/indelqual/test.yml
@@ -0,0 +1,8 @@
+- name: lofreq indelqual
+  command: nextflow run ./tests/modules/nf-core/lofreq/indelqual -entry test_lofreq_indelqual -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lofreq/indelqual/nextflow.config
+  tags:
+    - lofreq
+    - lofreq/indelqual
+  files:
+    - path: output/lofreq/test.indelqual.bam
+      md5sum: 18de975638c2633069bfe1a41ebc5ff7
diff --git a/tests/modules/nf-core/macrel/contigs/main.nf b/tests/modules/nf-core/macrel/contigs/main.nf
new file mode 100644
index 00000000000..1798753831e
--- /dev/null
+++ b/tests/modules/nf-core/macrel/contigs/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MACREL_CONTIGS } from '../../../../../modules/nf-core/macrel/contigs/main.nf'
+
+workflow test_macrel_contigs {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) 
+    ]
+
+    MACREL_CONTIGS ( input )
+}
diff --git a/tests/modules/macrel/contigs/nextflow.config b/tests/modules/nf-core/macrel/contigs/nextflow.config
similarity index 100%
rename from tests/modules/macrel/contigs/nextflow.config
rename to tests/modules/nf-core/macrel/contigs/nextflow.config
diff --git a/tests/modules/nf-core/macrel/contigs/test.yml b/tests/modules/nf-core/macrel/contigs/test.yml
new file mode 100644
index 00000000000..708aac9f7ae
--- /dev/null
+++ b/tests/modules/nf-core/macrel/contigs/test.yml
@@ -0,0 +1,16 @@
+- name: macrel contigs test_macrel_contigs
+  command: nextflow run ./tests/modules/nf-core/macrel/contigs -entry test_macrel_contigs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/macrel/contigs/nextflow.config
+  tags:
+    - macrel/contigs
+    - macrel
+  files:
+    - path: output/macrel/test/README.md
+      md5sum: fa3706dfc95d0538a52c4d0d824be5fb
+    - path: output/macrel/test/test.all_orfs.faa.gz
+    - path: output/macrel/test/test.prediction.gz
+    - path: output/macrel/test/test.smorfs.faa.gz
+      md5sum: 79704c6120c2f794518301af6f9b963d
+    - path: output/macrel/test/test_log.txt
+      md5sum: 6fdba143dce759597eb9f80e5d968729
+    - path: output/macrel/versions.yml
+      md5sum: be8bf0d0647751c635c3736655f29f85
diff --git a/tests/modules/nf-core/macs2/callpeak/main.nf b/tests/modules/nf-core/macs2/callpeak/main.nf
new file mode 100644
index 00000000000..0e41229f8a0
--- /dev/null
+++ b/tests/modules/nf-core/macs2/callpeak/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MACS2_CALLPEAK } from '../../../../../modules/nf-core/macs2/callpeak/main.nf'
+include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL    } from '../../../../../modules/nf-core/macs2/callpeak/main.nf'
+include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED     } from '../../../../../modules/nf-core/macs2/callpeak/main.nf'
+
+workflow test_macs2_callpeak_bed {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['pacbio']['genemodel1'], checkIfExists: true)],
+                  []]
+
+    MACS2_CALLPEAK_BED ( input, 4000 )
+}
+
+workflow test_macs2_callpeak {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
+                  []]
+
+    MACS2_CALLPEAK ( input, 40000 )
+}
+
+workflow test_macs2_callpeak_ctrl {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
+                  [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
+
+    MACS2_CALLPEAK_CTRL ( input, 40000 )
+}
diff --git a/tests/modules/macs2/callpeak/nextflow.config b/tests/modules/nf-core/macs2/callpeak/nextflow.config
similarity index 100%
rename from tests/modules/macs2/callpeak/nextflow.config
rename to tests/modules/nf-core/macs2/callpeak/nextflow.config
diff --git a/tests/modules/nf-core/macs2/callpeak/test.yml b/tests/modules/nf-core/macs2/callpeak/test.yml
new file mode 100644
index 00000000000..0934c07c830
--- /dev/null
+++ b/tests/modules/nf-core/macs2/callpeak/test.yml
@@ -0,0 +1,38 @@
+- name: macs2 callpeak test_macs2_callpeak_bed
+  command: nextflow run ./tests/modules/nf-core/macs2/callpeak -entry test_macs2_callpeak_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/macs2/callpeak/nextflow.config
+  tags:
+    - macs2
+    - macs2/callpeak
+  files:
+    - path: output/macs2/test_peaks.narrowPeak
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/macs2/test_peaks.xls
+      md5sum: 762383e3a35e1f9ac3834fd6b2926092
+    - path: output/macs2/test_summits.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+
+- name: macs2 callpeak test_macs2_callpeak
+  command: nextflow run ./tests/modules/nf-core/macs2/callpeak -entry test_macs2_callpeak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/macs2/callpeak/nextflow.config
+  tags:
+    - macs2
+    - macs2/callpeak
+  files:
+    - path: output/macs2/test_peaks.narrowPeak
+      md5sum: 2e4da1c1704595e12aaf99cc715ad70c
+    - path: output/macs2/test_peaks.xls
+      md5sum: 5d65cb3dbd5421ea3bb5b490a100e9a4
+    - path: output/macs2/test_summits.bed
+      md5sum: 26f0f97b6c14dbca129e947a58067c82
+
+- name: macs2 callpeak test_macs2_callpeak_ctrl
+  command: nextflow run ./tests/modules/nf-core/macs2/callpeak -entry test_macs2_callpeak_ctrl -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/macs2/callpeak/nextflow.config
+  tags:
+    - macs2
+    - macs2/callpeak
+  files:
+    - path: output/macs2/test_peaks.narrowPeak
+      md5sum: 653e1108cc57ca07d0f60fc0f4fb8ba3
+    - path: output/macs2/test_peaks.xls
+      md5sum: bf86546faa7b581b5209c29b22046a0a
+    - path: output/macs2/test_summits.bed
+      md5sum: 4f3c7c53a1d730d90d1b3dd9d3197af4
diff --git a/tests/modules/nf-core/mafft/main.nf b/tests/modules/nf-core/mafft/main.nf
new file mode 100644
index 00000000000..c3e7f0782ab
--- /dev/null
+++ b/tests/modules/nf-core/mafft/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MAFFT } from '../../../../modules/nf-core/mafft/main.nf'
+
+workflow test_mafft {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
+    ]
+
+    MAFFT ( input )
+}
diff --git a/tests/modules/mafft/nextflow.config b/tests/modules/nf-core/mafft/nextflow.config
similarity index 100%
rename from tests/modules/mafft/nextflow.config
rename to tests/modules/nf-core/mafft/nextflow.config
diff --git a/tests/modules/nf-core/mafft/test.yml b/tests/modules/nf-core/mafft/test.yml
new file mode 100644
index 00000000000..1d3bb3b15a0
--- /dev/null
+++ b/tests/modules/nf-core/mafft/test.yml
@@ -0,0 +1,9 @@
+- name: mafft test_mafft
+  command: nextflow run ./tests/modules/nf-core/mafft -entry test_mafft -c ./tests/config/nextflow.config
+  tags:
+    - mafft
+  files:
+    - path: output/mafft/test.fas
+      md5sum: 23426611f4a0df532b6708f072bd445b
+    - path: output/mafft/versions.yml
+      md5sum: b1b5ab3728ae17401808335f1c8f8215
diff --git a/tests/modules/malt/build b/tests/modules/nf-core/malt/build
similarity index 100%
rename from tests/modules/malt/build
rename to tests/modules/nf-core/malt/build
diff --git a/tests/modules/nf-core/malt/build_test/main.nf b/tests/modules/nf-core/malt/build_test/main.nf
new file mode 100644
index 00000000000..dbf7fd3ebe6
--- /dev/null
+++ b/tests/modules/nf-core/malt/build_test/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNZIP } from '../../../../../modules/nf-core/unzip/main.nf'
+include { MALT_BUILD } from '../../../../../modules/nf-core/malt/build/main.nf'
+
+workflow test_malt_build {
+    fastas        = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    seq_type      = "DNA"
+    map_accession = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/nucl_acc2tax-Jul2019.abin.zip", checkIfExists: true) ]
+    mapping_type  = 'ref'
+    mapping_db    = 'taxonomy'
+
+    UNZIP ( map_accession )
+    MALT_BUILD ( fastas, seq_type, UNZIP.out.unzipped_archive.map{ it[1] }, "ref", "taxonomy" )
+}
diff --git a/tests/modules/malt/build_test/nextflow.config b/tests/modules/nf-core/malt/build_test/nextflow.config
similarity index 100%
rename from tests/modules/malt/build_test/nextflow.config
rename to tests/modules/nf-core/malt/build_test/nextflow.config
diff --git a/tests/modules/nf-core/malt/build_test/test.yml b/tests/modules/nf-core/malt/build_test/test.yml
new file mode 100644
index 00000000000..a5db6c7d160
--- /dev/null
+++ b/tests/modules/nf-core/malt/build_test/test.yml
@@ -0,0 +1,27 @@
+- name: malt build test_malt_build
+  command: nextflow run ./tests/modules/nf-core/malt/build -entry test_malt_build -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/malt/build/nextflow.config
+  tags:
+    - malt
+    - malt/build
+  files:
+    - path: output/malt/malt-build.log
+      contains:
+        - "Peak memory"
+    - path: output/malt/malt_index/index0.idx
+      md5sum: 1954f2c00b418d00112829b0a6adb8ce
+    - path: output/malt/malt_index/ref.db
+      md5sum: 1fb74eccd5400fb23454454da1bd4c0c
+    - path: output/malt/malt_index/ref.idx
+      md5sum: 7dea362b3fac8e00956a4952a3d4f474
+    - path: output/malt/malt_index/ref.inf
+      md5sum: b146842067cf278ef1d23e6c2e7c0c35
+    - path: output/malt/malt_index/table0.db
+    - path: output/malt/malt_index/table0.idx
+    - path: output/malt/malt_index/taxonomy.idx
+      md5sum: 13aa81314892b5537319fca2a63a2c31
+    - path: output/malt/malt_index/taxonomy.map
+      md5sum: 1e972302ae6d705b8abb377cfafd380a
+    - path: output/malt/malt_index/taxonomy.tre
+      md5sum: 79c2322475a8eebc57607ff36c1e4728
+    - path: output/unzip/nucl_acc2tax-Jul2019.abin/nucl_acc2tax-Jul2019.abin
+      md5sum: b2deb1df50ebcec4de71a6beec6226d7
diff --git a/tests/modules/nf-core/malt/run/main.nf b/tests/modules/nf-core/malt/run/main.nf
new file mode 100644
index 00000000000..fb40f05b26e
--- /dev/null
+++ b/tests/modules/nf-core/malt/run/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNZIP      } from '../../../../../modules/nf-core/unzip/main.nf'
+include { MALT_BUILD } from  '../../../../../modules/nf-core/malt/build/main.nf'
+include { MALT_RUN   } from '../../../../../modules/nf-core/malt/run/main.nf'
+
+workflow test_malt_run {
+
+    fastas        = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    seq_type      = "DNA"
+    map_accession = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/nucl_acc2tax-Jul2019.abin.zip", checkIfExists: true) ]
+    mapping_type  = 'ref'
+    mapping_db    = 'taxonomy'
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    mode = "BlastN"
+
+    UNZIP ( map_accession )
+    MALT_BUILD ( fastas, seq_type, UNZIP.out.unzipped_archive.map{ it[1] }, "ref", "taxonomy" )
+    MALT_RUN ( input, mode, MALT_BUILD.out.index )
+}
+
diff --git a/tests/modules/malt/run/nextflow.config b/tests/modules/nf-core/malt/run/nextflow.config
similarity index 100%
rename from tests/modules/malt/run/nextflow.config
rename to tests/modules/nf-core/malt/run/nextflow.config
diff --git a/tests/modules/nf-core/malt/run/test.yml b/tests/modules/nf-core/malt/run/test.yml
new file mode 100644
index 00000000000..62cb3e8d866
--- /dev/null
+++ b/tests/modules/nf-core/malt/run/test.yml
@@ -0,0 +1,10 @@
+- name: malt run test_malt_run
+  command: nextflow run ./tests/modules/nf-core/malt/run -entry test_malt_run -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/malt/run/nextflow.config
+  tags:
+    - malt/run
+    - malt
+  files:
+    - path: output/malt/test-malt-run.log
+      contains:
+        - "Peak memory"
+    - path: output/malt/test_1.rma6
diff --git a/tests/modules/nf-core/maltextract/main.nf b/tests/modules/nf-core/maltextract/main.nf
new file mode 100644
index 00000000000..5ecbbab9515
--- /dev/null
+++ b/tests/modules/nf-core/maltextract/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNZIP as UNZIP_MALT        } from '../../../../modules/nf-core/unzip/main.nf'
+include { UNZIP as UNZIP_MALTEXTRACT }  from '../../../../modules/nf-core/unzip/main.nf'
+include { MALT_BUILD                 } from  '../../../../modules/nf-core/malt/build/main.nf'
+include { MALT_RUN                   } from '../../../../modules/nf-core/malt/run/main.nf'
+include { MALTEXTRACT                } from '../../../../modules/nf-core/maltextract/main.nf'
+
+workflow test_maltextract {
+
+    fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gff = []
+    seq_type = "DNA"
+    map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    mode = "BlastN"
+    taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
+    ncbi_dir = [ [], file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true) ]
+
+    UNZIP_MALT ( map_db )
+    UNZIP_MALTEXTRACT ( ncbi_dir )
+    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive.map{ it[1] } )
+    MALT_RUN ( input, mode, MALT_BUILD.out.index )
+    ch_input_to_maltextract = MALT_RUN.out.rma6.map{ it[1] }
+    MALTEXTRACT ( ch_input_to_maltextract, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive.map{ it[1] })
+}
diff --git a/tests/modules/maltextract/nextflow.config b/tests/modules/nf-core/maltextract/nextflow.config
similarity index 100%
rename from tests/modules/maltextract/nextflow.config
rename to tests/modules/nf-core/maltextract/nextflow.config
diff --git a/tests/modules/nf-core/maltextract/test.yml b/tests/modules/nf-core/maltextract/test.yml
new file mode 100644
index 00000000000..51b8dcd0abe
--- /dev/null
+++ b/tests/modules/nf-core/maltextract/test.yml
@@ -0,0 +1,9 @@
+- name: maltextract
+  command: nextflow run ./tests/modules/nf-core/maltextract -entry test_maltextract -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/maltextract/nextflow.config
+  tags:
+    - maltextract
+  files:
+    - path: output/maltextract/results/error.txt
+    - path: output/maltextract/results/log.txt
+      contains:
+        - "INFO: Peak memory"
diff --git a/tests/modules/nf-core/manta/convertinversion/main.nf b/tests/modules/nf-core/manta/convertinversion/main.nf
new file mode 100644
index 00000000000..b51b7057918
--- /dev/null
+++ b/tests/modules/nf-core/manta/convertinversion/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MANTA_CONVERTINVERSION } from '../../../../../modules/nf-core/manta/convertinversion/main.nf'
+include { MANTA_TUMORONLY        } from '../../../../../modules/nf-core/manta/tumoronly/main.nf'
+
+workflow test_manta_convertinversion {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        [], []
+    ]
+
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    MANTA_TUMORONLY ( input, fasta, fai )
+
+    MANTA_CONVERTINVERSION ( MANTA_TUMORONLY.out.tumor_sv_vcf, fasta )
+}
diff --git a/tests/modules/manta/convertinversion/nextflow.config b/tests/modules/nf-core/manta/convertinversion/nextflow.config
similarity index 100%
rename from tests/modules/manta/convertinversion/nextflow.config
rename to tests/modules/nf-core/manta/convertinversion/nextflow.config
diff --git a/tests/modules/nf-core/manta/convertinversion/test.yml b/tests/modules/nf-core/manta/convertinversion/test.yml
new file mode 100644
index 00000000000..35e19985201
--- /dev/null
+++ b/tests/modules/nf-core/manta/convertinversion/test.yml
@@ -0,0 +1,18 @@
+- name: manta convertinversion test_manta_convertinversion
+  command: nextflow run ./tests/modules/nf-core/manta/convertinversion -entry test_manta_convertinversion -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/manta/convertinversion/nextflow.config
+  tags:
+    - manta
+    - manta/convertinversion
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.tumor_sv.vcf.gz
+    - path: output/manta/test.tumor_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.vcf.gz
+    - path: output/manta/test.vcf.gz.tbi
+      md5sum: e7180bb953d2bd657c420a5f76a7164d
diff --git a/tests/modules/nf-core/manta/germline/main.nf b/tests/modules/nf-core/manta/germline/main.nf
new file mode 100644
index 00000000000..e949d73470d
--- /dev/null
+++ b/tests/modules/nf-core/manta/germline/main.nf
@@ -0,0 +1,48 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MANTA_GERMLINE } from '../../../../../modules/nf-core/manta/germline/main.nf'
+
+workflow test_manta_germline {
+    input = [
+        [ id:'test'], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)],
+        [],[]
+    ]
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    MANTA_GERMLINE ( input, fasta, fai )
+}
+
+workflow test_manta_germline_target_bed {
+    input = [
+        [ id:'test'], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)],
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
+    ]
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    MANTA_GERMLINE ( input, fasta, fai )
+}
+
+workflow test_manta_germline_target_bed_jointcalling {
+    input = [
+        [ id:'test'], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)],
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
+    ]
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    MANTA_GERMLINE ( input, fasta, fai )
+}
diff --git a/tests/modules/manta/germline/nextflow.config b/tests/modules/nf-core/manta/germline/nextflow.config
similarity index 100%
rename from tests/modules/manta/germline/nextflow.config
rename to tests/modules/nf-core/manta/germline/nextflow.config
diff --git a/tests/modules/nf-core/manta/germline/test.yml b/tests/modules/nf-core/manta/germline/test.yml
new file mode 100644
index 00000000000..7a7b32402d7
--- /dev/null
+++ b/tests/modules/nf-core/manta/germline/test.yml
@@ -0,0 +1,36 @@
+- name: manta germline
+  command: nextflow run ./tests/modules/nf-core/manta/germline -entry test_manta_germline -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/manta/germline/nextflow.config
+  tags:
+    - manta
+    - manta/germline
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+    - path: output/manta/test.diploid_sv.vcf.gz
+    - path: output/manta/test.diploid_sv.vcf.gz.tbi
+- name: manta germline target bed
+  command: nextflow run ./tests/modules/nf-core/manta/germline -entry test_manta_germline_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/manta/germline/nextflow.config
+  tags:
+    - manta
+    - manta/germline
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+    - path: output/manta/test.diploid_sv.vcf.gz
+    - path: output/manta/test.diploid_sv.vcf.gz.tbi
+- name: manta germline target bed jointcalling
+  command: nextflow run ./tests/modules/nf-core/manta/germline -entry test_manta_germline_target_bed_jointcalling -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/manta/germline/nextflow.config
+  tags:
+    - manta
+    - manta/germline
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+    - path: output/manta/test.diploid_sv.vcf.gz
+    - path: output/manta/test.diploid_sv.vcf.gz.tbi
diff --git a/tests/modules/nf-core/manta/somatic/main.nf b/tests/modules/nf-core/manta/somatic/main.nf
new file mode 100644
index 00000000000..2fdceb00011
--- /dev/null
+++ b/tests/modules/nf-core/manta/somatic/main.nf
@@ -0,0 +1,40 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MANTA_SOMATIC } from '../../../../../modules/nf-core/manta/somatic/main.nf'
+
+workflow test_manta_somatic {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        [], []
+    ]
+
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    MANTA_SOMATIC ( input, fasta, fai )
+}
+
+workflow test_manta_somatic_target_bed {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true),
+    ]
+
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    MANTA_SOMATIC ( input, fasta, fai )
+}
diff --git a/tests/modules/manta/somatic/nextflow.config b/tests/modules/nf-core/manta/somatic/nextflow.config
similarity index 100%
rename from tests/modules/manta/somatic/nextflow.config
rename to tests/modules/nf-core/manta/somatic/nextflow.config
diff --git a/tests/modules/nf-core/manta/somatic/test.yml b/tests/modules/nf-core/manta/somatic/test.yml
new file mode 100644
index 00000000000..b3acf544074
--- /dev/null
+++ b/tests/modules/nf-core/manta/somatic/test.yml
@@ -0,0 +1,18 @@
+- name: manta somatic test_manta_somatic
+  command: nextflow run ./tests/modules/nf-core/manta/somatic -entry test_manta_somatic -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/manta/somatic/nextflow.config
+  tags:
+    - manta/somatic
+    - manta
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.diploid_sv.vcf.gz
+    - path: output/manta/test.diploid_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.somatic_sv.vcf.gz
+    - path: output/manta/test.somatic_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
diff --git a/tests/modules/nf-core/manta/tumoronly/main.nf b/tests/modules/nf-core/manta/tumoronly/main.nf
new file mode 100644
index 00000000000..dccf5591ba2
--- /dev/null
+++ b/tests/modules/nf-core/manta/tumoronly/main.nf
@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MANTA_TUMORONLY } from '../../../../../modules/nf-core/manta/tumoronly/main.nf'
+
+workflow test_manta_tumoronly {
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        [], []
+    ]
+
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    MANTA_TUMORONLY ( input, fasta, fai )
+}
+
+workflow test_manta_tumoronly_target_bed {
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
+    ]
+
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    MANTA_TUMORONLY ( input, fasta, fai )
+}
diff --git a/tests/modules/manta/tumoronly/nextflow.config b/tests/modules/nf-core/manta/tumoronly/nextflow.config
similarity index 100%
rename from tests/modules/manta/tumoronly/nextflow.config
rename to tests/modules/nf-core/manta/tumoronly/nextflow.config
diff --git a/tests/modules/nf-core/manta/tumoronly/test.yml b/tests/modules/nf-core/manta/tumoronly/test.yml
new file mode 100644
index 00000000000..e566c711bea
--- /dev/null
+++ b/tests/modules/nf-core/manta/tumoronly/test.yml
@@ -0,0 +1,24 @@
+- name: manta tumoronly
+  command: nextflow run ./tests/modules/nf-core/manta/tumoronly -entry test_manta_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/manta/tumoronly/nextflow.config
+  tags:
+    - manta
+    - manta/tumoronly
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+    - path: output/manta/test.tumor_sv.vcf.gz
+    - path: output/manta/test.tumor_sv.vcf.gz.tbi
+- name: manta tumoronly target bed
+  command: nextflow run ./tests/modules/nf-core/manta/tumoronly -entry test_manta_tumoronly_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/manta/tumoronly/nextflow.config
+  tags:
+    - manta
+    - manta/tumoronly
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+    - path: output/manta/test.tumor_sv.vcf.gz
+    - path: output/manta/test.tumor_sv.vcf.gz.tbi
diff --git a/tests/modules/nf-core/mapdamage2/main.nf b/tests/modules/nf-core/mapdamage2/main.nf
new file mode 100644
index 00000000000..47e550c6e96
--- /dev/null
+++ b/tests/modules/nf-core/mapdamage2/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MAPDAMAGE2 } from '../../../../modules/nf-core/mapdamage2/main.nf'
+
+workflow test_mapdamage2 {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) 
+            ]                            
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    
+    MAPDAMAGE2 ( input, fasta )
+}
diff --git a/tests/modules/mapdamage2/nextflow.config b/tests/modules/nf-core/mapdamage2/nextflow.config
similarity index 100%
rename from tests/modules/mapdamage2/nextflow.config
rename to tests/modules/nf-core/mapdamage2/nextflow.config
diff --git a/tests/modules/nf-core/mapdamage2/test.yml b/tests/modules/nf-core/mapdamage2/test.yml
new file mode 100644
index 00000000000..4ac70c72356
--- /dev/null
+++ b/tests/modules/nf-core/mapdamage2/test.yml
@@ -0,0 +1,25 @@
+- name: mapdamage2 test_mapdamage2
+  command: nextflow run ./tests/modules/nf-core/mapdamage2 -entry test_mapdamage2 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mapdamage2/nextflow.config
+  tags:
+    - mapdamage2
+  files:
+    - path: output/mapdamage2/results_test.paired_end.sorted/3pGtoA_freq.txt
+      md5sum: 3b300b8d2842441675cb2b56740801f0
+    - path: output/mapdamage2/results_test.paired_end.sorted/5pCtoT_freq.txt
+      md5sum: 4c27465cd02e1fb8bf6fb2b01e98446d
+    - path: output/mapdamage2/results_test.paired_end.sorted/Fragmisincorporation_plot.pdf
+    - path: output/mapdamage2/results_test.paired_end.sorted/Runtime_log.txt
+    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_correct_prob.csv
+    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_hist.pdf
+    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_iter.csv
+    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_iter_summ_stat.csv
+    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_post_pred.pdf
+    - path: output/mapdamage2/results_test.paired_end.sorted/Stats_out_MCMC_trace.pdf
+    - path: output/mapdamage2/results_test.paired_end.sorted/dnacomp.txt
+      md5sum: 4244d9fa554bbfeebbcea8eba3ad6466
+    - path: output/mapdamage2/results_test.paired_end.sorted/dnacomp_genome.csv
+      md5sum: ea91a3d205717d3c6b3e0b77bb840945
+    - path: output/mapdamage2/results_test.paired_end.sorted/lgdistribution.txt
+      md5sum: f86dfc04b1fff4337cc91add6356e3a0
+    - path: output/mapdamage2/results_test.paired_end.sorted/misincorporation.txt
+      md5sum: 1c89b4c96d1f8996c3d0879cad5129a5
diff --git a/tests/modules/nf-core/mash/dist/main.nf b/tests/modules/nf-core/mash/dist/main.nf
new file mode 100644
index 00000000000..30b37a746c7
--- /dev/null
+++ b/tests/modules/nf-core/mash/dist/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MASH_DIST } from '../../../../../modules/nf-core/mash/dist/main.nf'
+
+workflow test_mash_dist {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+    ]
+
+    reference =  file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    MASH_DIST ( input, reference )
+}
diff --git a/tests/modules/mash/dist/nextflow.config b/tests/modules/nf-core/mash/dist/nextflow.config
similarity index 100%
rename from tests/modules/mash/dist/nextflow.config
rename to tests/modules/nf-core/mash/dist/nextflow.config
diff --git a/tests/modules/nf-core/mash/dist/test.yml b/tests/modules/nf-core/mash/dist/test.yml
new file mode 100644
index 00000000000..27fd099c3cf
--- /dev/null
+++ b/tests/modules/nf-core/mash/dist/test.yml
@@ -0,0 +1,10 @@
+- name: mash dist test_mash_dist
+  command: nextflow run ./tests/modules/nf-core/mash/dist -entry test_mash_dist -c ./tests/config/nextflow.config
+  tags:
+    - mash
+    - mash/dist
+  files:
+    - path: output/mash/test.txt
+      md5sum: 1dfd5b53e1996f9fdb9d260b3e81c4d6
+    - path: output/mash/versions.yml
+      md5sum: f786d48a9af59e823d19c171969d0d50
diff --git a/tests/modules/nf-core/mash/screen/main.nf b/tests/modules/nf-core/mash/screen/main.nf
new file mode 100644
index 00000000000..91675faa581
--- /dev/null
+++ b/tests/modules/nf-core/mash/screen/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MASH_SKETCH } from '../../../../../modules/nf-core/mash/sketch/main.nf'
+include { MASH_SCREEN } from '../../../../../modules/nf-core/mash/screen/main.nf'
+
+workflow test_mash_screen {
+
+    input = [
+        [ id:'test', single_end:false], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    sars_db = [
+        [ id: 'sars_db' ],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    MASH_SKETCH ( sars_db )
+    MASH_SCREEN ( input, MASH_SKETCH.out.mash.map { meta, sketch -> sketch } )
+}
diff --git a/tests/modules/mash/screen/nextflow.config b/tests/modules/nf-core/mash/screen/nextflow.config
similarity index 100%
rename from tests/modules/mash/screen/nextflow.config
rename to tests/modules/nf-core/mash/screen/nextflow.config
diff --git a/tests/modules/nf-core/mash/screen/test.yml b/tests/modules/nf-core/mash/screen/test.yml
new file mode 100644
index 00000000000..df486c04c46
--- /dev/null
+++ b/tests/modules/nf-core/mash/screen/test.yml
@@ -0,0 +1,12 @@
+- name: mash screen test_mash_screen
+  command: nextflow run ./tests/modules/nf-core/mash/screen -entry test_mash_screen -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mash/screen/nextflow.config
+  tags:
+    - mash
+    - mash/screen
+  files:
+    - path: output/mash/sars_db.mash_stats
+      md5sum: 1dafbd23e36e18bf4c87a007d0fc98f7
+    - path: output/mash/sars_db.msh
+      md5sum: 24289e4a13526e88eeb2abfca4a0f0a8
+    - path: output/mash/test.screen
+      md5sum: ac8701e1aab651b2f36c6380b1351b11
diff --git a/tests/modules/nf-core/mash/sketch/main.nf b/tests/modules/nf-core/mash/sketch/main.nf
new file mode 100644
index 00000000000..6fe6e93f0cd
--- /dev/null
+++ b/tests/modules/nf-core/mash/sketch/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MASH_SKETCH } from '../../../../../modules/nf-core/mash/sketch/main.nf'
+
+workflow test_mash_sketch {
+    
+    input = [ [ id:'test', single_end:false], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+              ]
+            ]
+
+    MASH_SKETCH ( input )
+}
diff --git a/tests/modules/mash/sketch/nextflow.config b/tests/modules/nf-core/mash/sketch/nextflow.config
similarity index 100%
rename from tests/modules/mash/sketch/nextflow.config
rename to tests/modules/nf-core/mash/sketch/nextflow.config
diff --git a/tests/modules/nf-core/mash/sketch/test.yml b/tests/modules/nf-core/mash/sketch/test.yml
new file mode 100644
index 00000000000..96696483a6d
--- /dev/null
+++ b/tests/modules/nf-core/mash/sketch/test.yml
@@ -0,0 +1,9 @@
+- name: mash sketch
+  command: nextflow run ./tests/modules/nf-core/mash/sketch -entry test_mash_sketch -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mash/sketch/nextflow.config
+  tags:
+    - mash/sketch
+  files:
+    - path: output/mash/test.msh
+      md5sum: d747145a43dad5f82342036f8f5d9133
+    - path: output/mash/test.mash_stats
+      md5sum: 2a6f297d8e69a5e4160243bc6c89129c
diff --git a/tests/modules/nf-core/mashtree/main.nf b/tests/modules/nf-core/mashtree/main.nf
new file mode 100644
index 00000000000..8ffbab037b1
--- /dev/null
+++ b/tests/modules/nf-core/mashtree/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MASHTREE } from '../../../../modules/nf-core/mashtree/main.nf'
+
+workflow test_mashtree {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    MASHTREE ( input )
+}
diff --git a/tests/modules/mashtree/nextflow.config b/tests/modules/nf-core/mashtree/nextflow.config
similarity index 100%
rename from tests/modules/mashtree/nextflow.config
rename to tests/modules/nf-core/mashtree/nextflow.config
diff --git a/tests/modules/nf-core/mashtree/test.yml b/tests/modules/nf-core/mashtree/test.yml
new file mode 100644
index 00000000000..9901d193f9d
--- /dev/null
+++ b/tests/modules/nf-core/mashtree/test.yml
@@ -0,0 +1,8 @@
+- name: mashtree test_mashtree
+  command: nextflow run ./tests/modules/nf-core/mashtree -entry test_mashtree -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mashtree/nextflow.config
+  tags:
+    - mashtree
+  files:
+    - path: output/mashtree/test.dnd
+      md5sum: 007b3949a9f0c991624791d2fb076824
+    - path: output/mashtree/test.tsv
diff --git a/tests/modules/nf-core/maxbin2/main.nf b/tests/modules/nf-core/maxbin2/main.nf
new file mode 100644
index 00000000000..2eb6cb45213
--- /dev/null
+++ b/tests/modules/nf-core/maxbin2/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MAXBIN2 } from '../../../../modules/nf-core/maxbin2/main.nf'
+
+workflow test_maxbin2 {
+
+    input = [ 
+        [ id:'test1', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true),
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+        []
+    ]
+
+    MAXBIN2 ( input )
+}
diff --git a/tests/modules/maxbin2/nextflow.config b/tests/modules/nf-core/maxbin2/nextflow.config
similarity index 100%
rename from tests/modules/maxbin2/nextflow.config
rename to tests/modules/nf-core/maxbin2/nextflow.config
diff --git a/tests/modules/nf-core/maxbin2/test.yml b/tests/modules/nf-core/maxbin2/test.yml
new file mode 100644
index 00000000000..92f2e5410de
--- /dev/null
+++ b/tests/modules/nf-core/maxbin2/test.yml
@@ -0,0 +1,15 @@
+- name: maxbin2
+  command: nextflow run ./tests/modules/nf-core/maxbin2 -entry test_maxbin2 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/maxbin2/nextflow.config
+  tags:
+    - maxbin2
+  files:
+    - path: output/maxbin2/test1.001.fasta.gz
+    - path: output/maxbin2/test1.002.fasta.gz
+    - path: output/maxbin2/test1.log.gz
+    - path: output/maxbin2/test1.marker.gz
+    - path: output/maxbin2/test1.marker_of_each_bin.tar.gz
+    - path: output/maxbin2/test1.noclass.gz
+    - path: output/maxbin2/test1.summary
+      contains:
+        - "Bin name\tAbundance\tCompleteness\tGenome size\tGC content"
+    - path: output/maxbin2/test1.tooshort.gz
diff --git a/tests/modules/nf-core/maxquant/lfq/main.nf b/tests/modules/nf-core/maxquant/lfq/main.nf
new file mode 100644
index 00000000000..bee3c82599b
--- /dev/null
+++ b/tests/modules/nf-core/maxquant/lfq/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MAXQUANT_LFQ } from '../../../../../modules/nf-core/maxquant/lfq/main.nf' addParams( options: [:] )
+
+workflow test_maxquant_lfq {
+        
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['proteomics']['database']['yeast_ups'], checkIfExists: true), file(params.test_data['proteomics']['parameter']['maxquant'] , checkIfExists: true)
+            ]
+
+
+    rawfiles = [file(params.test_data['proteomics']['msspectra']['ups_file1']) , file(params.test_data['proteomics']['msspectra']['ups_file2'])]
+
+    MAXQUANT_LFQ ( input, rawfiles.collect() )
+}
diff --git a/tests/modules/maxquant/lfq/nextflow.config b/tests/modules/nf-core/maxquant/lfq/nextflow.config
similarity index 100%
rename from tests/modules/maxquant/lfq/nextflow.config
rename to tests/modules/nf-core/maxquant/lfq/nextflow.config
diff --git a/tests/modules/nf-core/maxquant/lfq/test.yml b/tests/modules/nf-core/maxquant/lfq/test.yml
new file mode 100644
index 00000000000..fd2cf9a7fac
--- /dev/null
+++ b/tests/modules/nf-core/maxquant/lfq/test.yml
@@ -0,0 +1,8 @@
+- name: maxquant lfq
+  command: nextflow run ./tests/modules/nf-core/maxquant/lfq -entry test_maxquant_lfq  -c ./tests/config/nextflow.config
+  tags:
+    - maxquant
+    - maxquant/lfq
+  files:
+    - path: output/maxquant/proteinGroups.txt
+      md5sum: 0d0f6aab54fe6dc717d1307bbc207324
diff --git a/tests/modules/nf-core/mcroni/main.nf b/tests/modules/nf-core/mcroni/main.nf
new file mode 100644
index 00000000000..c1eeeb5fa30
--- /dev/null
+++ b/tests/modules/nf-core/mcroni/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MCRONI } from '../../../../modules/nf-core/mcroni/main.nf'
+
+workflow test_mcroni {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    MCRONI ( input )
+}
diff --git a/tests/modules/mcroni/nextflow.config b/tests/modules/nf-core/mcroni/nextflow.config
similarity index 100%
rename from tests/modules/mcroni/nextflow.config
rename to tests/modules/nf-core/mcroni/nextflow.config
diff --git a/tests/modules/nf-core/mcroni/test.yml b/tests/modules/nf-core/mcroni/test.yml
new file mode 100644
index 00000000000..83656baa466
--- /dev/null
+++ b/tests/modules/nf-core/mcroni/test.yml
@@ -0,0 +1,7 @@
+- name: mcroni test_mcroni
+  command: nextflow run ./tests/modules/nf-core/mcroni -entry test_mcroni -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mcroni/nextflow.config
+  tags:
+    - mcroni
+  files:
+    - path: output/mcroni/test_table.tsv
+      md5sum: 64f8438dcc476e8b4d762fedc2e3f69e
diff --git a/tests/modules/nf-core/md5sum/main.nf b/tests/modules/nf-core/md5sum/main.nf
new file mode 100644
index 00000000000..56b22acee1e
--- /dev/null
+++ b/tests/modules/nf-core/md5sum/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MD5SUM } from '../../../../modules/nf-core/md5sum/main.nf'
+
+workflow test_md5sum {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    MD5SUM ( input )
+}
diff --git a/tests/modules/md5sum/nextflow.config b/tests/modules/nf-core/md5sum/nextflow.config
similarity index 100%
rename from tests/modules/md5sum/nextflow.config
rename to tests/modules/nf-core/md5sum/nextflow.config
diff --git a/tests/modules/nf-core/md5sum/test.yml b/tests/modules/nf-core/md5sum/test.yml
new file mode 100644
index 00000000000..02b8efe5a28
--- /dev/null
+++ b/tests/modules/nf-core/md5sum/test.yml
@@ -0,0 +1,8 @@
+- name: md5sum test_md5sum
+  command: nextflow run ./tests/modules/nf-core/md5sum -entry test_md5sum -c ./tests/config/nextflow.config
+  tags:
+    - md5sum
+  files:
+    - path: output/md5sum/test.paired_end.bam.md5
+      md5sum: 1163095be8fdfb2acb3cc6c027389c4b
+    - path: output/md5sum/versions.yml
diff --git a/tests/modules/nf-core/medaka/main.nf b/tests/modules/nf-core/medaka/main.nf
new file mode 100644
index 00000000000..3ae6f6e7fdb
--- /dev/null
+++ b/tests/modules/nf-core/medaka/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MEDAKA } from '../../../../modules/nf-core/medaka/main.nf'
+
+workflow test_medaka {
+    
+    input = [ 
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+    
+    MEDAKA ( input )
+}
diff --git a/tests/modules/medaka/nextflow.config b/tests/modules/nf-core/medaka/nextflow.config
similarity index 100%
rename from tests/modules/medaka/nextflow.config
rename to tests/modules/nf-core/medaka/nextflow.config
diff --git a/tests/modules/nf-core/medaka/test.yml b/tests/modules/nf-core/medaka/test.yml
new file mode 100644
index 00000000000..8e853a38910
--- /dev/null
+++ b/tests/modules/nf-core/medaka/test.yml
@@ -0,0 +1,7 @@
+- name: medaka test_medaka
+  command: nextflow run ./tests/modules/nf-core/medaka -entry test_medaka -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/medaka/nextflow.config
+  tags:
+    - medaka
+  files:
+    - path: output/medaka/test.polished.genome.fa.gz
+      md5sum: f42303f1d6c2c79175faeb00e10b9a6e
diff --git a/tests/modules/nf-core/megahit/main.nf b/tests/modules/nf-core/megahit/main.nf
new file mode 100644
index 00000000000..57369265e98
--- /dev/null
+++ b/tests/modules/nf-core/megahit/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MEGAHIT } from '../../../../modules/nf-core/megahit/main.nf'
+
+workflow test_megahit {
+
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ] 
+    ]
+
+    MEGAHIT ( input )
+}
+
+workflow test_megahit_single {
+
+    input = [ 
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MEGAHIT ( input )
+}
diff --git a/tests/modules/megahit/nextflow.config b/tests/modules/nf-core/megahit/nextflow.config
similarity index 100%
rename from tests/modules/megahit/nextflow.config
rename to tests/modules/nf-core/megahit/nextflow.config
diff --git a/tests/modules/nf-core/megahit/test.yml b/tests/modules/nf-core/megahit/test.yml
new file mode 100644
index 00000000000..ac90e2a6fe4
--- /dev/null
+++ b/tests/modules/nf-core/megahit/test.yml
@@ -0,0 +1,71 @@
+- name: megahit
+  command: nextflow run ./tests/modules/nf-core/megahit -entry test_megahit -c ./tests/config/nextflow.config -process.cpus 1 -c ./tests/modules/nf-core/megahit/nextflow.config
+  tags:
+    - megahit
+  files:
+    - path: output/megahit/megahit_out/test.contigs.fa.gz
+      md5sum: 8ed114f22130e16df3532d3f6b03e116
+    - path: output/megahit/megahit_out/intermediate_contigs/k21.addi.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k21.contigs.fa.gz
+      md5sum: 4221d45f238045bbdb1eea04e4ce4261
+    - path: output/megahit/megahit_out/intermediate_contigs/k21.final.contigs.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k21.local.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k29.addi.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k29.contigs.fa.gz
+      md5sum: c72aeb242788542af0260098b4d61204
+    - path: output/megahit/megahit_out/intermediate_contigs/k29.final.contigs.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k29.local.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k39.addi.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k39.contigs.fa.gz
+      md5sum: aa188f4c92e69c1a4b396e8f2991236f
+    - path: output/megahit/megahit_out/intermediate_contigs/k39.final.contigs.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k39.local.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+
+- name: megahit_single
+  command: nextflow run ./tests/modules/nf-core/megahit -entry test_megahit_single -c ./tests/config/nextflow.config -process.cpus 1 -c ./tests/modules/nf-core/megahit/nextflow.config
+  tags:
+    - megahit
+  files:
+    - path: output/megahit/megahit_out/test.contigs.fa.gz
+      md5sum: f50352838b778cc67824f631197a8346
+    - path: output/megahit/megahit_out/intermediate_contigs/k21.addi.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k21.contigs.fa.gz
+      md5sum: 61554dc60ba8e95d9c1d9dca8d465bef
+    - path: output/megahit/megahit_out/intermediate_contigs/k21.final.contigs.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k21.local.fa.gz
+      md5sum: b916fc620fdf0d23ef33485352c168b3
+    - path: output/megahit/megahit_out/intermediate_contigs/k29.addi.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k29.contigs.fa.gz
+      md5sum: d916bc564854aa0fabaa5234035aa47b
+    - path: output/megahit/megahit_out/intermediate_contigs/k29.final.contigs.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k29.local.fa.gz
+      md5sum: cccf44441e65913b02fb64eb0835dcc1
+    - path: output/megahit/megahit_out/intermediate_contigs/k39.addi.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k39.contigs.fa.gz
+      md5sum: 4416a9e846ccbeb06b880ac2fdc02925
+    - path: output/megahit/megahit_out/intermediate_contigs/k39.final.contigs.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k39.local.fa.gz
+      md5sum: 590d0a08285226d24f7f984f7b3b4f65
+    - path: output/megahit/megahit_out/intermediate_contigs/k59.addi.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k59.contigs.fa.gz
+      md5sum: 51ef726b87a53b0cbdde762d7973a8a7
+    - path: output/megahit/megahit_out/intermediate_contigs/k59.final.contigs.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
+    - path: output/megahit/megahit_out/intermediate_contigs/k59.local.fa.gz
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
diff --git a/tests/modules/nf-core/megan/daa2info/main.nf b/tests/modules/nf-core/megan/daa2info/main.nf
new file mode 100644
index 00000000000..52f0ee2ef26
--- /dev/null
+++ b/tests/modules/nf-core/megan/daa2info/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DIAMOND_MAKEDB } from '../../../../../modules/nf-core/diamond/makedb/main.nf'
+include { DIAMOND_BLASTX } from '../../../../../modules/nf-core/diamond/blastx/main.nf'
+include { MEGAN_DAA2INFO } from '../../../../../modules/nf-core/megan/daa2info/main.nf'
+
+workflow test_megan_daa2info {
+
+    db = [ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true) ]
+    out_ext = 'daa'
+    blast_columns = []
+    megan_summary = true
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
+    MEGAN_DAA2INFO ( DIAMOND_BLASTX.out.daa, megan_summary )
+}
diff --git a/tests/modules/megan/daa2info/nextflow.config b/tests/modules/nf-core/megan/daa2info/nextflow.config
similarity index 100%
rename from tests/modules/megan/daa2info/nextflow.config
rename to tests/modules/nf-core/megan/daa2info/nextflow.config
diff --git a/tests/modules/nf-core/megan/daa2info/test.yml b/tests/modules/nf-core/megan/daa2info/test.yml
new file mode 100644
index 00000000000..d88a5817357
--- /dev/null
+++ b/tests/modules/nf-core/megan/daa2info/test.yml
@@ -0,0 +1,10 @@
+- name: megan daa2info test_megan_daa2info
+  command: nextflow run ./tests/modules/nf-core/megan/daa2info -entry test_megan_daa2info -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/megan/daa2info/nextflow.config
+  tags:
+    - megan/daa2info
+    - megan
+  files:
+    - path: output/megan/test.megan
+      contains: ["@Creator"]
+    - path: output/megan/test.txt.gz
+      contains: ["# Number of reads: 1"]
diff --git a/tests/modules/nf-core/megan/rma2info/main.nf b/tests/modules/nf-core/megan/rma2info/main.nf
new file mode 100644
index 00000000000..c8c76787724
--- /dev/null
+++ b/tests/modules/nf-core/megan/rma2info/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MEGAN_RMA2INFO } from '../../../../../modules/nf-core/megan/rma2info/main.nf'
+
+workflow test_megan_rma2info {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/a7e61654553887475a2f7178108587ecd9b54608/data/delete_me/malt/test.rma6', checkIfExists: true)
+    ]
+    megan_summary = true
+
+    MEGAN_RMA2INFO ( input, megan_summary )
+}
diff --git a/tests/modules/megan/rma2info/nextflow.config b/tests/modules/nf-core/megan/rma2info/nextflow.config
similarity index 100%
rename from tests/modules/megan/rma2info/nextflow.config
rename to tests/modules/nf-core/megan/rma2info/nextflow.config
diff --git a/tests/modules/nf-core/megan/rma2info/test.yml b/tests/modules/nf-core/megan/rma2info/test.yml
new file mode 100644
index 00000000000..dd39a159da8
--- /dev/null
+++ b/tests/modules/nf-core/megan/rma2info/test.yml
@@ -0,0 +1,12 @@
+- name: megan rma2info test_megan_rma2info
+  command: nextflow run ./tests/modules/nf-core/megan/rma2info -entry test_megan_rma2info -c ./tests/config/nextflow.config
+  tags:
+    - megan
+    - megan/rma2info
+  files:
+    - path: output/megan/test.megan
+      contains:
+        - "@Creator"
+    - path: output/megan/test.txt.gz
+      md5sum: 5c3b876aa0abef12158bcd7c3702740f
+    - path: output/megan/versions.yml
diff --git a/tests/modules/nf-core/meningotype/main.nf b/tests/modules/nf-core/meningotype/main.nf
new file mode 100644
index 00000000000..14ff4d00728
--- /dev/null
+++ b/tests/modules/nf-core/meningotype/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MENINGOTYPE } from '../../../../modules/nf-core/meningotype/main.nf'
+
+workflow test_meningotype {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    MENINGOTYPE ( input )
+}
diff --git a/tests/modules/meningotype/nextflow.config b/tests/modules/nf-core/meningotype/nextflow.config
similarity index 100%
rename from tests/modules/meningotype/nextflow.config
rename to tests/modules/nf-core/meningotype/nextflow.config
diff --git a/tests/modules/nf-core/meningotype/test.yml b/tests/modules/nf-core/meningotype/test.yml
new file mode 100644
index 00000000000..980040fae6b
--- /dev/null
+++ b/tests/modules/nf-core/meningotype/test.yml
@@ -0,0 +1,7 @@
+- name: meningotype test_meningotype
+  command: nextflow run ./tests/modules/nf-core/meningotype -entry test_meningotype -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/meningotype/nextflow.config
+  tags:
+    - meningotype
+  files:
+    - path: output/meningotype/test.tsv
+      md5sum: 25651bccb3d1c64cefcb7946fda30a6c
diff --git a/tests/modules/nf-core/merqury/main.nf b/tests/modules/nf-core/merqury/main.nf
new file mode 100644
index 00000000000..7d525446512
--- /dev/null
+++ b/tests/modules/nf-core/merqury/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERYL_COUNT    } from '../../../../modules/nf-core/meryl/count/main.nf'
+include { MERYL_UNIONSUM } from '../../../../modules/nf-core/meryl/unionsum/main.nf'
+include { MERQURY        } from '../../../../modules/nf-core/merqury/main.nf'
+
+workflow test_merqury {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    assembly = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    MERYL_COUNT ( input )
+    MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db )
+    MERQURY ( MERYL_UNIONSUM.out.meryl_db.join( Channel.value( assembly ) ) )
+}
diff --git a/tests/modules/merqury/nextflow.config b/tests/modules/nf-core/merqury/nextflow.config
similarity index 100%
rename from tests/modules/merqury/nextflow.config
rename to tests/modules/nf-core/merqury/nextflow.config
diff --git a/tests/modules/nf-core/merqury/test.yml b/tests/modules/nf-core/merqury/test.yml
new file mode 100644
index 00000000000..cbc02eba44b
--- /dev/null
+++ b/tests/modules/nf-core/merqury/test.yml
@@ -0,0 +1,34 @@
+- name: merqury test_merqury
+  command: nextflow run ./tests/modules/nf-core/merqury -entry test_merqury -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/merqury/nextflow.config
+  tags:
+    - merqury
+  files:
+    - path: output/merqury/genome_only.bed
+      md5sum: b611f22cde0e410a2ca07c1eefd042d3
+    - path: output/merqury/genome_only.wig
+      md5sum: 19cf44989af72af597ef80d3489b4882
+    - path: output/merqury/test.completeness.stats
+    - path: output/merqury/test.dist_only.hist
+      md5sum: e2e6b54b0febef1f0fcf24cd2afd0b7a
+    - path: output/merqury/test.genome.qv
+      md5sum: c554315aabcc4207c367805cf3090da3
+    - path: output/merqury/test.genome.spectra-cn.fl.png
+      md5sum: 3265701cbb1ddaed6d5cb6b4560564fd
+    - path: output/merqury/test.genome.spectra-cn.hist
+      md5sum: 6140a138ba47cb2b97814c93f80b2575
+    - path: output/merqury/test.genome.spectra-cn.ln.png
+      md5sum: 6386b604a8f0fbc43a1e3473ad9a779e
+    - path: output/merqury/test.genome.spectra-cn.st.png
+      md5sum: d5af80c91d23b182589b0ec131047f00
+    - path: output/merqury/test.qv
+      md5sum: 6e04952bc182221c8b9e242dc3298808
+    - path: output/merqury/test.spectra-asm.fl.png
+      md5sum: 60920481d988018a4f36a9be5b10c4ec
+    - path: output/merqury/test.spectra-asm.hist
+      md5sum: 541c9d1f87ab5c44df5e9e0acc440f8d
+    - path: output/merqury/test.spectra-asm.ln.png
+      md5sum: 54790dd54b5d8948d3676d32da1972df
+    - path: output/merqury/test.spectra-asm.st.png
+      md5sum: 010e013b5411ab2790e9a93ee70a574a
+    - path: output/merqury/test.unionsumdb.hist.ploidy
+      md5sum: f6904468b41a495c7ce255a7a5f3a302
diff --git a/tests/modules/nf-core/merquryfk/katcomp/main.nf b/tests/modules/nf-core/merquryfk/katcomp/main.nf
new file mode 100644
index 00000000000..78857f85494
--- /dev/null
+++ b/tests/modules/nf-core/merquryfk/katcomp/main.nf
@@ -0,0 +1,41 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTK_FASTK as FASTK1 } from '../../../../../modules/nf-core/fastk/fastk/main.nf'
+include { FASTK_FASTK as FASTK2 } from '../../../../../modules/nf-core/fastk/fastk/main.nf'
+include { MERQURYFK_KATCOMP } from '../../../../../modules/nf-core/merquryfk/katcomp/main.nf'
+
+workflow test_merquryfk_katcomp_png {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    FASTK1 ( input )
+    FASTK2 ( input )
+    MERQURYFK_KATCOMP (
+        FASTK1.out.hist
+            .join( FASTK1.out.ktab )
+            .join( FASTK2.out.hist )
+            .join( FASTK2.out.ktab )
+    )
+}
+
+workflow test_merquryfk_katcomp_pdf {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    FASTK1 ( input )
+    FASTK2 ( input )
+    MERQURYFK_KATCOMP (
+        FASTK1.out.hist
+            .join( FASTK1.out.ktab )
+            .join( FASTK2.out.hist )
+            .join( FASTK2.out.ktab )
+    )
+}
diff --git a/tests/modules/merquryfk/katcomp/nextflow.config b/tests/modules/nf-core/merquryfk/katcomp/nextflow.config
similarity index 100%
rename from tests/modules/merquryfk/katcomp/nextflow.config
rename to tests/modules/nf-core/merquryfk/katcomp/nextflow.config
diff --git a/tests/modules/nf-core/merquryfk/katcomp/test.yml b/tests/modules/nf-core/merquryfk/katcomp/test.yml
new file mode 100644
index 00000000000..21d80bf8a83
--- /dev/null
+++ b/tests/modules/nf-core/merquryfk/katcomp/test.yml
@@ -0,0 +1,22 @@
+- name: merquryfk katcomp test_merquryfk_katcomp_png
+  command: nextflow run ./tests/modules/nf-core/merquryfk/katcomp -entry test_merquryfk_katcomp_png -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/merquryfk/katcomp/nextflow.config
+  tags:
+    - merquryfk
+    - merquryfk/katcomp
+  files:
+    - path: output/merquryfk/test.fi.png
+      md5sum: 83b30d2f6103190887e66d3690c63d55
+    - path: output/merquryfk/test.ln.png
+      md5sum: 6d223a9b91937b1f984e3415fd1580bb
+    - path: output/merquryfk/test.st.png
+      md5sum: 00a851c8f1c7f2f5b8bb57c6f07b161c
+
+- name: merquryfk katcomp test_merquryfk_katcomp_pdf
+  command: nextflow run ./tests/modules/nf-core/merquryfk/katcomp -entry test_merquryfk_katcomp_pdf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/merquryfk/katcomp/nextflow.config
+  tags:
+    - merquryfk
+    - merquryfk/katcomp
+  files:
+    - path: output/merquryfk/test.fi.pdf
+    - path: output/merquryfk/test.ln.pdf
+    - path: output/merquryfk/test.st.pdf
diff --git a/tests/modules/nf-core/merquryfk/katgc/main.nf b/tests/modules/nf-core/merquryfk/katgc/main.nf
new file mode 100644
index 00000000000..d16ef2a1673
--- /dev/null
+++ b/tests/modules/nf-core/merquryfk/katgc/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTK_FASTK     } from '../../../../../modules/nf-core/fastk/fastk/main.nf'
+include { MERQURYFK_KATGC } from '../../../../../modules/nf-core/merquryfk/katgc/main.nf'
+
+workflow test_merquryfk_katgc_png {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    FASTK_FASTK ( input )
+    MERQURYFK_KATGC ( FASTK_FASTK.out.hist
+        .join( FASTK_FASTK.out.ktab )
+    )
+}
+
+workflow test_merquryfk_katgc_pdf {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    FASTK_FASTK ( input )
+    MERQURYFK_KATGC ( FASTK_FASTK.out.hist
+        .join( FASTK_FASTK.out.ktab )
+    )
+}
diff --git a/tests/modules/merquryfk/katgc/nextflow.config b/tests/modules/nf-core/merquryfk/katgc/nextflow.config
similarity index 100%
rename from tests/modules/merquryfk/katgc/nextflow.config
rename to tests/modules/nf-core/merquryfk/katgc/nextflow.config
diff --git a/tests/modules/nf-core/merquryfk/katgc/test.yml b/tests/modules/nf-core/merquryfk/katgc/test.yml
new file mode 100644
index 00000000000..41ef4f92f0d
--- /dev/null
+++ b/tests/modules/nf-core/merquryfk/katgc/test.yml
@@ -0,0 +1,22 @@
+- name: merquryfk katgc test_merquryfk_katgc_png
+  command: nextflow run ./tests/modules/nf-core/merquryfk/katgc -entry test_merquryfk_katgc_png -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/merquryfk/katgc/nextflow.config
+  tags:
+    - merquryfk
+    - merquryfk/katgc
+  files:
+    - path: output/merquryfk/test.fi.png
+      md5sum: bd4cf549d5c8eaaba82f78010f652dac
+    - path: output/merquryfk/test.ln.png
+      md5sum: 3f55f27a486c9be6187d71e3a570beb5
+    - path: output/merquryfk/test.st.png
+      md5sum: 636339e17af69c4b64f27f36d66edcd8
+
+- name: merquryfk katgc test_merquryfk_katgc_pdf
+  command: nextflow run ./tests/modules/nf-core/merquryfk/katgc -entry test_merquryfk_katgc_pdf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/merquryfk/katgc/nextflow.config
+  tags:
+    - merquryfk
+    - merquryfk/katgc
+  files:
+    - path: output/merquryfk/test.fi.pdf
+    - path: output/merquryfk/test.ln.pdf
+    - path: output/merquryfk/test.st.pdf
diff --git a/tests/modules/nf-core/merquryfk/merquryfk/main.nf b/tests/modules/nf-core/merquryfk/merquryfk/main.nf
new file mode 100644
index 00000000000..282833a4240
--- /dev/null
+++ b/tests/modules/nf-core/merquryfk/merquryfk/main.nf
@@ -0,0 +1,42 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTK_FASTK         } from '../../../../../modules/nf-core/fastk/fastk/main.nf'
+include { MERQURYFK_MERQURYFK } from '../../../../../modules/nf-core/merquryfk/merquryfk/main.nf'
+
+workflow test_merquryfk_merquryfk_png {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    assembly = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    FASTK_FASTK ( input )
+    MERQURYFK_MERQURYFK ( FASTK_FASTK.out.hist
+        .join( FASTK_FASTK.out.ktab )
+        .join( Channel.value( assembly ) )
+    )
+}
+
+workflow test_merquryfk_merquryfk_pdf {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    assembly = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    FASTK_FASTK ( input )
+    MERQURYFK_MERQURYFK ( FASTK_FASTK.out.hist
+        .join( FASTK_FASTK.out.ktab )
+        .join( Channel.value( assembly ) )
+    )
+}
diff --git a/tests/modules/merquryfk/merquryfk/nextflow.config b/tests/modules/nf-core/merquryfk/merquryfk/nextflow.config
similarity index 100%
rename from tests/modules/merquryfk/merquryfk/nextflow.config
rename to tests/modules/nf-core/merquryfk/merquryfk/nextflow.config
diff --git a/tests/modules/nf-core/merquryfk/merquryfk/test.yml b/tests/modules/nf-core/merquryfk/merquryfk/test.yml
new file mode 100644
index 00000000000..49f6281be8f
--- /dev/null
+++ b/tests/modules/nf-core/merquryfk/merquryfk/test.yml
@@ -0,0 +1,47 @@
+- name: merquryfk merquryfk test_merquryfk_merquryfk_png
+  command: nextflow run ./tests/modules/nf-core/merquryfk/merquryfk -entry test_merquryfk_merquryfk_png -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/merquryfk/merquryfk/nextflow.config
+  tags:
+    - merquryfk/merquryfk
+    - merquryfk
+  files:
+    - path: output/merquryfk/test.completeness.stats
+      md5sum: 797224fa75606bbda7f62caae7c9151c
+    - path: output/merquryfk/test.genome.qv
+      md5sum: 1e11be8abfa2230024042832f58f96f9
+    - path: output/merquryfk/test.genome.spectra-cn.fl.png
+      md5sum: 50bad6b85b8f80b8411b50e4119bc959
+    - path: output/merquryfk/test.genome.spectra-cn.ln.png
+      md5sum: 50bad6b85b8f80b8411b50e4119bc959
+    - path: output/merquryfk/test.genome.spectra-cn.st.png
+      md5sum: 50bad6b85b8f80b8411b50e4119bc959
+    - path: output/merquryfk/test.genome_only.bed
+      md5sum: 662d73e8a0019708feb538ec53c220f7
+    - path: output/merquryfk/test.qv
+      md5sum: 02b4d5c639ca706ff707bad89e29d90e
+    - path: output/merquryfk/test.spectra-asm.fl.png
+      md5sum: bb9ac38fe8991fbacbe791e562626d89
+    - path: output/merquryfk/test.spectra-asm.ln.png
+      md5sum: 48534a9d5e2ce9365eb1f0397c76f337
+    - path: output/merquryfk/test.spectra-asm.st.png
+      md5sum: 5e031a8b9ba2800e291721a11f4d9c00
+
+- name: merquryfk merquryfk test_merquryfk_merquryfk_pdf
+  command: nextflow run ./tests/modules/nf-core/merquryfk/merquryfk -entry test_merquryfk_merquryfk_pdf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/merquryfk/merquryfk/nextflow.config
+  tags:
+    - merquryfk/merquryfk
+    - merquryfk
+  files:
+    - path: output/merquryfk/test.completeness.stats
+      md5sum: 797224fa75606bbda7f62caae7c9151c
+    - path: output/merquryfk/test.genome.qv
+      md5sum: 1e11be8abfa2230024042832f58f96f9
+    - path: output/merquryfk/test.genome.spectra-cn.fl.pdf
+    - path: output/merquryfk/test.genome.spectra-cn.ln.pdf
+    - path: output/merquryfk/test.genome.spectra-cn.st.pdf
+    - path: output/merquryfk/test.genome_only.bed
+      md5sum: 662d73e8a0019708feb538ec53c220f7
+    - path: output/merquryfk/test.qv
+      md5sum: 02b4d5c639ca706ff707bad89e29d90e
+    - path: output/merquryfk/test.spectra-asm.fl.pdf
+    - path: output/merquryfk/test.spectra-asm.ln.pdf
+    - path: output/merquryfk/test.spectra-asm.st.pdf
diff --git a/tests/modules/nf-core/merquryfk/ploidyplot/main.nf b/tests/modules/nf-core/merquryfk/ploidyplot/main.nf
new file mode 100644
index 00000000000..26d228ed534
--- /dev/null
+++ b/tests/modules/nf-core/merquryfk/ploidyplot/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTK_FASTK          } from '../../../../../modules/nf-core/fastk/fastk/main.nf'
+include { MERQURYFK_PLOIDYPLOT } from '../../../../../modules/nf-core/merquryfk/ploidyplot/main.nf'
+
+workflow test_merquryfk_ploidyplot_png {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    FASTK_FASTK ( input )
+    MERQURYFK_PLOIDYPLOT ( FASTK_FASTK.out.hist
+        .join( FASTK_FASTK.out.ktab )
+    )
+}
+
+workflow test_merquryfk_ploidyplot_pdf {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    FASTK_FASTK ( input )
+    MERQURYFK_PLOIDYPLOT (
+        FASTK_FASTK.out.hist
+            .join( FASTK_FASTK.out.ktab )
+    )
+}
diff --git a/tests/modules/merquryfk/ploidyplot/nextflow.config b/tests/modules/nf-core/merquryfk/ploidyplot/nextflow.config
similarity index 100%
rename from tests/modules/merquryfk/ploidyplot/nextflow.config
rename to tests/modules/nf-core/merquryfk/ploidyplot/nextflow.config
diff --git a/tests/modules/nf-core/merquryfk/ploidyplot/test.yml b/tests/modules/nf-core/merquryfk/ploidyplot/test.yml
new file mode 100644
index 00000000000..1a0277a1dac
--- /dev/null
+++ b/tests/modules/nf-core/merquryfk/ploidyplot/test.yml
@@ -0,0 +1,22 @@
+- name: merquryfk ploidyplot test_merquryfk_ploidyplot_png
+  command: nextflow run ./tests/modules/nf-core/merquryfk/ploidyplot -entry test_merquryfk_ploidyplot_png -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/merquryfk/ploidyplot/nextflow.config
+  tags:
+    - merquryfk
+    - merquryfk/ploidyplot
+  files:
+    - path: output/merquryfk/test.fi.png
+      md5sum: c6f883f3d57ad64727219052e97d39b3
+    - path: output/merquryfk/test.ln.png
+      md5sum: bd299e2eceb258328d1a41c024d7fbf4
+    - path: output/merquryfk/test.st.png
+      md5sum: 4f858ed9712196606859675c3f3ba7a9
+
+- name: merquryfk ploidyplot test_merquryfk_ploidyplot_pdf
+  command: nextflow run ./tests/modules/nf-core/merquryfk/ploidyplot -entry test_merquryfk_ploidyplot_pdf -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/merquryfk/ploidyplot/nextflow.config
+  tags:
+    - merquryfk
+    - merquryfk/ploidyplot
+  files:
+    - path: output/merquryfk/test.fi.pdf
+    - path: output/merquryfk/test.ln.pdf
+    - path: output/merquryfk/test.st.pdf
diff --git a/tests/modules/nf-core/meryl/count/main.nf b/tests/modules/nf-core/meryl/count/main.nf
new file mode 100644
index 00000000000..cd71fb983da
--- /dev/null
+++ b/tests/modules/nf-core/meryl/count/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERYL_COUNT } from '../../../../../modules/nf-core/meryl/count/main.nf'
+
+workflow test_meryl_count_single_end {
+
+    input = [
+        [ id:'test' , single_end: true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MERYL_COUNT ( input )
+}
+
+workflow test_meryl_count_paired_end {
+
+    input = [
+        [ id:'test' , single_end: false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    MERYL_COUNT ( input )
+}
diff --git a/tests/modules/meryl/count/nextflow.config b/tests/modules/nf-core/meryl/count/nextflow.config
similarity index 100%
rename from tests/modules/meryl/count/nextflow.config
rename to tests/modules/nf-core/meryl/count/nextflow.config
diff --git a/tests/modules/nf-core/meryl/count/test.yml b/tests/modules/nf-core/meryl/count/test.yml
new file mode 100644
index 00000000000..7f4f9a50aac
--- /dev/null
+++ b/tests/modules/nf-core/meryl/count/test.yml
@@ -0,0 +1,17 @@
+- name: meryl count test_meryl_count_single_end
+  command: nextflow run ./tests/modules/nf-core/meryl/count -entry test_meryl_count_single_end -c ./tests/config/nextflow.config
+  tags:
+    - meryl/count
+    - meryl
+  files:
+    - path: output/meryl/versions.yml
+      md5sum: 5fe537d873925ccbcc4edf0983e9eda0
+
+- name: meryl count test_meryl_count_paired_end
+  command: nextflow run ./tests/modules/nf-core/meryl/count -entry test_meryl_count_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - meryl/count
+    - meryl
+  files:
+    - path: output/meryl/versions.yml
+      md5sum: 4961f13cfb60ba8764ed666e70dbf12c
diff --git a/tests/modules/nf-core/meryl/histogram/main.nf b/tests/modules/nf-core/meryl/histogram/main.nf
new file mode 100644
index 00000000000..153a76d44bf
--- /dev/null
+++ b/tests/modules/nf-core/meryl/histogram/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERYL_COUNT     } from '../../../../../modules/nf-core/meryl/count/main.nf'
+include { MERYL_HISTOGRAM } from '../../../../../modules/nf-core/meryl/histogram/main.nf'
+
+workflow test_meryl_histogram {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MERYL_COUNT ( input )
+    MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
+}
diff --git a/tests/modules/meryl/histogram/nextflow.config b/tests/modules/nf-core/meryl/histogram/nextflow.config
similarity index 100%
rename from tests/modules/meryl/histogram/nextflow.config
rename to tests/modules/nf-core/meryl/histogram/nextflow.config
diff --git a/tests/modules/nf-core/meryl/histogram/test.yml b/tests/modules/nf-core/meryl/histogram/test.yml
new file mode 100644
index 00000000000..7d794aa773b
--- /dev/null
+++ b/tests/modules/nf-core/meryl/histogram/test.yml
@@ -0,0 +1,10 @@
+- name: meryl histogram test_meryl_histogram
+  command: nextflow run ./tests/modules/nf-core/meryl/histogram -entry test_meryl_histogram -c ./tests/config/nextflow.config
+  tags:
+    - meryl/histogram
+    - meryl
+  files:
+    - path: output/meryl/test.hist
+      md5sum: 4bfdc8b287ee0cfd9922bbfa8cd64650
+    - path: output/meryl/versions.yml
+      md5sum: 050038f1b1df79977a393cce1b4b2ddb
diff --git a/tests/modules/nf-core/meryl/unionsum/main.nf b/tests/modules/nf-core/meryl/unionsum/main.nf
new file mode 100644
index 00000000000..e4e767375ce
--- /dev/null
+++ b/tests/modules/nf-core/meryl/unionsum/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERYL_COUNT    } from '../../../../../modules/nf-core/meryl/count/main.nf'
+include { MERYL_UNIONSUM } from '../../../../../modules/nf-core/meryl/unionsum/main.nf'
+
+workflow test_meryl_unionsum_single_end {
+
+    input = [
+        [ id:'test', single_end: true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MERYL_COUNT ( input )
+    MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db )
+}
+
+workflow test_meryl_unionsum_paired_end {
+
+    input = [
+        [ id:'test', single_end: false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    MERYL_COUNT ( input )
+    MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db )
+}
diff --git a/tests/modules/meryl/unionsum/nextflow.config b/tests/modules/nf-core/meryl/unionsum/nextflow.config
similarity index 100%
rename from tests/modules/meryl/unionsum/nextflow.config
rename to tests/modules/nf-core/meryl/unionsum/nextflow.config
diff --git a/tests/modules/nf-core/meryl/unionsum/test.yml b/tests/modules/nf-core/meryl/unionsum/test.yml
new file mode 100644
index 00000000000..244b2a58644
--- /dev/null
+++ b/tests/modules/nf-core/meryl/unionsum/test.yml
@@ -0,0 +1,17 @@
+- name: meryl unionsum test_meryl_unionsum_single_end
+  command: nextflow run ./tests/modules/nf-core/meryl/unionsum -entry test_meryl_unionsum_single_end -c ./tests/config/nextflow.config
+  tags:
+    - meryl
+    - meryl/unionsum
+  files:
+    - path: output/meryl/versions.yml
+      md5sum: 7de859c6d3a29d72f6c9c976609d0913
+
+- name: meryl unionsum test_meryl_unionsum_paired_end
+  command: nextflow run ./tests/modules/nf-core/meryl/unionsum -entry test_meryl_unionsum_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - meryl
+    - meryl/unionsum
+  files:
+    - path: output/meryl/versions.yml
+      md5sum: a16decdec014ccb9bdab69a4a1d30818
diff --git a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf
new file mode 100644
index 00000000000..861e0cb5f74
--- /dev/null
+++ b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf'
+
+workflow test_metabat2_jgisummarizebamcontigdepths {
+    
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input )
+}
diff --git a/tests/modules/metabat2/jgisummarizebamcontigdepths/nextflow.config b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/nextflow.config
similarity index 100%
rename from tests/modules/metabat2/jgisummarizebamcontigdepths/nextflow.config
rename to tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/nextflow.config
diff --git a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/test.yml b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/test.yml
new file mode 100644
index 00000000000..c68fac757b7
--- /dev/null
+++ b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/test.yml
@@ -0,0 +1,8 @@
+- name: metabat2 jgisummarizebamcontigdepths test_metabat2_jgisummarizebamcontigdepths
+  command: nextflow run ./tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths -entry test_metabat2_jgisummarizebamcontigdepths -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/nextflow.config
+  tags:
+    - metabat2/jgisummarizebamcontigdepths
+    - metabat2
+  files:
+    - path: output/metabat2/test.txt.gz
+      md5sum: 8f735aa408d6c90e5a0310e06ace7a9a
diff --git a/tests/modules/nf-core/metabat2/metabat2/main.nf b/tests/modules/nf-core/metabat2/metabat2/main.nf
new file mode 100644
index 00000000000..7bead547365
--- /dev/null
+++ b/tests/modules/nf-core/metabat2/metabat2/main.nf
@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { METABAT2_METABAT2 } from '../../../../../modules/nf-core/metabat2/metabat2/main.nf'
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf'
+
+workflow test_metabat2_no_depth {
+
+    input_depth = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+    Channel.fromPath(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+        .map { it -> [[ id:'test', single_end:false ], it, []] }
+        .set { input_metabat2 }
+    
+    METABAT2_METABAT2 ( input_metabat2 )
+}
+
+workflow test_metabat2_depth {
+
+    input_depth = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
+
+    Channel.fromPath(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+        .map { it -> [[ id:'test', single_end:false ], it] }
+        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+        .set { input_metabat2 }
+
+        METABAT2_METABAT2 ( input_metabat2 )
+}
diff --git a/tests/modules/metabat2/metabat2/nextflow.config b/tests/modules/nf-core/metabat2/metabat2/nextflow.config
similarity index 100%
rename from tests/modules/metabat2/metabat2/nextflow.config
rename to tests/modules/nf-core/metabat2/metabat2/nextflow.config
diff --git a/tests/modules/nf-core/metabat2/metabat2/test.yml b/tests/modules/nf-core/metabat2/metabat2/test.yml
new file mode 100644
index 00000000000..e1766921426
--- /dev/null
+++ b/tests/modules/nf-core/metabat2/metabat2/test.yml
@@ -0,0 +1,24 @@
+- name: metabat2 metabat2 test_metabat2_no_depth
+  command: nextflow run ./tests/modules/nf-core/metabat2/metabat2 -entry test_metabat2_no_depth -c ./tests/config/nextflow.config
+  tags:
+    - metabat2
+    - metabat2/metabat2
+  files:
+    - path: output/metabat2/bins/test.1.fa.gz
+      md5sum: 0e9bce5b5a0033fd4411a21dec881170
+    - path: output/metabat2/test.tsv.gz
+    - path: output/metabat2/versions.yml
+      md5sum: 5742a71af36c3a748fd5726d76924ba8
+
+- name: metabat2 metabat2 test_metabat2_depth
+  command: nextflow run ./tests/modules/nf-core/metabat2/metabat2 -entry test_metabat2_depth -c ./tests/config/nextflow.config
+  tags:
+    - metabat2
+    - metabat2/metabat2
+  files:
+    - path: output/metabat2/bins/test.1.fa.gz
+      md5sum: 0e9bce5b5a0033fd4411a21dec881170
+    - path: output/metabat2/test.tsv.gz
+    - path: output/metabat2/test.txt.gz
+    - path: output/metabat2/versions.yml
+      md5sum: 538c56b2df7d90580f05097218b5d5b1
diff --git a/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf
new file mode 100644
index 00000000000..eaa46a1acd5
--- /dev/null
+++ b/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR                           } from '../../../../../modules/nf-core/untar/main.nf'
+include { METAPHLAN3                      } from '../../../../../modules/nf-core/metaphlan3/metaphlan3/main.nf'
+include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../../../../modules/nf-core/metaphlan3/mergemetaphlantables/main.nf'
+
+workflow test_metaphlan3_mergemetaphlantables {
+
+    input = Channel.of(
+        [[ id:'test', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]],
+        [[ id:'test2', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]]
+    )
+
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
+
+    UNTAR ( db )
+    METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
+    METAPHLAN3_MERGEMETAPHLANTABLES ( METAPHLAN3.out.profile.map{ [[id:"test"], it[1]] }.groupTuple() )
+
+}
diff --git a/tests/modules/metaphlan3/mergemetaphlantables/nextflow.config b/tests/modules/nf-core/metaphlan3/mergemetaphlantables/nextflow.config
similarity index 100%
rename from tests/modules/metaphlan3/mergemetaphlantables/nextflow.config
rename to tests/modules/nf-core/metaphlan3/mergemetaphlantables/nextflow.config
diff --git a/tests/modules/nf-core/metaphlan3/mergemetaphlantables/test.yml b/tests/modules/nf-core/metaphlan3/mergemetaphlantables/test.yml
new file mode 100644
index 00000000000..7776a44b73f
--- /dev/null
+++ b/tests/modules/nf-core/metaphlan3/mergemetaphlantables/test.yml
@@ -0,0 +1,8 @@
+- name: metaphlan3 mergemetaphlantables test_metaphlan3_mergemetaphlantables
+  command: nextflow run ./tests/modules/nf-core/metaphlan3/mergemetaphlantables -entry test_metaphlan3_mergemetaphlantables -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/metaphlan3/mergemetaphlantables/nextflow.config
+  tags:
+    - metaphlan3/mergemetaphlantables
+    - metaphlan3
+  files:
+    - path: output/metaphlan3/test.txt
+      contains: ["clade_name	NCBI_tax_id"]
diff --git a/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf
new file mode 100644
index 00000000000..4a0f7948f5c
--- /dev/null
+++ b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf
@@ -0,0 +1,66 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR                 } from '../../../../../modules/nf-core/untar/main.nf'
+include { METAPHLAN3_METAPHLAN3 } from '../../../../../modules/nf-core/metaphlan3/metaphlan3/main.nf'
+
+workflow test_metaphlan3_single_end {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
+
+    UNTAR ( db )
+    METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
+}
+
+workflow test_metaphlan3_single_end_nodb {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    UNTAR ( db )
+    METAPHLAN3_METAPHLAN3 ( input, [] )
+}
+
+workflow test_metaphlan3_paired_end {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
+
+    UNTAR ( db )
+    METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
+}
+
+workflow test_metaphlan3_sam {
+
+    input = [ [ id:'test'], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
+            ]
+
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
+
+    UNTAR ( db )
+    SAMTOOLS_VIEW ( input, [] )
+    METAPHLAN3_METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar.map{ it[1] } )
+}
+
+workflow test_metaphlan3_fasta {
+
+    input = [ [ id:'test', single_end:true], // meta map
+              [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+            ]
+
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
+
+    UNTAR ( db )
+    METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
+}
diff --git a/tests/modules/metaphlan3/metaphlan3/nextflow.config b/tests/modules/nf-core/metaphlan3/metaphlan3/nextflow.config
similarity index 100%
rename from tests/modules/metaphlan3/metaphlan3/nextflow.config
rename to tests/modules/nf-core/metaphlan3/metaphlan3/nextflow.config
diff --git a/tests/modules/nf-core/metaphlan3/metaphlan3/test.yml b/tests/modules/nf-core/metaphlan3/metaphlan3/test.yml
new file mode 100644
index 00000000000..7c26575b352
--- /dev/null
+++ b/tests/modules/nf-core/metaphlan3/metaphlan3/test.yml
@@ -0,0 +1,123 @@
+- name: metaphlan3 test_metaphlan3_single_end
+  command: nextflow run ./tests/modules/nf-core/metaphlan3/metaphlan3 -entry test_metaphlan3_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/metaphlan3/metaphlan3/nextflow.config
+  tags:
+    - metaphlan3
+  files:
+    - path: output/metaphlan3/test.biom
+      contains:
+        - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"'
+    - path: output/metaphlan3/test.bowtie2out.txt
+      md5sum: ef46a9c6a8ce9cae26fbfd5527116fd5
+    - path: output/metaphlan3/test_profile.txt
+      md5sum: 72d40ee2304c162f3c165e1e578ed152
+    - path: output/untar/metaphlan_database/mpa_latest
+      md5sum: b1337362f607000384563a56a6ff4790
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.1.bt2
+      md5sum: d52a98fe273742ade7c744b819a7c5c1
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.2.bt2
+      md5sum: b14cc7faf3a4fae792160c917aebfe03
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.3.bt2
+      md5sum: 1bca5df879f2c6fad0c54984d0651bfb
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.4.bt2
+      md5sum: 249ee1c672d52d50cee41cb94b6adc42
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.fasta
+      md5sum: d3efe201c9eb449e877ead36656abf5f
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.pkl
+      md5sum: b208bb15eaef50d91cc7d5e35a1518ee
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
+      md5sum: ed05be063280e8629193e52903b07591
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
+      md5sum: 1ca16b905abf657b88ca2bc12e7ad404
+
+- name: metaphlan3 test_metaphlan3_paired_end
+  command: nextflow run ./tests/modules/nf-core/metaphlan3/metaphlan3 -entry test_metaphlan3_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/metaphlan3/metaphlan3/nextflow.config
+  tags:
+    - metaphlan3
+  files:
+    - path: output/metaphlan3/test.biom
+      contains:
+        - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"'
+    - path: output/metaphlan3/test.bowtie2out.txt
+      md5sum: ce11486fcc0e68fe7152867a3634e09a
+    - path: output/metaphlan3/test_profile.txt
+      md5sum: fcf99fec08ee00db6ef2c12fb93bc14b
+    - path: output/untar/metaphlan_database/mpa_latest
+      md5sum: b1337362f607000384563a56a6ff4790
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.1.bt2
+      md5sum: d52a98fe273742ade7c744b819a7c5c1
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.2.bt2
+      md5sum: b14cc7faf3a4fae792160c917aebfe03
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.3.bt2
+      md5sum: 1bca5df879f2c6fad0c54984d0651bfb
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.4.bt2
+      md5sum: 249ee1c672d52d50cee41cb94b6adc42
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.fasta
+      md5sum: d3efe201c9eb449e877ead36656abf5f
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.pkl
+      md5sum: b208bb15eaef50d91cc7d5e35a1518ee
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
+      md5sum: ed05be063280e8629193e52903b07591
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
+      md5sum: 1ca16b905abf657b88ca2bc12e7ad404
+
+- name: metaphlan3 test_metaphlan3_sam
+  command: nextflow run ./tests/modules/nf-core/metaphlan3/metaphlan3 -entry test_metaphlan3_sam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/metaphlan3/metaphlan3/nextflow.config
+  tags:
+    - metaphlan3
+  files:
+    - path: output/metaphlan3/test.biom
+      contains:
+        - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"'
+    - path: output/metaphlan3/test_profile.txt
+      md5sum: e050d49f7df8a23617880ef9ed7745a0
+    - path: output/samtools/test.sam.bam
+      md5sum: 1d5be3c91979ead358e3980e3e7c9acf
+    - path: output/untar/metaphlan_database/mpa_latest
+      md5sum: b1337362f607000384563a56a6ff4790
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.1.bt2
+      md5sum: d52a98fe273742ade7c744b819a7c5c1
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.2.bt2
+      md5sum: b14cc7faf3a4fae792160c917aebfe03
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.3.bt2
+      md5sum: 1bca5df879f2c6fad0c54984d0651bfb
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.4.bt2
+      md5sum: 249ee1c672d52d50cee41cb94b6adc42
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.fasta
+      md5sum: d3efe201c9eb449e877ead36656abf5f
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.pkl
+      md5sum: b208bb15eaef50d91cc7d5e35a1518ee
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
+      md5sum: ed05be063280e8629193e52903b07591
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
+      md5sum: 1ca16b905abf657b88ca2bc12e7ad404
+
+- name: metaphlan3 test_metaphlan3_fasta
+  command: nextflow run ./tests/modules/nf-core/metaphlan3/metaphlan3 -entry test_metaphlan3_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/metaphlan3/metaphlan3/nextflow.config
+  tags:
+    - metaphlan3
+  files:
+    - path: output/metaphlan3/test.biom
+      contains:
+        - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"'
+    - path: output/metaphlan3/test.bowtie2out.txt
+      md5sum: fece494a410b8328608a11de10af6396
+    - path: output/metaphlan3/test_profile.txt
+      md5sum: d148c4203e5a9d59f5eea57207e40769
+    - path: output/untar/metaphlan_database/mpa_latest
+      md5sum: b1337362f607000384563a56a6ff4790
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.1.bt2
+      md5sum: d52a98fe273742ade7c744b819a7c5c1
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.2.bt2
+      md5sum: b14cc7faf3a4fae792160c917aebfe03
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.3.bt2
+      md5sum: 1bca5df879f2c6fad0c54984d0651bfb
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.4.bt2
+      md5sum: 249ee1c672d52d50cee41cb94b6adc42
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.fasta
+      md5sum: d3efe201c9eb449e877ead36656abf5f
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.pkl
+      md5sum: b208bb15eaef50d91cc7d5e35a1518ee
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
+      md5sum: ed05be063280e8629193e52903b07591
+    - path: output/untar/metaphlan_database/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
+      md5sum: 1ca16b905abf657b88ca2bc12e7ad404
diff --git a/tests/modules/nf-core/methyldackel/extract/main.nf b/tests/modules/nf-core/methyldackel/extract/main.nf
new file mode 100644
index 00000000000..f5b686db25f
--- /dev/null
+++ b/tests/modules/nf-core/methyldackel/extract/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { METHYLDACKEL_EXTRACT } from '../../../../../modules/nf-core/methyldackel/extract/main.nf'
+
+workflow test_methyldackel_extract {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true) ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    METHYLDACKEL_EXTRACT ( input, fasta, fai )
+}
diff --git a/tests/modules/methyldackel/extract/nextflow.config b/tests/modules/nf-core/methyldackel/extract/nextflow.config
similarity index 100%
rename from tests/modules/methyldackel/extract/nextflow.config
rename to tests/modules/nf-core/methyldackel/extract/nextflow.config
diff --git a/tests/modules/nf-core/methyldackel/extract/test.yml b/tests/modules/nf-core/methyldackel/extract/test.yml
new file mode 100644
index 00000000000..6a3a66692ea
--- /dev/null
+++ b/tests/modules/nf-core/methyldackel/extract/test.yml
@@ -0,0 +1,8 @@
+- name: methyldackel extract
+  command: nextflow run ./tests/modules/nf-core/methyldackel/extract -entry test_methyldackel_extract -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/methyldackel/extract/nextflow.config
+  tags:
+    - methyldackel
+    - methyldackel/extract
+  files:
+    - path: output/methyldackel/test.paired_end.methylated.sorted_CpG.bedGraph
+      md5sum: abcc9d1db6e48d5aced567c337b563d4
diff --git a/tests/modules/nf-core/methyldackel/mbias/main.nf b/tests/modules/nf-core/methyldackel/mbias/main.nf
new file mode 100644
index 00000000000..49c08b9f2c3
--- /dev/null
+++ b/tests/modules/nf-core/methyldackel/mbias/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { METHYLDACKEL_MBIAS } from '../../../../../modules/nf-core/methyldackel/mbias/main.nf'
+
+workflow test_methyldackel_mbias {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true) ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    METHYLDACKEL_MBIAS ( input, fasta, fai )
+}
diff --git a/tests/modules/methyldackel/mbias/nextflow.config b/tests/modules/nf-core/methyldackel/mbias/nextflow.config
similarity index 100%
rename from tests/modules/methyldackel/mbias/nextflow.config
rename to tests/modules/nf-core/methyldackel/mbias/nextflow.config
diff --git a/tests/modules/nf-core/methyldackel/mbias/test.yml b/tests/modules/nf-core/methyldackel/mbias/test.yml
new file mode 100644
index 00000000000..9401c88def7
--- /dev/null
+++ b/tests/modules/nf-core/methyldackel/mbias/test.yml
@@ -0,0 +1,8 @@
+- name: methyldackel mbias
+  command: nextflow run ./tests/modules/nf-core/methyldackel/mbias -entry test_methyldackel_mbias -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/methyldackel/mbias/nextflow.config
+  tags:
+    - methyldackel
+    - methyldackel/mbias
+  files:
+    - path: output/methyldackel/test.mbias.txt
+      md5sum: 357bb944dc2cdffcc47fa0d34376e016
diff --git a/tests/modules/nf-core/minia/main.nf b/tests/modules/nf-core/minia/main.nf
new file mode 100644
index 00000000000..a2e73a91927
--- /dev/null
+++ b/tests/modules/nf-core/minia/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MINIA } from '../../../../modules/nf-core/minia/main.nf'
+
+workflow test_minia {
+    input = [ [ id:'test' ], // meta map
+              [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
+            ]
+
+    MINIA ( input )
+}
diff --git a/tests/modules/minia/nextflow.config b/tests/modules/nf-core/minia/nextflow.config
similarity index 100%
rename from tests/modules/minia/nextflow.config
rename to tests/modules/nf-core/minia/nextflow.config
diff --git a/tests/modules/nf-core/minia/test.yml b/tests/modules/nf-core/minia/test.yml
new file mode 100644
index 00000000000..bdef395dcee
--- /dev/null
+++ b/tests/modules/nf-core/minia/test.yml
@@ -0,0 +1,8 @@
+- name: minia
+  command: nextflow run ./tests/modules/nf-core/minia -entry test_minia -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/minia/nextflow.config
+  tags:
+    - minia
+  files:
+    - path: output/minia/test.h5
+    - path: output/minia/test.contigs.fa
+    - path: output/minia/test.unitigs.fa
diff --git a/tests/modules/nf-core/miniasm/main.nf b/tests/modules/nf-core/miniasm/main.nf
new file mode 100644
index 00000000000..5bc2a33416f
--- /dev/null
+++ b/tests/modules/nf-core/miniasm/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MINIASM } from '../../../../modules/nf-core/miniasm/main.nf'
+
+workflow test_miniasm {
+    
+    input = [ [ id:'test', single_end:true ], // meta map
+             file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true),
+             file(params.test_data['bacteroides_fragilis']['nanopore']['overlap_paf'], checkIfExists: true)
+            ]
+    
+    MINIASM ( input )
+}
diff --git a/tests/modules/miniasm/nextflow.config b/tests/modules/nf-core/miniasm/nextflow.config
similarity index 100%
rename from tests/modules/miniasm/nextflow.config
rename to tests/modules/nf-core/miniasm/nextflow.config
diff --git a/tests/modules/nf-core/miniasm/test.yml b/tests/modules/nf-core/miniasm/test.yml
new file mode 100644
index 00000000000..f67958c025f
--- /dev/null
+++ b/tests/modules/nf-core/miniasm/test.yml
@@ -0,0 +1,9 @@
+- name: miniasm test_miniasm
+  command: nextflow run ./tests/modules/nf-core/miniasm -entry test_miniasm -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/miniasm/nextflow.config
+  tags:
+    - miniasm
+  files:
+    - path: output/miniasm/test.assembly.gfa.gz
+      md5sum: c68e4c2b64338d1c0f5b79b32934da14
+    - path: output/miniasm/test.assembly.fasta.gz
+      md5sum: d2f78ae618c02744e7a57bf4706ab8b4
diff --git a/tests/modules/nf-core/minimap2/align/main.nf b/tests/modules/nf-core/minimap2/align/main.nf
new file mode 100644
index 00000000000..c956d2301c7
--- /dev/null
+++ b/tests/modules/nf-core/minimap2/align/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MINIMAP2_ALIGN } from '../../../../../modules/nf-core/minimap2/align/main.nf'
+
+workflow test_minimap2_align_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format = true
+    cigar_paf_format = false
+    cigar_bam = false
+
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam)
+}
+
+workflow test_minimap2_align_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format  = true
+    cigar_paf_format = false
+    cigar_bam = false
+
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam )
+}
diff --git a/tests/modules/minimap2/align/nextflow.config b/tests/modules/nf-core/minimap2/align/nextflow.config
similarity index 100%
rename from tests/modules/minimap2/align/nextflow.config
rename to tests/modules/nf-core/minimap2/align/nextflow.config
diff --git a/tests/modules/nf-core/minimap2/align/test.yml b/tests/modules/nf-core/minimap2/align/test.yml
new file mode 100644
index 00000000000..178c23a1c72
--- /dev/null
+++ b/tests/modules/nf-core/minimap2/align/test.yml
@@ -0,0 +1,17 @@
+- name: minimap2 align test_minimap2_align_single_end
+  command: nextflow run ./tests/modules/nf-core/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config
+  tags:
+    - minimap2
+    - minimap2/align
+  files:
+    - path: output/minimap2/test.bam
+    - path: output/minimap2/versions.yml
+
+- name: minimap2 align test_minimap2_align_paired_end
+  command: nextflow run ./tests/modules/nf-core/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - minimap2
+    - minimap2/align
+  files:
+    - path: output/minimap2/test.bam
+    - path: output/minimap2/versions.yml
diff --git a/tests/modules/nf-core/minimap2/index/main.nf b/tests/modules/nf-core/minimap2/index/main.nf
new file mode 100644
index 00000000000..212bb64e0ee
--- /dev/null
+++ b/tests/modules/nf-core/minimap2/index/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MINIMAP2_INDEX } from '../../../../../modules/nf-core/minimap2/index/main.nf'
+
+workflow test_minimap2_index {
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    MINIMAP2_INDEX ( [ [id:'test'], fasta ] )
+}
diff --git a/tests/modules/minimap2/index/nextflow.config b/tests/modules/nf-core/minimap2/index/nextflow.config
similarity index 100%
rename from tests/modules/minimap2/index/nextflow.config
rename to tests/modules/nf-core/minimap2/index/nextflow.config
diff --git a/tests/modules/nf-core/minimap2/index/test.yml b/tests/modules/nf-core/minimap2/index/test.yml
new file mode 100644
index 00000000000..a2e0199b8f0
--- /dev/null
+++ b/tests/modules/nf-core/minimap2/index/test.yml
@@ -0,0 +1,8 @@
+- name: minimap2 index
+  command: nextflow run ./tests/modules/nf-core/minimap2/index -entry test_minimap2_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/minimap2/index/nextflow.config
+  tags:
+    - minimap2
+    - minimap2/index
+  files:
+    - path: ./output/minimap2/genome.mmi
+      md5sum: 72e450f12dc691e763c697463bdb1571
diff --git a/tests/modules/nf-core/mlst/main.nf b/tests/modules/nf-core/mlst/main.nf
new file mode 100644
index 00000000000..863dc6b3ca2
--- /dev/null
+++ b/tests/modules/nf-core/mlst/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MLST } from '../../../../modules/nf-core/mlst/main.nf'
+
+workflow test_mlst {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://raw.githubusercontent.com/nf-core/test-datasets/bactmap/genome/NCTC13799.fna", checkIfExists: true) ]
+
+    MLST ( input )
+}
diff --git a/tests/modules/mlst/nextflow.config b/tests/modules/nf-core/mlst/nextflow.config
similarity index 100%
rename from tests/modules/mlst/nextflow.config
rename to tests/modules/nf-core/mlst/nextflow.config
diff --git a/tests/modules/nf-core/mlst/test.yml b/tests/modules/nf-core/mlst/test.yml
new file mode 100644
index 00000000000..ac4d769b518
--- /dev/null
+++ b/tests/modules/nf-core/mlst/test.yml
@@ -0,0 +1,7 @@
+- name: mlst test_mlst
+  command: nextflow run ./tests/modules/nf-core/mlst -entry test_mlst -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mlst/nextflow.config
+  tags:
+    - mlst
+  files:
+    - path: output/mlst/test.tsv
+      md5sum: b52df6178834a156c9402012718eb65e
diff --git a/tests/modules/nf-core/mobsuite/recon/main.nf b/tests/modules/nf-core/mobsuite/recon/main.nf
new file mode 100644
index 00000000000..cd04e1cb029
--- /dev/null
+++ b/tests/modules/nf-core/mobsuite/recon/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MOBSUITE_RECON } from '../../../../../modules/nf-core/mobsuite/recon/main.nf'
+
+workflow test_mobsuite_recon {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    MOBSUITE_RECON ( input )
+}
diff --git a/tests/modules/mobsuite/recon/nextflow.config b/tests/modules/nf-core/mobsuite/recon/nextflow.config
similarity index 100%
rename from tests/modules/mobsuite/recon/nextflow.config
rename to tests/modules/nf-core/mobsuite/recon/nextflow.config
diff --git a/tests/modules/nf-core/mobsuite/recon/test.yml b/tests/modules/nf-core/mobsuite/recon/test.yml
new file mode 100644
index 00000000000..47cfd00ed31
--- /dev/null
+++ b/tests/modules/nf-core/mobsuite/recon/test.yml
@@ -0,0 +1,12 @@
+- name: mobsuite recon test_mobsuite_recon
+  command: nextflow run ./tests/modules/nf-core/mobsuite/recon -entry test_mobsuite_recon -c ./tests/config/nextflow.config
+  tags:
+    - mobsuite/recon
+    - mobsuite
+  files:
+    - path: output/mobsuite/results/chromosome.fasta
+      md5sum: 33b2a0fa321c73c6ba8d8272dd53c6d4
+    - path: output/mobsuite/results/contig_report.txt
+      md5sum: a0ae364a9f2b475f77588d0b3c24b857
+    - path: output/mobsuite/versions.yml
+      md5sum: 7f7a0f8957394b0e526233a0edb8e20a
diff --git a/tests/modules/nf-core/mosdepth/main.nf b/tests/modules/nf-core/mosdepth/main.nf
new file mode 100644
index 00000000000..60b0e6cdb69
--- /dev/null
+++ b/tests/modules/nf-core/mosdepth/main.nf
@@ -0,0 +1,96 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MOSDEPTH                       } from '../../../../modules/nf-core/mosdepth/main.nf'
+include { MOSDEPTH as MOSDEPTH_FAIL      } from '../../../../modules/nf-core/mosdepth/main.nf'
+include { MOSDEPTH as MOSDEPTH_WINDOW    } from '../../../../modules/nf-core/mosdepth/main.nf'
+include { MOSDEPTH as MOSDEPTH_THRESHOLD } from '../../../../modules/nf-core/mosdepth/main.nf'
+include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../../modules/nf-core/mosdepth/main.nf'
+
+workflow test_mosdepth {
+    input = [
+        [ id:'test', single_end:true ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    MOSDEPTH ( input, [], [] )
+}
+
+workflow test_mosdepth_bed {
+    input = [
+        [ id:'test', single_end:true ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    MOSDEPTH ( input, bed, [] )
+}
+
+workflow test_mosdepth_cram {
+    input = [
+        [ id:'test', single_end:true ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    MOSDEPTH ( input, [], fasta )
+}
+
+workflow test_mosdepth_cram_bed {
+    input  = [
+        [ id:'test', single_end:true ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    MOSDEPTH ( input, bed, fasta )
+}
+
+workflow test_mosdepth_window {
+    input = [
+        [ id:'test', single_end:true ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    MOSDEPTH_WINDOW ( input, [], [] )
+}
+
+workflow test_mosdepth_quantized {
+    input = [
+        [ id:'test', single_end:true ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    MOSDEPTH_QUANTIZED ( input, [], [] )
+}
+
+workflow test_mosdepth_thresholds {
+    input = [
+        [ id:'test', single_end:true ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    MOSDEPTH_THRESHOLD ( input, bed, [] )
+}
+
+workflow test_mosdepth_fail {
+    input = [
+        [ id:'test', single_end:true ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    MOSDEPTH_FAIL ( input, bed, [] )
+}
diff --git a/tests/modules/mosdepth/nextflow.config b/tests/modules/nf-core/mosdepth/nextflow.config
similarity index 100%
rename from tests/modules/mosdepth/nextflow.config
rename to tests/modules/nf-core/mosdepth/nextflow.config
diff --git a/tests/modules/nf-core/mosdepth/test.yml b/tests/modules/nf-core/mosdepth/test.yml
new file mode 100644
index 00000000000..d0a0829a8af
--- /dev/null
+++ b/tests/modules/nf-core/mosdepth/test.yml
@@ -0,0 +1,135 @@
+- name: mosdepth test_mosdepth
+  command: nextflow run ./tests/modules/nf-core/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+
+- name: mosdepth test_mosdepth_bed
+  command: nextflow run ./tests/modules/nf-core/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.region.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 96c037f769974b904beb53edc4f56d82
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: output/mosdepth/test.regions.bed.gz
+      md5sum: 5d398caf7171ec4406278e2add3009ae
+    - path: output/mosdepth/test.regions.bed.gz.csi
+      md5sum: 47669cfe41f3e222e74d81e1b1be191f
+
+- name: mosdepth test_mosdepth_cram
+  command: nextflow run ./tests/modules/nf-core/mosdepth -entry test_mosdepth_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+
+- name: mosdepth test_mosdepth_cram_bed
+  command: nextflow run ./tests/modules/nf-core/mosdepth -entry test_mosdepth_cram_bed -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.region.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 96c037f769974b904beb53edc4f56d82
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: output/mosdepth/test.regions.bed.gz
+      md5sum: 5d398caf7171ec4406278e2add3009ae
+    - path: output/mosdepth/test.regions.bed.gz.csi
+      md5sum: 47669cfe41f3e222e74d81e1b1be191f
+
+- name: mosdepth test_mosdepth_window
+  command: nextflow run ./tests/modules/nf-core/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.region.dist.txt
+      md5sum: 39e0e707ec32feb5176fd20a95f1f468
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 96c037f769974b904beb53edc4f56d82
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: output/mosdepth/test.regions.bed.gz
+      md5sum: f02e2cb49cc050e13d76942d6960827a
+    - path: output/mosdepth/test.regions.bed.gz.csi
+      md5sum: 257d67678136963d9dd904330079609d
+
+- name: mosdepth test_mosdepth_quantized
+  command: nextflow run ./tests/modules/nf-core/mosdepth -entry test_mosdepth_quantized -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: output/mosdepth/test.quantized.bed.gz
+      md5sum: 3e434a8bafcf59a67841ae3d4d752838
+    - path: output/mosdepth/test.quantized.bed.gz.csi
+      md5sum: be9617f551f19a33923f1e886eaefb93
+
+- name: mosdepth test_mosdepth_thresholds
+  command: nextflow run ./tests/modules/nf-core/mosdepth -entry test_mosdepth_thresholds -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.region.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 96c037f769974b904beb53edc4f56d82
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: output/mosdepth/test.regions.bed.gz
+      md5sum: 5d398caf7171ec4406278e2add3009ae
+    - path: output/mosdepth/test.regions.bed.gz.csi
+      md5sum: 47669cfe41f3e222e74d81e1b1be191f
+    - path: output/mosdepth/test.thresholds.bed.gz
+      md5sum: 13101e326eea3cbfa1d569b69f494f4c
+    - path: output/mosdepth/test.thresholds.bed.gz.csi
+      md5sum: 912055ee9452229439df6fae95644196
+
+- name: mosdepth test_mosdepth_fail
+  command: nextflow run ./tests/modules/nf-core/mosdepth -entry test_mosdepth_fail -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  exit_code: 1
diff --git a/tests/modules/nf-core/motus/downloaddb/main.nf b/tests/modules/nf-core/motus/downloaddb/main.nf
new file mode 100644
index 00000000000..0331beb85d1
--- /dev/null
+++ b/tests/modules/nf-core/motus/downloaddb/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MOTUS_DOWNLOADDB } from '../../../../../modules/nf-core/motus/downloaddb/main.nf'
+
+workflow test_motus_downloaddb {
+
+    input = file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py')
+
+    MOTUS_DOWNLOADDB ( input )
+}
diff --git a/tests/modules/motus/downloaddb/nextflow.config b/tests/modules/nf-core/motus/downloaddb/nextflow.config
similarity index 100%
rename from tests/modules/motus/downloaddb/nextflow.config
rename to tests/modules/nf-core/motus/downloaddb/nextflow.config
diff --git a/tests/modules/nf-core/motus/downloaddb/test.yml b/tests/modules/nf-core/motus/downloaddb/test.yml
new file mode 100644
index 00000000000..5a85b5f3b76
--- /dev/null
+++ b/tests/modules/nf-core/motus/downloaddb/test.yml
@@ -0,0 +1,7 @@
+- name: motus downloaddb test_motus_downloaddb
+  command: nextflow run ./tests/modules/nf-core/motus/downloaddb -entry test_motus_downloaddb -c ./tests/config/nextflow.config
+  tags:
+    - motus
+    - motus/downloaddb
+  files:
+    - path: output/motus/db_mOTU/db_mOTU_versions
diff --git a/tests/modules/nf-core/motus/merge/main.nf b/tests/modules/nf-core/motus/merge/main.nf
new file mode 100644
index 00000000000..22260b3f433
--- /dev/null
+++ b/tests/modules/nf-core/motus/merge/main.nf
@@ -0,0 +1,51 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MOTUS_DOWNLOADDB                } from '../../../../../modules/nf-core/motus/downloaddb/main.nf'
+include { MOTUS_PROFILE                   } from '../../../../../modules/nf-core/motus/profile/main.nf'
+include { MOTUS_MERGE                     } from '../../../../../modules/nf-core/motus/merge/main.nf'
+include { MOTUS_MERGE as MOTUS_MERGE_BIOM } from '../../../../../modules/nf-core/motus/merge/main.nf'
+
+workflow test_motus_merge {
+
+    input = Channel.fromList(
+        [
+            [
+                [ id:'test', single_end:true ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ],
+            [
+                [ id:'test2', single_end:true ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ]
+        ]
+    )
+
+    MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') )
+    MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db )
+    MOTUS_MERGE ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first() )
+
+}
+
+workflow test_motus_merge_biom {
+
+    input = Channel.fromList(
+        [
+            [
+                [ id:'test', single_end:true ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ],
+            [
+                [ id:'test2', single_end:true ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+            ]
+        ]
+    )
+
+    MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') )
+    MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db )
+    MOTUS_MERGE_BIOM ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first() )
+
+}
+
diff --git a/tests/modules/motus/merge/nextflow.config b/tests/modules/nf-core/motus/merge/nextflow.config
similarity index 100%
rename from tests/modules/motus/merge/nextflow.config
rename to tests/modules/nf-core/motus/merge/nextflow.config
diff --git a/tests/modules/nf-core/motus/merge/test.yml b/tests/modules/nf-core/motus/merge/test.yml
new file mode 100644
index 00000000000..aa786fecd2a
--- /dev/null
+++ b/tests/modules/nf-core/motus/merge/test.yml
@@ -0,0 +1,19 @@
+- name: motus merge test_motus_merge
+  command: nextflow run ./tests/modules/nf-core/motus/merge -entry test_motus_merge -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/motus/merge/nextflow.config
+  tags:
+    - motus
+    - motus/merge
+  files:
+    - path: output/motus/test.txt
+      contains:
+        - "consensus_taxonomy"
+
+- name: motus merge test_motus_merge_biom
+  command: nextflow run ./tests/modules/nf-core/motus/merge -entry test_motus_merge_biom -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/motus/merge/nextflow.config
+  tags:
+    - motus
+    - motus/merge
+  files:
+    - path: output/motus/test.biom
+      contains:
+        - "Biological Observation Matrix 1.0.0"
diff --git a/tests/modules/nf-core/motus/profile/main.nf b/tests/modules/nf-core/motus/profile/main.nf
new file mode 100644
index 00000000000..1add4dcf903
--- /dev/null
+++ b/tests/modules/nf-core/motus/profile/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MOTUS_DOWNLOADDB } from '../../../../../modules/nf-core/motus/downloaddb/main.nf'
+include { MOTUS_PROFILE    } from '../../../../../modules/nf-core/motus/profile/main.nf'
+
+workflow test_motus_profile_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
+
+    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db )
+}
+
diff --git a/tests/modules/motus/profile/nextflow.config b/tests/modules/nf-core/motus/profile/nextflow.config
similarity index 100%
rename from tests/modules/motus/profile/nextflow.config
rename to tests/modules/nf-core/motus/profile/nextflow.config
diff --git a/tests/modules/nf-core/motus/profile/test.yml b/tests/modules/nf-core/motus/profile/test.yml
new file mode 100644
index 00000000000..fff6ad1dca5
--- /dev/null
+++ b/tests/modules/nf-core/motus/profile/test.yml
@@ -0,0 +1,10 @@
+- name: motus profile test_motus_profile_single_end
+  command: nextflow run ./tests/modules/nf-core/motus/profile -entry test_motus_profile_single_end -c ./tests/config/nextflow.config
+  tags:
+    - motus
+    - motus/profile
+  files:
+    - path: output/motus/test.out
+      contains: ["#consensus_taxonomy\ttest"]
+    - path: output/motus/test.log
+      contains: ["Finished computation"]
diff --git a/tests/modules/nf-core/msisensor/msi/main.nf b/tests/modules/nf-core/msisensor/msi/main.nf
new file mode 100644
index 00000000000..5d052c5b9c5
--- /dev/null
+++ b/tests/modules/nf-core/msisensor/msi/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MSISENSOR_SCAN } from '../../../../../modules/nf-core/msisensor/scan/main.nf'
+include { MSISENSOR_MSI } from '../../../../../modules/nf-core/msisensor/msi/main.nf'
+
+workflow test_msisensor_msi {
+
+    def scaninput  = []
+    scaninput = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    scan = MSISENSOR_SCAN ( scaninput )
+
+    // IMPERFECT TEST:
+    // USING SARS-COV2 DATA AS NORMAL:TUMOR PAIR THIS WILL SUFFICE TO
+    // TEST MODULE EXECUTION, BUT NOT FUNCTIONALITY.
+    // FUNCTIONALITY HAS BEEN TESTED MANUALY USING AUTHOR-PROVIDED TEST
+    // DATA (https://github.com/ding-lab/msisensor/tree/master/test)
+    def input      = []
+
+    input = Channel.from([ [ id:'test', single_end:false ], // meta map
+               file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'],     checkIfExists: true),
+               file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
+               file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'],         checkIfExists: true),
+               file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'],     checkIfExists: true) ])
+    //scan.txt.view()
+    input.concat(scan.txt).collect().view()
+    // BIT CLUMSY:
+    MSISENSOR_MSI ( input.concat(scan.txt).collect() )
+}
diff --git a/tests/modules/msisensor/msi/nextflow.config b/tests/modules/nf-core/msisensor/msi/nextflow.config
similarity index 100%
rename from tests/modules/msisensor/msi/nextflow.config
rename to tests/modules/nf-core/msisensor/msi/nextflow.config
diff --git a/tests/modules/nf-core/msisensor/msi/test.yml b/tests/modules/nf-core/msisensor/msi/test.yml
new file mode 100644
index 00000000000..06bb1a09c11
--- /dev/null
+++ b/tests/modules/nf-core/msisensor/msi/test.yml
@@ -0,0 +1,14 @@
+- name: msisensor msi
+  command: nextflow run ./tests/modules/nf-core/msisensor/msi -entry test_msisensor_msi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/msisensor/msi/nextflow.config
+  tags:
+    - msisensor
+    - msisensor/msi
+  files:
+    - path: output/msisensor/test
+      md5sum: a3290f7539dbbf83777e8590156c0e28
+    - path: output/msisensor/test_dis
+      md5sum: 060a3fc3701f3b10f6b19da9b21a32b7
+    - path: output/msisensor/test_germline
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/msisensor/test_somatic
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/nf-core/msisensor/scan/main.nf b/tests/modules/nf-core/msisensor/scan/main.nf
new file mode 100644
index 00000000000..6b6383db1f3
--- /dev/null
+++ b/tests/modules/nf-core/msisensor/scan/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MSISENSOR_SCAN } from '../../../../../modules/nf-core/msisensor/scan/main.nf'
+
+workflow test_msisensor_scan {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+
+    MSISENSOR_SCAN ( input )
+}
diff --git a/tests/modules/msisensor/scan/nextflow.config b/tests/modules/nf-core/msisensor/scan/nextflow.config
similarity index 100%
rename from tests/modules/msisensor/scan/nextflow.config
rename to tests/modules/nf-core/msisensor/scan/nextflow.config
diff --git a/tests/modules/nf-core/msisensor/scan/test.yml b/tests/modules/nf-core/msisensor/scan/test.yml
new file mode 100644
index 00000000000..20ec3a9a2d8
--- /dev/null
+++ b/tests/modules/nf-core/msisensor/scan/test.yml
@@ -0,0 +1,8 @@
+- name: msisensor scan
+  command: nextflow run ./tests/modules/nf-core/msisensor/scan -entry test_msisensor_scan -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/msisensor/scan/nextflow.config
+  tags:
+    - msisensor
+    - msisensor/scan
+  files:
+    - path: output/msisensor/test.msisensor_scan.tab
+      md5sum: b7ae85acdcfc1a51e867ab3446d6fb59
diff --git a/tests/modules/nf-core/msisensor2/msi/main.nf b/tests/modules/nf-core/msisensor2/msi/main.nf
new file mode 100644
index 00000000000..78738d27f67
--- /dev/null
+++ b/tests/modules/nf-core/msisensor2/msi/main.nf
@@ -0,0 +1,84 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MSISENSOR2_SCAN } from '../../../../../modules/nf-core/msisensor2/scan/main.nf'
+include { MSISENSOR2_MSI } from '../../../../../modules/nf-core/msisensor2/msi/main.nf'
+
+workflow test_msisensor2_msi_tumor_only {
+
+    reference = [
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    MSISENSOR2_SCAN ( reference, "outputfile" )
+
+    input = [
+        [ id:'test' ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        [],
+        [],
+        [],
+    ]
+
+    MSISENSOR2_MSI ( input, MSISENSOR2_SCAN.out.scan, [] )
+}
+
+
+workflow test_msisensor2_msi_tumor_normal {
+
+    reference = [
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    MSISENSOR2_SCAN ( reference, "outputfile" )
+
+    input = [
+        [ id:'test' ],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
+        [],
+    ]
+
+    MSISENSOR2_MSI ( input, MSISENSOR2_SCAN.out.scan, [] )
+}
+
+workflow test_msisensor2_msi_tumor_only_ml {
+
+    input = [
+        [ id:'test' ],
+        file('https://github.com/niu-lab/msisensor2/raw/master/test/example.tumor.only.hg19.bam', checkIfExists: true),
+        file('https://github.com/niu-lab/msisensor2/raw/master/test/example.tumor.only.hg19.bam.bai', checkIfExists: true),
+        [],
+        [],
+        [],
+    ]
+
+    models = Channel.fromPath(
+        [
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/016a16e12aca2bdba3713a3be76f72cd",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/02d42c2bda19aac304d6e86390c7f328",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/1030c0aa35ca5c263daeae866ad18632",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/15c3f5ec1c020d8f44283e40a2d9b6bb",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/15d6012f9a234b7adbbeecec524aea7d",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/2cf9a58f57e78b88acd86d792fe6a7b3",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/3ba04410c7ccbfc33e8b1b11d8132ae9",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/4431c9dc08be932c460a9e67192e7c57",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/4f5fa7bed97b48093375222d242fc982",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/71e6c0d59ea09d2a7acc566560841e34",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/8144b15900bba7086e86b31a0e1f8cfd",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/9bf6f7a544f369c3262a3a6f72cfdd7b",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/b8a36f2274b33cb0ed932e85cd1ddd5a",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/c08f164ded323a8c2606c408c555d73d",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/ceaa36ddbb76dc6eb6199ed946945788",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/e05d5da7208a924762311eddc4ec96c0",
+            "https://github.com/niu-lab/msisensor2/raw/master/test/tmp/models_hg19_17sites/f8a20acf51ccb2b0ce6af42f24a8b5ef",
+        ],
+        checkIfExists: true
+    )
+
+    MSISENSOR2_MSI ( input, [], models.collect() )
+}
diff --git a/tests/modules/msisensor2/msi/nextflow.config b/tests/modules/nf-core/msisensor2/msi/nextflow.config
similarity index 100%
rename from tests/modules/msisensor2/msi/nextflow.config
rename to tests/modules/nf-core/msisensor2/msi/nextflow.config
diff --git a/tests/modules/nf-core/msisensor2/msi/test.yml b/tests/modules/nf-core/msisensor2/msi/test.yml
new file mode 100644
index 00000000000..f2c1b5e9d22
--- /dev/null
+++ b/tests/modules/nf-core/msisensor2/msi/test.yml
@@ -0,0 +1,39 @@
+- name: msisensor2 msi test_msisensor2_msi_tumor_only
+  command: nextflow run ./tests/modules/nf-core/msisensor2/msi -entry test_msisensor2_msi_tumor_only -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/msisensor2/msi/nextflow.config
+  tags:
+    - msisensor2
+    - msisensor2/msi
+  files:
+    - path: output/msisensor2/outputfile
+      md5sum: b1fa373ada56fd5027b705d5e2faa374
+    - path: output/msisensor2/test
+      md5sum: a3290f7539dbbf83777e8590156c0e28
+    - path: output/msisensor2/test_dis
+      md5sum: 236e814ddeb95e21a17b48250f92250d
+    - path: output/msisensor2/test_somatic
+
+- name: msisensor2 msi test_msisensor2_msi_tumor_normal
+  command: nextflow run ./tests/modules/nf-core/msisensor2/msi -entry test_msisensor2_msi_tumor_normal -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/msisensor2/msi/nextflow.config
+  tags:
+    - msisensor2
+    - msisensor2/msi
+  files:
+    - path: output/msisensor2/outputfile
+      md5sum: b1fa373ada56fd5027b705d5e2faa374
+    - path: output/msisensor2/test
+      md5sum: a3290f7539dbbf83777e8590156c0e28
+    - path: output/msisensor2/test_dis
+      md5sum: d47b22c13092707ed64645f118e82cc1
+    - path: output/msisensor2/test_somatic
+
+- name: msisensor2 msi test_msisensor2_msi_tumor_only_ml
+  command: nextflow run ./tests/modules/nf-core/msisensor2/msi -entry test_msisensor2_msi_tumor_only_ml -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/msisensor2/msi/nextflow.config
+  tags:
+    - msisensor2
+    - msisensor2/msi
+  files:
+    - path: output/msisensor2/test
+      md5sum: a3290f7539dbbf83777e8590156c0e28
+    - path: output/msisensor2/test_dis
+      md5sum: 85205504ea8652ebdee46ac07ee1a8f6
+    - path: output/msisensor2/test_somatic
diff --git a/tests/modules/nf-core/msisensor2/scan/main.nf b/tests/modules/nf-core/msisensor2/scan/main.nf
new file mode 100644
index 00000000000..a5bc912f776
--- /dev/null
+++ b/tests/modules/nf-core/msisensor2/scan/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MSISENSOR2_SCAN } from '../../../../../modules/nf-core/msisensor2/scan/main.nf'
+
+workflow test_msisensor2_scan {
+
+    input = [
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true)
+    ]
+
+    MSISENSOR2_SCAN ( input, "outputfile" )
+}
diff --git a/tests/modules/msisensor2/scan/nextflow.config b/tests/modules/nf-core/msisensor2/scan/nextflow.config
similarity index 100%
rename from tests/modules/msisensor2/scan/nextflow.config
rename to tests/modules/nf-core/msisensor2/scan/nextflow.config
diff --git a/tests/modules/nf-core/msisensor2/scan/test.yml b/tests/modules/nf-core/msisensor2/scan/test.yml
new file mode 100644
index 00000000000..f76075e543c
--- /dev/null
+++ b/tests/modules/nf-core/msisensor2/scan/test.yml
@@ -0,0 +1,8 @@
+- name: msisensor2 scan test_msisensor2_scan
+  command: nextflow run ./tests/modules/nf-core/msisensor2/scan -entry test_msisensor2_scan -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/msisensor2/scan/nextflow.config
+  tags:
+    - msisensor2/scan
+    - msisensor2
+  files:
+    - path: output/msisensor2/outputfile
+      md5sum: bdc0a576f37bd95a59692f387d083092
diff --git a/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf b/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf
new file mode 100644
index 00000000000..ed0a9d6f70c
--- /dev/null
+++ b/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MSISENSORPRO_MSI_SOMATIC } from '../../../../../modules/nf-core/msisensorpro/msi_somatic/main.nf'
+include { MSISENSORPRO_SCAN } from '../../../../../modules/nf-core/msisensorpro/scan/main.nf'
+
+workflow test_msisensorpro_msi {
+
+    scan_in = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    ]
+
+    println scan_in
+
+    MSISENSORPRO_SCAN ( scan_in )
+
+    input = [// meta map
+        [ id:'test'],
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        []
+    ]
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+
+    MSISENSORPRO_SCAN.out.list.map{meta, list -> [list]}.set{list}
+    MSISENSORPRO_MSI_SOMATIC(input, fasta, list)
+
+
+}
diff --git a/tests/modules/msisensorpro/msi_somatic/nextflow.config b/tests/modules/nf-core/msisensorpro/msi_somatic/nextflow.config
similarity index 100%
rename from tests/modules/msisensorpro/msi_somatic/nextflow.config
rename to tests/modules/nf-core/msisensorpro/msi_somatic/nextflow.config
diff --git a/tests/modules/nf-core/msisensorpro/msi_somatic/test.yml b/tests/modules/nf-core/msisensorpro/msi_somatic/test.yml
new file mode 100644
index 00000000000..ca92fc798eb
--- /dev/null
+++ b/tests/modules/nf-core/msisensorpro/msi_somatic/test.yml
@@ -0,0 +1,18 @@
+- name: msisensorpro msi_somatic test_msisensorpro_msi
+  command: nextflow run ./tests/modules/nf-core/msisensorpro/msi_somatic -entry test_msisensorpro_msi -c ./tests/config/nextflow.config
+  tags:
+    - msisensorpro/msi_somatic
+    - msisensorpro
+  files:
+    - path: output/msisensorpro/test
+      md5sum: db7f2cc99ea79f79b0ba011c4bcbb43d
+    - path: output/msisensorpro/test.msisensor_scan.list
+      md5sum: 309d41b136993db24a9f3dade877753b
+    - path: output/msisensorpro/test_dis
+      md5sum: fc3e205b7ca50c9ecf3f70c87781e96f
+    - path: output/msisensorpro/test_germline
+      md5sum: ba585b355c08877b8bca4901f49d9311
+    - path: output/msisensorpro/test_somatic
+      md5sum: 836e617ddded07ec1e39089fd595c3d8
+    - path: output/msisensorpro/versions.yml
+      md5sum: b57279502ca6863c5406ed46e6b42994
diff --git a/tests/modules/nf-core/msisensorpro/scan/main.nf b/tests/modules/nf-core/msisensorpro/scan/main.nf
new file mode 100644
index 00000000000..9647dc36ffb
--- /dev/null
+++ b/tests/modules/nf-core/msisensorpro/scan/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MSISENSORPRO_SCAN } from '../../../../../modules/nf-core/msisensorpro/scan/main.nf'
+
+workflow test_msisensorpro_scan {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    ]
+
+    MSISENSORPRO_SCAN ( input )
+}
diff --git a/tests/modules/msisensorpro/scan/nextflow.config b/tests/modules/nf-core/msisensorpro/scan/nextflow.config
similarity index 100%
rename from tests/modules/msisensorpro/scan/nextflow.config
rename to tests/modules/nf-core/msisensorpro/scan/nextflow.config
diff --git a/tests/modules/nf-core/msisensorpro/scan/test.yml b/tests/modules/nf-core/msisensorpro/scan/test.yml
new file mode 100644
index 00000000000..d86d022fce5
--- /dev/null
+++ b/tests/modules/nf-core/msisensorpro/scan/test.yml
@@ -0,0 +1,10 @@
+- name: msisensorpro scan test_msisensorpro_scan
+  command: nextflow run ./tests/modules/nf-core/msisensorpro/scan -entry test_msisensorpro_scan -c ./tests/config/nextflow.config
+  tags:
+    - msisensorpro
+    - msisensorpro/scan
+  files:
+    - path: output/msisensorpro/test.msisensor_scan.list
+      md5sum: 309d41b136993db24a9f3dade877753b
+    - path: output/msisensorpro/versions.yml
+      md5sum: ed713232c854bce5c74d10097101ed06
diff --git a/tests/modules/nf-core/mtnucratio/main.nf b/tests/modules/nf-core/mtnucratio/main.nf
new file mode 100644
index 00000000000..080210ee600
--- /dev/null
+++ b/tests/modules/nf-core/mtnucratio/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MTNUCRATIO } from '../../../../modules/nf-core/mtnucratio/main.nf'
+
+workflow test_mtnucratio {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)]
+    mt_id = 'mt_id'
+
+    MTNUCRATIO ( input, mt_id )
+}
diff --git a/tests/modules/mtnucratio/nextflow.config b/tests/modules/nf-core/mtnucratio/nextflow.config
similarity index 100%
rename from tests/modules/mtnucratio/nextflow.config
rename to tests/modules/nf-core/mtnucratio/nextflow.config
diff --git a/tests/modules/nf-core/mtnucratio/test.yml b/tests/modules/nf-core/mtnucratio/test.yml
new file mode 100644
index 00000000000..ea9a4b3cb02
--- /dev/null
+++ b/tests/modules/nf-core/mtnucratio/test.yml
@@ -0,0 +1,9 @@
+- name: mtnucratio
+  command: nextflow run ./tests/modules/nf-core/mtnucratio -entry test_mtnucratio -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mtnucratio/nextflow.config
+  tags:
+    - mtnucratio
+  files:
+    - path: output/mtnucratio/test.single_end.sorted.bam.mtnucratio
+      md5sum: 19e96849802c70aa0694785f716274b7
+    - path: output/mtnucratio/test.single_end.sorted.bam.mtnucratiomtnuc.json
+      md5sum: 14d24be6272854d6762f0dfad5918ef6
diff --git a/tests/modules/nf-core/multiqc/main.nf b/tests/modules/nf-core/multiqc/main.nf
new file mode 100644
index 00000000000..f8ea220ca5e
--- /dev/null
+++ b/tests/modules/nf-core/multiqc/main.nf
@@ -0,0 +1,45 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTQC            } from '../../../../modules/nf-core/fastqc/main.nf'
+include { FASTQC as FASTQC2 } from '../../../../modules/nf-core/fastqc/main.nf'
+include { MULTIQC           } from '../../../../modules/nf-core/multiqc/main.nf'
+
+workflow test_multiqc {
+    input = [
+        [ id: 'test', single_end: false ],
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+    ]
+
+    FASTQC  ( input )
+    MULTIQC ( FASTQC.out.zip.collect { it[1] }, [], [], [] )
+}
+
+workflow test_multiqc_fn_collision {
+    fqc_input = [
+        [ id: 'test', single_end: false ],
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+    ]
+    mqc_input = Channel.empty()
+
+    FASTQC  ( fqc_input  )
+    mqc_input = mqc_input.mix(FASTQC.out.zip.collect { it[1] })
+
+    FASTQC2  ( fqc_input )
+    mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] })
+
+    MULTIQC ( mqc_input, [], [], [] )
+}
+
+workflow test_multiqc_config {
+    input = [
+        [ id: 'test', single_end: false ],
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+    ]
+    mqc_config = file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)
+    mqc_input = Channel.empty()
+
+    FASTQC  ( input )
+    MULTIQC ( FASTQC.out.zip.collect { it[1] }, mqc_config, [], [] )
+}
diff --git a/tests/modules/multiqc/nextflow.config b/tests/modules/nf-core/multiqc/nextflow.config
similarity index 100%
rename from tests/modules/multiqc/nextflow.config
rename to tests/modules/nf-core/multiqc/nextflow.config
diff --git a/tests/modules/nf-core/multiqc/test.yml b/tests/modules/nf-core/multiqc/test.yml
new file mode 100644
index 00000000000..bd70ffd8d1a
--- /dev/null
+++ b/tests/modules/nf-core/multiqc/test.yml
@@ -0,0 +1,41 @@
+- name: multiqc test_multiqc
+  command: nextflow run ./tests/modules/nf-core/multiqc -entry test_multiqc -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/multiqc/nextflow.config
+  tags:
+    - multiqc
+  files:
+    - path: output/multiqc/multiqc_data/multiqc.log
+      contains: ["MultiQC complete"]
+    - path: output/multiqc/multiqc_data/multiqc_citations.txt
+      contains: ["10.1093/bioinformatics/btw354"]
+    - path: output/multiqc/multiqc_data/multiqc_data.json
+      contains: ["report_data_sources"]
+    - path: output/multiqc/multiqc_report.html
+      contains: ["Abandon hope all ye who enter here.."]
+
+- name: multiqc test_multiqc_fn_collision
+  command: nextflow run ./tests/modules/nf-core/multiqc -entry test_multiqc_fn_collision -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/multiqc/nextflow.config
+  tags:
+    - multiqc
+  files:
+    - path: output/multiqc/multiqc_data/multiqc.log
+      contains: ["MultiQC complete"]
+    - path: output/multiqc/multiqc_data/multiqc_citations.txt
+      contains: ["10.1093/bioinformatics/btw354"]
+    - path: output/multiqc/multiqc_data/multiqc_data.json
+      contains: ["report_data_sources"]
+    - path: output/multiqc/multiqc_report.html
+      contains: ["Abandon hope all ye who enter here.."]
+
+- name: multiqc test_multiqc_config
+  command: nextflow run ./tests/modules/nf-core/multiqc -entry test_multiqc_config -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/multiqc/nextflow.config
+  tags:
+    - multiqc
+  files:
+    - path: output/multiqc/multiqc_data/multiqc.log
+      contains: ["MultiQC complete"]
+    - path: output/multiqc/multiqc_data/multiqc_citations.txt
+      contains: ["10.1093/bioinformatics/btw354"]
+    - path: output/multiqc/multiqc_data/multiqc_data.json
+      contains: ["report_data_sources"]
+    - path: output/multiqc/multiqc_report.html
+      contains: ["Abandon hope all ye who enter here.."]
diff --git a/tests/modules/nf-core/multivcfanalyzer/main.nf b/tests/modules/nf-core/multivcfanalyzer/main.nf
new file mode 100644
index 00000000000..11bfd415c85
--- /dev/null
+++ b/tests/modules/nf-core/multivcfanalyzer/main.nf
@@ -0,0 +1,41 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf'
+include { GUNZIP                } from '../../../../modules/nf-core/gunzip/main.nf'
+include { MULTIVCFANALYZER      } from '../../../../modules/nf-core/multivcfanalyzer/main.nf'
+
+workflow test_multivcfanalyzer {
+
+    input     = Channel.of([ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                ],
+                [ [ id:'test2' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true),
+                ],
+                )
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [], [], [], [])
+
+    mva_vcf = GUNZIP ( GATK_UNIFIEDGENOTYPER.out.vcf ).gunzip
+        .map{it[1]}
+        .collect()
+        .dump()
+
+    snpeff_results          = []
+    gff                     = []
+    allele_freqs            = true
+    genotype_quality        = 30
+    coverage                = 5
+    homozygous_freq         = 0.8
+    heterozygous_freq       = 0.2
+    gff_exclude             = []
+
+    MULTIVCFANALYZER ( mva_vcf, fasta, snpeff_results, gff, allele_freqs, genotype_quality, coverage, homozygous_freq, heterozygous_freq, gff_exclude )
+}
diff --git a/tests/modules/multivcfanalyzer/nextflow.config b/tests/modules/nf-core/multivcfanalyzer/nextflow.config
similarity index 100%
rename from tests/modules/multivcfanalyzer/nextflow.config
rename to tests/modules/nf-core/multivcfanalyzer/nextflow.config
diff --git a/tests/modules/nf-core/multivcfanalyzer/test.yml b/tests/modules/nf-core/multivcfanalyzer/test.yml
new file mode 100644
index 00000000000..e4ec251c683
--- /dev/null
+++ b/tests/modules/nf-core/multivcfanalyzer/test.yml
@@ -0,0 +1,31 @@
+- name: multivcfanalyzer test_multivcfanalyzer
+  command: nextflow run ./tests/modules/nf-core/multivcfanalyzer -entry test_multivcfanalyzer -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/multivcfanalyzer/nextflow.config
+  tags:
+    - multivcfanalyzer
+  files:
+    - path: output/multivcfanalyzer/MultiVCFAnalyzer.json
+      md5sum: c841c9f04c6114911f308ea09a08980e
+    - path: output/multivcfanalyzer/fullAlignment.fasta.gz
+      contains:
+        - ">Reference_MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome"
+    - path: output/multivcfanalyzer/info.txt
+      contains:
+        - "Run finished"
+    - path: output/multivcfanalyzer/snpAlignment.fasta.gz
+      contains:
+        - "test.vcf"
+    - path: output/multivcfanalyzer/snpAlignmentIncludingRefGenome.fasta.gz
+      contains:
+        - ">Reference_MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome"
+    - path: output/multivcfanalyzer/snpStatistics.tsv
+      contains: ["statistics", "test.vcf", "test2.vcf"]
+    - path: output/multivcfanalyzer/snpTable.tsv
+      contains: ["Position", "test.vcf", "test2.vcf"]
+    - path: output/multivcfanalyzer/snpTableForSnpEff.tsv
+      md5sum: 8d7ab4ec98a89d290e301d6feae461aa
+    - path: output/multivcfanalyzer/snpTableWithUncertaintyCalls.tsv
+      contains: ["Position", "test.vcf", "test2.vcf"]
+    - path: output/multivcfanalyzer/structureGenotypes.tsv
+      contains: ["test.vcf", "test2.vcf"]
+    - path: output/multivcfanalyzer/structureGenotypes_noMissingData-Columns.tsv
+      contains: ["test.vcf", "test2.vcf"]
diff --git a/tests/modules/nf-core/mummer/main.nf b/tests/modules/nf-core/mummer/main.nf
new file mode 100644
index 00000000000..68cfcfceb9d
--- /dev/null
+++ b/tests/modules/nf-core/mummer/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MUMMER } from '../../../../modules/nf-core/mummer/main.nf'
+
+workflow test_mummer {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+
+    MUMMER ( input )
+}
diff --git a/tests/modules/mummer/nextflow.config b/tests/modules/nf-core/mummer/nextflow.config
similarity index 100%
rename from tests/modules/mummer/nextflow.config
rename to tests/modules/nf-core/mummer/nextflow.config
diff --git a/tests/modules/nf-core/mummer/test.yml b/tests/modules/nf-core/mummer/test.yml
new file mode 100644
index 00000000000..a110f8cb32d
--- /dev/null
+++ b/tests/modules/nf-core/mummer/test.yml
@@ -0,0 +1,7 @@
+- name: mummer test_mummer
+  command: nextflow run ./tests/modules/nf-core/mummer -entry test_mummer -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mummer/nextflow.config
+  tags:
+    - mummer
+  files:
+    - path: output/mummer/test.coords
+      md5sum: 6084fe43c7cb2eca8b96d674560bdefc
diff --git a/tests/modules/nf-core/muscle/main.nf b/tests/modules/nf-core/muscle/main.nf
new file mode 100644
index 00000000000..06759966b23
--- /dev/null
+++ b/tests/modules/nf-core/muscle/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MUSCLE } from '../../../../modules/nf-core/muscle/main.nf'
+include { MUSCLE as MUSCLE_TREE } from '../../../../modules/nf-core/muscle/main.nf'
+
+workflow test_muscle {
+
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
+
+    MUSCLE ( input )
+    MUSCLE_TREE ( MUSCLE.out.aligned_fasta )
+}
diff --git a/tests/modules/muscle/nextflow.config b/tests/modules/nf-core/muscle/nextflow.config
similarity index 100%
rename from tests/modules/muscle/nextflow.config
rename to tests/modules/nf-core/muscle/nextflow.config
diff --git a/tests/modules/nf-core/muscle/test.yml b/tests/modules/nf-core/muscle/test.yml
new file mode 100644
index 00000000000..ffb7ec2031b
--- /dev/null
+++ b/tests/modules/nf-core/muscle/test.yml
@@ -0,0 +1,14 @@
+- name: muscle test_muscle
+  command: nextflow run ./tests/modules/nf-core/muscle -entry test_muscle -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/muscle/nextflow.config
+  tags:
+    - muscle
+  files:
+    - path: output/muscle/muscle_msa.log
+    - path: output/muscle/test_muscle_msa.afa
+      md5sum: 93732f6876054d82b0cd252d702c143f
+    - path: output/muscle/test_muscle_msa.phyi
+      md5sum: 1f2a246dcca53125456149770763d5d1
+    - path: output/muscle/test_muscle_msa.phys
+      md5sum: 12f9dd45672a3d92ba1205fcc8010490
+    - path: output/muscle/test_muscle_msa.tree
+      md5sum: 6bf1080bca2440f08ffa2675f74f732a
diff --git a/tests/modules/nf-core/mykrobe/predict/main.nf b/tests/modules/nf-core/mykrobe/predict/main.nf
new file mode 100644
index 00000000000..6fbe60c36a5
--- /dev/null
+++ b/tests/modules/nf-core/mykrobe/predict/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MYKROBE_PREDICT } from '../../../../../modules/nf-core/mykrobe/predict/main.nf'
+
+workflow test_mykrobe_predict {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    MYKROBE_PREDICT ( input, "typhi" )
+}
diff --git a/tests/modules/mykrobe/predict/nextflow.config b/tests/modules/nf-core/mykrobe/predict/nextflow.config
similarity index 100%
rename from tests/modules/mykrobe/predict/nextflow.config
rename to tests/modules/nf-core/mykrobe/predict/nextflow.config
diff --git a/tests/modules/nf-core/mykrobe/predict/test.yml b/tests/modules/nf-core/mykrobe/predict/test.yml
new file mode 100644
index 00000000000..cacf955b4b3
--- /dev/null
+++ b/tests/modules/nf-core/mykrobe/predict/test.yml
@@ -0,0 +1,10 @@
+- name: mykrobe predict test_mykrobe_predict
+  command: nextflow run ./tests/modules/nf-core/mykrobe/predict -entry test_mykrobe_predict -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/mykrobe/predict/nextflow.config
+  tags:
+    - mykrobe/predict
+    - mykrobe
+  files:
+    - path: output/mykrobe/test.csv
+      contains: ["susceptibility", "genotype_model", "variants", "test.paired_end.bam"]
+    - path: output/mykrobe/test.json
+      contains: ["susceptibility", "kmer_count", "files", "test.paired_end.bam"]
diff --git a/tests/modules/nf-core/nanolyse/main.nf b/tests/modules/nf-core/nanolyse/main.nf
new file mode 100644
index 00000000000..a5ed562f2cb
--- /dev/null
+++ b/tests/modules/nf-core/nanolyse/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NANOLYSE } from '../../../../modules/nf-core/nanolyse/main.nf'
+
+workflow test_nanolyse {
+    input = [ 
+        [ id:'test' ], // meta map
+        [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)]
+    ]
+
+    fasta = file("https://github.com/wdecoster/nanolyse/raw/master/reference/lambda.fasta.gz", checkIfExists: true)
+
+    NANOLYSE ( input, fasta )
+}
diff --git a/tests/modules/nanolyse/nextflow.config b/tests/modules/nf-core/nanolyse/nextflow.config
similarity index 100%
rename from tests/modules/nanolyse/nextflow.config
rename to tests/modules/nf-core/nanolyse/nextflow.config
diff --git a/tests/modules/nf-core/nanolyse/test.yml b/tests/modules/nf-core/nanolyse/test.yml
new file mode 100644
index 00000000000..cf508089a03
--- /dev/null
+++ b/tests/modules/nf-core/nanolyse/test.yml
@@ -0,0 +1,6 @@
+- name: nanolyse
+  command: nextflow run ./tests/modules/nf-core/nanolyse -entry test_nanolyse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/nanolyse/nextflow.config
+  tags:
+    - nanolyse
+  files:
+    - path: ./output/nanolyse/test.clean.fastq.gz
diff --git a/tests/modules/nf-core/nanoplot/main.nf b/tests/modules/nf-core/nanoplot/main.nf
new file mode 100644
index 00000000000..e5e2bd59f6e
--- /dev/null
+++ b/tests/modules/nf-core/nanoplot/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NANOPLOT  } from '../../../../modules/nf-core/nanoplot/main.nf'
+
+workflow test_nanoplot_summary {
+    def input = []
+    input = [ [ id:'test' ], // meta map
+            [ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ] ]
+              
+    NANOPLOT ( input )
+}
+
+workflow test_nanoplot_fastq {
+    def input = []
+    input = [ [ id:'test' ], // meta map
+            [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ] ]
+
+    NANOPLOT ( input )
+}
diff --git a/tests/modules/nanoplot/nextflow.config b/tests/modules/nf-core/nanoplot/nextflow.config
similarity index 100%
rename from tests/modules/nanoplot/nextflow.config
rename to tests/modules/nf-core/nanoplot/nextflow.config
diff --git a/tests/modules/nf-core/nanoplot/test.yml b/tests/modules/nf-core/nanoplot/test.yml
new file mode 100644
index 00000000000..c00b1a797a4
--- /dev/null
+++ b/tests/modules/nf-core/nanoplot/test.yml
@@ -0,0 +1,16 @@
+- name: nanoplot_summary
+  command: nextflow run ./tests/modules/nf-core/nanoplot -entry test_nanoplot_summary -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/nanoplot/nextflow.config
+  tags:
+    - nanoplot
+  files:
+    - path: ./output/nanoplot/NanoPlot-report.html
+      contains:
+        - "report"
+- name: nanoplot_fastq
+  command: nextflow run ./tests/modules/nf-core/nanoplot -entry test_nanoplot_fastq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/nanoplot/nextflow.config
+  tags:
+    - nanoplot
+  files:
+    - path: ./output/nanoplot/NanoPlot-report.html
+      contains:
+        - "report"
diff --git a/tests/modules/nf-core/ncbigenomedownload/main.nf b/tests/modules/nf-core/ncbigenomedownload/main.nf
new file mode 100644
index 00000000000..63a41517e46
--- /dev/null
+++ b/tests/modules/nf-core/ncbigenomedownload/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NCBIGENOMEDOWNLOAD } from '../../../../modules/nf-core/ncbigenomedownload/main.nf'
+
+workflow test_ncbigenomedownload {
+    
+    input = [ [ id:'test', single_end:false ] ]
+
+    accessions = []
+
+    NCBIGENOMEDOWNLOAD ( input, accessions)
+}
+
+
diff --git a/tests/modules/ncbigenomedownload/nextflow.config b/tests/modules/nf-core/ncbigenomedownload/nextflow.config
similarity index 100%
rename from tests/modules/ncbigenomedownload/nextflow.config
rename to tests/modules/nf-core/ncbigenomedownload/nextflow.config
diff --git a/tests/modules/nf-core/ncbigenomedownload/test.yml b/tests/modules/nf-core/ncbigenomedownload/test.yml
new file mode 100644
index 00000000000..5f6f1649c38
--- /dev/null
+++ b/tests/modules/nf-core/ncbigenomedownload/test.yml
@@ -0,0 +1,11 @@
+- name: ncbigenomedownload test_ncbigenomedownload
+  command: nextflow run ./tests/modules/nf-core/ncbigenomedownload -entry test_ncbigenomedownload -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ncbigenomedownload/nextflow.config
+  tags:
+    - ncbigenomedownload
+  files:
+    - path: output/ncbigenomedownload/GCF_000013425.1_ASM1342v1_assembly_stats.txt
+      md5sum: f78c6a373130e50fac5472962a5fdf44
+    - path: output/ncbigenomedownload/GCF_000013425.1_ASM1342v1_genomic.fna.gz
+      md5sum: b086eb1020e7df022afa545dc6d93297
+    - path: output/ncbigenomedownload/GCF_000013425.1_ASM1342v1_genomic.gbff.gz
+      md5sum: ae2da70e32c783858e6c60c72e9eeb7a
diff --git a/tests/modules/nf-core/nextclade/datasetget/main.nf b/tests/modules/nf-core/nextclade/datasetget/main.nf
new file mode 100644
index 00000000000..5935f8bbaaf
--- /dev/null
+++ b/tests/modules/nf-core/nextclade/datasetget/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NEXTCLADE_DATASETGET } from '../../../../../modules/nf-core/nextclade/datasetget/main.nf'
+
+workflow test_nextclade_datasetget {
+
+    dataset = 'sars-cov-2'
+    reference = 'MN908947'
+    tag = '2022-01-18T12:00:00Z'
+
+    NEXTCLADE_DATASETGET ( dataset, reference, tag )
+
+}
diff --git a/tests/modules/nextclade/datasetget/nextflow.config b/tests/modules/nf-core/nextclade/datasetget/nextflow.config
similarity index 100%
rename from tests/modules/nextclade/datasetget/nextflow.config
rename to tests/modules/nf-core/nextclade/datasetget/nextflow.config
diff --git a/tests/modules/nf-core/nextclade/datasetget/test.yml b/tests/modules/nf-core/nextclade/datasetget/test.yml
new file mode 100644
index 00000000000..9639700e1b3
--- /dev/null
+++ b/tests/modules/nf-core/nextclade/datasetget/test.yml
@@ -0,0 +1,22 @@
+- name: nextclade datasetget
+  command: nextflow run ./tests/modules/nf-core/nextclade/datasetget -entry test_nextclade_datasetget -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/nextclade/datasetget/nextflow.config
+  tags:
+    - nextclade
+    - nextclade/datasetget
+  files:
+    - path: output/nextclade/sars-cov-2/genemap.gff
+      md5sum: 21ebebfd0f416eeb959e55ebffd808e8
+    - path: output/nextclade/sars-cov-2/primers.csv
+      md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
+    - path: output/nextclade/sars-cov-2/qc.json
+      md5sum: c512f51fda0212b21ffff05779180963
+    - path: output/nextclade/sars-cov-2/reference.fasta
+      md5sum: c7ce05f28e4ec0322c96f24e064ef55c
+    - path: output/nextclade/sars-cov-2/sequences.fasta
+      md5sum: 41129d255b99e0e92bdf20e866b99a1b
+    - path: output/nextclade/sars-cov-2/tag.json
+      md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3
+    - path: output/nextclade/sars-cov-2/tree.json
+      md5sum: b8f32f547ff9e2131d6fc66b68fc54b1
+    - path: output/nextclade/sars-cov-2/virus_properties.json
+      md5sum: 5f2de3949e07cb633f3d9e4a7654dc81
diff --git a/tests/modules/nf-core/nextclade/run/main.nf b/tests/modules/nf-core/nextclade/run/main.nf
new file mode 100644
index 00000000000..5c44ea4e7f3
--- /dev/null
+++ b/tests/modules/nf-core/nextclade/run/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NEXTCLADE_DATASETGET } from '../../../../../modules/nf-core/nextclade/datasetget/main.nf'
+include { NEXTCLADE_RUN        } from '../../../../../modules/nf-core/nextclade/run/main.nf'
+
+workflow test_nextclade_run {
+
+    dataset = 'sars-cov-2'
+    reference = 'MN908947'
+    tag = '2022-01-18T12:00:00Z'
+
+    NEXTCLADE_DATASETGET ( dataset, reference, tag )
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset )
+}
+
diff --git a/tests/modules/nextclade/run/nextflow.config b/tests/modules/nf-core/nextclade/run/nextflow.config
similarity index 100%
rename from tests/modules/nextclade/run/nextflow.config
rename to tests/modules/nf-core/nextclade/run/nextflow.config
diff --git a/tests/modules/nf-core/nextclade/run/test.yml b/tests/modules/nf-core/nextclade/run/test.yml
new file mode 100644
index 00000000000..f8ee2cf322b
--- /dev/null
+++ b/tests/modules/nf-core/nextclade/run/test.yml
@@ -0,0 +1,62 @@
+- name: nextclade run test_nextclade_run
+  command: nextflow run ./tests/modules/nf-core/nextclade/run -entry test_nextclade_run -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/nextclade/run/nextflow.config
+  tags:
+    - nextclade/run
+    - nextclade
+  files:
+    - path: output/nextclade/sars-cov-2/genemap.gff
+      md5sum: 21ebebfd0f416eeb959e55ebffd808e8
+    - path: output/nextclade/sars-cov-2/primers.csv
+      md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
+    - path: output/nextclade/sars-cov-2/qc.json
+      md5sum: c512f51fda0212b21ffff05779180963
+    - path: output/nextclade/sars-cov-2/reference.fasta
+      md5sum: c7ce05f28e4ec0322c96f24e064ef55c
+    - path: output/nextclade/sars-cov-2/sequences.fasta
+      md5sum: 41129d255b99e0e92bdf20e866b99a1b
+    - path: output/nextclade/sars-cov-2/tag.json
+      md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3
+    - path: output/nextclade/sars-cov-2/tree.json
+      md5sum: b8f32f547ff9e2131d6fc66b68fc54b1
+    - path: output/nextclade/sars-cov-2/virus_properties.json
+      md5sum: 5f2de3949e07cb633f3d9e4a7654dc81
+    - path: output/nextclade/test.aligned.fasta
+      md5sum: 1bf54662837b0df37f1857c7fa631225
+    - path: output/nextclade/test.auspice.json
+      md5sum: 04d8c32f141435ca45bf430dcb59bcba
+    - path: output/nextclade/test.csv
+      md5sum: 9489bab7f58c07c0b6949182789aa435
+    - path: output/nextclade/test.errors.csv
+      md5sum: 810d1c72e1ed010a9a017afba7ce8063
+    - path: output/nextclade/test.insertions.csv
+      md5sum: c3aa7071d06122ec07ba7c7c4ba6e84a
+    - path: output/nextclade/test.json
+      contains: ["nextcladeAlgoVersion"]
+    - path: output/nextclade/test.ndjson
+      md5sum: 32e3c1e733be19509faa0a45260a3d96
+    - path: output/nextclade/test.tsv
+      md5sum: 7f4bea521bcef4d1bca02c51d11b2fe1
+    - path: output/nextclade/test_gene_E.translation.fasta
+      md5sum: 1a6d93bd7abfeb193476a86950f07202
+    - path: output/nextclade/test_gene_M.translation.fasta
+      md5sum: 6f79ab0742c078fcd9d2a474518c7022
+    - path: output/nextclade/test_gene_N.translation.fasta
+      md5sum: bef9912f101777bfff36225d7e5c3c1f
+    - path: output/nextclade/test_gene_ORF1a.translation.fasta
+      md5sum: 4dc0e2eb1f2a61939ba49500ee3fa41a
+    - path: output/nextclade/test_gene_ORF1b.translation.fasta
+      md5sum: 9c2e83d26161b5c887ff51cd64bd15bb
+    - path: output/nextclade/test_gene_ORF3a.translation.fasta
+      md5sum: adcbede4ebc2cac7af755a9d29d28ea3
+    - path: output/nextclade/test_gene_ORF6.translation.fasta
+      md5sum: 3785b34cce978c95256f83db6ee82af0
+    - path: output/nextclade/test_gene_ORF7a.translation.fasta
+      md5sum: 6ede1acb9e75afc84aa30bbc40551d37
+    - path: output/nextclade/test_gene_ORF7b.translation.fasta
+      md5sum: 460e4cbc5f8c632c2bc9a8aedad5cf43
+    - path: output/nextclade/test_gene_ORF8.translation.fasta
+      md5sum: c733c88e61b29542664368fbf6dd4c76
+    - path: output/nextclade/test_gene_ORF9b.translation.fasta
+      md5sum: 0aa13afc6cbf445fc92caa2e6c0a7548
+    - path: output/nextclade/test_gene_S.translation.fasta
+      md5sum: 77740927a3f00b7e5bfac392fa6d264c
diff --git a/tests/modules/nf-core/nextgenmap/main.nf b/tests/modules/nf-core/nextgenmap/main.nf
new file mode 100644
index 00000000000..89db132e2b0
--- /dev/null
+++ b/tests/modules/nf-core/nextgenmap/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NEXTGENMAP } from '../../../../modules/nf-core/nextgenmap/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_nextgenmap_single {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    NEXTGENMAP ( input, fasta )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_bwamem2_mem_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    NEXTGENMAP ( input, fasta )
+}
diff --git a/tests/modules/nextgenmap/nextflow.config b/tests/modules/nf-core/nextgenmap/nextflow.config
similarity index 100%
rename from tests/modules/nextgenmap/nextflow.config
rename to tests/modules/nf-core/nextgenmap/nextflow.config
diff --git a/tests/modules/nf-core/nextgenmap/test.yml b/tests/modules/nf-core/nextgenmap/test.yml
new file mode 100644
index 00000000000..6b6f8dc35b5
--- /dev/null
+++ b/tests/modules/nf-core/nextgenmap/test.yml
@@ -0,0 +1,15 @@
+- name: nextgenmap test_nextgenmap_single
+  command: nextflow run ./tests/modules/nf-core/nextgenmap -entry test_nextgenmap_single -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/nextgenmap/nextflow.config
+  tags:
+    - nextgenmap
+  files:
+    - path: output/nextgenmap/test.bam
+      md5sum: ada069bc5c670ffee23871f3ca525d0a
+
+- name: nextgenmap test_bwamem2_mem_paired_end
+  command: nextflow run ./tests/modules/nf-core/nextgenmap -entry test_bwamem2_mem_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/nextgenmap/nextflow.config
+  tags:
+    - nextgenmap
+  files:
+    - path: output/nextgenmap/test.bam
+      md5sum: fa76167e236cf1aabdafdbb0632253cd
diff --git a/tests/modules/nf-core/ngmaster/main.nf b/tests/modules/nf-core/ngmaster/main.nf
new file mode 100644
index 00000000000..a6d4c12f19d
--- /dev/null
+++ b/tests/modules/nf-core/ngmaster/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NGMASTER } from '../../../../modules/nf-core/ngmaster/main.nf'
+
+workflow test_ngmaster {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    NGMASTER ( input )
+}
diff --git a/tests/modules/ngmaster/nextflow.config b/tests/modules/nf-core/ngmaster/nextflow.config
similarity index 100%
rename from tests/modules/ngmaster/nextflow.config
rename to tests/modules/nf-core/ngmaster/nextflow.config
diff --git a/tests/modules/nf-core/ngmaster/test.yml b/tests/modules/nf-core/ngmaster/test.yml
new file mode 100644
index 00000000000..706bb40e69c
--- /dev/null
+++ b/tests/modules/nf-core/ngmaster/test.yml
@@ -0,0 +1,7 @@
+- name: ngmaster test_ngmaster
+  command: nextflow run ./tests/modules/nf-core/ngmaster -entry test_ngmaster -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ngmaster/nextflow.config
+  tags:
+    - ngmaster
+  files:
+    - path: output/ngmaster/test.tsv
+      md5sum: cf674474eaf8ac6abfcebce0af0226cf
diff --git a/tests/modules/nf-core/ngscheckmate/ncm/main.nf b/tests/modules/nf-core/ngscheckmate/ncm/main.nf
new file mode 100644
index 00000000000..00025215095
--- /dev/null
+++ b/tests/modules/nf-core/ngscheckmate/ncm/main.nf
@@ -0,0 +1,63 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_BAM} from '../../../../../modules/nf-core/ngscheckmate/ncm/main.nf'
+include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_VCF} from '../../../../../modules/nf-core/ngscheckmate/ncm/main.nf'
+
+include { BEDTOOLS_MAKEWINDOWS } from '../../../../../modules/nf-core/bedtools/makewindows/main.nf'
+
+include { BCFTOOLS_MPILEUP } from '../../../../../modules/nf-core/bcftools/mpileup/main.nf'
+include { BCFTOOLS_MPILEUP as BCFTOOLS_MPILEUP2 } from '../../../../../modules/nf-core/bcftools/mpileup/main.nf'
+
+workflow test_ngscheckmate_ncm_bam {
+    input    = [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
+
+    fasta    = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    inputBed = [ [ id:'test'],
+                 file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
+
+    BEDTOOLS_MAKEWINDOWS(inputBed, true).
+    tab.
+    map{it[1]}.
+    view().
+    set{snp_channel}
+
+    NGSCHECKMATE_NCM_BAM(input, snp_channel, fasta)
+}
+
+workflow test_ngscheckmate_ncm_vcf {
+    input1   = [ [ id:'test1' ], // meta map
+                 [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+               ]
+
+    input2   = [ [ id:'test2' ], // meta map
+                 [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+               ]
+
+    fasta    = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    inputBed = [ [ id:'test'],
+                 file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
+
+    BCFTOOLS_MPILEUP ( input1, fasta, false )
+    BCFTOOLS_MPILEUP2 ( input2, fasta, false )
+
+    BCFTOOLS_MPILEUP2.out.vcf.
+        combine( BCFTOOLS_MPILEUP.out.vcf ).
+        map { [ it[1], it[3] ] }.
+        set { vcf_channel }
+
+    BEDTOOLS_MAKEWINDOWS( inputBed, true ).tab.
+        map { it[1] }.
+        view().
+        set { snp_channel }
+
+    NGSCHECKMATE_NCM_VCF(vcf_channel, snp_channel, fasta)
+}
+
+
diff --git a/tests/modules/ngscheckmate/ncm/nextflow.config b/tests/modules/nf-core/ngscheckmate/ncm/nextflow.config
similarity index 100%
rename from tests/modules/ngscheckmate/ncm/nextflow.config
rename to tests/modules/nf-core/ngscheckmate/ncm/nextflow.config
diff --git a/tests/modules/nf-core/ngscheckmate/ncm/test.yml b/tests/modules/nf-core/ngscheckmate/ncm/test.yml
new file mode 100644
index 00000000000..0d690400285
--- /dev/null
+++ b/tests/modules/nf-core/ngscheckmate/ncm/test.yml
@@ -0,0 +1,29 @@
+- name: ngscheckmate ncm test_ngscheckmate_ncm_bam
+  command: nextflow run ./tests/modules/nf-core/ngscheckmate/ncm -entry test_ngscheckmate_ncm_bam -c ./tests/config/nextflow.config
+  tags:
+    - ngscheckmate/ncm
+    - ngscheckmate
+  files:
+    - path: output/ngscheckmate/output_all.txt
+      md5sum: f71a712c3f6ecf64dd526365212f1b7c
+    - path: output/ngscheckmate/output_corr_matrix.txt
+      md5sum: 6777377aa9ae3d57f841b12896318db0
+    - path: output/ngscheckmate/output_matched.txt
+      md5sum: f71a712c3f6ecf64dd526365212f1b7c
+    - path: output/ngscheckmate/versions.yml
+      md5sum: fbb2bebd65b4f4e1e93c6bf5c08a6829
+
+- name: ngscheckmate ncm test_ngscheckmate_ncm_vcf
+  command: nextflow run ./tests/modules/nf-core/ngscheckmate/ncm -entry test_ngscheckmate_ncm_vcf -c ./tests/config/nextflow.config
+  tags:
+    - ngscheckmate/ncm
+    - ngscheckmate
+  files:
+    - path: output/ngscheckmate/output_all.txt
+      md5sum: fd74956dcac279b6f58e82ea73e344f8
+    - path: output/ngscheckmate/output_corr_matrix.txt
+      md5sum: 0c86bdad2721c470fe6be119f291c8e5
+    - path: output/ngscheckmate/output_matched.txt
+      md5sum: fd74956dcac279b6f58e82ea73e344f8
+    - path: output/ngscheckmate/versions.yml
+      md5sum: f06910b83dde194a47870c553cefe193
diff --git a/tests/modules/nf-core/nucmer/main.nf b/tests/modules/nf-core/nucmer/main.nf
new file mode 100644
index 00000000000..0799c7ff375
--- /dev/null
+++ b/tests/modules/nf-core/nucmer/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NUCMER } from '../../../../modules/nf-core/nucmer/main.nf'
+
+workflow test_nucmer {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+
+    NUCMER ( input )
+}
diff --git a/tests/modules/nucmer/nextflow.config b/tests/modules/nf-core/nucmer/nextflow.config
similarity index 100%
rename from tests/modules/nucmer/nextflow.config
rename to tests/modules/nf-core/nucmer/nextflow.config
diff --git a/tests/modules/nf-core/nucmer/test.yml b/tests/modules/nf-core/nucmer/test.yml
new file mode 100644
index 00000000000..9899eea4acb
--- /dev/null
+++ b/tests/modules/nf-core/nucmer/test.yml
@@ -0,0 +1,9 @@
+- name: nucmer test_nucmer
+  command: nextflow run ./tests/modules/nf-core/nucmer -entry test_nucmer -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/nucmer/nextflow.config
+  tags:
+    - nucmer
+  files:
+    - path: output/nucmer/test.coords
+      contains: ["MT192765.1"]
+    - path: output/nucmer/test.delta
+      contains: ["MT192765.1"]
diff --git a/tests/modules/nf-core/optitype/main.nf b/tests/modules/nf-core/optitype/main.nf
new file mode 100644
index 00000000000..7771f682fb0
--- /dev/null
+++ b/tests/modules/nf-core/optitype/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { OPTITYPE } from '../../../../modules/nf-core/optitype/main.nf'
+
+workflow test_optitype {
+    input = [ [ id:'test', seq_type:'dna' ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam_bai'], checkIfExists: true)
+            ]
+
+    OPTITYPE ( input )
+}
diff --git a/tests/modules/optitype/nextflow.config b/tests/modules/nf-core/optitype/nextflow.config
similarity index 100%
rename from tests/modules/optitype/nextflow.config
rename to tests/modules/nf-core/optitype/nextflow.config
diff --git a/tests/modules/nf-core/optitype/test.yml b/tests/modules/nf-core/optitype/test.yml
new file mode 100644
index 00000000000..b823742b053
--- /dev/null
+++ b/tests/modules/nf-core/optitype/test.yml
@@ -0,0 +1,9 @@
+- name: optitype test_optitype
+  command: nextflow run ./tests/modules/nf-core/optitype -entry test_optitype -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/optitype/nextflow.config
+  tags:
+    - optitype
+  files:
+    - path: output/optitype/test/test_coverage_plot.pdf
+    - path: output/optitype/test/test_result.tsv
+      contains:
+        - "1439"
diff --git a/tests/modules/nf-core/pairix/main.nf b/tests/modules/nf-core/pairix/main.nf
new file mode 100644
index 00000000000..04591eaf0c3
--- /dev/null
+++ b/tests/modules/nf-core/pairix/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PAIRIX } from '../../../../modules/nf-core/pairix/main.nf'
+
+workflow test_pairix {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://raw.githubusercontent.com/4dn-dcic/pairix/master/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz", checkIfExists: true) ]
+
+    PAIRIX ( input )
+}
diff --git a/tests/modules/pairix/nextflow.config b/tests/modules/nf-core/pairix/nextflow.config
similarity index 100%
rename from tests/modules/pairix/nextflow.config
rename to tests/modules/nf-core/pairix/nextflow.config
diff --git a/tests/modules/nf-core/pairix/test.yml b/tests/modules/nf-core/pairix/test.yml
new file mode 100644
index 00000000000..88cd5fcf985
--- /dev/null
+++ b/tests/modules/nf-core/pairix/test.yml
@@ -0,0 +1,9 @@
+- name: pairix test_pairix
+  command: nextflow run ./tests/modules/nf-core/pairix -entry test_pairix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pairix/nextflow.config
+  tags:
+    - pairix
+  files:
+    - path: output/pairix/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz
+      md5sum: a0165859d0151f45fe6fb206f2f4814b
+    - path: output/pairix/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2
+      md5sum: a6e41cc7cff16fd15b5ee505549ec99a
diff --git a/tests/modules/nf-core/pairtools/dedup/main.nf b/tests/modules/nf-core/pairtools/dedup/main.nf
new file mode 100644
index 00000000000..6772b0bfe09
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/dedup/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PAIRTOOLS_DEDUP } from '../../../../../modules/nf-core/pairtools/dedup/main.nf'
+
+workflow test_pairtools_dedup {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.4dedup.pairsam", checkIfExists: true) ]
+
+    PAIRTOOLS_DEDUP ( input )
+}
diff --git a/tests/modules/pairtools/dedup/nextflow.config b/tests/modules/nf-core/pairtools/dedup/nextflow.config
similarity index 100%
rename from tests/modules/pairtools/dedup/nextflow.config
rename to tests/modules/nf-core/pairtools/dedup/nextflow.config
diff --git a/tests/modules/nf-core/pairtools/dedup/test.yml b/tests/modules/nf-core/pairtools/dedup/test.yml
new file mode 100644
index 00000000000..65de086fafa
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/dedup/test.yml
@@ -0,0 +1,10 @@
+- name: pairtools dedup test_pairtools_dedup
+  command: nextflow run ./tests/modules/nf-core/pairtools/dedup -entry test_pairtools_dedup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pairtools/dedup/nextflow.config
+  tags:
+    - pairtools/dedup
+    - pairtools
+  files:
+    - path: output/pairtools/test.dedup.pairs.gz
+      md5sum: 785ffc9495731fd3d0f6f679a0a0e988
+    - path: output/pairtools/test.dedup.pairs.stat
+      md5sum: a554a846567cbcda66f070c76a9173bc
diff --git a/tests/modules/nf-core/pairtools/flip/main.nf b/tests/modules/nf-core/pairtools/flip/main.nf
new file mode 100644
index 00000000000..d891f6ae752
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/flip/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PAIRTOOLS_FLIP } from '../../../../../modules/nf-core/pairtools/flip/main.nf'
+
+workflow test_pairtools_flip {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.4flip.pairs", checkIfExists: true) ]
+    sizes = file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.chrom.sizes", checkIfExists:true)
+
+    PAIRTOOLS_FLIP ( input, sizes )
+}
diff --git a/tests/modules/pairtools/flip/nextflow.config b/tests/modules/nf-core/pairtools/flip/nextflow.config
similarity index 100%
rename from tests/modules/pairtools/flip/nextflow.config
rename to tests/modules/nf-core/pairtools/flip/nextflow.config
diff --git a/tests/modules/nf-core/pairtools/flip/test.yml b/tests/modules/nf-core/pairtools/flip/test.yml
new file mode 100644
index 00000000000..39235c00786
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/flip/test.yml
@@ -0,0 +1,7 @@
+- name: pairtools flip test_pairtools_flip
+  command: nextflow run ./tests/modules/nf-core/pairtools/flip -entry test_pairtools_flip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pairtools/flip/nextflow.config
+  tags:
+    - pairtools/flip
+    - pairtools
+  files:
+    - path: output/pairtools/test.flip.gz
diff --git a/tests/modules/nf-core/pairtools/parse/main.nf b/tests/modules/nf-core/pairtools/parse/main.nf
new file mode 100644
index 00000000000..4b387e1c4e1
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/parse/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PAIRTOOLS_PARSE } from '../../../../../modules/nf-core/pairtools/parse/main.nf'
+
+workflow test_pairtools_parse {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.sam", checkIfExists: true) ]
+    sizes = file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.chrom.sizes", checkIfExists:true)
+
+    PAIRTOOLS_PARSE ( input, sizes )
+}
diff --git a/tests/modules/pairtools/parse/nextflow.config b/tests/modules/nf-core/pairtools/parse/nextflow.config
similarity index 100%
rename from tests/modules/pairtools/parse/nextflow.config
rename to tests/modules/nf-core/pairtools/parse/nextflow.config
diff --git a/tests/modules/nf-core/pairtools/parse/test.yml b/tests/modules/nf-core/pairtools/parse/test.yml
new file mode 100644
index 00000000000..8bf033278c9
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/parse/test.yml
@@ -0,0 +1,9 @@
+- name: pairtools parse test_pairtools_parse
+  command: nextflow run ./tests/modules/nf-core/pairtools/parse -entry test_pairtools_parse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pairtools/parse/nextflow.config
+  tags:
+    - pairtools
+    - pairtools/parse
+  files:
+    - path: output/pairtools/test.raw.pairsam.gz
+    - path: output/pairtools/test.raw.pairsam.stat
+      md5sum: 11e90f346f855ffd750c7c348ac1d456
diff --git a/tests/modules/nf-core/pairtools/restrict/main.nf b/tests/modules/nf-core/pairtools/restrict/main.nf
new file mode 100644
index 00000000000..62302473002
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/restrict/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PAIRTOOLS_RESTRICT } from '../../../../../modules/nf-core/pairtools/restrict/main.nf'
+
+workflow test_pairtools_restrict {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.4flip.pairs", checkIfExists: true) ]
+    File dig  = new File("${workflow.workDir}/frag.bed")
+    dig.write("chr1\t0\t50\r\nchr1\t50\t100\r\nchr2\t0\t50\r\nchr2\t50\t100\r\n!\t0\t1\r\n")
+    frag  = file(dig)
+
+    PAIRTOOLS_RESTRICT ( input, frag )
+}
diff --git a/tests/modules/pairtools/restrict/nextflow.config b/tests/modules/nf-core/pairtools/restrict/nextflow.config
similarity index 100%
rename from tests/modules/pairtools/restrict/nextflow.config
rename to tests/modules/nf-core/pairtools/restrict/nextflow.config
diff --git a/tests/modules/nf-core/pairtools/restrict/test.yml b/tests/modules/nf-core/pairtools/restrict/test.yml
new file mode 100644
index 00000000000..04f1b4bbba8
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/restrict/test.yml
@@ -0,0 +1,7 @@
+- name: pairtools restrict test_pairtools_restrict
+  command: nextflow run ./tests/modules/nf-core/pairtools/restrict -entry test_pairtools_restrict -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pairtools/restrict/nextflow.config
+  tags:
+    - pairtools/restrict
+    - pairtools
+  files:
+    - path: output/pairtools/test.restrict.pairs.gz
diff --git a/tests/modules/nf-core/pairtools/select/main.nf b/tests/modules/nf-core/pairtools/select/main.nf
new file mode 100644
index 00000000000..2eddb21bee4
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/select/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PAIRTOOLS_SELECT } from '../../../../../modules/nf-core/pairtools/select/main.nf'
+
+workflow test_pairtools_select {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.pairsam", checkIfExists: true) ]
+
+    PAIRTOOLS_SELECT ( input )
+}
diff --git a/tests/modules/pairtools/select/nextflow.config b/tests/modules/nf-core/pairtools/select/nextflow.config
similarity index 100%
rename from tests/modules/pairtools/select/nextflow.config
rename to tests/modules/nf-core/pairtools/select/nextflow.config
diff --git a/tests/modules/nf-core/pairtools/select/test.yml b/tests/modules/nf-core/pairtools/select/test.yml
new file mode 100644
index 00000000000..8532a7350df
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/select/test.yml
@@ -0,0 +1,8 @@
+- name: pairtools select test_pairtools_select
+  command: nextflow run ./tests/modules/nf-core/pairtools/select -entry test_pairtools_select -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pairtools/select/nextflow.config
+  tags:
+    - pairtools/select
+    - pairtools
+  files:
+    - path: output/pairtools/test.selected.pairs.gz
+    - path: output/pairtools/test.unselected.pairs.gz
diff --git a/tests/modules/nf-core/pairtools/sort/main.nf b/tests/modules/nf-core/pairtools/sort/main.nf
new file mode 100644
index 00000000000..6ec22c67f91
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/sort/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PAIRTOOLS_SORT } from '../../../../../modules/nf-core/pairtools/sort/main.nf'
+
+workflow test_pairtools_sort {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.pairsam", checkIfExists: true) ]
+
+    PAIRTOOLS_SORT ( input )
+}
diff --git a/tests/modules/pairtools/sort/nextflow.config b/tests/modules/nf-core/pairtools/sort/nextflow.config
similarity index 100%
rename from tests/modules/pairtools/sort/nextflow.config
rename to tests/modules/nf-core/pairtools/sort/nextflow.config
diff --git a/tests/modules/nf-core/pairtools/sort/test.yml b/tests/modules/nf-core/pairtools/sort/test.yml
new file mode 100644
index 00000000000..10ea983fe95
--- /dev/null
+++ b/tests/modules/nf-core/pairtools/sort/test.yml
@@ -0,0 +1,7 @@
+- name: pairtools sort test_pairtools_sort
+  command: nextflow run ./tests/modules/nf-core/pairtools/sort -entry test_pairtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pairtools/sort/nextflow.config
+  tags:
+    - pairtools/sort
+    - pairtools
+  files:
+    - path: output/pairtools/test.sorted.pairs.gz
diff --git a/tests/modules/nf-core/panaroo/run/main.nf b/tests/modules/nf-core/panaroo/run/main.nf
new file mode 100644
index 00000000000..ac7329bcd8f
--- /dev/null
+++ b/tests/modules/nf-core/panaroo/run/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PANAROO_RUN } from '../../../../../modules/nf-core/panaroo/run/main.nf'
+
+workflow test_panaroo_run {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
+        ]
+    ]
+
+    PANAROO_RUN ( input )
+}
diff --git a/tests/modules/panaroo/run/nextflow.config b/tests/modules/nf-core/panaroo/run/nextflow.config
similarity index 100%
rename from tests/modules/panaroo/run/nextflow.config
rename to tests/modules/nf-core/panaroo/run/nextflow.config
diff --git a/tests/modules/nf-core/panaroo/run/test.yml b/tests/modules/nf-core/panaroo/run/test.yml
new file mode 100644
index 00000000000..7c198c68846
--- /dev/null
+++ b/tests/modules/nf-core/panaroo/run/test.yml
@@ -0,0 +1,38 @@
+- name: panaroo run test_panaroo_run
+  command: nextflow run ./tests/modules/nf-core/panaroo/run -entry test_panaroo_run -c ./tests/config/nextflow.config
+  tags:
+    - panaroo/run
+    - panaroo
+  files:
+    - path: output/panaroo/results/combined_DNA_CDS.fasta
+      md5sum: 92bd4f6b9c84c84c0989d77d2558b7d1
+    - path: output/panaroo/results/combined_protein_CDS.fasta
+      md5sum: 7a5636c4f2abc190f5dd4dfbb1da7034
+    - path: output/panaroo/results/combined_protein_cdhit_out.txt
+      md5sum: 2164b81606712b53af2198b4d50eed08
+    - path: output/panaroo/results/combined_protein_cdhit_out.txt.clstr
+      md5sum: aaa9fc2b797c932b6d9ff2df640113f1
+    - path: output/panaroo/results/core_alignment_header.embl
+      contains: ["DNA", "feature", "locus_tag"]
+    - path: output/panaroo/results/core_gene_alignment.aln
+      contains: ["test1", "test2", "test3"]
+    - path: output/panaroo/results/final_graph.gml
+      contains: ["graph", "isolateNames", "test3"]
+    - path: output/panaroo/results/gene_data.csv
+      md5sum: 45df2d26ac81754b858c0e4757e834b2
+    - path: output/panaroo/results/gene_presence_absence.Rtab
+      md5sum: 9efbed5df121dc0c4fbb58869b65c3e4
+    - path: output/panaroo/results/gene_presence_absence.csv
+      contains: ["Gene", "unique", "test3"]
+    - path: output/panaroo/results/gene_presence_absence_roary.csv
+      contains: ["Gene", "Max", "Fragment"]
+    - path: output/panaroo/results/pan_genome_reference.fa
+      md5sum: d0b03cdfaab8965d86cb1045db3c2d20
+    - path: output/panaroo/results/pre_filt_graph.gml
+      contains: ["graph", "node", "id"]
+    - path: output/panaroo/results/struct_presence_absence.Rtab
+      md5sum: 246017db1175f9b1683dfe60cb2e9b5b
+    - path: output/panaroo/results/summary_statistics.txt
+      md5sum: 9c73c416e1758bea06c67b4ec9fd0720
+    - path: output/panaroo/versions.yml
+      md5sum: 909e7b046a8a87319986d34b7328641c
diff --git a/tests/modules/nf-core/pangolin/main.nf b/tests/modules/nf-core/pangolin/main.nf
new file mode 100644
index 00000000000..6bed60ae0d7
--- /dev/null
+++ b/tests/modules/nf-core/pangolin/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PANGOLIN } from '../../../../modules/nf-core/pangolin/main.nf'
+
+workflow test_pangolin {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ]
+
+    PANGOLIN ( input )
+}
diff --git a/tests/modules/pangolin/nextflow.config b/tests/modules/nf-core/pangolin/nextflow.config
similarity index 100%
rename from tests/modules/pangolin/nextflow.config
rename to tests/modules/nf-core/pangolin/nextflow.config
diff --git a/tests/modules/nf-core/pangolin/test.yml b/tests/modules/nf-core/pangolin/test.yml
new file mode 100644
index 00000000000..0b408d08659
--- /dev/null
+++ b/tests/modules/nf-core/pangolin/test.yml
@@ -0,0 +1,7 @@
+- name: pangolin
+  command: nextflow run ./tests/modules/nf-core/pangolin -entry test_pangolin -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pangolin/nextflow.config
+  tags:
+    - pangolin
+  files:
+    - path: ./output/pangolin/test.pangolin.csv
+      md5sum: 3484156c2f2e2e638431be7934cfc5b7
diff --git a/tests/modules/nf-core/paraclu/main.nf b/tests/modules/nf-core/paraclu/main.nf
new file mode 100644
index 00000000000..1e7b71382a5
--- /dev/null
+++ b/tests/modules/nf-core/paraclu/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PARACLU } from '../../../../modules/nf-core/paraclu/main.nf'
+
+workflow test_paraclu {
+
+    input = [[  id:'test' ], // meta map
+                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                ]
+    min_cluster = 30
+
+    PARACLU ( input, min_cluster )
+}
diff --git a/tests/modules/paraclu/nextflow.config b/tests/modules/nf-core/paraclu/nextflow.config
similarity index 100%
rename from tests/modules/paraclu/nextflow.config
rename to tests/modules/nf-core/paraclu/nextflow.config
diff --git a/tests/modules/nf-core/paraclu/test.yml b/tests/modules/nf-core/paraclu/test.yml
new file mode 100644
index 00000000000..85eab3e9d34
--- /dev/null
+++ b/tests/modules/nf-core/paraclu/test.yml
@@ -0,0 +1,7 @@
+- name: paraclu test_paraclu
+  command: nextflow run ./tests/modules/nf-core/paraclu -entry test_paraclu -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/paraclu/nextflow.config
+  tags:
+    - paraclu
+  files:
+    - path: output/paraclu/test.clustered.simplified.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/nf-core/pasty/main.nf b/tests/modules/nf-core/pasty/main.nf
new file mode 100644
index 00000000000..d4e8f397a63
--- /dev/null
+++ b/tests/modules/nf-core/pasty/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PASTY } from '../../../../modules/nf-core/pasty/main.nf'
+
+workflow test_pasty {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    PASTY ( input )
+}
diff --git a/tests/modules/pasty/nextflow.config b/tests/modules/nf-core/pasty/nextflow.config
similarity index 100%
rename from tests/modules/pasty/nextflow.config
rename to tests/modules/nf-core/pasty/nextflow.config
diff --git a/tests/modules/nf-core/pasty/test.yml b/tests/modules/nf-core/pasty/test.yml
new file mode 100644
index 00000000000..6241971111e
--- /dev/null
+++ b/tests/modules/nf-core/pasty/test.yml
@@ -0,0 +1,11 @@
+- name: pasty test_pasty
+  command: nextflow run ./tests/modules/nf-core/pasty -entry test_pasty -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/pasty/nextflow.config
+  tags:
+    - pasty
+  files:
+    - path: output/pasty/test.blastn.tsv
+      md5sum: 45de2825f0bb3cc8fe9f2b7c419f66f2
+    - path: output/pasty/test.details.tsv
+      md5sum: d6822beea048a27af839087dfc14a536
+    - path: output/pasty/test.tsv
+      md5sum: edbae35d3edc17283ea73f7f3eb22087
diff --git a/tests/modules/nf-core/pbbam/pbmerge/main.nf b/tests/modules/nf-core/pbbam/pbmerge/main.nf
new file mode 100644
index 00000000000..52334508896
--- /dev/null
+++ b/tests/modules/nf-core/pbbam/pbmerge/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PBBAM_PBMERGE } from '../../../../../modules/nf-core/pbbam/pbmerge/main.nf'
+
+workflow test_pbbam_pbmerge {
+
+    input = [
+        [ id:'test' ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['pacbio']['cluster']   , checkIfExists: true),
+            file(params.test_data['homo_sapiens']['pacbio']['singletons'], checkIfExists: true)
+        ]
+    ]
+
+    PBBAM_PBMERGE ( input )
+}
diff --git a/tests/modules/pbbam/pbmerge/nextflow.config b/tests/modules/nf-core/pbbam/pbmerge/nextflow.config
similarity index 100%
rename from tests/modules/pbbam/pbmerge/nextflow.config
rename to tests/modules/nf-core/pbbam/pbmerge/nextflow.config
diff --git a/tests/modules/nf-core/pbbam/pbmerge/test.yml b/tests/modules/nf-core/pbbam/pbmerge/test.yml
new file mode 100644
index 00000000000..49a885512d9
--- /dev/null
+++ b/tests/modules/nf-core/pbbam/pbmerge/test.yml
@@ -0,0 +1,10 @@
+- name: pbbam pbmerge test_pbbam_pbmerge
+  command: nextflow run ./tests/modules/nf-core/pbbam/pbmerge -entry test_pbbam_pbmerge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pbbam/pbmerge/nextflow.config
+  tags:
+    - pbbam/pbmerge
+    - pbbam
+  files:
+    - path: output/pbbam/test.merged.bam
+      md5sum: 727c7ba1289192085c06890dda70f973
+    - path: output/pbbam/test.merged.bam.pbi
+      md5sum: edfadd3a81c598d1ee051899792db75d
diff --git a/tests/modules/nf-core/pbccs/main.nf b/tests/modules/nf-core/pbccs/main.nf
new file mode 100644
index 00000000000..17c8f8e0992
--- /dev/null
+++ b/tests/modules/nf-core/pbccs/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PBCCS } from '../../../../modules/nf-core/pbccs/main.nf'
+
+workflow test_pbccs {
+
+    input = [
+        [ id:'alz' ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['alz'],    checkIfExists: true),
+        file(params.test_data['homo_sapiens']['pacbio']['alzpbi'], checkIfExists: true)
+    ]
+
+    chunk_num = 2
+    chunk_on  = 3
+
+    PBCCS ( input, chunk_num, chunk_on )
+}
diff --git a/tests/modules/pbccs/nextflow.config b/tests/modules/nf-core/pbccs/nextflow.config
similarity index 100%
rename from tests/modules/pbccs/nextflow.config
rename to tests/modules/nf-core/pbccs/nextflow.config
diff --git a/tests/modules/nf-core/pbccs/test.yml b/tests/modules/nf-core/pbccs/test.yml
new file mode 100644
index 00000000000..7fa5ffac8f8
--- /dev/null
+++ b/tests/modules/nf-core/pbccs/test.yml
@@ -0,0 +1,15 @@
+- name: pbccs test_pbccs
+  command: nextflow run ./tests/modules/nf-core/pbccs -entry test_pbccs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pbccs/nextflow.config
+  tags:
+    - pbccs
+  files:
+    - path: output/pbccs/alz.chunk2.bam
+      md5sum: 2b6451f2d0454eb08359cb84e2e4069c
+    - path: output/pbccs/alz.chunk2.bam.pbi
+      md5sum: 3112cda9744e3facbf38245d41aaf080
+    - path: output/pbccs/alz.chunk2.metrics.json.gz
+      contains: ["zmws"]
+    - path: output/pbccs/alz.chunk2.report.json
+      contains: ["Created by pbcopper"]
+    - path: output/pbccs/alz.chunk2.report.txt
+      md5sum: bbc5bd7a1269345cf7a7f3d4c746024b
diff --git a/tests/modules/nf-core/pbptyper/main.nf b/tests/modules/nf-core/pbptyper/main.nf
new file mode 100644
index 00000000000..39a310b9016
--- /dev/null
+++ b/tests/modules/nf-core/pbptyper/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PBPTYPER } from '../../../../modules/nf-core/pbptyper/main.nf'
+
+workflow test_pbptyper {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    PBPTYPER ( input, [] )
+}
diff --git a/tests/modules/pbptyper/nextflow.config b/tests/modules/nf-core/pbptyper/nextflow.config
similarity index 100%
rename from tests/modules/pbptyper/nextflow.config
rename to tests/modules/nf-core/pbptyper/nextflow.config
diff --git a/tests/modules/nf-core/pbptyper/test.yml b/tests/modules/nf-core/pbptyper/test.yml
new file mode 100644
index 00000000000..7c6c9f73f3f
--- /dev/null
+++ b/tests/modules/nf-core/pbptyper/test.yml
@@ -0,0 +1,13 @@
+- name: pbptyper test_pbptyper
+  command: nextflow run ./tests/modules/nf-core/pbptyper -entry test_pbptyper -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/pbptyper/nextflow.config
+  tags:
+    - pbptyper
+  files:
+    - path: output/pbptyper/test-1A.tblastn.tsv
+      md5sum: 16bb26284bd7bf2327337fc95c055429
+    - path: output/pbptyper/test-2B.tblastn.tsv
+      md5sum: 16bb26284bd7bf2327337fc95c055429
+    - path: output/pbptyper/test-2X.tblastn.tsv
+      md5sum: 16bb26284bd7bf2327337fc95c055429
+    - path: output/pbptyper/test.tsv
+      md5sum: 7115fb3533ee30f0a7dde61a42f69185
diff --git a/tests/modules/nf-core/pear/main.nf b/tests/modules/nf-core/pear/main.nf
new file mode 100644
index 00000000000..0b49c247479
--- /dev/null
+++ b/tests/modules/nf-core/pear/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PEAR } from '../../../../modules/nf-core/pear/main.nf'
+
+workflow test_pear {
+
+    input = [
+        [ id:'test' ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    PEAR ( input )
+}
diff --git a/tests/modules/pear/nextflow.config b/tests/modules/nf-core/pear/nextflow.config
similarity index 100%
rename from tests/modules/pear/nextflow.config
rename to tests/modules/nf-core/pear/nextflow.config
diff --git a/tests/modules/nf-core/pear/test.yml b/tests/modules/nf-core/pear/test.yml
new file mode 100644
index 00000000000..98fc4782fd9
--- /dev/null
+++ b/tests/modules/nf-core/pear/test.yml
@@ -0,0 +1,12 @@
+- name: pear test_pear
+  command: nextflow run ./tests/modules/nf-core/pear -entry test_pear -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/pear/nextflow.config
+  tags:
+    - pear
+  files:
+    - path: output/pear/test.assembled.fastq.gz
+      md5sum: d02799ee04909655e7be5c9161c876b2
+    - path: output/pear/test.discarded.fastq.gz # Known empty file
+    - path: output/pear/test.unassembled.forward.fastq.gz
+      md5sum: 2e35f09a6abbb4559127c512f5652e7e
+    - path: output/pear/test.unassembled.reverse.fastq.gz
+      md5sum: 6e1c73c502230869c21b03a41faddafb
diff --git a/tests/modules/nf-core/peddy/main.nf b/tests/modules/nf-core/peddy/main.nf
new file mode 100644
index 00000000000..c5a605fa2ad
--- /dev/null
+++ b/tests/modules/nf-core/peddy/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PEDDY } from '../../../../modules/nf-core/peddy/main.nf'
+
+workflow test_peddy {
+
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz_tbi'], checkIfExists: true)
+    ]
+    ped = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+
+    PEDDY ( input, ped )
+}
diff --git a/tests/modules/peddy/nextflow.config b/tests/modules/nf-core/peddy/nextflow.config
similarity index 100%
rename from tests/modules/peddy/nextflow.config
rename to tests/modules/nf-core/peddy/nextflow.config
diff --git a/tests/modules/nf-core/peddy/test.yml b/tests/modules/nf-core/peddy/test.yml
new file mode 100644
index 00000000000..dc5c317664e
--- /dev/null
+++ b/tests/modules/nf-core/peddy/test.yml
@@ -0,0 +1,17 @@
+- name: peddy test_peddy
+  command: nextflow run ./tests/modules/nf-core/peddy -entry test_peddy -c ./tests/config/nextflow.config ./tests/modules/nf-core/peddy/nextflow.config
+  tags:
+    - peddy
+  files:
+    - path: output/peddy/justhusky_minimal.het_check.csv
+      md5sum: f4006d47355f2a760e40215b403926c3
+    - path: output/peddy/justhusky_minimal.html
+      md5sum: 4f189cdbe8f03fe5c32d343c183506a5
+    - path: output/peddy/justhusky_minimal.ped_check.csv
+      md5sum: d79a98558e280afe794d1374d2b985d4
+    - path: output/peddy/justhusky_minimal.ped_check.rel-difference.csv
+      md5sum: 9de7e287cb30c742db2ff3622b0e63b1
+    - path: output/peddy/justhusky_minimal.sex_check.csv
+      md5sum: 60848489bc697490da6a53b5170baf3b
+    - path: output/peddy/justhusky_minimal.vs.html
+      md5sum: 20f5f3a97fa781057c876ac79e044010
diff --git a/tests/modules/nf-core/phantompeakqualtools/main.nf b/tests/modules/nf-core/phantompeakqualtools/main.nf
new file mode 100644
index 00000000000..57ac3ac8c5c
--- /dev/null
+++ b/tests/modules/nf-core/phantompeakqualtools/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PHANTOMPEAKQUALTOOLS } from '../../../../modules/nf-core/phantompeakqualtools/main.nf'
+
+workflow test_phantompeakqualtools_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+    ]
+
+    PHANTOMPEAKQUALTOOLS ( input )
+}
+
+workflow test_phantompeakqualtools_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    PHANTOMPEAKQUALTOOLS ( input )
+}
diff --git a/tests/modules/phantompeakqualtools/nextflow.config b/tests/modules/nf-core/phantompeakqualtools/nextflow.config
similarity index 100%
rename from tests/modules/phantompeakqualtools/nextflow.config
rename to tests/modules/nf-core/phantompeakqualtools/nextflow.config
diff --git a/tests/modules/nf-core/phantompeakqualtools/test.yml b/tests/modules/nf-core/phantompeakqualtools/test.yml
new file mode 100644
index 00000000000..8138cd0adc5
--- /dev/null
+++ b/tests/modules/nf-core/phantompeakqualtools/test.yml
@@ -0,0 +1,23 @@
+- name: phantompeakqualtools test_phantompeakqualtools_single_end
+  command: nextflow run ./tests/modules/nf-core/phantompeakqualtools -entry test_phantompeakqualtools_single_end -c ./tests/config/nextflow.config
+  tags:
+    - phantompeakqualtools
+  files:
+    - path: output/phantompeakqualtools/test.spp.Rdata
+    - path: output/phantompeakqualtools/test.spp.out
+      md5sum: b01d976506b6fe45b66c821b1e8a1d15
+    - path: output/phantompeakqualtools/test.spp.pdf
+    - path: output/phantompeakqualtools/versions.yml
+      md5sum: 6c2ede1aac4c574e3c72fbe09f15c03f
+
+- name: phantompeakqualtools test_phantompeakqualtools_paired_end
+  command: nextflow run ./tests/modules/nf-core/phantompeakqualtools -entry test_phantompeakqualtools_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - phantompeakqualtools
+  files:
+    - path: output/phantompeakqualtools/test.spp.Rdata
+    - path: output/phantompeakqualtools/test.spp.out
+      md5sum: eed46e75eab119224f397a7a8b5924e6
+    - path: output/phantompeakqualtools/test.spp.pdf
+    - path: output/phantompeakqualtools/versions.yml
+      md5sum: 383d2dd583fcb40451bde0d3840bdb72
diff --git a/tests/modules/nf-core/phyloflash/main.nf b/tests/modules/nf-core/phyloflash/main.nf
new file mode 100644
index 00000000000..3e7549a676b
--- /dev/null
+++ b/tests/modules/nf-core/phyloflash/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PHYLOFLASH } from '../../../../modules/nf-core/phyloflash/main.nf'
+
+process STUB_PHYLOFLASH_DATABASE {
+    output:
+    path "ref"    , emit: silva_db
+    path "UniVec" , emit: univec_db
+
+    stub:
+    """
+    mkdir ref
+    touch UniVec
+    """
+}
+
+workflow test_phyloflash_single_end {
+
+    STUB_PHYLOFLASH_DATABASE ()
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db, STUB_PHYLOFLASH_DATABASE.out.univec_db )
+}
+
+workflow test_phyloflash_paired_end {
+
+    STUB_PHYLOFLASH_DATABASE ()
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db,  STUB_PHYLOFLASH_DATABASE.out.univec_db )
+}
diff --git a/tests/modules/phyloflash/nextflow.config b/tests/modules/nf-core/phyloflash/nextflow.config
similarity index 100%
rename from tests/modules/phyloflash/nextflow.config
rename to tests/modules/nf-core/phyloflash/nextflow.config
diff --git a/tests/modules/nf-core/phyloflash/test.yml b/tests/modules/nf-core/phyloflash/test.yml
new file mode 100644
index 00000000000..fcf75b22c52
--- /dev/null
+++ b/tests/modules/nf-core/phyloflash/test.yml
@@ -0,0 +1,15 @@
+- name: phyloflash single-end
+  command: nextflow run ./tests/modules/nf-core/phyloflash -entry test_phyloflash_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/phyloflash/nextflow.config -stub-run
+  tags:
+    - phyloflash
+  files:
+    - path: output/phyloflash/test/test.SSU.collection.fasta
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+
+- name: phyloflash paired-end
+  command: nextflow run ./tests/modules/nf-core/phyloflash -entry test_phyloflash_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/phyloflash/nextflow.config -stub-run
+  tags:
+    - phyloflash
+  files:
+    - path: output/phyloflash/test/test.SSU.collection.fasta
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf b/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf
new file mode 100644
index 00000000000..e0196f34016
--- /dev/null
+++ b/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_ADDORREPLACEREADGROUPS } from '../../../../../modules/nf-core/picard/addorreplacereadgroups/main.nf'
+
+workflow test_picard_addorreplacereadgroups {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
+    ]
+
+    PICARD_ADDORREPLACEREADGROUPS ( input )
+}
diff --git a/tests/modules/picard/addorreplacereadgroups/nextflow.config b/tests/modules/nf-core/picard/addorreplacereadgroups/nextflow.config
similarity index 100%
rename from tests/modules/picard/addorreplacereadgroups/nextflow.config
rename to tests/modules/nf-core/picard/addorreplacereadgroups/nextflow.config
diff --git a/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml b/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml
new file mode 100644
index 00000000000..26335c4f6f1
--- /dev/null
+++ b/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml
@@ -0,0 +1,17 @@
+- name: picard addorreplacereadgroups test_picard_addorreplacereadgroups
+  command: nextflow run ./tests/modules/nf-core/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c ./tests/config/nextflow.config
+  tags:
+    - picard
+    - picard/addorreplacereadgroups
+  files:
+    - path: output/picard/test.bam
+      md5sum: 7b82f3461c2d80fc6a10385e78c9427f
+    - path: output/picard/versions.yml
+- name: picard addorreplacereadgroups test_picard_addorreplacereadgroups stub
+  command: nextflow run ./tests/modules/nf-core/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c ./tests/config/nextflow.config -stub
+  tags:
+    - picard
+    - picard/addorreplacereadgroups
+  files:
+    - path: output/picard/test.bam
+    - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/cleansam/main.nf b/tests/modules/nf-core/picard/cleansam/main.nf
new file mode 100644
index 00000000000..d337aca51ee
--- /dev/null
+++ b/tests/modules/nf-core/picard/cleansam/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_CLEANSAM } from '../../../../../modules/nf-core/picard/cleansam/main.nf'
+
+workflow test_picard_cleansam {
+    
+    input = [ 
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) 
+    ]
+
+    PICARD_CLEANSAM ( input )
+}
diff --git a/tests/modules/picard/cleansam/nextflow.config b/tests/modules/nf-core/picard/cleansam/nextflow.config
similarity index 100%
rename from tests/modules/picard/cleansam/nextflow.config
rename to tests/modules/nf-core/picard/cleansam/nextflow.config
diff --git a/tests/modules/nf-core/picard/cleansam/test.yml b/tests/modules/nf-core/picard/cleansam/test.yml
new file mode 100644
index 00000000000..9c05391e984
--- /dev/null
+++ b/tests/modules/nf-core/picard/cleansam/test.yml
@@ -0,0 +1,9 @@
+- name: picard cleansam test_picard_cleansam
+  command: nextflow run ./tests/modules/nf-core/picard/cleansam -entry test_picard_cleansam -c ./tests/config/nextflow.config
+  tags:
+    - picard/cleansam
+    - picard
+  files:
+    - path: output/picard/test.bam
+      md5sum: a48f8e77a1480445efc57570c3a38a68
+    - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/collecthsmetrics/main.nf b/tests/modules/nf-core/picard/collecthsmetrics/main.nf
new file mode 100644
index 00000000000..2876353b047
--- /dev/null
+++ b/tests/modules/nf-core/picard/collecthsmetrics/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_COLLECTHSMETRICS } from '../../../../../modules/nf-core/picard/collecthsmetrics/main.nf'
+
+workflow test_picard_collecthsmetrics {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
+    target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+
+    PICARD_COLLECTHSMETRICS ( input, fasta, fai, bait_intervals, target_intervals )
+}
+
+workflow test_picard_collecthsmetrics_nofasta {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+
+    bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
+    target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+
+    PICARD_COLLECTHSMETRICS ( input, [], [], bait_intervals, target_intervals )
+}
diff --git a/tests/modules/picard/collecthsmetrics/nextflow.config b/tests/modules/nf-core/picard/collecthsmetrics/nextflow.config
similarity index 100%
rename from tests/modules/picard/collecthsmetrics/nextflow.config
rename to tests/modules/nf-core/picard/collecthsmetrics/nextflow.config
diff --git a/tests/modules/nf-core/picard/collecthsmetrics/test.yml b/tests/modules/nf-core/picard/collecthsmetrics/test.yml
new file mode 100644
index 00000000000..8bf60191838
--- /dev/null
+++ b/tests/modules/nf-core/picard/collecthsmetrics/test.yml
@@ -0,0 +1,15 @@
+- name: picard collecthsmetrics test_picard_collecthsmetrics
+  command: nextflow run ./tests/modules/nf-core/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/collecthsmetrics/nextflow.config
+  tags:
+    - picard/collecthsmetrics
+    - picard
+  files:
+    - path: output/picard/test.CollectHsMetrics.coverage_metrics
+
+- name: picard collecthsmetrics test_picard_collecthsmetrics_nofasta
+  command: nextflow run ./tests/modules/nf-core/picard/collecthsmetrics -entry test_picard_collecthsmetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/collecthsmetrics/nextflow.config
+  tags:
+    - picard/collecthsmetrics
+    - picard
+  files:
+    - path: output/picard/test.CollectHsMetrics.coverage_metrics
diff --git a/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf b/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf
new file mode 100644
index 00000000000..0271a293779
--- /dev/null
+++ b/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf
@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../../modules/nf-core/picard/collectmultiplemetrics/main.nf'
+
+workflow test_picard_collectmultiplemetrics {
+    input = [
+                [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, [] )
+}
+
+workflow test_picard_collectmultiplemetrics_nofasta {
+    input = [
+                [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    PICARD_COLLECTMULTIPLEMETRICS ( input, [], [] )
+}
+
+workflow test_picard_collectmultiplemetrics_cram {
+    input = [
+                [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, fai )
+}
diff --git a/tests/modules/picard/collectmultiplemetrics/nextflow.config b/tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
similarity index 100%
rename from tests/modules/picard/collectmultiplemetrics/nextflow.config
rename to tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
diff --git a/tests/modules/nf-core/picard/collectmultiplemetrics/test.yml b/tests/modules/nf-core/picard/collectmultiplemetrics/test.yml
new file mode 100644
index 00000000000..f16bb7d49ad
--- /dev/null
+++ b/tests/modules/nf-core/picard/collectmultiplemetrics/test.yml
@@ -0,0 +1,96 @@
+- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics
+  command: nextflow run ./tests/modules/nf-core/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
+  tags:
+    - picard
+    - picard/collectmultiplemetrics
+  files:
+    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+      contains:
+        - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+      contains:
+        - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
+        - "1\t1\t20\t26\t32\t22\t0"
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
+      contains:
+        - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
+        - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311"
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+      contains:
+        - "CYCLE\tMEAN_QUALITY"
+        - "1\t32"
+        - "2\t31.35"
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+      contains:
+        - "QUALITY\tCOUNT_OF_Q"
+        - "14\t1926"
+    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
+
+- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta
+  command: nextflow run ./tests/modules/nf-core/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
+  tags:
+    - picard
+    - picard/collectmultiplemetrics
+  files:
+    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+      contains:
+        - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+      contains:
+        - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
+        - "1\t1\t20\t26\t32\t22\t0"
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
+      contains:
+        - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
+        - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311"
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+      contains:
+        - "CYCLE\tMEAN_QUALITY"
+        - "1\t32"
+        - "2\t31.35"
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+      contains:
+        - "QUALITY\tCOUNT_OF_Q"
+        - "14\t1926"
+    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
+
+- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_cram
+  command: nextflow run ./tests/modules/nf-core/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
+  tags:
+    - picard
+    - picard/collectmultiplemetrics
+  files:
+    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+      contains:
+        - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+      contains:
+        - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
+        - "1\t1\t34.065934\t15.242822\t16.093584\t34.526764\t0.070897"
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
+      contains:
+        - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
+        - "123\t96\t23\t32\t300\t125.684397\t32.447863\t2820\tFR\t11\t17\t27\t37\t47\t57\t69\t83\t103\t125\t169"
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+      contains:
+        - "CYCLE\tMEAN_QUALITY"
+        - "1\t41.018079"
+        - "2\t40.981921"
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+      contains:
+        - "QUALITY\tCOUNT_OF_Q"
+        - "3\t2"
+        - "4\t44"
+    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
diff --git a/tests/modules/nf-core/picard/collectwgsmetrics/main.nf b/tests/modules/nf-core/picard/collectwgsmetrics/main.nf
new file mode 100644
index 00000000000..42ac40fb89e
--- /dev/null
+++ b/tests/modules/nf-core/picard/collectwgsmetrics/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_COLLECTWGSMETRICS } from '../../../../../modules/nf-core/picard/collectwgsmetrics/main.nf'
+
+workflow test_picard_collectwgsmetrics {
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    PICARD_COLLECTWGSMETRICS ( input, fasta )
+}
diff --git a/tests/modules/picard/collectwgsmetrics/nextflow.config b/tests/modules/nf-core/picard/collectwgsmetrics/nextflow.config
similarity index 100%
rename from tests/modules/picard/collectwgsmetrics/nextflow.config
rename to tests/modules/nf-core/picard/collectwgsmetrics/nextflow.config
diff --git a/tests/modules/nf-core/picard/collectwgsmetrics/test.yml b/tests/modules/nf-core/picard/collectwgsmetrics/test.yml
new file mode 100644
index 00000000000..b1f317c01c3
--- /dev/null
+++ b/tests/modules/nf-core/picard/collectwgsmetrics/test.yml
@@ -0,0 +1,15 @@
+- name: picard collectwgsmetrics test_picard_collectwgsmetrics
+  command: nextflow run ./tests/modules/nf-core/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/collectwgsmetrics/nextflow.config
+  tags:
+    - picard/collectwgsmetrics
+    - picard
+  files:
+    - path: output/picard/test.CollectWgsMetrics.coverage_metrics
+
+- name: picard collectwgsmetrics test_picard_collectwgsmetrics stub
+  command: nextflow run ./tests/modules/nf-core/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/collectwgsmetrics/nextflow.config -stub-run
+  tags:
+    - picard/collectwgsmetrics
+    - picard
+  files:
+    - path: output/picard/test.CollectWgsMetrics.coverage_metrics
diff --git a/tests/modules/nf-core/picard/createsequencedictionary/main.nf b/tests/modules/nf-core/picard/createsequencedictionary/main.nf
new file mode 100644
index 00000000000..fcdc50b641d
--- /dev/null
+++ b/tests/modules/nf-core/picard/createsequencedictionary/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../../../modules/nf-core/picard/createsequencedictionary/main.nf'
+
+workflow test_picard_createsequencedictionary {
+    
+    input = [ 
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
+    ]
+
+    PICARD_CREATESEQUENCEDICTIONARY ( input )
+}
diff --git a/tests/modules/picard/createsequencedictionary/nextflow.config b/tests/modules/nf-core/picard/createsequencedictionary/nextflow.config
similarity index 100%
rename from tests/modules/picard/createsequencedictionary/nextflow.config
rename to tests/modules/nf-core/picard/createsequencedictionary/nextflow.config
diff --git a/tests/modules/nf-core/picard/createsequencedictionary/test.yml b/tests/modules/nf-core/picard/createsequencedictionary/test.yml
new file mode 100644
index 00000000000..ba2f1248264
--- /dev/null
+++ b/tests/modules/nf-core/picard/createsequencedictionary/test.yml
@@ -0,0 +1,9 @@
+- name: picard createsequencedictionary test_picard_createsequencedictionary
+  command: nextflow run ./tests/modules/nf-core/picard/createsequencedictionary -entry test_picard_createsequencedictionary -c ./tests/config/nextflow.config
+  tags:
+    - picard/createsequencedictionary
+    - picard
+  files:
+    - path: output/picard/test.dict
+      contains: ["SN:MT192765.1"]
+    - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf b/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf
new file mode 100644
index 00000000000..bef0537205a
--- /dev/null
+++ b/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_CROSSCHECKFINGERPRINTS } from '../../../../../modules/nf-core/picard/crosscheckfingerprints/main.nf'
+
+workflow test_picard_crosscheckfingerprints {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
+    ]
+    PICARD_CROSSCHECKFINGERPRINTS ( input,[], file(params.test_data['homo_sapiens']['genome']['haplotype_map'], checkIfExists: true))
+}
diff --git a/tests/modules/picard/crosscheckfingerprints/nextflow.config b/tests/modules/nf-core/picard/crosscheckfingerprints/nextflow.config
similarity index 100%
rename from tests/modules/picard/crosscheckfingerprints/nextflow.config
rename to tests/modules/nf-core/picard/crosscheckfingerprints/nextflow.config
diff --git a/tests/modules/nf-core/picard/crosscheckfingerprints/test.yml b/tests/modules/nf-core/picard/crosscheckfingerprints/test.yml
new file mode 100644
index 00000000000..48bb2ab52c4
--- /dev/null
+++ b/tests/modules/nf-core/picard/crosscheckfingerprints/test.yml
@@ -0,0 +1,8 @@
+- name: "picard crosscheckfingerprints"
+  command: nextflow run ./tests/modules/nf-core/picard/crosscheckfingerprints -entry test_picard_crosscheckfingerprints -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/crosscheckfingerprints/nextflow.config
+  tags:
+    - "picard"
+    - "picard/crosscheckfingerprints"
+  files:
+    - path: "output/picard/test.crosscheck_metrics.txt"
+    - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/fastqtosam/main.nf b/tests/modules/nf-core/picard/fastqtosam/main.nf
new file mode 100644
index 00000000000..5b1af7ea9fc
--- /dev/null
+++ b/tests/modules/nf-core/picard/fastqtosam/main.nf
@@ -0,0 +1,43 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_FASTQTOSAM } from '../../../../../modules/nf-core/picard/fastqtosam/main.nf'
+
+workflow test_picard_fastqtosam_single {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    PICARD_FASTQTOSAM ( input )
+}
+
+workflow test_picard_fastqtosam_paired {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    PICARD_FASTQTOSAM ( input )
+}
+
+workflow test_picard_fastqtosam_paired_custom_samplename {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    PICARD_FASTQTOSAM ( input )
+}
diff --git a/tests/modules/picard/fastqtosam/nextflow.config b/tests/modules/nf-core/picard/fastqtosam/nextflow.config
similarity index 100%
rename from tests/modules/picard/fastqtosam/nextflow.config
rename to tests/modules/nf-core/picard/fastqtosam/nextflow.config
diff --git a/tests/modules/nf-core/picard/fastqtosam/test.yml b/tests/modules/nf-core/picard/fastqtosam/test.yml
new file mode 100644
index 00000000000..348337c46b9
--- /dev/null
+++ b/tests/modules/nf-core/picard/fastqtosam/test.yml
@@ -0,0 +1,26 @@
+- name: picard fastqtosam test_picard_fastqtosam_single
+  command: nextflow run ./tests/modules/nf-core/picard/fastqtosam -entry test_picard_fastqtosam_single -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/fastqtosam/nextflow.config
+  tags:
+    - picard
+    - picard/fastqtosam
+  files:
+    - path: output/picard/test.bam
+      md5sum: fe2882efe8f13a8da20fcc63469ed0aa
+
+- name: picard fastqtosam test_picard_fastqtosam_paired
+  command: nextflow run ./tests/modules/nf-core/picard/fastqtosam -entry test_picard_fastqtosam_paired -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/fastqtosam/nextflow.config
+  tags:
+    - picard
+    - picard/fastqtosam
+  files:
+    - path: output/picard/test.bam
+      md5sum: 90e4f59f9d942f96c3f3c41160f3fd5d
+
+- name: picard fastqtosam test_picard_fastqtosam_paired_custom_samplename
+  command: nextflow run ./tests/modules/nf-core/picard/fastqtosam -entry test_picard_fastqtosam_paired_custom_samplename -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/picard/fastqtosam/nextflow.config
+  tags:
+    - picard
+    - picard/fastqtosam
+  files:
+    - path: output/picard/test.bam
+      md5sum: 69d35ee2b5dc263d022eaf59a9e383d3
diff --git a/tests/modules/nf-core/picard/filtersamreads/main.nf b/tests/modules/nf-core/picard/filtersamreads/main.nf
new file mode 100644
index 00000000000..3687bbfb19b
--- /dev/null
+++ b/tests/modules/nf-core/picard/filtersamreads/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_SORTSAM        } from '../../../../../modules/nf-core/picard/sortsam/main.nf'
+include { PICARD_FILTERSAMREADS } from '../../../../../modules/nf-core/picard/filtersamreads/main.nf'
+
+workflow test_picard_filtersamreads {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
+    sort_order = 'queryname'
+    filter = 'includeAligned'
+
+    PICARD_SORTSAM ( input, sort_order )
+    PICARD_SORTSAM.out.bam
+        .map {
+            [ it[0], it[1], [] ]
+        }
+        .set{ ch_sorted_for_filtersamreads }
+    PICARD_FILTERSAMREADS ( ch_sorted_for_filtersamreads, filter )
+}
+
+workflow test_picard_filtersamreads_readlist {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam_readlist_txt'], checkIfExists: true) ]
+    filter = 'includeReadList'
+
+    PICARD_FILTERSAMREADS ( input, filter )
+}
diff --git a/tests/modules/picard/filtersamreads/nextflow.config b/tests/modules/nf-core/picard/filtersamreads/nextflow.config
similarity index 100%
rename from tests/modules/picard/filtersamreads/nextflow.config
rename to tests/modules/nf-core/picard/filtersamreads/nextflow.config
diff --git a/tests/modules/nf-core/picard/filtersamreads/test.yml b/tests/modules/nf-core/picard/filtersamreads/test.yml
new file mode 100644
index 00000000000..ed641144b20
--- /dev/null
+++ b/tests/modules/nf-core/picard/filtersamreads/test.yml
@@ -0,0 +1,17 @@
+- name: picard filtersamreads
+  command: nextflow run ./tests/modules/nf-core/picard/filtersamreads -entry test_picard_filtersamreads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/filtersamreads/nextflow.config
+  tags:
+    - picard
+    - picard/filtersamreads
+  files:
+    - path: output/picard/test.filtered.bam
+      md5sum: b44a6ca04811a9470c7813c3c9465fd5
+
+- name: picard filtersamreads readlist
+  command: nextflow run ./tests/modules/nf-core/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/filtersamreads/nextflow.config
+  tags:
+    - picard
+    - picard/filtersamreads
+  files:
+    - path: output/picard/test.filtered.bam
+      md5sum: 1e86b738b56f2c2b09f4cab52baf05c7
diff --git a/tests/modules/nf-core/picard/fixmateinformation/main.nf b/tests/modules/nf-core/picard/fixmateinformation/main.nf
new file mode 100644
index 00000000000..92277611f29
--- /dev/null
+++ b/tests/modules/nf-core/picard/fixmateinformation/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_FIXMATEINFORMATION } from '../../../../../modules/nf-core/picard/fixmateinformation/main.nf'
+
+workflow test_picard_fixmateinformation {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
+    ]
+
+    PICARD_FIXMATEINFORMATION ( input )
+}
diff --git a/tests/modules/picard/fixmateinformation/nextflow.config b/tests/modules/nf-core/picard/fixmateinformation/nextflow.config
similarity index 100%
rename from tests/modules/picard/fixmateinformation/nextflow.config
rename to tests/modules/nf-core/picard/fixmateinformation/nextflow.config
diff --git a/tests/modules/nf-core/picard/fixmateinformation/test.yml b/tests/modules/nf-core/picard/fixmateinformation/test.yml
new file mode 100644
index 00000000000..27de7cf3966
--- /dev/null
+++ b/tests/modules/nf-core/picard/fixmateinformation/test.yml
@@ -0,0 +1,9 @@
+- name: picard fixmateinformation test_picard_fixmateinformation
+  command: nextflow run ./tests/modules/nf-core/picard/fixmateinformation -entry test_picard_fixmateinformation -c ./tests/config/nextflow.config
+  tags:
+    - picard
+    - picard/fixmateinformation
+  files:
+    - path: output/picard/test.bam
+      md5sum: 746102e8c242c0ef42e045c49d320030
+    - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/liftovervcf/main.nf b/tests/modules/nf-core/picard/liftovervcf/main.nf
new file mode 100644
index 00000000000..94a78fbcd85
--- /dev/null
+++ b/tests/modules/nf-core/picard/liftovervcf/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_LIFTOVERVCF } from '../../../../../modules/nf-core/picard/liftovervcf/main.nf'
+
+workflow test_picard_liftovervcf {
+
+    input_vcf = [ [ id:'test' ],
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
+            ]
+    dict =  file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    chain =  file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
+    fasta  = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
+}
+
+workflow test_picard_liftovervcf_stubs {
+
+    input_vcf = [ [ id:'test' ],
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
+            ]
+    dict =  file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    chain =  file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
+    fasta  = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
+}
diff --git a/tests/modules/picard/liftovervcf/nextflow.config b/tests/modules/nf-core/picard/liftovervcf/nextflow.config
similarity index 100%
rename from tests/modules/picard/liftovervcf/nextflow.config
rename to tests/modules/nf-core/picard/liftovervcf/nextflow.config
diff --git a/tests/modules/nf-core/picard/liftovervcf/test.yml b/tests/modules/nf-core/picard/liftovervcf/test.yml
new file mode 100644
index 00000000000..09bd2dd14c2
--- /dev/null
+++ b/tests/modules/nf-core/picard/liftovervcf/test.yml
@@ -0,0 +1,21 @@
+- name: picard liftovervcf test_picard_liftovervcf
+  command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf -c ./tests/config/nextflow.config
+  tags:
+    - picard/liftovervcf
+    - picard
+  files:
+    - path: output/picard/test.lifted.vcf.gz
+      contains:
+        - "chr22"
+    - path: output/picard/test.unlifted.vcf.gz
+    - path: output/picard/versions.yml
+
+- name: picard liftovervcf test_picard_liftovervcf_stubs
+  command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf_stubs -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - picard/liftovervcf
+    - picard
+  files:
+    - path: output/picard/test.lifted.vcf.gz
+    - path: output/picard/test.unlifted.vcf.gz
+    - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/markduplicates/main.nf b/tests/modules/nf-core/picard/markduplicates/main.nf
new file mode 100644
index 00000000000..941bec1ca41
--- /dev/null
+++ b/tests/modules/nf-core/picard/markduplicates/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_MARKDUPLICATES } from '../../../../../modules/nf-core/picard/markduplicates/main.nf'
+include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED}  from '../../../../../modules/nf-core/picard/markduplicates/main.nf'
+
+workflow test_picard_markduplicates_sorted_bam  {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    PICARD_MARKDUPLICATES ( input )
+}
+
+workflow test_picard_markduplicates_unsorted_bam  {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+            ]
+
+    PICARD_MARKDUPLICATES_UNSORTED ( input )
+}
diff --git a/tests/modules/picard/markduplicates/nextflow.config b/tests/modules/nf-core/picard/markduplicates/nextflow.config
similarity index 100%
rename from tests/modules/picard/markduplicates/nextflow.config
rename to tests/modules/nf-core/picard/markduplicates/nextflow.config
diff --git a/tests/modules/nf-core/picard/markduplicates/test.yml b/tests/modules/nf-core/picard/markduplicates/test.yml
new file mode 100644
index 00000000000..4b17f31aba7
--- /dev/null
+++ b/tests/modules/nf-core/picard/markduplicates/test.yml
@@ -0,0 +1,20 @@
+- name: picard markduplicates sorted bam
+  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config
+  tags:
+    - picard
+    - picard/markduplicates
+  files:
+    - path: ./output/picard/test.MarkDuplicates.metrics.txt
+      contains:
+        - "1.0	97	97"
+    - path: ./output/picard/test.bam
+- name: picard markduplicates unsorted bam
+  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config
+  tags:
+    - picard
+    - picard/markduplicates
+  files:
+    - path: ./output/picard/test.MarkDuplicates.metrics.txt
+      contains:
+        - "1.0	97	97"
+    - path: ./output/picard/test.bam
diff --git a/tests/modules/nf-core/picard/mergesamfiles/main.nf b/tests/modules/nf-core/picard/mergesamfiles/main.nf
new file mode 100644
index 00000000000..360cfd7ed0d
--- /dev/null
+++ b/tests/modules/nf-core/picard/mergesamfiles/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_MERGESAMFILES } from '../../../../../modules/nf-core/picard/mergesamfiles/main.nf'
+
+workflow test_picard_mergesamfiles {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true), ]
+            ]
+
+    PICARD_MERGESAMFILES ( input )
+}
diff --git a/tests/modules/picard/mergesamfiles/nextflow.config b/tests/modules/nf-core/picard/mergesamfiles/nextflow.config
similarity index 100%
rename from tests/modules/picard/mergesamfiles/nextflow.config
rename to tests/modules/nf-core/picard/mergesamfiles/nextflow.config
diff --git a/tests/modules/nf-core/picard/mergesamfiles/test.yml b/tests/modules/nf-core/picard/mergesamfiles/test.yml
new file mode 100644
index 00000000000..97dc1b785e7
--- /dev/null
+++ b/tests/modules/nf-core/picard/mergesamfiles/test.yml
@@ -0,0 +1,7 @@
+- name: picard mergesamfiles
+  command: nextflow run ./tests/modules/nf-core/picard/mergesamfiles -entry test_picard_mergesamfiles -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/mergesamfiles/nextflow.config
+  tags:
+    - picard
+    - picard/mergesamfiles
+  files:
+    - path: ./output/picard/test.bam
diff --git a/tests/modules/nf-core/picard/sortsam/main.nf b/tests/modules/nf-core/picard/sortsam/main.nf
new file mode 100644
index 00000000000..4b4e801355a
--- /dev/null
+++ b/tests/modules/nf-core/picard/sortsam/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_SORTSAM } from '../../../../../modules/nf-core/picard/sortsam/main.nf'
+
+workflow test_picard_sortsam {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
+    sort_order = "queryname"
+
+    PICARD_SORTSAM ( input, sort_order )
+}
diff --git a/tests/modules/picard/sortsam/nextflow.config b/tests/modules/nf-core/picard/sortsam/nextflow.config
similarity index 100%
rename from tests/modules/picard/sortsam/nextflow.config
rename to tests/modules/nf-core/picard/sortsam/nextflow.config
diff --git a/tests/modules/nf-core/picard/sortsam/test.yml b/tests/modules/nf-core/picard/sortsam/test.yml
new file mode 100644
index 00000000000..9530019b3e6
--- /dev/null
+++ b/tests/modules/nf-core/picard/sortsam/test.yml
@@ -0,0 +1,8 @@
+- name: picard sortsam
+  command: nextflow run ./tests/modules/nf-core/picard/sortsam -entry test_picard_sortsam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/sortsam/nextflow.config
+  tags:
+    - picard
+    - picard/sortsam
+  files:
+    - path: output/picard/test.sorted.bam
+      md5sum: b44a6ca04811a9470c7813c3c9465fd5
diff --git a/tests/modules/nf-core/picard/sortvcf/main.nf b/tests/modules/nf-core/picard/sortvcf/main.nf
new file mode 100644
index 00000000000..f4d9c391411
--- /dev/null
+++ b/tests/modules/nf-core/picard/sortvcf/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_SORTVCF } from '../../../../../modules/nf-core/picard/sortvcf/main.nf'
+
+workflow test_picard_sortvcf {
+
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+            ]
+
+    fasta  = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    dict  = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
+
+    PICARD_SORTVCF ( input, fasta, dict )
+}
diff --git a/tests/modules/picard/sortvcf/nextflow.config b/tests/modules/nf-core/picard/sortvcf/nextflow.config
similarity index 100%
rename from tests/modules/picard/sortvcf/nextflow.config
rename to tests/modules/nf-core/picard/sortvcf/nextflow.config
diff --git a/tests/modules/nf-core/picard/sortvcf/test.yml b/tests/modules/nf-core/picard/sortvcf/test.yml
new file mode 100644
index 00000000000..67458bdf65a
--- /dev/null
+++ b/tests/modules/nf-core/picard/sortvcf/test.yml
@@ -0,0 +1,7 @@
+- name: picard sortvcf
+  command: nextflow run ./tests/modules/nf-core/picard/sortvcf -entry test_picard_sortvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/sortvcf/nextflow.config
+  tags:
+    - picard
+    - picard/sortvcf
+  files:
+    - path: output/picard/test_sorted.vcf.gz
diff --git a/tests/modules/nf-core/pints/caller/main.nf b/tests/modules/nf-core/pints/caller/main.nf
new file mode 100644
index 00000000000..a5cccca59f4
--- /dev/null
+++ b/tests/modules/nf-core/pints/caller/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PINTS_CALLER } from '../../../../../modules/nf-core/pints/caller/main.nf'
+
+workflow test_pints_caller {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        // FIXME Fails if it doesn't find any signals
+        [file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S0mR1.bam", checkIfExists: true),
+         file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S40mR1.bam", checkIfExists: true)]
+    ]
+
+    PINTS_CALLER ( input )
+}
+
+// TODO Test single bam input
+// TODO Test single bigwig input
+// TODO Test multiple bigwig input
diff --git a/tests/modules/pints/caller/nextflow.config b/tests/modules/nf-core/pints/caller/nextflow.config
similarity index 100%
rename from tests/modules/pints/caller/nextflow.config
rename to tests/modules/nf-core/pints/caller/nextflow.config
diff --git a/tests/modules/nf-core/pints/caller/test.yml b/tests/modules/nf-core/pints/caller/test.yml
new file mode 100644
index 00000000000..0feb4a09639
--- /dev/null
+++ b/tests/modules/nf-core/pints/caller/test.yml
@@ -0,0 +1,16 @@
+- name: "pints caller"
+  command: nextflow run ./tests/modules/nf-core/pints/caller -entry test_pints_caller -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pints/caller/nextflow.config
+  tags:
+    - "pints"
+    - "pints/caller"
+  files:
+    - path: output/pints/test_1_bidirectional_peaks.bed
+      md5sum: 8c69305ab896bd772e450e938ddf45f0
+    - path: output/pints/test_1_divergent_peaks.bed
+      md5sum: 2078c643951071f5836d365e5dc7ba1c
+    - path: output/pints/test_1_unidirectional_peaks.bed
+    - path: output/pints/test_2_bidirectional_peaks.bed
+      md5sum: c4efa0f297ba4cdb00659c5e6700ebe5
+    - path: output/pints/test_2_divergent_peaks.bed
+      md5sum: 213a2ba5d9930768d76bf2a7d8c3f7fb
+    - path: output/pints/test_2_unidirectional_peaks.bed
diff --git a/tests/modules/nf-core/pirate/main.nf b/tests/modules/nf-core/pirate/main.nf
new file mode 100644
index 00000000000..0def80c4bfe
--- /dev/null
+++ b/tests/modules/nf-core/pirate/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PIRATE } from '../../../../modules/nf-core/pirate/main.nf'
+
+workflow test_pirate {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
+        ]
+    ]
+
+    PIRATE ( input )
+}
diff --git a/tests/modules/pirate/nextflow.config b/tests/modules/nf-core/pirate/nextflow.config
similarity index 100%
rename from tests/modules/pirate/nextflow.config
rename to tests/modules/nf-core/pirate/nextflow.config
diff --git a/tests/modules/nf-core/pirate/test.yml b/tests/modules/nf-core/pirate/test.yml
new file mode 100644
index 00000000000..b81457957fe
--- /dev/null
+++ b/tests/modules/nf-core/pirate/test.yml
@@ -0,0 +1,98 @@
+- name: pirate test_pirate
+  command: nextflow run ./tests/modules/nf-core/pirate -entry test_pirate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pirate/nextflow.config
+  tags:
+    - pirate
+  files:
+    - path: output/pirate/results/PIRATE.gene_families.ordered.tsv
+      contains: ["allele_name"]
+    - path: output/pirate/results/PIRATE.gene_families.tsv
+      contains: ["allele_name"]
+    - path: output/pirate/results/PIRATE.genomes_per_allele.tsv
+      contains: ["g0197"]
+    - path: output/pirate/results/PIRATE.log
+      contains: ["PIRATE input options"]
+    - path: output/pirate/results/PIRATE.pangenome_summary.txt
+      md5sum: 4551c291bc06b21f984f25c09329ed7d
+    - path: output/pirate/results/PIRATE.unique_alleles.tsv
+      contains: ["allele_name"]
+    - path: output/pirate/results/binary_presence_absence.fasta
+      contains: ["test1"]
+    - path: output/pirate/results/binary_presence_absence.nwk
+      md5sum: 1fcf7434911bbab39b74791259f1f989
+    - path: output/pirate/results/cluster_alleles.tab
+      contains: ["g0001"]
+    - path: output/pirate/results/co-ords/test1.co-ords.tab
+      md5sum: f1e75c045b35bae260dadb1a2f000dfa
+    - path: output/pirate/results/co-ords/test2.co-ords.tab
+      md5sum: 953b0d2f1dfd4c3a6a6dd246c9174703
+    - path: output/pirate/results/co-ords/test3.co-ords.tab
+      md5sum: 61f2c52ef77dc9a97a200c57b89b7d69
+    - path: output/pirate/results/genome2loci.tab
+      md5sum: 2d9cdefd5b1a7f5e20b0a70a6e5fa588
+    - path: output/pirate/results/genome_list.txt
+      md5sum: c19ac63da7949b15179f42093cbf95b8
+    - path: output/pirate/results/link_clusters.log
+      contains: ["parsing paralog file"]
+    - path: output/pirate/results/loci_list.tab
+      contains: ["test1_00242"]
+    - path: output/pirate/results/loci_paralog_categories.tab
+      md5sum: f8c3d31f445c3cb66bd95ba77be0a7b8
+    - path: output/pirate/results/modified_gffs/test1.gff
+      md5sum: 5dc220e472165c3b693e1017f38fc0e3
+    - path: output/pirate/results/modified_gffs/test2.gff
+      md5sum: 975f5c7fb363caf1be9c53e5e237bb5d
+    - path: output/pirate/results/modified_gffs/test3.gff
+      md5sum: a4735a5ac75ce82aadba8a3de6cabc2e
+    - path: output/pirate/results/pan_sequences.fasta
+      md5sum: 0492833706f0f969b49a3555c16ec40d
+    - path: output/pirate/results/pangenome.connected_blocks.tsv
+      contains: ["block_number"]
+    - path: output/pirate/results/pangenome.edges
+      contains: ["g0259"]
+    - path: output/pirate/results/pangenome.gfa
+      contains: ["g0001"]
+    - path: output/pirate/results/pangenome.order.tsv
+      contains: ["g0172"]
+    - path: output/pirate/results/pangenome.reversed.tsv
+      md5sum: b2396ce09a6e4178761eca6dc7f4434f
+    - path: output/pirate/results/pangenome.syntenic_blocks.tsv
+      contains: ["g0091"]
+    - path: output/pirate/results/pangenome.temp
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
+      contains: ["test1_00242"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
+      contains: ["test1_00242"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
+      contains: ["test1_00242"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
+      contains: ["test1_00242"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
+      contains: ["test1_00242"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
+      contains: ["test1_00242"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
+      contains: ["test1_00242"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
+      md5sum: ffb3b5bf1ba24bf2bd0be677500139a2
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
+      contains: ["test1_00081"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
+      contains: ["test1_00242"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
+      contains: ["chaos"]
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
+      md5sum: 6e483c773ed90bd50b33f2bd569343e4
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
+    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pto
+    - path: output/pirate/results/pangenome_log.txt
+      contains: ["Creating pangenome on amino acid"]
+    - path: output/pirate/results/paralog_clusters.tab
+      contains: ["g0216"]
+    - path: output/pirate/results/representative_sequences.faa
+      contains: ["representative_genome"]
+    - path: output/pirate/results/representative_sequences.ffn
+      contains: ["representative_genome"]
+    - path: output/pirate/results/split_groups.log
+      contains: ["g0"]
diff --git a/tests/modules/nf-core/plasmidfinder/main.nf b/tests/modules/nf-core/plasmidfinder/main.nf
new file mode 100644
index 00000000000..9b79e37310c
--- /dev/null
+++ b/tests/modules/nf-core/plasmidfinder/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLASMIDFINDER } from '../../../../modules/nf-core/plasmidfinder/main.nf'
+
+workflow test_plasmidfinder {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    PLASMIDFINDER ( input )
+}
diff --git a/tests/modules/plasmidfinder/nextflow.config b/tests/modules/nf-core/plasmidfinder/nextflow.config
similarity index 100%
rename from tests/modules/plasmidfinder/nextflow.config
rename to tests/modules/nf-core/plasmidfinder/nextflow.config
diff --git a/tests/modules/nf-core/plasmidfinder/test.yml b/tests/modules/nf-core/plasmidfinder/test.yml
new file mode 100644
index 00000000000..cdb053ab3ac
--- /dev/null
+++ b/tests/modules/nf-core/plasmidfinder/test.yml
@@ -0,0 +1,13 @@
+- name: plasmidfinder test_plasmidfinder
+  command: nextflow run ./tests/modules/nf-core/plasmidfinder -entry test_plasmidfinder -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/plasmidfinder/nextflow.config
+  tags:
+    - plasmidfinder
+  files:
+    - path: output/plasmidfinder/test-hit_in_genome_seq.fsa
+    - path: output/plasmidfinder/test-plasmid_seqs.fsa
+    - path: output/plasmidfinder/test.json
+      contains: ["plasmidfinder", "filename", "results", "Rep_trans"]
+    - path: output/plasmidfinder/test.tsv
+      contains: ["Database", "Accession", "Query"]
+    - path: output/plasmidfinder/test.txt
+      contains: ["plasmidfinder", "Results", "Contig", "found"]
diff --git a/tests/modules/nf-core/plasmidid/main.nf b/tests/modules/nf-core/plasmidid/main.nf
new file mode 100644
index 00000000000..4ef7fc64ac8
--- /dev/null
+++ b/tests/modules/nf-core/plasmidid/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLASMIDID } from '../../../../modules/nf-core/plasmidid/main.nf'
+
+workflow test_plasmidid {
+
+    contigs = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+              ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    PLASMIDID ( contigs, fasta )
+}
diff --git a/tests/modules/plasmidid/nextflow.config b/tests/modules/nf-core/plasmidid/nextflow.config
similarity index 100%
rename from tests/modules/plasmidid/nextflow.config
rename to tests/modules/nf-core/plasmidid/nextflow.config
diff --git a/tests/modules/nf-core/plasmidid/test.yml b/tests/modules/nf-core/plasmidid/test.yml
new file mode 100644
index 00000000000..1cd9633ccb6
--- /dev/null
+++ b/tests/modules/nf-core/plasmidid/test.yml
@@ -0,0 +1,55 @@
+- name: plasmidid
+  command: nextflow run ./tests/modules/nf-core/plasmidid -entry test_plasmidid -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/plasmidid/nextflow.config
+  tags:
+    - plasmidid
+  files:
+    - path: output/plasmidid/test/data/database_reconstruct_test.length
+      md5sum: a57c401f27ae5133823fb09fb21c8a3c
+    - path: output/plasmidid/test/data/test.coverage_adapted_clustered_ac
+      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
+    - path: output/plasmidid/test/data/test.err
+      md5sum: 011108fd8b0bb4a4c0b5b2cf46452a90
+    - path: output/plasmidid/test/data/test.fna
+      md5sum: 503a5e1d4654bb2df19420e211070db3
+    - path: output/plasmidid/test/data/test.gbk
+    - path: output/plasmidid/test/data/test.gff
+      md5sum: 3ed8912ee9b0712ca491fa78ff5f4da1
+    - path: output/plasmidid/test/data/test.karyotype_individual.txt
+      md5sum: aaf0f5bfe297fb9846ace761ff018d22
+    - path: output/plasmidid/test/data/test.karyotype_summary.txt
+      md5sum: aaf0f5bfe297fb9846ace761ff018d22
+    - path: output/plasmidid/test/data/test.plasmids.blast
+      md5sum: 241045ea62156c1ca9bc1eb734ac9526
+    - path: output/plasmidid/test/data/test.plasmids.blast.links
+      md5sum: a44d6aa388b582da8ad53c5b49467b8f
+    - path: output/plasmidid/test/data/test.plasmids.complete
+      md5sum: fbc7235285dbb963b07561dd6972a883
+    - path: output/plasmidid/test/database/test.fna
+      md5sum: 6b843fe652b4369addb382f61952c3dd
+    - path: output/plasmidid/test/database/test.gbk
+    - path: output/plasmidid/test/database/test.gff
+      md5sum: 7e65da147d0a413020b0d92b7b03ffcd
+    - path: output/plasmidid/test/fasta_files/MT192765.1_term.fasta
+      md5sum: 8a8537dd3b21e6905f9367b51c3b3074
+    - path: output/plasmidid/test/images/test_individual.circos.conf
+      md5sum: f74467ab77232e2b342e2bd408897b12
+    - path: output/plasmidid/test/images/test_MT192765.1_individual.circos.conf
+      md5sum: 548443ba0a68065a69383fe32b226780
+    - path: output/plasmidid/test/images/test_summary.circos.conf
+      md5sum: e59dc3b77ee610a48b79230da705aba0
+    - path: output/plasmidid/test/images/test_MT192765.1.png
+    - path: output/plasmidid/test/images/test_summary.png
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.clusters.tab
+      md5sum: cf75e4418631796bb4675129b575915d
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.representative.fasta
+      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.representative.fasta.blast.tmp.ndb
+      md5sum: f67f8be1e00eb7d3512869071fb4c2c2
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.fasta
+      md5sum: c7fe0e9e9a94d98d7f85a7be99c032fd
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.mash.distances.tab
+      md5sum: fd5408c3c2f8f68dc01e0123bb6a9079
+    - path: output/plasmidid/test/logs/draw_circos_images.log
+    - path: output/plasmidid/test/logs/plasmidID.log
+    - path: output/plasmidid/test/test_final_results.html
+    - path: output/plasmidid/test/test_final_results.tab
diff --git a/tests/modules/nf-core/plink/extract/main.nf b/tests/modules/nf-core/plink/extract/main.nf
new file mode 100644
index 00000000000..f0a50a5ac49
--- /dev/null
+++ b/tests/modules/nf-core/plink/extract/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLINK_VCF     } from '../../../../../modules/nf-core/plink/vcf/main.nf'
+include { PLINK_EXTRACT } from '../../../../../modules/nf-core/plink/extract/main.nf'
+
+workflow test_plink_extract {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true) 
+    ]
+
+    PLINK_VCF ( input )
+    
+    PLINK_VCF.out.bim
+        .splitText(file: 'variants.keep', keepHeader: false, by: 10)
+        .first()
+        .set { ch_variants }
+
+    PLINK_VCF.out.bed
+        .concat(PLINK_VCF.out.bim, PLINK_VCF.out.fam.concat(ch_variants))
+        .groupTuple()
+        .map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
+        .set { ch_extract }
+
+    PLINK_EXTRACT ( ch_extract )
+}
diff --git a/tests/modules/plink/extract/nextflow.config b/tests/modules/nf-core/plink/extract/nextflow.config
similarity index 100%
rename from tests/modules/plink/extract/nextflow.config
rename to tests/modules/nf-core/plink/extract/nextflow.config
diff --git a/tests/modules/nf-core/plink/extract/test.yml b/tests/modules/nf-core/plink/extract/test.yml
new file mode 100644
index 00000000000..1543aefb3ac
--- /dev/null
+++ b/tests/modules/nf-core/plink/extract/test.yml
@@ -0,0 +1,18 @@
+- name: plink extract test_plink_extract
+  command: nextflow run ./tests/modules/nf-core/plink/extract -entry test_plink_extract -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/plink/extract/nextflow.config
+  tags:
+    - plink
+    - plink/extract
+  files:
+    - path: output/plink/test.bed
+      md5sum: 9121010aba9905eee965e96bc983611d
+    - path: output/plink/test.bim
+      md5sum: 510ec606219ee5daaf5c207cb01554bf
+    - path: output/plink/test.extract.bed
+      md5sum: 9e02f7143bcc756a51f20d50ca7f8032
+    - path: output/plink/test.extract.bim
+      md5sum: 63d190aea4094aa5d042aacd63397f94
+    - path: output/plink/test.extract.fam
+      md5sum: c499456df4da78792ef29934ef3cd47d
+    - path: output/plink/test.fam
+      md5sum: c499456df4da78792ef29934ef3cd47d
diff --git a/tests/modules/nf-core/plink/vcf/main.nf b/tests/modules/nf-core/plink/vcf/main.nf
new file mode 100644
index 00000000000..59119c238db
--- /dev/null
+++ b/tests/modules/nf-core/plink/vcf/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLINK_VCF } from '../../../../../modules/nf-core/plink/vcf/main.nf'
+
+workflow test_plink_vcf {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+
+    PLINK_VCF ( input )
+}
diff --git a/tests/modules/plink/vcf/nextflow.config b/tests/modules/nf-core/plink/vcf/nextflow.config
similarity index 100%
rename from tests/modules/plink/vcf/nextflow.config
rename to tests/modules/nf-core/plink/vcf/nextflow.config
diff --git a/tests/modules/nf-core/plink/vcf/test.yml b/tests/modules/nf-core/plink/vcf/test.yml
new file mode 100644
index 00000000000..996b3b8b92c
--- /dev/null
+++ b/tests/modules/nf-core/plink/vcf/test.yml
@@ -0,0 +1,12 @@
+- name: plink vcf test_plink_vcf
+  command: nextflow run ./tests/modules/nf-core/plink/vcf -entry test_plink_vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/plink/vcf/nextflow.config
+  tags:
+    - plink
+    - plink/vcf
+  files:
+    - path: output/plink/test.bed
+      md5sum: 55c3ab2636212911b5f952ef6f5d855c
+    - path: output/plink/test.bim
+      md5sum: 54164b6f103e152de05712c6bb317db8
+    - path: output/plink/test.fam
+      md5sum: 22d32d7daa3ae6b819a24895e82b2a70
diff --git a/tests/modules/nf-core/plink2/extract/main.nf b/tests/modules/nf-core/plink2/extract/main.nf
new file mode 100644
index 00000000000..f442edb8f24
--- /dev/null
+++ b/tests/modules/nf-core/plink2/extract/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLINK2_VCF     } from '../../../../../modules/nf-core/plink2/vcf/main.nf'
+include { PLINK2_EXTRACT } from '../../../../../modules/nf-core/plink2/extract/main.nf'
+
+workflow test_plink2_extract {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
+    ]
+    PLINK2_VCF ( input )
+
+    PLINK2_VCF.out.pvar
+        .splitText(file: 'variants.keep', keepHeader: false, by: 10)
+        .last()
+        .set { ch_variants }
+
+    ch_variants.view()
+
+    PLINK2_VCF.out.pgen
+        .concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar.concat(ch_variants))
+        .groupTuple()
+        .map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
+        .set { ch_extract }
+
+    PLINK2_EXTRACT ( ch_extract )
+}
diff --git a/tests/modules/plink2/extract/nextflow.config b/tests/modules/nf-core/plink2/extract/nextflow.config
similarity index 100%
rename from tests/modules/plink2/extract/nextflow.config
rename to tests/modules/nf-core/plink2/extract/nextflow.config
diff --git a/tests/modules/nf-core/plink2/extract/test.yml b/tests/modules/nf-core/plink2/extract/test.yml
new file mode 100644
index 00000000000..457a31112b3
--- /dev/null
+++ b/tests/modules/nf-core/plink2/extract/test.yml
@@ -0,0 +1,20 @@
+- name: plink2 extract test_plink2_extract
+  command: nextflow run ./tests/modules/nf-core/plink2/extract -entry test_plink2_extract -c ./tests/config/nextflow.config
+  tags:
+    - plink2/extract
+    - plink2
+  files:
+    - path: output/plink2/test.extract.pgen
+      md5sum: 785e729a293ecabb0d39394865316bda
+    - path: output/plink2/test.extract.psam
+      md5sum: e6c714488754cb8448c3dfda08c4c0ea
+    - path: output/plink2/test.extract.pvar.zst
+      md5sum: 076767e6695e681115eabb924a447ee9
+    - path: output/plink2/test.pgen
+      md5sum: fac12ca9041d6950f6b7d60ac2120721
+    - path: output/plink2/test.psam
+      md5sum: e6c714488754cb8448c3dfda08c4c0ea
+    - path: output/plink2/test.pvar
+      md5sum: ff9e44f8e5f4035d8cf2bfe7be6755b3
+    - path: output/plink2/versions.yml
+      md5sum: c477b7c9f6e39b89710fe1a0bceee50d
diff --git a/tests/modules/nf-core/plink2/score/main.nf b/tests/modules/nf-core/plink2/score/main.nf
new file mode 100644
index 00000000000..75cedf22f5f
--- /dev/null
+++ b/tests/modules/nf-core/plink2/score/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLINK2_VCF } from '../../../../../modules/nf-core/plink2/vcf/main.nf'
+include { PLINK2_SCORE } from '../../../../../modules/nf-core/plink2/score/main.nf'
+
+workflow test_plink2_score {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
+    ]
+    PLINK2_VCF ( input )
+
+    scorefile = file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_score'], checkIfExists: true)
+
+    PLINK2_VCF.out.pgen
+        .concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar)
+        .groupTuple()
+        .map { it.flatten() }
+        .set { ch_target_genome }
+
+    PLINK2_SCORE ( ch_target_genome, scorefile )
+}
diff --git a/tests/modules/plink2/score/nextflow.config b/tests/modules/nf-core/plink2/score/nextflow.config
similarity index 100%
rename from tests/modules/plink2/score/nextflow.config
rename to tests/modules/nf-core/plink2/score/nextflow.config
diff --git a/tests/modules/nf-core/plink2/score/test.yml b/tests/modules/nf-core/plink2/score/test.yml
new file mode 100644
index 00000000000..78f8a5354f2
--- /dev/null
+++ b/tests/modules/nf-core/plink2/score/test.yml
@@ -0,0 +1,16 @@
+- name: plink2 score test_plink2_score
+  command: nextflow run ./tests/modules/nf-core/plink2/score -entry test_plink2_score -c ./tests/config/nextflow.config
+  tags:
+    - plink2
+    - plink2/score
+  files:
+    - path: output/plink2/test.pgen
+      md5sum: fac12ca9041d6950f6b7d60ac2120721
+    - path: output/plink2/test.psam
+      md5sum: e6c714488754cb8448c3dfda08c4c0ea
+    - path: output/plink2/test.pvar.zst
+      md5sum: 98d59e9779a8b62d5032cd98b642a63b
+    - path: output/plink2/test.sscore
+      md5sum: 97bde840f69febd65f2c00e9243126e9
+    - path: output/plink2/versions.yml
+      md5sum: 71499ab14e1583c88ced3a7a4f05bfa7
diff --git a/tests/modules/nf-core/plink2/vcf/main.nf b/tests/modules/nf-core/plink2/vcf/main.nf
new file mode 100644
index 00000000000..abdfb9b0bef
--- /dev/null
+++ b/tests/modules/nf-core/plink2/vcf/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLINK2_VCF } from '../../../../../modules/nf-core/plink2/vcf/main.nf'
+
+workflow test_plink2_vcf {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+
+    PLINK2_VCF ( input )
+}
diff --git a/tests/modules/plink2/vcf/nextflow.config b/tests/modules/nf-core/plink2/vcf/nextflow.config
similarity index 100%
rename from tests/modules/plink2/vcf/nextflow.config
rename to tests/modules/nf-core/plink2/vcf/nextflow.config
diff --git a/tests/modules/nf-core/plink2/vcf/test.yml b/tests/modules/nf-core/plink2/vcf/test.yml
new file mode 100644
index 00000000000..59a1e852f00
--- /dev/null
+++ b/tests/modules/nf-core/plink2/vcf/test.yml
@@ -0,0 +1,14 @@
+- name: plink2 vcf test_plink2_vcf
+  command: nextflow run ./tests/modules/nf-core/plink2/vcf -entry test_plink2_vcf -c ./tests/config/nextflow.config
+  tags:
+    - plink2
+    - plink2/vcf
+  files:
+    - path: output/plink2/test.pgen
+      md5sum: d66d3cd4a6c9cca1a4073d7f4b277041
+    - path: output/plink2/test.psam
+      md5sum: dc3b77d7753a7bed41734323e3549b10
+    - path: output/plink2/test.pvar.zst
+      md5sum: b53cccb83e024a39789af5eab8de1c28
+    - path: output/plink2/versions.yml
+      md5sum: 82ada74bc81473b7cba377f696acf54c
diff --git a/tests/modules/nf-core/pmdtools/filter/main.nf b/tests/modules/nf-core/pmdtools/filter/main.nf
new file mode 100644
index 00000000000..5c8531b3e0f
--- /dev/null
+++ b/tests/modules/nf-core/pmdtools/filter/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PMDTOOLS_FILTER } from '../../../../../modules/nf-core/pmdtools/filter/main.nf'
+
+workflow test_pmdtools_filter {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]]
+    threshold = 3
+    reference = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+    PMDTOOLS_FILTER ( input, threshold, reference )
+}
diff --git a/tests/modules/pmdtools/filter/nextflow.config b/tests/modules/nf-core/pmdtools/filter/nextflow.config
similarity index 100%
rename from tests/modules/pmdtools/filter/nextflow.config
rename to tests/modules/nf-core/pmdtools/filter/nextflow.config
diff --git a/tests/modules/nf-core/pmdtools/filter/test.yml b/tests/modules/nf-core/pmdtools/filter/test.yml
new file mode 100644
index 00000000000..c2aef35f8f2
--- /dev/null
+++ b/tests/modules/nf-core/pmdtools/filter/test.yml
@@ -0,0 +1,8 @@
+- name: pmdtools filter
+  command: nextflow run ./tests/modules/nf-core/pmdtools/filter -entry test_pmdtools_filter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pmdtools/filter/nextflow.config
+  tags:
+    - pmdtools
+    - pmdtools/filter
+  files:
+    - path: output/pmdtools/test.bam
+      md5sum: 0fa64cb87d0439d4482938a4b6990b9d
diff --git a/tests/modules/nf-core/porechop/main.nf b/tests/modules/nf-core/porechop/main.nf
new file mode 100644
index 00000000000..59f68c5c5d9
--- /dev/null
+++ b/tests/modules/nf-core/porechop/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PORECHOP } from '../../../../modules/nf-core/porechop/main.nf'
+
+workflow test_porechop {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+                file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+
+    PORECHOP ( input )
+}
diff --git a/tests/modules/porechop/nextflow.config b/tests/modules/nf-core/porechop/nextflow.config
similarity index 100%
rename from tests/modules/porechop/nextflow.config
rename to tests/modules/nf-core/porechop/nextflow.config
diff --git a/tests/modules/nf-core/porechop/test.yml b/tests/modules/nf-core/porechop/test.yml
new file mode 100644
index 00000000000..9e6a8be3ea2
--- /dev/null
+++ b/tests/modules/nf-core/porechop/test.yml
@@ -0,0 +1,9 @@
+- name: porechop test_porechop
+  command: nextflow run ./tests/modules/nf-core/porechop -entry test_porechop -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/porechop/nextflow.config
+  tags:
+    - porechop
+  files:
+    - path: output/porechop/test_porechop.fastq.gz
+      md5sum: 08f314ae9f162c8dcc27e5b513d2064d
+    - path: output/porechop/test_porechop.log
+      contains: ["Saving trimmed reads to file"]
diff --git a/tests/modules/nf-core/preseq/ccurve/main.nf b/tests/modules/nf-core/preseq/ccurve/main.nf
new file mode 100644
index 00000000000..cee8a6c52bb
--- /dev/null
+++ b/tests/modules/nf-core/preseq/ccurve/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRESEQ_CCURVE } from '../../../../../modules/nf-core/preseq/ccurve/main.nf'
+
+workflow test_preseq_ccurve_single_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
+    ]
+
+    PRESEQ_CCURVE ( input )
+}
+
+workflow test_preseq_ccurve_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    PRESEQ_CCURVE ( input )
+}
diff --git a/tests/modules/preseq/ccurve/nextflow.config b/tests/modules/nf-core/preseq/ccurve/nextflow.config
similarity index 100%
rename from tests/modules/preseq/ccurve/nextflow.config
rename to tests/modules/nf-core/preseq/ccurve/nextflow.config
diff --git a/tests/modules/nf-core/preseq/ccurve/test.yml b/tests/modules/nf-core/preseq/ccurve/test.yml
new file mode 100644
index 00000000000..a2be2924e76
--- /dev/null
+++ b/tests/modules/nf-core/preseq/ccurve/test.yml
@@ -0,0 +1,19 @@
+- name: preseq ccurve single-end
+  command: nextflow run ./tests/modules/nf-core/preseq/ccurve -entry test_preseq_ccurve_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/preseq/ccurve/nextflow.config
+  tags:
+    - preseq
+    - preseq/ccurve
+  files:
+    - path: output/preseq/test.c_curve.txt
+      md5sum: cf4743abdd355595d6ec1fb3f38e66e5
+    - path: output/preseq/test.command.log
+
+- name: preseq ccurve paired-end
+  command: nextflow run ./tests/modules/nf-core/preseq/ccurve -entry test_preseq_ccurve_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/preseq/ccurve/nextflow.config
+  tags:
+    - preseq
+    - preseq/ccurve
+  files:
+    - path: output/preseq/test.c_curve.txt
+      md5sum: cf4743abdd355595d6ec1fb3f38e66e5
+    - path: output/preseq/test.command.log
diff --git a/tests/modules/nf-core/preseq/lcextrap/main.nf b/tests/modules/nf-core/preseq/lcextrap/main.nf
new file mode 100644
index 00000000000..be87f23362c
--- /dev/null
+++ b/tests/modules/nf-core/preseq/lcextrap/main.nf
@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRESEQ_LCEXTRAP } from '../../../../../modules/nf-core/preseq/lcextrap/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_preseq_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true) ]
+            ]
+    PRESEQ_LCEXTRAP ( input )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_preseq_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true) ]
+            ]
+
+    PRESEQ_LCEXTRAP ( input )
+}
+
diff --git a/tests/modules/preseq/lcextrap/nextflow.config b/tests/modules/nf-core/preseq/lcextrap/nextflow.config
similarity index 100%
rename from tests/modules/preseq/lcextrap/nextflow.config
rename to tests/modules/nf-core/preseq/lcextrap/nextflow.config
diff --git a/tests/modules/nf-core/preseq/lcextrap/test.yml b/tests/modules/nf-core/preseq/lcextrap/test.yml
new file mode 100644
index 00000000000..975bf90dcf9
--- /dev/null
+++ b/tests/modules/nf-core/preseq/lcextrap/test.yml
@@ -0,0 +1,19 @@
+- name: preseq lcextrap single-end
+  command: nextflow run ./tests/modules/nf-core/preseq/lcextrap -entry test_preseq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/preseq/lcextrap/nextflow.config
+  tags:
+    - preseq
+    - preseq/lcextrap
+  files:
+    - path: output/preseq/test.lc_extrap.txt
+      md5sum: 1fa5cdd601079329618f61660bee00de
+    - path: output/preseq/test.command.log
+
+- name: preseq lcextrap paired-end
+  command: nextflow run ./tests/modules/nf-core/preseq/lcextrap -entry test_preseq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/preseq/lcextrap/nextflow.config
+  tags:
+    - preseq
+    - preseq/lcextrap
+  files:
+    - path: output/preseq/test.lc_extrap.txt
+      md5sum: 10e5ea860e87fb6f5dc10f4f20c62040
+    - path: output/preseq/test.command.log
diff --git a/tests/modules/nf-core/prinseqplusplus/main.nf b/tests/modules/nf-core/prinseqplusplus/main.nf
new file mode 100644
index 00000000000..b604b8091ec
--- /dev/null
+++ b/tests/modules/nf-core/prinseqplusplus/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRINSEQPLUSPLUS } from '../../../../modules/nf-core/prinseqplusplus/main.nf'
+
+workflow test_prinseqplusplus_single_end {
+
+        input = [ [ id:'test', single_end:true ], // meta map
+            [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+        ]
+
+    PRINSEQPLUSPLUS ( input )
+}
+
+workflow test_prinseqplusplus_paired_end {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+        ]
+
+    PRINSEQPLUSPLUS ( input )
+}
diff --git a/tests/modules/prinseqplusplus/nextflow.config b/tests/modules/nf-core/prinseqplusplus/nextflow.config
similarity index 100%
rename from tests/modules/prinseqplusplus/nextflow.config
rename to tests/modules/nf-core/prinseqplusplus/nextflow.config
diff --git a/tests/modules/nf-core/prinseqplusplus/test.yml b/tests/modules/nf-core/prinseqplusplus/test.yml
new file mode 100644
index 00000000000..4b125043712
--- /dev/null
+++ b/tests/modules/nf-core/prinseqplusplus/test.yml
@@ -0,0 +1,27 @@
+- name: prinseqplusplus test_prinseqplusplus_single_end
+  command: nextflow run ./tests/modules/nf-core/prinseqplusplus -entry test_prinseqplusplus_single_end -c ./tests/config/nextflow.config
+  tags:
+    - prinseqplusplus
+  files:
+    - path: output/prinseqplusplus/test.log
+      contains:
+        - "reads removed by -lc_entropy"
+    - path: output/prinseqplusplus/test_bad_out.fastq.gz
+    - path: output/prinseqplusplus/test_good_out.fastq.gz
+    - path: output/prinseqplusplus/versions.yml
+
+- name: prinseqplusplus test_prinseqplusplus_paired_end
+  command: nextflow run ./tests/modules/nf-core/prinseqplusplus -entry test_prinseqplusplus_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - prinseqplusplus
+  files:
+    - path: output/prinseqplusplus/test.log
+      contains:
+        - "reads removed by -lc_entropy"
+    - path: output/prinseqplusplus/test_bad_out_R1.fastq.gz
+    - path: output/prinseqplusplus/test_bad_out_R2.fastq.gz
+    - path: output/prinseqplusplus/test_good_out_R1.fastq.gz
+    - path: output/prinseqplusplus/test_good_out_R2.fastq.gz
+    - path: output/prinseqplusplus/test_single_out_R1.fastq.gz
+    - path: output/prinseqplusplus/test_single_out_R2.fastq.gz
+    - path: output/prinseqplusplus/versions.yml
diff --git a/tests/modules/nf-core/prodigal/main.nf b/tests/modules/nf-core/prodigal/main.nf
new file mode 100644
index 00000000000..c69f887e5fa
--- /dev/null
+++ b/tests/modules/nf-core/prodigal/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRODIGAL } from '../../../../modules/nf-core/prodigal/main.nf'
+
+workflow test_prodigal {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
+            ]
+
+    PRODIGAL ( input , "gff")
+}
diff --git a/tests/modules/prodigal/nextflow.config b/tests/modules/nf-core/prodigal/nextflow.config
similarity index 100%
rename from tests/modules/prodigal/nextflow.config
rename to tests/modules/nf-core/prodigal/nextflow.config
diff --git a/tests/modules/nf-core/prodigal/test.yml b/tests/modules/nf-core/prodigal/test.yml
new file mode 100644
index 00000000000..0c83b3fbd35
--- /dev/null
+++ b/tests/modules/nf-core/prodigal/test.yml
@@ -0,0 +1,13 @@
+- name: prodigal test_prodigal
+  command: nextflow run ./tests/modules/nf-core/prodigal -entry test_prodigal -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/prodigal/nextflow.config
+  tags:
+    - prodigal
+  files:
+    - path: output/prodigal/test.fna
+      md5sum: 1bc8a05bcb72a3c324f5e4ffaa716d3b
+    - path: output/prodigal/test.gff
+      md5sum: 612c2724c2891c63350f171f74165757
+    - path: output/prodigal/test.faa
+      md5sum: 7168b854103f3586ccfdb71a44c389f7
+    - path: output/prodigal/test_all.txt
+      md5sum: e6d6c50f0c39e5169f84ae3c90837fa9
diff --git a/tests/modules/nf-core/prokka/main.nf b/tests/modules/nf-core/prokka/main.nf
new file mode 100644
index 00000000000..ff17e956831
--- /dev/null
+++ b/tests/modules/nf-core/prokka/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PROKKA } from '../../../../modules/nf-core/prokka/main.nf'
+
+workflow test_prokka {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            ]
+    
+    PROKKA ( input, [], [] )
+}
diff --git a/tests/modules/prokka/nextflow.config b/tests/modules/nf-core/prokka/nextflow.config
similarity index 100%
rename from tests/modules/prokka/nextflow.config
rename to tests/modules/nf-core/prokka/nextflow.config
diff --git a/tests/modules/nf-core/prokka/test.yml b/tests/modules/nf-core/prokka/test.yml
new file mode 100644
index 00000000000..746bc25368d
--- /dev/null
+++ b/tests/modules/nf-core/prokka/test.yml
@@ -0,0 +1,27 @@
+- name: prokka
+  command: nextflow run ./tests/modules/nf-core/prokka -entry test_prokka -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/prokka/nextflow.config
+  tags:
+    - prokka
+  files:
+    - path: output/prokka/test/test.err
+      md5sum: b3daedc646fddd422824e2b3e5e9229d
+    - path: output/prokka/test/test.faa
+      md5sum: a4ceda83262b3c222a6b1f508fb9e24b
+    - path: output/prokka/test/test.ffn
+      md5sum: 80f474b5367b7ea5ed23791935f65e34
+    - path: output/prokka/test/test.fna
+      md5sum: 787307f29a263e5657cc276ebbf7e2b3
+    - path: output/prokka/test/test.fsa
+      md5sum: 71bbefcb7f12046bcd3263f58cfd5404
+    - path: output/prokka/test/test.gff
+      md5sum: 5dbfb8fcf2db020564c16045976a0933
+    - path: output/prokka/test/test.tbl
+      md5sum: d8f816a066ced94b62d9618b13fb8add
+    - path: output/prokka/test/test.tsv
+      md5sum: da7c720c3018c5081d6a70b517b7d450
+    - path: output/prokka/test/test.txt
+      md5sum: b40e485ffc8eaf1feacf8d79d9751a33
+    # Contain time stamps
+    - path: output/prokka/test/test.gbk
+    - path: output/prokka/test/test.log
+    - path: output/prokka/test/test.sqn
diff --git a/tests/modules/nf-core/pycoqc/main.nf b/tests/modules/nf-core/pycoqc/main.nf
new file mode 100644
index 00000000000..8256d3f1350
--- /dev/null
+++ b/tests/modules/nf-core/pycoqc/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PYCOQC } from '../../../../modules/nf-core/pycoqc/main.nf'
+
+workflow test_pycoqc {
+
+    input = [ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ]
+
+    PYCOQC ( input )
+}
diff --git a/tests/modules/pycoqc/nextflow.config b/tests/modules/nf-core/pycoqc/nextflow.config
similarity index 100%
rename from tests/modules/pycoqc/nextflow.config
rename to tests/modules/nf-core/pycoqc/nextflow.config
diff --git a/tests/modules/nf-core/pycoqc/test.yml b/tests/modules/nf-core/pycoqc/test.yml
new file mode 100644
index 00000000000..a83ad9a0cc5
--- /dev/null
+++ b/tests/modules/nf-core/pycoqc/test.yml
@@ -0,0 +1,11 @@
+- name: pycoqc
+  command: nextflow run ./tests/modules/nf-core/pycoqc -entry test_pycoqc -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pycoqc/nextflow.config
+  tags:
+    - pycoqc
+  files:
+    - path: output/pycoqc/pycoqc.json
+      contains:
+        - '"reads_number": 100,'
+        - '"bases_number": 1160,'
+        - '"N50": 12,'
+    - path: output/pycoqc/pycoqc.html
diff --git a/tests/modules/nf-core/pydamage/analyze/main.nf b/tests/modules/nf-core/pydamage/analyze/main.nf
new file mode 100644
index 00000000000..786eb11622b
--- /dev/null
+++ b/tests/modules/nf-core/pydamage/analyze/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PYDAMAGE_ANALYZE } from '../../../../../modules/nf-core/pydamage/analyze/main.nf'
+
+workflow test_pydamage {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+    PYDAMAGE_ANALYZE ( input )
+}
diff --git a/tests/modules/pydamage/analyze/nextflow.config b/tests/modules/nf-core/pydamage/analyze/nextflow.config
similarity index 100%
rename from tests/modules/pydamage/analyze/nextflow.config
rename to tests/modules/nf-core/pydamage/analyze/nextflow.config
diff --git a/tests/modules/nf-core/pydamage/analyze/test.yml b/tests/modules/nf-core/pydamage/analyze/test.yml
new file mode 100644
index 00000000000..57397e763c6
--- /dev/null
+++ b/tests/modules/nf-core/pydamage/analyze/test.yml
@@ -0,0 +1,8 @@
+- name: pydamage analyze test workflow
+  command: nextflow run ./tests/modules/nf-core/pydamage/analyze -entry test_pydamage -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pydamage/analyze/nextflow.config
+  tags:
+    - pydamage
+    - pydamage/analyze
+  files:
+    - path: output/pydamage/pydamage_results/pydamage_results.csv
+      md5sum: 37ee6b4dee6890fd2ec8550337f21ac9
diff --git a/tests/modules/nf-core/pydamage/filter/main.nf b/tests/modules/nf-core/pydamage/filter/main.nf
new file mode 100644
index 00000000000..bc2d1e30bf4
--- /dev/null
+++ b/tests/modules/nf-core/pydamage/filter/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PYDAMAGE_ANALYZE } from '../../../../../modules/nf-core/pydamage/analyze/main.nf'
+include { PYDAMAGE_FILTER } from '../../../../../modules/nf-core/pydamage/filter/main.nf'
+
+workflow test_pydamage {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+    PYDAMAGE_ANALYZE ( input )
+    PYDAMAGE_FILTER (PYDAMAGE_ANALYZE.out.csv)
+}
diff --git a/tests/modules/pydamage/filter/nextflow.config b/tests/modules/nf-core/pydamage/filter/nextflow.config
similarity index 100%
rename from tests/modules/pydamage/filter/nextflow.config
rename to tests/modules/nf-core/pydamage/filter/nextflow.config
diff --git a/tests/modules/nf-core/pydamage/filter/test.yml b/tests/modules/nf-core/pydamage/filter/test.yml
new file mode 100644
index 00000000000..0b98214476c
--- /dev/null
+++ b/tests/modules/nf-core/pydamage/filter/test.yml
@@ -0,0 +1,10 @@
+- name: pydamage filter test workflow
+  command: nextflow run ./tests/modules/nf-core/pydamage/filter -entry test_pydamage -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pydamage/filter/nextflow.config
+  tags:
+    - pydamage
+    - pydamage/filter
+  files:
+    - path: output/pydamage/pydamage_results/pydamage_filtered_results.csv
+      md5sum: 9f297233cf4932d7d7e52cc72d4727dc
+    - path: output/pydamage/pydamage_results/pydamage_results.csv
+      md5sum: 37ee6b4dee6890fd2ec8550337f21ac9
diff --git a/tests/modules/nf-core/qcat/main.nf b/tests/modules/nf-core/qcat/main.nf
new file mode 100644
index 00000000000..c64d6367a66
--- /dev/null
+++ b/tests/modules/nf-core/qcat/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { QCAT } from '../../../../modules/nf-core/qcat/main.nf'
+
+workflow test_qcat {
+    input = [ [ id:'test' ], // meta map
+              [ file("https://github.com/nf-core/test-datasets/raw/nanoseq/fastq/nondemultiplexed/sample_nobc_dx.fastq.gz", checkIfExists: true) ]
+            ]
+    barcode_kit = 'NBD103/NBD104'
+
+    QCAT ( input, barcode_kit )
+}
diff --git a/tests/modules/qcat/nextflow.config b/tests/modules/nf-core/qcat/nextflow.config
similarity index 100%
rename from tests/modules/qcat/nextflow.config
rename to tests/modules/nf-core/qcat/nextflow.config
diff --git a/tests/modules/nf-core/qcat/test.yml b/tests/modules/nf-core/qcat/test.yml
new file mode 100644
index 00000000000..2aa0795071c
--- /dev/null
+++ b/tests/modules/nf-core/qcat/test.yml
@@ -0,0 +1,8 @@
+- name: qcat
+  command: nextflow run ./tests/modules/nf-core/qcat -entry test_qcat -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/qcat/nextflow.config
+  tags:
+    - qcat
+  files:
+    - path: ./output/qcat/fastq/barcode06.fastq.gz
+    - path: ./output/qcat/fastq/barcode12.fastq.gz
+    - path: ./output/qcat/fastq/none.fastq.gz
diff --git a/tests/modules/nf-core/qualimap/bamqc/main.nf b/tests/modules/nf-core/qualimap/bamqc/main.nf
new file mode 100644
index 00000000000..f3f6b8c16fc
--- /dev/null
+++ b/tests/modules/nf-core/qualimap/bamqc/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { QUALIMAP_BAMQC } from '../../../../../modules/nf-core/qualimap/bamqc/main.nf'
+
+workflow test_qualimap_bamqc {
+    input   = [ [ id:'test', single_end:false ], // meta map
+                [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+              ]
+    gff     = []
+
+    QUALIMAP_BAMQC ( input, gff )
+}
diff --git a/tests/modules/qualimap/bamqc/nextflow.config b/tests/modules/nf-core/qualimap/bamqc/nextflow.config
similarity index 100%
rename from tests/modules/qualimap/bamqc/nextflow.config
rename to tests/modules/nf-core/qualimap/bamqc/nextflow.config
diff --git a/tests/modules/nf-core/qualimap/bamqc/test.yml b/tests/modules/nf-core/qualimap/bamqc/test.yml
new file mode 100644
index 00000000000..ffa6d0ff044
--- /dev/null
+++ b/tests/modules/nf-core/qualimap/bamqc/test.yml
@@ -0,0 +1,81 @@
+- name: qualimap bamqc test workflow
+  command: nextflow run ./tests/modules/nf-core/qualimap/bamqc -entry test_qualimap_bamqc -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/qualimap/bamqc/nextflow.config
+  tags:
+    - qualimap
+    - qualimap/bamqc
+  files:
+    - path: ./output/qualimap/test/qualimapReport.html
+    - path: ./output/qualimap/test/genome_results.txt
+      md5sum: 5ec87ea86ad734d512c8c76fe8eb37b1
+    - path: ./output/qualimap/test/css/plus.png
+      md5sum: 0125e6faa04e2cf0141a2d599d3bb220
+    - path: ./output/qualimap/test/css/down-pressed.png
+      md5sum: ebe8979581eda700fb234a73c661a4b9
+    - path: ./output/qualimap/test/css/underscore.js
+      md5sum: db5ba047a66617d4cd3e8c5099cc51db
+    - path: ./output/qualimap/test/css/ajax-loader.gif
+      md5sum: ae6667053ad118020b8e68ccf307b519
+    - path: ./output/qualimap/test/css/searchtools.js
+      md5sum: d550841adeedc8ed47c40ee607620937
+    - path: ./output/qualimap/test/css/up.png
+    - path: ./output/qualimap/test/css/file.png
+    - path: ./output/qualimap/test/css/up-pressed.png
+    - path: ./output/qualimap/test/css/down.png
+    - path: ./output/qualimap/test/css/minus.png
+    - path: ./output/qualimap/test/css/bgtop.png
+    - path: ./output/qualimap/test/css/comment.png
+    - path: ./output/qualimap/test/css/basic.css
+      md5sum: 25b2823342c0604924a2870eeb4e7e94
+    - path: ./output/qualimap/test/css/report.css
+      md5sum: 7a5f09eaf7c176f966f4e8854168b812
+    - path: ./output/qualimap/test/css/pygments.css
+      md5sum: d625a0adb949f181bd0d3f1432b0fa7f
+    - path: ./output/qualimap/test/css/comment-close.png
+    - path: ./output/qualimap/test/css/doctools.js
+      md5sum: 5ff571aa60e63f69c1890283e240ff8d
+    - path: ./output/qualimap/test/css/comment-bright.png
+    - path: ./output/qualimap/test/css/qualimap_logo_small.png
+    - path: ./output/qualimap/test/css/websupport.js
+      md5sum: 9e61e1e8a7433c56bd7e5a615affcf85
+    - path: ./output/qualimap/test/css/agogo.css
+      md5sum: bd757b1a7ce6fdc0288ba148680f4583
+    - path: ./output/qualimap/test/css/bgfooter.png
+    - path: ./output/qualimap/test/css/jquery.js
+      md5sum: 10092eee563dec2dca82b77d2cf5a1ae
+    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_histogram.txt
+      md5sum: 749630484c5b24b4973ad613d85a2341
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt
+      md5sum: dbcb28c1ab2f0c78f6e803a24a2a695f
+    - path: ./output/qualimap/test/raw_data_qualimapReport/genome_fraction_coverage.txt
+      md5sum: d5ba8feb5418091d6e00e4ad0c865cf1
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_histogram.txt
+      md5sum: 8b638330338758c156200a37602c53d5
+    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_across_reference.txt
+      md5sum: dc553f58b5e361b9e5c894f118347bc1
+    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_histogram.txt
+      md5sum: f57a631c72f2373ca4d3f6c8deb1ad6d
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_across_reference.txt
+      md5sum: 42223637499a2221cf99b4dd08badb6f
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
+      md5sum: c7c7db9fa3febd58b27e95cff857df90
+    - path: ./output/qualimap/test/raw_data_qualimapReport/homopolymer_indels.txt
+      md5sum: ba7484d97ab505ab8642d73074afef04
+    - path: ./output/qualimap/test/raw_data_qualimapReport/duplication_rate_histogram.txt
+      md5sum: 7875c892eb75a6da5115b10e3b2b767e
+    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_across_reference.txt
+      md5sum: fbabd3fea386712fa453e7c9825107af
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_clipping_profile.txt
+      md5sum: e199f6930d4bda5f9e871cb5c628a69a
+    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_content_per_read_position.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_gc_content_per_window.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_0to50_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_uniq_read_starts_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_across_reference.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_across_reference.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_homopolymer_indels.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_across_reference.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_clipping_profile.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_quotes.png
diff --git a/tests/modules/nf-core/qualimap/bamqccram/main.nf b/tests/modules/nf-core/qualimap/bamqccram/main.nf
new file mode 100644
index 00000000000..cd375985414
--- /dev/null
+++ b/tests/modules/nf-core/qualimap/bamqccram/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { QUALIMAP_BAMQCCRAM } from '../../../../../modules/nf-core/qualimap/bamqccram/main.nf'
+
+workflow test_qualimap_bamqc {
+    input   = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+              ]
+    gff     = []
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    QUALIMAP_BAMQCCRAM ( input, gff, fasta, fai )
+}
diff --git a/tests/modules/qualimap/bamqccram/nextflow.config b/tests/modules/nf-core/qualimap/bamqccram/nextflow.config
similarity index 100%
rename from tests/modules/qualimap/bamqccram/nextflow.config
rename to tests/modules/nf-core/qualimap/bamqccram/nextflow.config
diff --git a/tests/modules/nf-core/qualimap/bamqccram/test.yml b/tests/modules/nf-core/qualimap/bamqccram/test.yml
new file mode 100644
index 00000000000..7b9a6495aa3
--- /dev/null
+++ b/tests/modules/nf-core/qualimap/bamqccram/test.yml
@@ -0,0 +1,80 @@
+- name: qualimap bamqccram test_qualimap_bamqc
+  command: nextflow run ./tests/modules/nf-core/qualimap/bamqccram -entry test_qualimap_bamqc -c ./tests/config/nextflow.config
+  tags:
+    - qualimap/bamqccram
+    - qualimap
+  files:
+    - path: ./output/qualimap/test/qualimapReport.html
+    - path: ./output/qualimap/test/genome_results.txt
+      md5sum: 61d8b36507652fd7d7db9583de708161
+    - path: ./output/qualimap/test/css/plus.png
+      md5sum: 0125e6faa04e2cf0141a2d599d3bb220
+    - path: ./output/qualimap/test/css/down-pressed.png
+      md5sum: ebe8979581eda700fb234a73c661a4b9
+    - path: ./output/qualimap/test/css/underscore.js
+      md5sum: db5ba047a66617d4cd3e8c5099cc51db
+    - path: ./output/qualimap/test/css/ajax-loader.gif
+      md5sum: ae6667053ad118020b8e68ccf307b519
+    - path: ./output/qualimap/test/css/searchtools.js
+      md5sum: d550841adeedc8ed47c40ee607620937
+    - path: ./output/qualimap/test/css/up.png
+    - path: ./output/qualimap/test/css/file.png
+    - path: ./output/qualimap/test/css/up-pressed.png
+    - path: ./output/qualimap/test/css/down.png
+    - path: ./output/qualimap/test/css/minus.png
+    - path: ./output/qualimap/test/css/bgtop.png
+    - path: ./output/qualimap/test/css/comment.png
+    - path: ./output/qualimap/test/css/basic.css
+      md5sum: 25b2823342c0604924a2870eeb4e7e94
+    - path: ./output/qualimap/test/css/report.css
+      md5sum: 7a5f09eaf7c176f966f4e8854168b812
+    - path: ./output/qualimap/test/css/pygments.css
+      md5sum: d625a0adb949f181bd0d3f1432b0fa7f
+    - path: ./output/qualimap/test/css/comment-close.png
+    - path: ./output/qualimap/test/css/doctools.js
+      md5sum: 5ff571aa60e63f69c1890283e240ff8d
+    - path: ./output/qualimap/test/css/comment-bright.png
+    - path: ./output/qualimap/test/css/qualimap_logo_small.png
+    - path: ./output/qualimap/test/css/websupport.js
+      md5sum: 9e61e1e8a7433c56bd7e5a615affcf85
+    - path: ./output/qualimap/test/css/agogo.css
+      md5sum: bd757b1a7ce6fdc0288ba148680f4583
+    - path: ./output/qualimap/test/css/bgfooter.png
+    - path: ./output/qualimap/test/css/jquery.js
+      md5sum: 10092eee563dec2dca82b77d2cf5a1ae
+    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_histogram.txt
+      md5sum: b7aeda7558e9b31f027f7dc530df90b8
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt
+      md5sum: 42774c6edd6e36538acbdb6ffbd019c2
+    - path: ./output/qualimap/test/raw_data_qualimapReport/genome_fraction_coverage.txt
+      md5sum: 972a19d4846bf4e93ba32ae3dff5289c
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_histogram.txt
+      md5sum: 4e3918da81202b52395a576f99c1a50f
+    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_across_reference.txt
+    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_histogram.txt
+      md5sum: 353e74d2a6c4281686c9063de570a64d
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_across_reference.txt
+      md5sum: 9bf33149528be9a0e154e4ba7cb89420
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
+      md5sum: be36d9346a402ba580718497d5075d06
+    - path: ./output/qualimap/test/raw_data_qualimapReport/homopolymer_indels.txt
+      md5sum: b0e19fcfb60e5f039eb0986ef61ab3ed
+    - path: ./output/qualimap/test/raw_data_qualimapReport/duplication_rate_histogram.txt
+      md5sum: 76e80e4ce8d0e01bbd65f1c28f5a92e7
+    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_across_reference.txt
+      md5sum: b609d33a1f98d24aa84a04e60513cbee
+    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_clipping_profile.txt
+      md5sum: 7c86f7b225b99bc60008d7e4e55d6adb
+    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_content_per_read_position.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_gc_content_per_window.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_0to50_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_uniq_read_starts_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_across_reference.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_across_reference.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_homopolymer_indels.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_histogram.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_across_reference.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_clipping_profile.png
+    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_quotes.png
diff --git a/tests/modules/nf-core/quast/main.nf b/tests/modules/nf-core/quast/main.nf
new file mode 100644
index 00000000000..58377d43e2d
--- /dev/null
+++ b/tests/modules/nf-core/quast/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { QUAST }   from '../../../../modules/nf-core/quast/main.nf'
+
+workflow test_quast_ref {
+    fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    gff       = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+    consensus = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    use_fasta = true
+    use_gtf   = true
+
+    QUAST ( consensus, fasta, gff, use_fasta, use_gtf )
+}
+
+workflow test_quast_noref {
+    fasta     = file('fasta_dummy')
+    gff       = file('gff_dummy')
+    consensus = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    use_fasta = false
+    use_gtf   = false
+
+    QUAST ( consensus, fasta, gff, use_fasta, use_gtf )
+}
diff --git a/tests/modules/quast/nextflow.config b/tests/modules/nf-core/quast/nextflow.config
similarity index 100%
rename from tests/modules/quast/nextflow.config
rename to tests/modules/nf-core/quast/nextflow.config
diff --git a/tests/modules/nf-core/quast/test.yml b/tests/modules/nf-core/quast/test.yml
new file mode 100644
index 00000000000..542d48daa9a
--- /dev/null
+++ b/tests/modules/nf-core/quast/test.yml
@@ -0,0 +1,107 @@
+- name: quast with reference
+  command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config
+  tags:
+    - quast
+  files:
+    - path: ./output/quast/report.tsv
+    - path: ./output/quast/quast/transposed_report.txt
+      md5sum: 1dacbc04dfea073cbd74488d8b3cf821
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: 8d74e5b3d7967820b0e61acdeeee6dcb
+    - path: ./output/quast/quast/icarus.html
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: c0a0d2f998087b307f1a372ed31f5cde
+    - path: ./output/quast/quast/report.tex
+      md5sum: 881df38fdcd5ce2a7b78ac3cbfebbde1
+    - path: ./output/quast/quast/report.txt
+      md5sum: dd24fa9b6f95676006dc0928130d7d0b
+    - path: ./output/quast/quast/report.tsv
+      md5sum: f9b9f817bde917c1672a17ad1d072d6c
+    - path: ./output/quast/quast/report.html
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/quast/genome_stats/transcriptome_genomic_features_any.txt
+      md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
+    - path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
+    - path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
+    - path: ./output/quast/quast/genome_stats/genome_info.txt
+      md5sum: d0193b322079565dc78608291e9c44d1
+    - path: ./output/quast/quast/genome_stats/transcriptome_gaps.txt
+      md5sum: c52381f09ea40b6141be5232494727b6
+    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
+    - path: ./output/quast/quast/basic_stats/transcriptome_GC_content_plot.pdf
+    - path: ./output/quast/quast/basic_stats/gc.icarus.txt
+      md5sum: bdf3e7481880ee7dafbd53add5291da1
+    - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
+    - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.mis_contigs.info
+    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.unaligned.info
+      md5sum: a8505cf206bf53ca369f7e3073fee587
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
+      md5sum: d778f337899736cc62ed837b739b375c
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
+      md5sum: 8b9a6d675a41bab6bf344dde2a20a939
+    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stdout
+    - path: ./output/quast/quast/contigs_reports/all_alignments_transcriptome.tsv
+      md5sum: c247152eb82b361106492642fd796e2c
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
+      md5sum: ec1f7a1d1fb4a1b465057cf897b90b51
+    - path: ./output/quast/quast/contigs_reports/transcriptome.mis_contigs.fa
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
+      md5sum: fdb440c653e2f0306286798cacceaadb
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
+      md5sum: 81d9597314356363a6b4e0d67027345a
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
+      md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
+      md5sum: a32a09a0df811d1a75fbfe124081d1ca
+    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stderr
+    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
+      md5sum: e8e3bcb86da2cbd8eded980de80fa45c
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords.filtered
+      md5sum: ec9191d0acb5d5bce56b4842551a8598
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords
+      md5sum: dda3fc0addc41ecc0d5183dee6f95886
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.sf
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.unaligned
+    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords_tmp
+      md5sum: e5e26685b36489cbcff906fb07320cde
+    - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
+    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
+
+- name: quast without reference
+  command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_noref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config
+  tags:
+    - quast
+  files:
+    - path: ./output/quast/report.tsv
+      md5sum: 40e321250db460120563bd0449d76fe3
+    - path: ./output/quast/quast/transposed_report.txt
+      md5sum: 28d6c8051278e9fe4e2facef69329b67
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: 1cb47c314d9b0c1759375e88f7f91018
+    - path: ./output/quast/quast/icarus.html
+      md5sum: ecc0b67f3d4ff54568dfb83d8ac5911b
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: 5de57a794763ced1015c1e81eaa0b32b
+    - path: ./output/quast/quast/report.tex
+      md5sum: a2c8b9b1811fa948b0ccad1907f8d21b
+    - path: ./output/quast/quast/report.txt
+      md5sum: 97f0306d20056e0efd213de88488b895
+    - path: ./output/quast/quast/report.tsv
+      md5sum: 40e321250db460120563bd0449d76fe3
+    - path: ./output/quast/quast/report.html
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
+    - path: ./output/quast/quast/basic_stats/genome_GC_content_plot.pdf
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
diff --git a/tests/modules/nf-core/racon/main.nf b/tests/modules/nf-core/racon/main.nf
new file mode 100644
index 00000000000..416e498be99
--- /dev/null
+++ b/tests/modules/nf-core/racon/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RACON } from '../../../../modules/nf-core/racon/main.nf'
+
+workflow test_racon {
+    input = [ [ id:'test', single_end:true ], // meta map
+              file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['genome']['genome_paf'], checkIfExists: true)
+            ]
+
+    RACON ( input )
+}
\ No newline at end of file
diff --git a/tests/modules/racon/nextflow.config b/tests/modules/nf-core/racon/nextflow.config
similarity index 100%
rename from tests/modules/racon/nextflow.config
rename to tests/modules/nf-core/racon/nextflow.config
diff --git a/tests/modules/nf-core/racon/test.yml b/tests/modules/nf-core/racon/test.yml
new file mode 100644
index 00000000000..45521cc3073
--- /dev/null
+++ b/tests/modules/nf-core/racon/test.yml
@@ -0,0 +1,7 @@
+- name: racon test_racon
+  command: nextflow run ./tests/modules/nf-core/racon -entry test_racon -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/racon/nextflow.config
+  tags:
+    - racon
+  files:
+    - path: output/racon/test_assembly_consensus.fasta.gz
+      md5sum: 96a0ba94c6154f6f37b5a76a0207eb6f
diff --git a/tests/modules/nf-core/rapidnj/main.nf b/tests/modules/nf-core/rapidnj/main.nf
new file mode 100644
index 00000000000..af9caac2f95
--- /dev/null
+++ b/tests/modules/nf-core/rapidnj/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RAPIDNJ } from '../../../../modules/nf-core/rapidnj/main.nf'
+
+workflow test_rapidnj {
+    
+    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
+
+    RAPIDNJ ( input )
+}
diff --git a/tests/modules/rapidnj/nextflow.config b/tests/modules/nf-core/rapidnj/nextflow.config
similarity index 100%
rename from tests/modules/rapidnj/nextflow.config
rename to tests/modules/nf-core/rapidnj/nextflow.config
diff --git a/tests/modules/nf-core/rapidnj/test.yml b/tests/modules/nf-core/rapidnj/test.yml
new file mode 100644
index 00000000000..2372aa02154
--- /dev/null
+++ b/tests/modules/nf-core/rapidnj/test.yml
@@ -0,0 +1,9 @@
+- name: rapidnj
+  command: nextflow run ./tests/modules/nf-core/rapidnj -entry test_rapidnj -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rapidnj/nextflow.config
+  tags:
+    - rapidnj
+  files:
+    - path: output/rapidnj/alignment.sth
+      md5sum: d2e995c5dd3e3a8212a98414ae5b5de7
+    - path: output/rapidnj/rapidnj_phylogeny.tre
+      md5sum: 775909ea40138101976592cfa1814a1d
diff --git a/tests/modules/nf-core/rasusa/main.nf b/tests/modules/nf-core/rasusa/main.nf
new file mode 100644
index 00000000000..d8ffdb74d06
--- /dev/null
+++ b/tests/modules/nf-core/rasusa/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RASUSA } from '../../../../modules/nf-core/rasusa/main.nf'
+
+workflow test_rasusa {
+    input = [ [ id:'test', single_end:false], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+              ],
+              "1000000b"
+            ]
+
+    depth_cutoff = 100
+
+    RASUSA ( input, depth_cutoff )
+}
diff --git a/tests/modules/rasusa/nextflow.config b/tests/modules/nf-core/rasusa/nextflow.config
similarity index 100%
rename from tests/modules/rasusa/nextflow.config
rename to tests/modules/nf-core/rasusa/nextflow.config
diff --git a/tests/modules/nf-core/rasusa/test.yml b/tests/modules/nf-core/rasusa/test.yml
new file mode 100644
index 00000000000..df61b111198
--- /dev/null
+++ b/tests/modules/nf-core/rasusa/test.yml
@@ -0,0 +1,9 @@
+- name: rasusa test_rasusa
+  command: nextflow run ./tests/modules/nf-core/rasusa -entry test_rasusa -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rasusa/nextflow.config
+  tags:
+    - rasusa
+  files:
+    - path: output/rasusa/test_100X_1.fastq.gz
+      md5sum: b9d6f0bef1ef0c21576330d882a7edbb
+    - path: output/rasusa/test_100X_2.fastq.gz
+      md5sum: 479bc4cdce2511a9af219e6c39db8d30
diff --git a/tests/modules/nf-core/raven/main.nf b/tests/modules/nf-core/raven/main.nf
new file mode 100644
index 00000000000..d354c209583
--- /dev/null
+++ b/tests/modules/nf-core/raven/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RAVEN } from '../../../../modules/nf-core/raven/main.nf'
+
+workflow test_raven {
+    
+    input = [ 
+              [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true) ] 
+            ]
+
+    RAVEN ( input )
+}
diff --git a/tests/modules/raven/nextflow.config b/tests/modules/nf-core/raven/nextflow.config
similarity index 100%
rename from tests/modules/raven/nextflow.config
rename to tests/modules/nf-core/raven/nextflow.config
diff --git a/tests/modules/nf-core/raven/test.yml b/tests/modules/nf-core/raven/test.yml
new file mode 100644
index 00000000000..057ff3ed012
--- /dev/null
+++ b/tests/modules/nf-core/raven/test.yml
@@ -0,0 +1,9 @@
+- name: raven test_raven
+  command: nextflow run ./tests/modules/nf-core/raven -entry test_raven -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/raven/nextflow.config
+  tags:
+    - raven
+  files:
+    - path: output/raven/test.fasta.gz
+      md5sum: b026b6aba793a9f2bbfb17f732c91926
+    - path: output/raven/test.gfa.gz
+      md5sum: 09053490495f6deb7a3941e559cda626
diff --git a/tests/modules/nf-core/raxmlng/main.nf b/tests/modules/nf-core/raxmlng/main.nf
new file mode 100644
index 00000000000..78f1107fcec
--- /dev/null
+++ b/tests/modules/nf-core/raxmlng/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RAXMLNG as RAXMLNG_NO_BOOTSTRAP } from '../../../../modules/nf-core/raxmlng/main.nf'
+include { RAXMLNG as RAXMLNG_BOOTSTRAP    } from '../../../../modules/nf-core/raxmlng/main.nf'
+
+//
+// Test without bootstrapping
+//
+workflow test_raxmlng_no_bootstrap {
+
+    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
+
+    RAXMLNG_NO_BOOTSTRAP ( input )
+}
+
+//
+// Test with bootstrapping
+//
+workflow test_raxmlng_bootstrap {
+
+    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
+
+    RAXMLNG_BOOTSTRAP ( input )
+}
diff --git a/tests/modules/raxmlng/nextflow.config b/tests/modules/nf-core/raxmlng/nextflow.config
similarity index 100%
rename from tests/modules/raxmlng/nextflow.config
rename to tests/modules/nf-core/raxmlng/nextflow.config
diff --git a/tests/modules/nf-core/raxmlng/test.yml b/tests/modules/nf-core/raxmlng/test.yml
new file mode 100644
index 00000000000..cc30d8e9814
--- /dev/null
+++ b/tests/modules/nf-core/raxmlng/test.yml
@@ -0,0 +1,31 @@
+- name: raxmlng no_bootstrap
+  command: nextflow run ./tests/modules/nf-core/raxmlng -entry test_raxmlng_no_bootstrap -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/raxmlng/nextflow.config
+  tags:
+    - raxmlng
+  files:
+    - path: output/raxmlng/output.raxml.bestTree
+      contains:
+        - "sample1:0.359"
+        - "sample2:1.50"
+        - "sample3:0.000001"
+        - "sample4:0.111"
+
+- name: raxmlng bootstrap
+  command: nextflow run ./tests/modules/nf-core/raxmlng -entry test_raxmlng_bootstrap -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/raxmlng/nextflow.config
+  tags:
+    - raxmlng
+  files:
+    - path: output/raxmlng/output.raxml.bestTree
+      contains:
+        - "sample1:0.359"
+        - "sample2:1.50"
+        - "sample3:0.000001"
+        - "sample4:0.111"
+    - path: output/raxmlng/output.raxml.support
+      contains:
+        - "sample1:0.359"
+        - "sample2:1.50"
+        - "sample3:0.000001"
+        - "sample4:0.111"
+      contains_regex:
+        - '\)[89]\d:'
diff --git a/tests/modules/nf-core/rgi/main/main.nf b/tests/modules/nf-core/rgi/main/main.nf
new file mode 100644
index 00000000000..f1cd67fe5cc
--- /dev/null
+++ b/tests/modules/nf-core/rgi/main/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RGI_MAIN } from '../../../../../modules/nf-core/rgi/main/main.nf'
+
+workflow test_rgi_main {
+
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    RGI_MAIN ( input )
+}
diff --git a/tests/modules/rgi/main/nextflow.config b/tests/modules/nf-core/rgi/main/nextflow.config
similarity index 100%
rename from tests/modules/rgi/main/nextflow.config
rename to tests/modules/nf-core/rgi/main/nextflow.config
diff --git a/tests/modules/nf-core/rgi/main/test.yml b/tests/modules/nf-core/rgi/main/test.yml
new file mode 100644
index 00000000000..5564d6bba1e
--- /dev/null
+++ b/tests/modules/nf-core/rgi/main/test.yml
@@ -0,0 +1,10 @@
+- name: rgi main
+  command: nextflow run ./tests/modules/nf-core/rgi/main -entry test_rgi_main -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rgi/main/nextflow.config
+  tags:
+    - rgi
+    - rgi/main
+  files:
+    - path: output/rgi/test.json
+      contains: ["NZ_LS483480", "orf_end", "perc_identity", "Pulvomycin"]
+    - path: output/rgi/test.txt
+      contains: ["NZ_LS483480", "ORF_ID", "Model_type", "Pulvomycin"]
diff --git a/tests/modules/nf-core/rhocall/annotate/main.nf b/tests/modules/nf-core/rhocall/annotate/main.nf
new file mode 100644
index 00000000000..9dd7c01414e
--- /dev/null
+++ b/tests/modules/nf-core/rhocall/annotate/main.nf
@@ -0,0 +1,40 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RHOCALL_ANNOTATE } from '../../../../../modules/nf-core/rhocall/annotate/main.nf'
+include { BCFTOOLS_ROH } from '../../../../../modules/nf-core/bcftools/roh/main.nf'
+
+workflow test_rhocall_annotate {
+
+    input = [ [ id:'test' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+
+    af_file = [[],[]]
+    gen_map = []
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
+    RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
+
+}
+
+workflow test_rhocall_annotate_stub {
+
+    input = [ [ id:'test' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+
+    af_file = [[],[]]
+    gen_map = []
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
+    RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
+
+}
diff --git a/tests/modules/rhocall/annotate/nextflow.config b/tests/modules/nf-core/rhocall/annotate/nextflow.config
similarity index 100%
rename from tests/modules/rhocall/annotate/nextflow.config
rename to tests/modules/nf-core/rhocall/annotate/nextflow.config
diff --git a/tests/modules/nf-core/rhocall/annotate/test.yml b/tests/modules/nf-core/rhocall/annotate/test.yml
new file mode 100644
index 00000000000..e7468628fe6
--- /dev/null
+++ b/tests/modules/nf-core/rhocall/annotate/test.yml
@@ -0,0 +1,17 @@
+- name: "rhocall annotate"
+  command: nextflow run ./tests/modules/nf-core/rhocall/annotate -entry test_rhocall_annotate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rhocall/annotate/nextflow.config
+  tags:
+    - "rhocall"
+    - "rhocall/annotate"
+  files:
+    - path: "output/rhocall/test_rhocall.vcf"
+    - path: "output/rhocall/versions.yml"
+
+- name: "rhocall annotate stub"
+  command: nextflow run ./tests/modules/nf-core/rhocall/annotate -entry test_rhocall_annotate_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rhocall/annotate/nextflow.config -stub-run
+  tags:
+    - "rhocall"
+    - "rhocall/annotate"
+  files:
+    - path: "output/rhocall/test_rhocall.vcf"
+    - path: "output/rhocall/versions.yml"
diff --git a/tests/modules/nf-core/rmarkdownnotebook/main.nf b/tests/modules/nf-core/rmarkdownnotebook/main.nf
new file mode 100644
index 00000000000..6e628854bf1
--- /dev/null
+++ b/tests/modules/nf-core/rmarkdownnotebook/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RMARKDOWNNOTEBOOK } from '../../../../modules/nf-core/rmarkdownnotebook/main.nf'
+include { RMARKDOWNNOTEBOOK as RMARKDOWNNOTEBOOK_PARAMETRIZE } from '../../../../modules/nf-core/rmarkdownnotebook/main.nf'
+
+workflow test_rmarkdown {
+
+    input = [ [ id:'test_rmd' ], // meta map
+              file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) ]
+
+    RMARKDOWNNOTEBOOK ( input, [:], [])
+
+}
+
+workflow test_rmarkdown_parametrize {
+
+    input = [ [ id:'test_rmd' ], // meta map
+              file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) ]
+
+    RMARKDOWNNOTEBOOK_PARAMETRIZE(
+        input,
+        [input_filename: "hello.txt", n_iter: 12],
+        file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
+    )
+
+}
+
diff --git a/tests/modules/rmarkdownnotebook/nextflow.config b/tests/modules/nf-core/rmarkdownnotebook/nextflow.config
similarity index 100%
rename from tests/modules/rmarkdownnotebook/nextflow.config
rename to tests/modules/nf-core/rmarkdownnotebook/nextflow.config
diff --git a/tests/modules/nf-core/rmarkdownnotebook/test.yml b/tests/modules/nf-core/rmarkdownnotebook/test.yml
new file mode 100644
index 00000000000..fdf77a18fa7
--- /dev/null
+++ b/tests/modules/nf-core/rmarkdownnotebook/test.yml
@@ -0,0 +1,27 @@
+- name: rmarkdownnotebook test_rmarkdown
+  command: nextflow run ./tests/modules/nf-core/rmarkdownnotebook -entry test_rmarkdown -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rmarkdownnotebook/nextflow.config
+  tags:
+    - rmarkdownnotebook
+  files:
+    - path: output/rmarkdownnotebook/session_info.log
+      contains:
+        - R version 4.1.0
+        - yaml_2.2.1
+    - path: output/rmarkdownnotebook/test_rmd.html
+      contains:
+        - "n_iter = 10"
+
+- name: rmarkdownnotebook test_rmarkdown_parametrize
+  command: nextflow run ./tests/modules/nf-core/rmarkdownnotebook -entry test_rmarkdown_parametrize -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rmarkdownnotebook/nextflow.config
+  tags:
+    - rmarkdownnotebook
+  files:
+    - path: output/rmarkdownnotebook/artifacts/artifact.txt
+      md5sum: b10a8db164e0754105b7a99be72e3fe5
+    - path: output/rmarkdownnotebook/session_info.log
+      contains:
+        - R version 4.1.0
+        - yaml_2.2.1
+    - path: output/rmarkdownnotebook/test_rmd.html
+      contains:
+        - "n_iter = 12"
diff --git a/tests/modules/nf-core/roary/main.nf b/tests/modules/nf-core/roary/main.nf
new file mode 100644
index 00000000000..4fd915a09d7
--- /dev/null
+++ b/tests/modules/nf-core/roary/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ROARY } from '../../../../modules/nf-core/roary/main.nf'
+
+workflow test_roary {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
+        ]
+    ]
+
+    ROARY ( input )
+}
diff --git a/tests/modules/roary/nextflow.config b/tests/modules/nf-core/roary/nextflow.config
similarity index 100%
rename from tests/modules/roary/nextflow.config
rename to tests/modules/nf-core/roary/nextflow.config
diff --git a/tests/modules/nf-core/roary/test.yml b/tests/modules/nf-core/roary/test.yml
new file mode 100644
index 00000000000..ce2314bed0d
--- /dev/null
+++ b/tests/modules/nf-core/roary/test.yml
@@ -0,0 +1,39 @@
+- name: roary test_roary
+  command: nextflow run ./tests/modules/nf-core/roary -entry test_roary -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/roary/nextflow.config
+  tags:
+    - roary
+  files:
+    - path: output/roary/results/accessory.header.embl
+      contains: ["ID   Genome standard; DNA; PRO; 1234 BP."]
+    - path: output/roary/results/accessory.tab
+      contains: ["FT"]
+    - path: output/roary/results/accessory_binary_genes.fa
+      md5sum: d4191cf748dd8016ad877857a034bef3
+    - path: output/roary/results/accessory_binary_genes.fa.newick
+      md5sum: d4a2a64e781263ca1b9b3a4bc9d3a6ea
+    - path: output/roary/results/accessory_graph.dot
+      contains: ["/* list of nodes */"]
+    - path: output/roary/results/blast_identity_frequency.Rtab
+      md5sum: 829baa25c3fad94b1af207265452a692
+    - path: output/roary/results/clustered_proteins
+      contains: ["JKHLNHAL_00087"]
+    - path: output/roary/results/core_accessory.header.embl
+      contains: ["ID   Genome standard; DNA; PRO; 1234 BP."]
+    - path: output/roary/results/core_accessory.tab
+      contains: ['FT                   /taxa="test1 test2 test3"']
+    - path: output/roary/results/core_accessory_graph.dot
+      contains: ["/* list of nodes */"]
+    - path: output/roary/results/gene_presence_absence.Rtab
+      contains: ["Gene"]
+    - path: output/roary/results/gene_presence_absence.csv
+      contains: ['"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"']
+    - path: output/roary/results/number_of_conserved_genes.Rtab
+      contains: ["2"]
+    - path: output/roary/results/number_of_genes_in_pan_genome.Rtab
+      contains: ["2"]
+    - path: output/roary/results/number_of_new_genes.Rtab
+      contains: ["2"]
+    - path: output/roary/results/number_of_unique_genes.Rtab
+      contains: ["2"]
+    - path: output/roary/results/summary_statistics.txt
+      md5sum: 3921b5445df6a7ed59408119b8860a58
diff --git a/tests/modules/nf-core/rsem/calculateexpression/main.nf b/tests/modules/nf-core/rsem/calculateexpression/main.nf
new file mode 100644
index 00000000000..d4989d64423
--- /dev/null
+++ b/tests/modules/nf-core/rsem/calculateexpression/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEM_PREPAREREFERENCE    } from '../../../../../modules/nf-core/rsem/preparereference/main.nf'
+include { RSEM_CALCULATEEXPRESSION } from '../../../../../modules/nf-core/rsem/calculateexpression/main.nf'
+
+workflow test_rsem_calculateexpression {
+
+    input = [
+        [ id:'test', single_end:false, strandedness: 'forward' ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+
+    RSEM_PREPAREREFERENCE ( fasta, gtf )
+    RSEM_CALCULATEEXPRESSION( input, RSEM_PREPAREREFERENCE.out.index )
+}
diff --git a/tests/modules/rsem/calculateexpression/nextflow.config b/tests/modules/nf-core/rsem/calculateexpression/nextflow.config
similarity index 100%
rename from tests/modules/rsem/calculateexpression/nextflow.config
rename to tests/modules/nf-core/rsem/calculateexpression/nextflow.config
diff --git a/tests/modules/nf-core/rsem/calculateexpression/test.yml b/tests/modules/nf-core/rsem/calculateexpression/test.yml
new file mode 100644
index 00000000000..a3a80612130
--- /dev/null
+++ b/tests/modules/nf-core/rsem/calculateexpression/test.yml
@@ -0,0 +1,66 @@
+- name: rsem calculateexpression test_rsem_calculateexpression
+  command: nextflow run ./tests/modules/nf-core/rsem/calculateexpression -entry test_rsem_calculateexpression -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rsem/calculateexpression/nextflow.config
+  tags:
+    - rsem
+    - rsem/calculateexpression
+  files:
+    - path: output/rsem/rsem/Genome
+      md5sum: a654229fbca6071dcb6b01ce7df704da
+    - path: output/rsem/rsem/Log.out
+    - path: output/rsem/rsem/SA
+      md5sum: 8c3edc46697b72c9e92440d4cf43506c
+    - path: output/rsem/rsem/SAindex
+      md5sum: fd05c149960e72642a8d7c860528ae81
+    - path: output/rsem/rsem/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/rsem/rsem/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/rsem/rsem/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/rsem/rsem/chrStart.txt
+      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
+    - path: output/rsem/rsem/exonGeTrInfo.tab
+      md5sum: d04497f69d6ef889efd4d34fe63edcc4
+    - path: output/rsem/rsem/exonInfo.tab
+      md5sum: 0d560290fab688b7268d88d5494bf9fe
+    - path: output/rsem/rsem/geneInfo.tab
+      md5sum: 8b608537307443ffaee4927d2b428805
+    - path: output/rsem/rsem/genome.chrlist
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/rsem/rsem/genome.fasta
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/rsem/rsem/genome.grp
+      md5sum: c2848a8b6d495956c11ec53efc1de67e
+    - path: output/rsem/rsem/genome.idx.fa
+      md5sum: 050c521a2719c2ae48267c1e65218f29
+    - path: output/rsem/rsem/genome.n2g.idx.fa
+      md5sum: 050c521a2719c2ae48267c1e65218f29
+    - path: output/rsem/rsem/genome.seq
+      md5sum: 94da0c6b88c33e63c9a052a11f4f57c1
+    - path: output/rsem/rsem/genome.ti
+      md5sum: c9e4ae8d4d13a504eec2acf1b8589a66
+    - path: output/rsem/rsem/genome.transcripts.fa
+      md5sum: 050c521a2719c2ae48267c1e65218f29
+    - path: output/rsem/rsem/genomeParameters.txt
+      md5sum: df5a456e3242520cc36e0083a6a7d9dd
+    - path: output/rsem/rsem/sjdbInfo.txt
+      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
+    - path: output/rsem/rsem/sjdbList.fromGTF.out.tab
+      md5sum: 8760c33e966dad0b39f440301ebbdee4
+    - path: output/rsem/rsem/sjdbList.out.tab
+      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
+    - path: output/rsem/rsem/transcriptInfo.tab
+      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
+    - path: output/rsem/test.genes.results
+      md5sum: c7ec226f76736ea805771e73553ae359
+    - path: output/rsem/test.isoforms.results
+      md5sum: 99f7f80aa505b44ca429fdebbd7dd5d8
+    - path: output/rsem/test.log
+    - path: output/rsem/test.stat/test.cnt
+      md5sum: 76249e6b2f3c104f414aae596ba2c2f4
+    - path: output/rsem/test.stat/test.model
+      md5sum: a7a4bc1734918ef5848604e3362b83e2
+    - path: output/rsem/test.stat/test.theta
+      md5sum: de2e4490c98cc5383a86ae8225fd0a28
+    - path: output/rsem/test.transcript.bam
+      md5sum: ed681d39f5700ffc74d6321525330d93
diff --git a/tests/modules/nf-core/rsem/preparereference/main.nf b/tests/modules/nf-core/rsem/preparereference/main.nf
new file mode 100644
index 00000000000..4b1e409491e
--- /dev/null
+++ b/tests/modules/nf-core/rsem/preparereference/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEM_PREPAREREFERENCE }   from '../../../../../modules/nf-core/rsem/preparereference/main.nf'
+
+workflow test_rsem_preparereference {
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+
+    RSEM_PREPAREREFERENCE ( fasta, gtf )
+}
diff --git a/tests/modules/rsem/preparereference/nextflow.config b/tests/modules/nf-core/rsem/preparereference/nextflow.config
similarity index 100%
rename from tests/modules/rsem/preparereference/nextflow.config
rename to tests/modules/nf-core/rsem/preparereference/nextflow.config
diff --git a/tests/modules/nf-core/rsem/preparereference/test.yml b/tests/modules/nf-core/rsem/preparereference/test.yml
new file mode 100644
index 00000000000..e82a5098195
--- /dev/null
+++ b/tests/modules/nf-core/rsem/preparereference/test.yml
@@ -0,0 +1,22 @@
+- name: rsem preparereference test_rsem_preparereference
+  command: nextflow run ./tests/modules/nf-core/rsem/preparereference -entry test_rsem_preparereference -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rsem/preparereference/nextflow.config
+  tags:
+    - rsem
+    - rsem/preparereference
+  files:
+    - path: output/rsem/rsem/genome.chrlist
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/rsem/rsem/genome.fasta
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/rsem/rsem/genome.grp
+      md5sum: c2848a8b6d495956c11ec53efc1de67e
+    - path: output/rsem/rsem/genome.idx.fa
+      md5sum: 050c521a2719c2ae48267c1e65218f29
+    - path: output/rsem/rsem/genome.n2g.idx.fa
+      md5sum: 050c521a2719c2ae48267c1e65218f29
+    - path: output/rsem/rsem/genome.seq
+      md5sum: 94da0c6b88c33e63c9a052a11f4f57c1
+    - path: output/rsem/rsem/genome.ti
+      md5sum: c9e4ae8d4d13a504eec2acf1b8589a66
+    - path: output/rsem/rsem/genome.transcripts.fa
+      md5sum: 050c521a2719c2ae48267c1e65218f29
diff --git a/tests/modules/nf-core/rseqc/bamstat/main.nf b/tests/modules/nf-core/rseqc/bamstat/main.nf
new file mode 100644
index 00000000000..489d5b5cdab
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/bamstat/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_BAMSTAT }   from '../../../../../modules/nf-core/rseqc/bamstat/main.nf'
+
+workflow test_rseqc_bamstat {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    RSEQC_BAMSTAT ( input )
+}
diff --git a/tests/modules/rseqc/bamstat/nextflow.config b/tests/modules/nf-core/rseqc/bamstat/nextflow.config
similarity index 100%
rename from tests/modules/rseqc/bamstat/nextflow.config
rename to tests/modules/nf-core/rseqc/bamstat/nextflow.config
diff --git a/tests/modules/nf-core/rseqc/bamstat/test.yml b/tests/modules/nf-core/rseqc/bamstat/test.yml
new file mode 100644
index 00000000000..460dd92734b
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/bamstat/test.yml
@@ -0,0 +1,8 @@
+- name: rseqc bamstat test_rseqc_bamstat
+  command: nextflow run ./tests/modules/nf-core/rseqc/bamstat -entry test_rseqc_bamstat -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rseqc/bamstat/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/bamstat
+  files:
+    - path: output/rseqc/test.bam_stat.txt
+      md5sum: 2675857864c1d1139b2a19d25dc36b09
diff --git a/tests/modules/nf-core/rseqc/inferexperiment/main.nf b/tests/modules/nf-core/rseqc/inferexperiment/main.nf
new file mode 100644
index 00000000000..65f358107fb
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/inferexperiment/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_INFEREXPERIMENT }   from '../../../../../modules/nf-core/rseqc/inferexperiment/main.nf'
+
+workflow test_rseqc_inferexperiment {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+
+    RSEQC_INFEREXPERIMENT ( input, bed )
+}
diff --git a/tests/modules/rseqc/inferexperiment/nextflow.config b/tests/modules/nf-core/rseqc/inferexperiment/nextflow.config
similarity index 100%
rename from tests/modules/rseqc/inferexperiment/nextflow.config
rename to tests/modules/nf-core/rseqc/inferexperiment/nextflow.config
diff --git a/tests/modules/nf-core/rseqc/inferexperiment/test.yml b/tests/modules/nf-core/rseqc/inferexperiment/test.yml
new file mode 100644
index 00000000000..b033bdbaa36
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/inferexperiment/test.yml
@@ -0,0 +1,8 @@
+- name: rseqc inferexperiment test_rseqc_inferexperiment
+  command: nextflow run ./tests/modules/nf-core/rseqc/inferexperiment -entry test_rseqc_inferexperiment -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rseqc/inferexperiment/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/inferexperiment
+  files:
+    - path: output/rseqc/test.infer_experiment.txt
+      md5sum: f9d0bfc239df637cd8aeda40ade3c59a
diff --git a/tests/modules/nf-core/rseqc/innerdistance/main.nf b/tests/modules/nf-core/rseqc/innerdistance/main.nf
new file mode 100644
index 00000000000..48130d493e9
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/innerdistance/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_INNERDISTANCE }   from '../../../../../modules/nf-core/rseqc/innerdistance/main.nf'
+
+workflow test_rseqc_innerdistance {
+    input = [ [ id:'test', single_end: false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    bed = file(params.test_data['sarscov2']['genome']['test_bed12'], checkIfExists: true)
+
+    RSEQC_INNERDISTANCE ( input, bed )
+}
diff --git a/tests/modules/rseqc/innerdistance/nextflow.config b/tests/modules/nf-core/rseqc/innerdistance/nextflow.config
similarity index 100%
rename from tests/modules/rseqc/innerdistance/nextflow.config
rename to tests/modules/nf-core/rseqc/innerdistance/nextflow.config
diff --git a/tests/modules/nf-core/rseqc/innerdistance/test.yml b/tests/modules/nf-core/rseqc/innerdistance/test.yml
new file mode 100644
index 00000000000..4d5c81bca7b
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/innerdistance/test.yml
@@ -0,0 +1,15 @@
+- name: rseqc innerdistance test_rseqc_innerdistance
+  command: nextflow run ./tests/modules/nf-core/rseqc/innerdistance -entry test_rseqc_innerdistance -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rseqc/innerdistance/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/innerdistance
+  files:
+    - path: output/rseqc/test.inner_distance.txt
+      md5sum: a1acc9def0f64a5500d4c4cb47cbe32b
+    - path: output/rseqc/test.inner_distance_freq.txt
+      md5sum: 3fc037501f5899b5da009c8ce02fc25e
+    - path: output/rseqc/test.inner_distance_mean.txt
+      md5sum: 58398b7d5a29a5e564f9e3c50b55996c
+    - path: output/rseqc/test.inner_distance_plot.pdf
+    - path: output/rseqc/test.inner_distance_plot.r
+      md5sum: 5859fbd5b42046d47e8b9aa85077f4ea
diff --git a/tests/modules/nf-core/rseqc/junctionannotation/main.nf b/tests/modules/nf-core/rseqc/junctionannotation/main.nf
new file mode 100644
index 00000000000..90fbbc9660b
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/junctionannotation/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_JUNCTIONANNOTATION }   from '../../../../../modules/nf-core/rseqc/junctionannotation/main.nf'
+
+workflow test_rseqc_junctionannotation {
+    input = [ 
+        [ id:'test', single_end: false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+
+    RSEQC_JUNCTIONANNOTATION ( input, bed )
+}
diff --git a/tests/modules/rseqc/junctionannotation/nextflow.config b/tests/modules/nf-core/rseqc/junctionannotation/nextflow.config
similarity index 100%
rename from tests/modules/rseqc/junctionannotation/nextflow.config
rename to tests/modules/nf-core/rseqc/junctionannotation/nextflow.config
diff --git a/tests/modules/nf-core/rseqc/junctionannotation/test.yml b/tests/modules/nf-core/rseqc/junctionannotation/test.yml
new file mode 100644
index 00000000000..77f9924314d
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/junctionannotation/test.yml
@@ -0,0 +1,9 @@
+- name: rseqc junctionannotation test_rseqc_junctionannotation
+  command: nextflow run ./tests/modules/nf-core/rseqc/junctionannotation -entry test_rseqc_junctionannotation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rseqc/junctionannotation/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/junctionannotation
+  files:
+    - path: output/rseqc/test.junction_annotation.log
+    - path: output/rseqc/test.junction.xls
+    - path: output/rseqc/test.junction_plot.r
diff --git a/tests/modules/nf-core/rseqc/junctionsaturation/main.nf b/tests/modules/nf-core/rseqc/junctionsaturation/main.nf
new file mode 100644
index 00000000000..bcb8981c085
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/junctionsaturation/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_JUNCTIONSATURATION }   from '../../../../../modules/nf-core/rseqc/junctionsaturation/main.nf'
+
+workflow test_rseqc_junctionsaturation {
+    input = [
+        [ id:'test', single_end: false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+
+    RSEQC_JUNCTIONSATURATION ( input, bed )
+}
diff --git a/tests/modules/rseqc/junctionsaturation/nextflow.config b/tests/modules/nf-core/rseqc/junctionsaturation/nextflow.config
similarity index 100%
rename from tests/modules/rseqc/junctionsaturation/nextflow.config
rename to tests/modules/nf-core/rseqc/junctionsaturation/nextflow.config
diff --git a/tests/modules/nf-core/rseqc/junctionsaturation/test.yml b/tests/modules/nf-core/rseqc/junctionsaturation/test.yml
new file mode 100644
index 00000000000..e350cb4284a
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/junctionsaturation/test.yml
@@ -0,0 +1,9 @@
+- name: rseqc junctionsaturation test_rseqc_junctionsaturation
+  command: nextflow run ./tests/modules/nf-core/rseqc/junctionsaturation -entry test_rseqc_junctionsaturation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rseqc/junctionsaturation/nextflow.config
+  tags:
+    - rseqc/junctionsaturation
+    - rseqc
+  files:
+    - path: output/rseqc/test.junctionSaturation_plot.pdf
+    - path: output/rseqc/test.junctionSaturation_plot.r
+      md5sum: caa6e63dcb477aabb169882b2f30dadd
diff --git a/tests/modules/nf-core/rseqc/readdistribution/main.nf b/tests/modules/nf-core/rseqc/readdistribution/main.nf
new file mode 100644
index 00000000000..5bcbe38324d
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/readdistribution/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_READDISTRIBUTION }   from '../../../../../modules/nf-core/rseqc/readdistribution/main.nf'
+
+workflow test_rseqc_readdistribution {
+    input = [ [ id:'test', single_end: false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    bed = file(params.test_data['sarscov2']['genome']['test_bed12'], checkIfExists: true)
+
+    RSEQC_READDISTRIBUTION ( input, bed )
+}
diff --git a/tests/modules/rseqc/readdistribution/nextflow.config b/tests/modules/nf-core/rseqc/readdistribution/nextflow.config
similarity index 100%
rename from tests/modules/rseqc/readdistribution/nextflow.config
rename to tests/modules/nf-core/rseqc/readdistribution/nextflow.config
diff --git a/tests/modules/nf-core/rseqc/readdistribution/test.yml b/tests/modules/nf-core/rseqc/readdistribution/test.yml
new file mode 100644
index 00000000000..e84f93aee0b
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/readdistribution/test.yml
@@ -0,0 +1,8 @@
+- name: rseqc readdistribution test_rseqc_readdistribution
+  command: nextflow run ./tests/modules/nf-core/rseqc/readdistribution -entry test_rseqc_readdistribution -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rseqc/readdistribution/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/readdistribution
+  files:
+    - path: output/rseqc/test.read_distribution.txt
+      md5sum: 56893fdc0809d968629a363551a1655f
diff --git a/tests/modules/nf-core/rseqc/readduplication/main.nf b/tests/modules/nf-core/rseqc/readduplication/main.nf
new file mode 100644
index 00000000000..f641d265a0d
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/readduplication/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_READDUPLICATION }   from '../../../../../modules/nf-core/rseqc/readduplication/main.nf'
+
+workflow test_rseqc_readduplication {
+    input = [ [ id:'test', single_end: false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    RSEQC_READDUPLICATION ( input )
+}
diff --git a/tests/modules/rseqc/readduplication/nextflow.config b/tests/modules/nf-core/rseqc/readduplication/nextflow.config
similarity index 100%
rename from tests/modules/rseqc/readduplication/nextflow.config
rename to tests/modules/nf-core/rseqc/readduplication/nextflow.config
diff --git a/tests/modules/nf-core/rseqc/readduplication/test.yml b/tests/modules/nf-core/rseqc/readduplication/test.yml
new file mode 100644
index 00000000000..f5cedb7ae1a
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/readduplication/test.yml
@@ -0,0 +1,13 @@
+- name: rseqc readduplication test_rseqc_readduplication
+  command: nextflow run ./tests/modules/nf-core/rseqc/readduplication -entry test_rseqc_readduplication -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rseqc/readduplication/nextflow.config
+  tags:
+    - rseqc/readduplication
+    - rseqc
+  files:
+    - path: output/rseqc/test.DupRate_plot.pdf
+    - path: output/rseqc/test.DupRate_plot.r
+      md5sum: 3c0325095cee4835b921e57d61c23dca
+    - path: output/rseqc/test.pos.DupRate.xls
+      md5sum: a859bc2031d46bf1cc4336205847caa3
+    - path: output/rseqc/test.seq.DupRate.xls
+      md5sum: ee8783399eec5a18522a6f08bece338b
diff --git a/tests/modules/nf-core/rseqc/tin/main.nf b/tests/modules/nf-core/rseqc/tin/main.nf
new file mode 100644
index 00000000000..a91fb3e2302
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/tin/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RSEQC_TIN } from '../../../../../modules/nf-core/rseqc/tin/main.nf'
+
+workflow test_rseqc_tin {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+
+    RSEQC_TIN ( input, bed )
+}
diff --git a/tests/modules/rseqc/tin/nextflow.config b/tests/modules/nf-core/rseqc/tin/nextflow.config
similarity index 100%
rename from tests/modules/rseqc/tin/nextflow.config
rename to tests/modules/nf-core/rseqc/tin/nextflow.config
diff --git a/tests/modules/nf-core/rseqc/tin/test.yml b/tests/modules/nf-core/rseqc/tin/test.yml
new file mode 100644
index 00000000000..5303ec09cb2
--- /dev/null
+++ b/tests/modules/nf-core/rseqc/tin/test.yml
@@ -0,0 +1,10 @@
+- name: rseqc tin
+  command: nextflow run ./tests/modules/nf-core/rseqc/tin -entry test_rseqc_tin -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rseqc/tin/nextflow.config
+  tags:
+    - rseqc
+    - rseqc/tin
+  files:
+    - path: output/rseqc/test.paired_end.sorted.summary.txt
+      md5sum: 9d98447e178b89a89f6f5aba7a772fe6
+    - path: output/rseqc/test.paired_end.sorted.tin.xls
+      md5sum: 6b1b1b0dc1dc265342ba8c3f27fa60e6
diff --git a/tests/modules/nf-core/rtgtools/pedfilter/main.nf b/tests/modules/nf-core/rtgtools/pedfilter/main.nf
new file mode 100644
index 00000000000..97421523e1f
--- /dev/null
+++ b/tests/modules/nf-core/rtgtools/pedfilter/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RTGTOOLS_PEDFILTER } from '../../../../../modules/nf-core/rtgtools/pedfilter/main.nf'
+
+workflow test_rtgtools_pedfilter {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+    ]
+
+    RTGTOOLS_PEDFILTER ( input )
+}
diff --git a/tests/modules/rtgtools/pedfilter/nextflow.config b/tests/modules/nf-core/rtgtools/pedfilter/nextflow.config
similarity index 100%
rename from tests/modules/rtgtools/pedfilter/nextflow.config
rename to tests/modules/nf-core/rtgtools/pedfilter/nextflow.config
diff --git a/tests/modules/nf-core/rtgtools/pedfilter/test.yml b/tests/modules/nf-core/rtgtools/pedfilter/test.yml
new file mode 100644
index 00000000000..5817bc7b9fc
--- /dev/null
+++ b/tests/modules/nf-core/rtgtools/pedfilter/test.yml
@@ -0,0 +1,7 @@
+- name: rtgtools pedfilter test_rtgtools_pedfilter
+  command: nextflow run ./tests/modules/nf-core/rtgtools/pedfilter -entry test_rtgtools_pedfilter -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/rtgtools/pedfilter/nextflow.config
+  tags:
+    - rtgtools/pedfilter
+    - rtgtools
+  files:
+    - path: output/rtgtools/test.vcf.gz
diff --git a/tests/modules/nf-core/rtgtools/vcfeval/main.nf b/tests/modules/nf-core/rtgtools/vcfeval/main.nf
new file mode 100644
index 00000000000..df6a9850b95
--- /dev/null
+++ b/tests/modules/nf-core/rtgtools/vcfeval/main.nf
@@ -0,0 +1,69 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RTGTOOLS_VCFEVAL } from '../../../../../modules/nf-core/rtgtools/vcfeval/main.nf'
+include { UNTAR } from '../../../../modules/nf-core/untar/main.nf'
+
+workflow test_rtgtools_vcfeval {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true),        
+    ]
+
+    truth = [
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    truth_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    evaluation_regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    compressed_sdf = [
+        [],
+        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
+    ]
+
+    sdf = UNTAR( compressed_sdf ).untar
+        .map({
+            meta, folder ->
+                folder
+        })
+    
+
+    RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
+}
+
+workflow test_rtgtools_vcfeval_no_optional_inputs {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
+        [],
+    ]
+
+    truth = [
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
+        []
+    ]
+
+    truth_regions = []
+
+    evaluation_regions = []
+
+    compressed_sdf = [
+        [],
+        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
+    ]
+
+    sdf = UNTAR( compressed_sdf ).untar
+        .map({
+            meta, folder ->
+                [folder]
+        })
+
+    RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
+}
diff --git a/tests/modules/rtgtools/vcfeval/nextflow.config b/tests/modules/nf-core/rtgtools/vcfeval/nextflow.config
similarity index 100%
rename from tests/modules/rtgtools/vcfeval/nextflow.config
rename to tests/modules/nf-core/rtgtools/vcfeval/nextflow.config
diff --git a/tests/modules/nf-core/rtgtools/vcfeval/test.yml b/tests/modules/nf-core/rtgtools/vcfeval/test.yml
new file mode 100644
index 00000000000..6fcbd2c25cf
--- /dev/null
+++ b/tests/modules/nf-core/rtgtools/vcfeval/test.yml
@@ -0,0 +1,75 @@
+- name: rtgtools vcfeval test_rtgtools_vcfeval
+  command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c ./tests/config/nextflow.config
+  tags:
+    - rtgtools
+    - rtgtools/vcfeval
+  files:
+    - path: output/rtgtools/test_results/done
+    - path: output/rtgtools/test_results/fn.vcf.gz
+      md5sum: be9c9106055bfad4c5985bc0d33efd56
+    - path: output/rtgtools/test_results/fn.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test_results/fp.vcf.gz
+      md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
+    - path: output/rtgtools/test_results/fp.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test_results/non_snp_roc.tsv.gz
+      md5sum: ad5bad32c48f05aef232e2c0e708877a
+    - path: output/rtgtools/test_results/phasing.txt
+      md5sum: 133677dbd8be657439ea2b03fdfb8795
+    - path: output/rtgtools/test_results/progress
+    - path: output/rtgtools/test_results/snp_roc.tsv.gz
+      md5sum: 6785b83d66486e7e6c75c5a5b1574c09
+    - path: output/rtgtools/test_results/summary.txt
+      md5sum: f4c8df93c8bdab603036bbc27b4a28c3
+    - path: output/rtgtools/test_results/tp-baseline.vcf.gz
+      md5sum: be9c9106055bfad4c5985bc0d33efd56
+    - path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test_results/tp.vcf.gz
+      md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
+    - path: output/rtgtools/test_results/tp.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test_results/vcfeval.log
+    - path: output/rtgtools/test_results/weighted_roc.tsv.gz
+      md5sum: fa7c046ea0084172f1ef91f19de07b2b
+    - path: output/rtgtools/versions.yml
+      md5sum: 270ed7a5a8e347b251eb4aa2198f98e8
+
+- name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs
+  command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c ./tests/config/nextflow.config
+  tags:
+    - rtgtools
+    - rtgtools/vcfeval
+  files:
+    - path: output/rtgtools/test_results/done
+    - path: output/rtgtools/test_results/fn.vcf.gz
+      md5sum: c11c889a4f42c8ea325748bd768ea34d
+    - path: output/rtgtools/test_results/fn.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test_results/fp.vcf.gz
+      md5sum: 138e85c1cd79f8fea9a33e81ce0c734c
+    - path: output/rtgtools/test_results/fp.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test_results/non_snp_roc.tsv.gz
+      md5sum: 34fb78a008dfc0bef02807b8a7012b07
+    - path: output/rtgtools/test_results/phasing.txt
+      md5sum: 133677dbd8be657439ea2b03fdfb8795
+    - path: output/rtgtools/test_results/progress
+    - path: output/rtgtools/test_results/snp_roc.tsv.gz
+      md5sum: a4c5761c2653e2d04fc84c1cea13b1f0
+    - path: output/rtgtools/test_results/summary.txt
+      md5sum: f33feb32f84958fb931063044fba369b
+    - path: output/rtgtools/test_results/tp-baseline.vcf.gz
+      md5sum: d1c2d990899edf127ea5fcca8866fcb0
+    - path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
+      md5sum: 3307008fea47adb75c46d395c5567bc0
+    - path: output/rtgtools/test_results/tp.vcf.gz
+      md5sum: e35b4dab82894eee9b77c81f9bc89cca
+    - path: output/rtgtools/test_results/tp.vcf.gz.tbi
+      md5sum: 45d8f8793140944f129e728299918c88
+    - path: output/rtgtools/test_results/vcfeval.log
+    - path: output/rtgtools/test_results/weighted_roc.tsv.gz
+      md5sum: 5b8efc9e9381f604880412800f58e4e9
+    - path: output/rtgtools/versions.yml
+      md5sum: 55568e4bbe5ab7e634a1f392abb89cc4
diff --git a/tests/modules/nf-core/salmon/index/main.nf b/tests/modules/nf-core/salmon/index/main.nf
new file mode 100644
index 00000000000..4ebb83688cd
--- /dev/null
+++ b/tests/modules/nf-core/salmon/index/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SALMON_INDEX } from '../../../../../modules/nf-core/salmon/index/main.nf'
+
+workflow test_salmon_index {
+    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
+}
diff --git a/tests/modules/salmon/index/nextflow.config b/tests/modules/nf-core/salmon/index/nextflow.config
similarity index 100%
rename from tests/modules/salmon/index/nextflow.config
rename to tests/modules/nf-core/salmon/index/nextflow.config
diff --git a/tests/modules/nf-core/salmon/index/test.yml b/tests/modules/nf-core/salmon/index/test.yml
new file mode 100644
index 00000000000..f3c4fecafc5
--- /dev/null
+++ b/tests/modules/nf-core/salmon/index/test.yml
@@ -0,0 +1,31 @@
+- name: salmon index
+  command: nextflow run ./tests/modules/nf-core/salmon/index -entry test_salmon_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/salmon/index/nextflow.config
+  tags:
+    - salmon
+    - salmon/index
+  files:
+    - path: ./output/salmon/salmon/ref_indexing.log
+    - path: ./output/salmon/salmon/refseq.bin
+      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
+    - path: ./output/salmon/salmon/versionInfo.json
+      md5sum: 6c764bd219b7bc17168a99d232c0fe09
+    - path: ./output/salmon/salmon/complete_ref_lens.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/mphf.bin
+      md5sum: 53669a47610e33e031faafd32703b714
+    - path: ./output/salmon/salmon/pre_indexing.log
+    - path: ./output/salmon/salmon/ctable.bin
+    - path: ./output/salmon/salmon/duplicate_clusters.tsv
+      md5sum: 51b5292e3a874119c0e1aa566e95d70c
+    - path: ./output/salmon/salmon/reflengths.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/info.json
+      md5sum: 61ff4d3471134c280668355ddd39e99f
+    - path: ./output/salmon/salmon/refAccumLengths.bin
+      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
+    - path: ./output/salmon/salmon/ctg_offsets.bin
+      md5sum: 27a76542337df436436e66017f66dd25
+    - path: ./output/salmon/salmon/rank.bin
+      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
+    - path: ./output/salmon/salmon/pos.bin
+    - path: ./output/salmon/salmon/seq.bin
diff --git a/tests/modules/nf-core/salmon/quant/main.nf b/tests/modules/nf-core/salmon/quant/main.nf
new file mode 100644
index 00000000000..5f402193db5
--- /dev/null
+++ b/tests/modules/nf-core/salmon/quant/main.nf
@@ -0,0 +1,59 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SALMON_INDEX } from '../../../../../modules/nf-core/salmon/index/main.nf'
+include { SALMON_QUANT } from '../../../../../modules/nf-core/salmon/quant/main.nf'
+
+workflow test_salmon_quant_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    gtf              = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
+    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false, '' )
+
+}
+
+workflow test_salmon_quant_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    gtf              = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
+    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false, '' )
+
+}
+
+workflow test_salmon_quant_single_end_lib_type_A {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    gtf              = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
+    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false, 'A' )
+
+}
+
diff --git a/tests/modules/salmon/quant/nextflow.config b/tests/modules/nf-core/salmon/quant/nextflow.config
similarity index 100%
rename from tests/modules/salmon/quant/nextflow.config
rename to tests/modules/nf-core/salmon/quant/nextflow.config
diff --git a/tests/modules/nf-core/salmon/quant/test.yml b/tests/modules/nf-core/salmon/quant/test.yml
new file mode 100644
index 00000000000..ef3de792257
--- /dev/null
+++ b/tests/modules/nf-core/salmon/quant/test.yml
@@ -0,0 +1,151 @@
+- name: salmon quant single-end
+  command: nextflow run ./tests/modules/nf-core/salmon/quant -entry test_salmon_quant_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/salmon/quant/nextflow.config
+  tags:
+    - salmon
+    - salmon/quant
+  files:
+    - path: ./output/salmon/test/cmd_info.json
+    - path: ./output/salmon/test/quant.sf
+      md5sum: 687368b9963874c1797d210310b38516
+    - path: ./output/salmon/test/lib_format_counts.json
+    - path: ./output/salmon/test/quant.genes.sf
+      md5sum: af6d88f109e0d0d6a0826bdf2b3b7e97
+    - path: ./output/salmon/test/logs/salmon_quant.log
+    - path: ./output/salmon/test/aux_info/expected_bias.gz
+      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
+    - path: ./output/salmon/test/aux_info/observed_bias_3p.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/test/aux_info/meta_info.json
+    - path: ./output/salmon/test/aux_info/fld.gz
+    - path: ./output/salmon/test/aux_info/ambig_info.tsv
+      md5sum: 2ee3dc3080ad7222e0687481e7a1ee03
+    - path: ./output/salmon/test/aux_info/observed_bias.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/test/libParams/flenDist.txt
+      md5sum: 2de170bdc9f6fd237d286429b292bb28
+    - path: ./output/salmon/salmon/ref_indexing.log
+    - path: ./output/salmon/salmon/refseq.bin
+      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
+    - path: ./output/salmon/salmon/versionInfo.json
+      md5sum: 6c764bd219b7bc17168a99d232c0fe09
+    - path: ./output/salmon/salmon/complete_ref_lens.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/mphf.bin
+      md5sum: 53669a47610e33e031faafd32703b714
+    - path: ./output/salmon/salmon/pre_indexing.log
+    - path: ./output/salmon/salmon/ctable.bin
+    - path: ./output/salmon/salmon/duplicate_clusters.tsv
+      md5sum: 51b5292e3a874119c0e1aa566e95d70c
+    - path: ./output/salmon/salmon/reflengths.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/info.json
+      md5sum: 61ff4d3471134c280668355ddd39e99f
+    - path: ./output/salmon/salmon/refAccumLengths.bin
+      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
+    - path: ./output/salmon/salmon/ctg_offsets.bin
+      md5sum: 27a76542337df436436e66017f66dd25
+    - path: ./output/salmon/salmon/rank.bin
+      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
+    - path: ./output/salmon/salmon/pos.bin
+    - path: ./output/salmon/salmon/seq.bin
+
+- name: salmon quant paired end
+  command: nextflow run ./tests/modules/nf-core/salmon/quant -entry test_salmon_quant_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/salmon/quant/nextflow.config
+  tags:
+    - salmon
+    - salmon/quant
+  files:
+    - path: ./output/salmon/test/cmd_info.json
+    - path: ./output/salmon/test/quant.sf
+      md5sum: 4abd35d0a60b5279b394424f0e6ea42d
+    - path: ./output/salmon/test/lib_format_counts.json
+    - path: ./output/salmon/test/quant.genes.sf
+      md5sum: 29c8cd26f609cacd4fb88713df9c71c2
+    - path: ./output/salmon/test/logs/salmon_quant.log
+    - path: ./output/salmon/test/aux_info/expected_bias.gz
+      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
+    - path: ./output/salmon/test/aux_info/observed_bias_3p.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/test/aux_info/meta_info.json
+    - path: ./output/salmon/test/aux_info/fld.gz
+    - path: ./output/salmon/test/aux_info/ambig_info.tsv
+      md5sum: 33c0df069da554344869604ea8c18b22
+    - path: ./output/salmon/test/aux_info/observed_bias.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/test/libParams/flenDist.txt
+      md5sum: 221f754ed55dd1e34874f9b7b3f9d240
+    - path: ./output/salmon/salmon/ref_indexing.log
+    - path: ./output/salmon/salmon/refseq.bin
+      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
+    - path: ./output/salmon/salmon/versionInfo.json
+      md5sum: 6c764bd219b7bc17168a99d232c0fe09
+    - path: ./output/salmon/salmon/complete_ref_lens.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/mphf.bin
+      md5sum: 53669a47610e33e031faafd32703b714
+    - path: ./output/salmon/salmon/pre_indexing.log
+    - path: ./output/salmon/salmon/ctable.bin
+    - path: ./output/salmon/salmon/duplicate_clusters.tsv
+      md5sum: 51b5292e3a874119c0e1aa566e95d70c
+    - path: ./output/salmon/salmon/reflengths.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/info.json
+      md5sum: 61ff4d3471134c280668355ddd39e99f
+    - path: ./output/salmon/salmon/refAccumLengths.bin
+      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
+    - path: ./output/salmon/salmon/ctg_offsets.bin
+      md5sum: 27a76542337df436436e66017f66dd25
+
+    - path: ./output/salmon/salmon/rank.bin
+      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
+    - path: ./output/salmon/salmon/pos.bin
+    - path: ./output/salmon/salmon/seq.bin
+
+- name: salmon quant test_salmon_quant_single_end_lib_type_A
+  command: nextflow run ./tests/modules/nf-core/salmon/quant -entry test_salmon_quant_single_end_lib_type_A -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/salmon/quant/nextflow.config
+  tags:
+    - salmon/quant
+    - salmon
+  files:
+    - path: ./output/salmon/test/cmd_info.json
+    - path: output/salmon/test/quant.sf
+      md5sum: 687368b9963874c1797d210310b38516
+    - path: ./output/salmon/test/lib_format_counts.json
+    - path: ./output/salmon/test/quant.genes.sf
+      md5sum: af6d88f109e0d0d6a0826bdf2b3b7e97
+    - path: ./output/salmon/test/logs/salmon_quant.log
+    - path: output/salmon/test/aux_info/expected_bias.gz
+      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
+    - path: output/salmon/test/aux_info/observed_bias_3p.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/test/aux_info/meta_info.json
+    - path: ./output/salmon/test/aux_info/fld.gz
+    - path: output/salmon/test/aux_info/ambig_info.tsv
+      md5sum: 2ee3dc3080ad7222e0687481e7a1ee03
+    - path: ./output/salmon/test/aux_info/observed_bias.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: output/salmon/test/libParams/flenDist.txt
+      md5sum: 2de170bdc9f6fd237d286429b292bb28
+    - path: ./output/salmon/salmon/ref_indexing.log
+    - path: output/salmon/salmon/refseq.bin
+      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
+    - path: output/salmon/salmon/versionInfo.json
+      md5sum: 6c764bd219b7bc17168a99d232c0fe09
+    - path: output/salmon/salmon/complete_ref_lens.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: output/salmon/salmon/mphf.bin
+      md5sum: 53669a47610e33e031faafd32703b714
+    - path: output/salmon/salmon/duplicate_clusters.tsv
+      md5sum: 51b5292e3a874119c0e1aa566e95d70c
+    - path: output/salmon/salmon/reflengths.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: output/salmon/salmon/info.json
+      md5sum: 61ff4d3471134c280668355ddd39e99f
+    - path: output/salmon/salmon/refAccumLengths.bin
+      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
+    - path: output/salmon/salmon/ctg_offsets.bin
+      md5sum: 27a76542337df436436e66017f66dd25
+    - path: output/salmon/salmon/rank.bin
+      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
+    - path: ./output/salmon/salmon/pos.bin
+    - path: ./output/salmon/salmon/seq.bin
diff --git a/tests/modules/nf-core/samblaster/main.nf b/tests/modules/nf-core/samblaster/main.nf
new file mode 100644
index 00000000000..2e54aefe862
--- /dev/null
+++ b/tests/modules/nf-core/samblaster/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMBLASTER } from '../../../../modules/nf-core/samblaster/main.nf'
+
+workflow test_samblaster {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_unsorted_bam'], checkIfExists: true) ]
+
+    SAMBLASTER ( input )
+}
diff --git a/tests/modules/samblaster/nextflow.config b/tests/modules/nf-core/samblaster/nextflow.config
similarity index 100%
rename from tests/modules/samblaster/nextflow.config
rename to tests/modules/nf-core/samblaster/nextflow.config
diff --git a/tests/modules/nf-core/samblaster/test.yml b/tests/modules/nf-core/samblaster/test.yml
new file mode 100644
index 00000000000..9a4b5cc2111
--- /dev/null
+++ b/tests/modules/nf-core/samblaster/test.yml
@@ -0,0 +1,7 @@
+- name: samblaster test_samblaster
+  command: nextflow run ./tests/modules/nf-core/samblaster -entry test_samblaster -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samblaster/nextflow.config
+  tags:
+    - samblaster
+  files:
+    - path: output/samblaster/test.processed.bam
+      md5sum: 3009528be9f69e7fc8951921583b0016
diff --git a/tests/modules/nf-core/samtools/ampliconclip/main.nf b/tests/modules/nf-core/samtools/ampliconclip/main.nf
new file mode 100644
index 00000000000..9f571ad6f1c
--- /dev/null
+++ b/tests/modules/nf-core/samtools/ampliconclip/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_AMPLICONCLIP } from '../../../../../modules/nf-core/samtools/ampliconclip/main.nf'
+
+workflow test_samtools_ampliconclip_no_stats_no_rejects {
+
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    save_cliprejects = false
+    save_clipstats   = false
+
+    SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
+}
+
+workflow test_samtools_ampliconclip_no_stats_with_rejects {
+
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    save_cliprejects = true
+    save_clipstats   = false
+
+    SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
+}
+
+workflow test_samtools_ampliconclip_with_stats_with_rejects {
+
+    input = [ 
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    save_cliprejects = true
+    save_clipstats   = true
+
+    SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
+}
diff --git a/tests/modules/samtools/ampliconclip/nextflow.config b/tests/modules/nf-core/samtools/ampliconclip/nextflow.config
similarity index 100%
rename from tests/modules/samtools/ampliconclip/nextflow.config
rename to tests/modules/nf-core/samtools/ampliconclip/nextflow.config
diff --git a/tests/modules/nf-core/samtools/ampliconclip/test.yml b/tests/modules/nf-core/samtools/ampliconclip/test.yml
new file mode 100644
index 00000000000..add1215e5db
--- /dev/null
+++ b/tests/modules/nf-core/samtools/ampliconclip/test.yml
@@ -0,0 +1,32 @@
+- name: samtools ampliconclip no stats no rejects
+  command: nextflow run ./tests/modules/nf-core/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_no_rejects -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/ampliconclip/nextflow.config
+  tags:
+    - samtools
+    - samtools/ampliconclip
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 69e4ba713447864231f6cbbaf036c51d
+
+- name: samtools ampliconclip no stats with rejects
+  command: nextflow run ./tests/modules/nf-core/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/ampliconclip/nextflow.config
+  tags:
+    - samtools
+    - samtools/ampliconclip
+  files:
+    - path: output/samtools/test.bam
+      md5sum: dd2ed9d7cc4ddc070ece2dccc577f94b
+    - path: output/samtools/test.cliprejects.bam
+      md5sum: 7d641f6da838f41d75eaabbd897f60bd
+
+- name: samtools ampliconclip with stats with rejects
+  command: nextflow run ./tests/modules/nf-core/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/ampliconclip/nextflow.config
+  tags:
+    - samtools
+    - samtools/ampliconclip
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 6c19afc0873fba2f4e530eabf61c0735
+    - path: output/samtools/test.cliprejects.bam
+      md5sum: 1dfb61aa80d8e90add324ed61ed17061
+    - path: output/samtools/test.clipstats.txt
+      md5sum: 05ead360a98fab6a678056e326c4f1f3
diff --git a/tests/modules/nf-core/samtools/bam2fq/main.nf b/tests/modules/nf-core/samtools/bam2fq/main.nf
new file mode 100644
index 00000000000..847e6cf6723
--- /dev/null
+++ b/tests/modules/nf-core/samtools/bam2fq/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_BAM2FQ } from '../../../../../modules/nf-core/samtools/bam2fq/main.nf'
+
+workflow test_samtools_bam2fq_nosplit {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_converted_bam'], checkIfExists: true) ]
+    split = false
+
+    SAMTOOLS_BAM2FQ ( input, split )
+}
+
+
+workflow test_samtools_bam2fq_withsplit {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_converted_bam'], checkIfExists: true) ]
+    split = true
+
+    SAMTOOLS_BAM2FQ ( input, split )
+}
diff --git a/tests/modules/samtools/bam2fq/nextflow.config b/tests/modules/nf-core/samtools/bam2fq/nextflow.config
similarity index 100%
rename from tests/modules/samtools/bam2fq/nextflow.config
rename to tests/modules/nf-core/samtools/bam2fq/nextflow.config
diff --git a/tests/modules/nf-core/samtools/bam2fq/test.yml b/tests/modules/nf-core/samtools/bam2fq/test.yml
new file mode 100644
index 00000000000..ab06fd3c8ca
--- /dev/null
+++ b/tests/modules/nf-core/samtools/bam2fq/test.yml
@@ -0,0 +1,26 @@
+- name: samtools bam2fq test_samtools_bam2fq_nosplit
+  command: nextflow run ./tests/modules/nf-core/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c ./tests/config/nextflow.config
+  tags:
+    - samtools/bam2fq
+    - samtools
+  files:
+    - path: output/samtools/test_interleaved.fq.gz
+    - path: output/samtools/versions.yml
+      md5sum: 4973eac1b6a8f090d5fcd4456d65a894
+
+- name: samtools bam2fq test_samtools_bam2fq_withsplit
+  command: nextflow run ./tests/modules/nf-core/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c ./tests/config/nextflow.config
+  tags:
+    - samtools/bam2fq
+    - samtools
+  files:
+    - path: output/samtools/test_1.fq.gz
+      md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed
+    - path: output/samtools/test_2.fq.gz
+      md5sum: e679ec035d3208785e704458d6b68c8c
+    - path: output/samtools/test_other.fq.gz
+      md5sum: 709872fc2910431b1e8b7074bfe38c67
+    - path: output/samtools/test_singleton.fq.gz
+      md5sum: 709872fc2910431b1e8b7074bfe38c67
+    - path: output/samtools/versions.yml
+      md5sum: e92d21bbcda2fed7cb438d95c51edff0
diff --git a/tests/modules/nf-core/samtools/collate/main.nf b/tests/modules/nf-core/samtools/collate/main.nf
new file mode 100644
index 00000000000..9e3e8805c71
--- /dev/null
+++ b/tests/modules/nf-core/samtools/collate/main.nf
@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_COLLATE } from '../../../../../modules/nf-core/samtools/collate/main.nf'
+
+workflow test_samtools_collate {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    SAMTOOLS_COLLATE ( input, [] )
+}
+
+workflow test_samtools_collate_cram {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    SAMTOOLS_COLLATE ( input, fasta )
+}
diff --git a/tests/modules/samtools/collate/nextflow.config b/tests/modules/nf-core/samtools/collate/nextflow.config
similarity index 100%
rename from tests/modules/samtools/collate/nextflow.config
rename to tests/modules/nf-core/samtools/collate/nextflow.config
diff --git a/tests/modules/nf-core/samtools/collate/test.yml b/tests/modules/nf-core/samtools/collate/test.yml
new file mode 100644
index 00000000000..b2fb9ee28b0
--- /dev/null
+++ b/tests/modules/nf-core/samtools/collate/test.yml
@@ -0,0 +1,17 @@
+- name: samtools collate test_samtools_collate
+  command: nextflow run ./tests/modules/nf-core/samtools/collate -entry test_samtools_collate -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/collate/nextflow.config
+  tags:
+    - samtools/collate
+    - samtools
+  files:
+    - path: output/samtools/test.bam
+      md5sum: dbb8244c28778a970e49577731b158df
+
+- name: samtools collate test_samtools_collate_cram
+  command: nextflow run ./tests/modules/nf-core/samtools/collate -entry test_samtools_collate_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/collate/nextflow.config
+  tags:
+    - samtools/collate
+    - samtools
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 81aa61ed1f6f3bf6b9c94f70cbf2a177
diff --git a/tests/modules/nf-core/samtools/collatefastq/main.nf b/tests/modules/nf-core/samtools/collatefastq/main.nf
new file mode 100644
index 00000000000..57c732a6ff2
--- /dev/null
+++ b/tests/modules/nf-core/samtools/collatefastq/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_COLLATEFASTQ } from '../../../../../modules/nf-core/samtools/collatefastq/main.nf'
+
+workflow test_samtools_collatefastq {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_COLLATEFASTQ ( input )
+}
diff --git a/tests/modules/samtools/collatefastq/nextflow.config b/tests/modules/nf-core/samtools/collatefastq/nextflow.config
similarity index 100%
rename from tests/modules/samtools/collatefastq/nextflow.config
rename to tests/modules/nf-core/samtools/collatefastq/nextflow.config
diff --git a/tests/modules/nf-core/samtools/collatefastq/test.yml b/tests/modules/nf-core/samtools/collatefastq/test.yml
new file mode 100644
index 00000000000..8e529fa4f01
--- /dev/null
+++ b/tests/modules/nf-core/samtools/collatefastq/test.yml
@@ -0,0 +1,14 @@
+- name: samtools fastq test_samtools_collatefastq
+  command: nextflow run ./tests/modules/nf-core/samtools/collatefastq -entry test_samtools_collatefastq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/collatefastq/nextflow.config
+  tags:
+    - samtools
+    - samtools/collatefastq
+  files:
+    - path: output/samtools/test_1.fq.gz
+      md5sum: 829732de4e937edca90f27b07e5b501a
+    - path: output/samtools/test_2.fq.gz
+      md5sum: ef27d3809e495620fd93df894280c03a
+    - path: output/samtools/test_other.fq.gz
+      md5sum: 709872fc2910431b1e8b7074bfe38c67
+    - path: output/samtools/test_singleton.fq.gz
+      md5sum: 709872fc2910431b1e8b7074bfe38c67
diff --git a/tests/modules/nf-core/samtools/convert/main.nf b/tests/modules/nf-core/samtools/convert/main.nf
new file mode 100644
index 00000000000..38b00b96d05
--- /dev/null
+++ b/tests/modules/nf-core/samtools/convert/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../../modules/nf-core/samtools/convert/main.nf'
+include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../../modules/nf-core/samtools/convert/main.nf'
+
+workflow test_samtools_convert_bamtocram {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
+}
+
+workflow test_samtools_convert_cramtobam {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    SAMTOOLS_CRAMTOBAM ( input, fasta, fai )
+}
diff --git a/tests/modules/samtools/convert/nextflow.config b/tests/modules/nf-core/samtools/convert/nextflow.config
similarity index 100%
rename from tests/modules/samtools/convert/nextflow.config
rename to tests/modules/nf-core/samtools/convert/nextflow.config
diff --git a/tests/modules/nf-core/samtools/convert/test.yml b/tests/modules/nf-core/samtools/convert/test.yml
new file mode 100644
index 00000000000..aa0750b5670
--- /dev/null
+++ b/tests/modules/nf-core/samtools/convert/test.yml
@@ -0,0 +1,21 @@
+- name: samtools convert test_samtools_convert_bamtocram
+  command: nextflow run ./tests/modules/nf-core/samtools/convert -entry test_samtools_convert_bamtocram -c ./tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/convert
+  files:
+    - path: output/samtools/test.cram
+    - path: output/samtools/test.cram.crai
+    - path: output/samtools/versions.yml
+
+- name: samtools convert test_samtools_convert_cramtobam
+  command: nextflow run ./tests/modules/nf-core/samtools/convert -entry test_samtools_convert_cramtobam -c ./tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/convert
+  files:
+    - path: output/samtools/test.bam
+      md5sum: c262b6dc15f9b480bdb47d6d018b4b56
+    - path: output/samtools/test.bam.bai
+      md5sum: 6e8f5034f728401bfa841c8e70c62463
+    - path: output/samtools/versions.yml
diff --git a/tests/modules/nf-core/samtools/depth/main.nf b/tests/modules/nf-core/samtools/depth/main.nf
new file mode 100644
index 00000000000..23dae538463
--- /dev/null
+++ b/tests/modules/nf-core/samtools/depth/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_DEPTH } from '../../../../../modules/nf-core/samtools/depth/main.nf'
+
+workflow test_samtools_depth {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) ]
+
+    SAMTOOLS_DEPTH ( input )
+}
diff --git a/tests/modules/samtools/depth/nextflow.config b/tests/modules/nf-core/samtools/depth/nextflow.config
similarity index 100%
rename from tests/modules/samtools/depth/nextflow.config
rename to tests/modules/nf-core/samtools/depth/nextflow.config
diff --git a/tests/modules/nf-core/samtools/depth/test.yml b/tests/modules/nf-core/samtools/depth/test.yml
new file mode 100644
index 00000000000..419cf022a5d
--- /dev/null
+++ b/tests/modules/nf-core/samtools/depth/test.yml
@@ -0,0 +1,8 @@
+- name: samtools depth
+  command: nextflow run ./tests/modules/nf-core/samtools/depth -entry test_samtools_depth -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/depth/nextflow.config
+  tags:
+    - samtools/depth
+    - samtools
+  files:
+    - path: output/samtools/test.tsv
+      md5sum: aa27ebf69663ebded553b4d6538219d9
diff --git a/tests/modules/nf-core/samtools/dict/main.nf b/tests/modules/nf-core/samtools/dict/main.nf
new file mode 100644
index 00000000000..7bac114a4f1
--- /dev/null
+++ b/tests/modules/nf-core/samtools/dict/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_DICT } from '../../../../../modules/nf-core/samtools/dict/main.nf'
+
+workflow test_samtools_dict {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    SAMTOOLS_DICT ( input )
+}
diff --git a/tests/modules/samtools/dict/nextflow.config b/tests/modules/nf-core/samtools/dict/nextflow.config
similarity index 100%
rename from tests/modules/samtools/dict/nextflow.config
rename to tests/modules/nf-core/samtools/dict/nextflow.config
diff --git a/tests/modules/nf-core/samtools/dict/test.yml b/tests/modules/nf-core/samtools/dict/test.yml
new file mode 100644
index 00000000000..388b2bc0216
--- /dev/null
+++ b/tests/modules/nf-core/samtools/dict/test.yml
@@ -0,0 +1,13 @@
+- name: samtools dict test_samtools_dict
+  command: nextflow run ./tests/modules/nf-core/samtools/dict -entry test_samtools_dict -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/dict/nextflow.config
+  tags:
+    - samtools
+    - samtools/dict
+  files:
+    - path: output/samtools/genome.fasta.dict
+      contains:
+        - "SN:MT192765.1"
+        - "LN:29829"
+        - "M5:c95f3e5592d0ad9974e41e7f0ea14eb0"
+    - path: output/samtools/versions.yml
+      md5sum: 12cd0c5ce466eefb2dff72625ecbe5c2
diff --git a/tests/modules/nf-core/samtools/faidx/main.nf b/tests/modules/nf-core/samtools/faidx/main.nf
new file mode 100644
index 00000000000..e07229915db
--- /dev/null
+++ b/tests/modules/nf-core/samtools/faidx/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_FAIDX } from '../../../../../modules/nf-core/samtools/faidx/main.nf'
+
+workflow test_samtools_faidx {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    SAMTOOLS_FAIDX ( input )
+}
+
+workflow test_samtools_faidx_bgzip {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) ]
+
+    SAMTOOLS_FAIDX ( input )
+}
diff --git a/tests/modules/samtools/faidx/nextflow.config b/tests/modules/nf-core/samtools/faidx/nextflow.config
similarity index 100%
rename from tests/modules/samtools/faidx/nextflow.config
rename to tests/modules/nf-core/samtools/faidx/nextflow.config
diff --git a/tests/modules/nf-core/samtools/faidx/test.yml b/tests/modules/nf-core/samtools/faidx/test.yml
new file mode 100644
index 00000000000..7ad833de740
--- /dev/null
+++ b/tests/modules/nf-core/samtools/faidx/test.yml
@@ -0,0 +1,20 @@
+- name: samtools faidx test_samtools_faidx
+  command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx -c ./tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/faidx
+  files:
+    - path: output/samtools/genome.fasta.fai
+      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
+    - path: output/samtools/versions.yml
+- name: samtools faidx test_samtools_faidx_bgzip
+  command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx_bgzip -c ./tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/faidx
+  files:
+    - path: output/samtools/genome.fasta.gz.fai
+      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
+    - path: output/samtools/genome.fasta.gz.gzi
+      md5sum: 7dea362b3fac8e00956a4952a3d4f474
+    - path: output/samtools/versions.yml
diff --git a/tests/modules/nf-core/samtools/fasta/main.nf b/tests/modules/nf-core/samtools/fasta/main.nf
new file mode 100644
index 00000000000..f477209bcf1
--- /dev/null
+++ b/tests/modules/nf-core/samtools/fasta/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_FASTA } from '../../../../../modules/nf-core/samtools/fasta/main.nf'
+
+workflow test_samtools_fasta {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    SAMTOOLS_FASTA ( input )
+}
diff --git a/tests/modules/samtools/fasta/nextflow.config b/tests/modules/nf-core/samtools/fasta/nextflow.config
similarity index 100%
rename from tests/modules/samtools/fasta/nextflow.config
rename to tests/modules/nf-core/samtools/fasta/nextflow.config
diff --git a/tests/modules/nf-core/samtools/fasta/test.yml b/tests/modules/nf-core/samtools/fasta/test.yml
new file mode 100644
index 00000000000..22282bcab76
--- /dev/null
+++ b/tests/modules/nf-core/samtools/fasta/test.yml
@@ -0,0 +1,10 @@
+- name: samtools fasta test_samtools_fasta
+  command: nextflow run ./tests/modules/nf-core/samtools/fasta -entry test_samtools_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/fasta/nextflow.config
+  tags:
+    - samtools
+    - samtools/fasta
+  files:
+    - path: output/samtools/test_1.fasta.gz
+      md5sum: 3abd682290bc7c75f1ce2b80db995237
+    - path: output/samtools/test_2.fasta.gz
+      md5sum: 6ada09ce66f68b8732985e14aac1bf1f
diff --git a/tests/modules/nf-core/samtools/fastq/main.nf b/tests/modules/nf-core/samtools/fastq/main.nf
new file mode 100644
index 00000000000..b7997101d63
--- /dev/null
+++ b/tests/modules/nf-core/samtools/fastq/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_FASTQ } from '../../../../../modules/nf-core/samtools/fastq/main.nf'
+
+workflow test_samtools_fastq {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_FASTQ ( input )
+}
diff --git a/tests/modules/samtools/fastq/nextflow.config b/tests/modules/nf-core/samtools/fastq/nextflow.config
similarity index 100%
rename from tests/modules/samtools/fastq/nextflow.config
rename to tests/modules/nf-core/samtools/fastq/nextflow.config
diff --git a/tests/modules/nf-core/samtools/fastq/test.yml b/tests/modules/nf-core/samtools/fastq/test.yml
new file mode 100644
index 00000000000..9ae83c63d46
--- /dev/null
+++ b/tests/modules/nf-core/samtools/fastq/test.yml
@@ -0,0 +1,10 @@
+- name: samtools fastq test_samtools_fastq
+  command: nextflow run ./tests/modules/nf-core/samtools/fastq -entry test_samtools_fastq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/fastq/nextflow.config
+  tags:
+    - samtools
+    - samtools/fastq
+  files:
+    - path: output/samtools/test_2.fastq.gz
+      md5sum: 51e7a469b554de694799bec982fd722e
+    - path: output/samtools/test_1.fastq.gz
+      md5sum: 6c2d5b467eb94e058300271a542e34e6
diff --git a/tests/modules/nf-core/samtools/fixmate/main.nf b/tests/modules/nf-core/samtools/fixmate/main.nf
new file mode 100644
index 00000000000..e2a1725f5a4
--- /dev/null
+++ b/tests/modules/nf-core/samtools/fixmate/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_FIXMATE } from '../../../../../modules/nf-core/samtools/fixmate/main.nf'
+
+workflow test_samtools_fixmate {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+
+    SAMTOOLS_FIXMATE ( input )
+
+}
diff --git a/tests/modules/samtools/fixmate/nextflow.config b/tests/modules/nf-core/samtools/fixmate/nextflow.config
similarity index 100%
rename from tests/modules/samtools/fixmate/nextflow.config
rename to tests/modules/nf-core/samtools/fixmate/nextflow.config
diff --git a/tests/modules/nf-core/samtools/fixmate/test.yml b/tests/modules/nf-core/samtools/fixmate/test.yml
new file mode 100644
index 00000000000..c7c05c10a78
--- /dev/null
+++ b/tests/modules/nf-core/samtools/fixmate/test.yml
@@ -0,0 +1,8 @@
+- name: samtools fixmate test_samtools_fixmate
+  command: nextflow run ./tests/modules/nf-core/samtools/fixmate -entry test_samtools_fixmate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/fixmate/nextflow.config
+  tags:
+    - samtools
+    - samtools/fixmate
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 13805ea1a9212496a8cb4ce395b25119
diff --git a/tests/modules/nf-core/samtools/flagstat/main.nf b/tests/modules/nf-core/samtools/flagstat/main.nf
new file mode 100644
index 00000000000..c1a435f02a7
--- /dev/null
+++ b/tests/modules/nf-core/samtools/flagstat/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_FLAGSTAT } from '../../../../../modules/nf-core/samtools/flagstat/main.nf'
+
+workflow test_samtools_flagstat {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    SAMTOOLS_FLAGSTAT ( input )
+}
diff --git a/tests/modules/samtools/flagstat/nextflow.config b/tests/modules/nf-core/samtools/flagstat/nextflow.config
similarity index 100%
rename from tests/modules/samtools/flagstat/nextflow.config
rename to tests/modules/nf-core/samtools/flagstat/nextflow.config
diff --git a/tests/modules/nf-core/samtools/flagstat/test.yml b/tests/modules/nf-core/samtools/flagstat/test.yml
new file mode 100644
index 00000000000..ad58ad5dc62
--- /dev/null
+++ b/tests/modules/nf-core/samtools/flagstat/test.yml
@@ -0,0 +1,8 @@
+- name: samtools flagstat test_samtools_flagstat
+  command: nextflow run ./tests/modules/nf-core/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/flagstat/nextflow.config
+  tags:
+    - samtools/flagstat
+    - samtools
+  files:
+    - path: output/samtools/test.flagstat
+      md5sum: 4f7ffd1e6a5e85524d443209ac97d783
diff --git a/tests/modules/nf-core/samtools/getrg/main.nf b/tests/modules/nf-core/samtools/getrg/main.nf
new file mode 100644
index 00000000000..19403d2f124
--- /dev/null
+++ b/tests/modules/nf-core/samtools/getrg/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_GETRG } from '../../../../../modules/nf-core/samtools/getrg/main.nf'
+
+workflow test_samtools_getrg {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    SAMTOOLS_GETRG ( input )
+}
diff --git a/tests/modules/samtools/getrg/nextflow.config b/tests/modules/nf-core/samtools/getrg/nextflow.config
similarity index 100%
rename from tests/modules/samtools/getrg/nextflow.config
rename to tests/modules/nf-core/samtools/getrg/nextflow.config
diff --git a/tests/modules/nf-core/samtools/getrg/test.yml b/tests/modules/nf-core/samtools/getrg/test.yml
new file mode 100644
index 00000000000..272054a385b
--- /dev/null
+++ b/tests/modules/nf-core/samtools/getrg/test.yml
@@ -0,0 +1,8 @@
+- name: samtools getrg test_samtools_getrg
+  command: nextflow run ./tests/modules/nf-core/samtools/getrg -entry test_samtools_getrg -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/getrg/nextflow.config
+  tags:
+    - samtools/getrg
+    - samtools
+  files:
+    - path: output/samtools/readgroups.txt
+      md5sum: 7b1d2d10a82a0c4fa6b22673559e41f6
diff --git a/tests/modules/nf-core/samtools/idxstats/main.nf b/tests/modules/nf-core/samtools/idxstats/main.nf
new file mode 100644
index 00000000000..4a29252eb3b
--- /dev/null
+++ b/tests/modules/nf-core/samtools/idxstats/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_IDXSTATS } from '../../../../../modules/nf-core/samtools/idxstats/main.nf'
+
+workflow test_samtools_idxstats {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_IDXSTATS ( input )
+}
diff --git a/tests/modules/samtools/idxstats/nextflow.config b/tests/modules/nf-core/samtools/idxstats/nextflow.config
similarity index 100%
rename from tests/modules/samtools/idxstats/nextflow.config
rename to tests/modules/nf-core/samtools/idxstats/nextflow.config
diff --git a/tests/modules/nf-core/samtools/idxstats/test.yml b/tests/modules/nf-core/samtools/idxstats/test.yml
new file mode 100644
index 00000000000..8c596c21bb0
--- /dev/null
+++ b/tests/modules/nf-core/samtools/idxstats/test.yml
@@ -0,0 +1,8 @@
+- name: samtools idxstats test_samtools_idxstats
+  command: nextflow run ./tests/modules/nf-core/samtools/idxstats -entry test_samtools_idxstats -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/idxstats/nextflow.config
+  tags:
+    - samtools/idxstats
+    - samtools
+  files:
+    - path: output/samtools/test.idxstats
+      md5sum: df60a8c8d6621100d05178c93fb053a2
diff --git a/tests/modules/nf-core/samtools/index/main.nf b/tests/modules/nf-core/samtools/index/main.nf
new file mode 100644
index 00000000000..880f44f3308
--- /dev/null
+++ b/tests/modules/nf-core/samtools/index/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI  } from '../../../../../modules/nf-core/samtools/index/main.nf'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../../modules/nf-core/samtools/index/main.nf'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI  } from '../../../../../modules/nf-core/samtools/index/main.nf'
+
+workflow test_samtools_index_bai {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_INDEX_BAI ( input )
+}
+
+workflow test_samtools_index_crai {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_INDEX_CRAI ( input )
+}
+
+workflow test_samtools_index_csi {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_INDEX_CSI ( input )
+}
diff --git a/tests/modules/samtools/index/nextflow.config b/tests/modules/nf-core/samtools/index/nextflow.config
similarity index 100%
rename from tests/modules/samtools/index/nextflow.config
rename to tests/modules/nf-core/samtools/index/nextflow.config
diff --git a/tests/modules/nf-core/samtools/index/test.yml b/tests/modules/nf-core/samtools/index/test.yml
new file mode 100644
index 00000000000..496a301c6cd
--- /dev/null
+++ b/tests/modules/nf-core/samtools/index/test.yml
@@ -0,0 +1,26 @@
+- name: samtools index test_samtools_index_bai
+  command: nextflow run ./tests/modules/nf-core/samtools/index -entry test_samtools_index_bai -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/index/nextflow.config
+  tags:
+    - samtools
+    - samtools/index
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.bai
+      md5sum: 704c10dd1326482448ca3073fdebc2f4
+
+- name: samtools index test_samtools_index_crai
+  command: nextflow run ./tests/modules/nf-core/samtools/index -entry test_samtools_index_crai -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/index/nextflow.config
+  tags:
+    - samtools
+    - samtools/index
+  files:
+    - path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai
+      md5sum: 14bc3bd5c89cacc8f4541f9062429029
+
+- name: samtools index test_samtools_index_csi
+  command: nextflow run ./tests/modules/nf-core/samtools/index -entry test_samtools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/index/nextflow.config
+  tags:
+    - samtools
+    - samtools/index
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.csi
+      md5sum: 8d63373007553e74d823fc2b9cbcf84d
diff --git a/tests/modules/nf-core/samtools/markdup/main.nf b/tests/modules/nf-core/samtools/markdup/main.nf
new file mode 100644
index 00000000000..6d8cb99394b
--- /dev/null
+++ b/tests/modules/nf-core/samtools/markdup/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_COLLATE } from '../../../../../modules/nf-core/samtools/collate/main.nf'
+include { SAMTOOLS_FIXMATE } from '../../../../../modules/nf-core/samtools/fixmate/main.nf'
+include { SAMTOOLS_SORT    } from '../../../../../modules/nf-core/samtools/sort/main.nf'
+include { SAMTOOLS_MARKDUP } from '../../../../../modules/nf-core/samtools/markdup/main.nf'
+
+workflow test_samtools_markdup {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    SAMTOOLS_COLLATE ( input, [] )
+    SAMTOOLS_FIXMATE ( SAMTOOLS_COLLATE.out.bam )
+    SAMTOOLS_SORT ( SAMTOOLS_FIXMATE.out.bam )
+    SAMTOOLS_MARKDUP ( SAMTOOLS_SORT.out.bam, [] )
+
+}
diff --git a/tests/modules/samtools/markdup/nextflow.config b/tests/modules/nf-core/samtools/markdup/nextflow.config
similarity index 100%
rename from tests/modules/samtools/markdup/nextflow.config
rename to tests/modules/nf-core/samtools/markdup/nextflow.config
diff --git a/tests/modules/nf-core/samtools/markdup/test.yml b/tests/modules/nf-core/samtools/markdup/test.yml
new file mode 100644
index 00000000000..56663ab1910
--- /dev/null
+++ b/tests/modules/nf-core/samtools/markdup/test.yml
@@ -0,0 +1,8 @@
+- name: samtools markdup test_samtools_markdup
+  command: nextflow run ./tests/modules/nf-core/samtools/markdup -entry test_samtools_markdup -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/markdup/nextflow.config
+  tags:
+    - samtools/markdup
+    - samtools
+  files:
+    - path: output/samtools/test.markdup.bam
+      md5sum: 75f35284e20970d279a0baac5bbf8ee0
diff --git a/tests/modules/nf-core/samtools/merge/main.nf b/tests/modules/nf-core/samtools/merge/main.nf
new file mode 100644
index 00000000000..34d96d1ec7c
--- /dev/null
+++ b/tests/modules/nf-core/samtools/merge/main.nf
@@ -0,0 +1,39 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_MERGE } from '../../../../../modules/nf-core/samtools/merge/main.nf'
+
+workflow test_samtools_merge {
+    input = [ [ id: 'test' ], // meta map
+              [ 
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
+              ]
+            ]
+
+    SAMTOOLS_MERGE ( input, [], [] )
+}
+
+workflow test_samtools_merge_cram {
+    input = [ [ id: 'test' ], // meta map
+              [ 
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+              ]
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    SAMTOOLS_MERGE ( input, fasta, fai )
+}
+
+workflow test_samtools_merge_single_file {
+    input = [ [ id: 'test' ], // meta map
+              [
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+              ]
+            ]
+
+    SAMTOOLS_MERGE ( input, [], [] )
+}
diff --git a/tests/modules/samtools/merge/nextflow.config b/tests/modules/nf-core/samtools/merge/nextflow.config
similarity index 100%
rename from tests/modules/samtools/merge/nextflow.config
rename to tests/modules/nf-core/samtools/merge/nextflow.config
diff --git a/tests/modules/nf-core/samtools/merge/test.yml b/tests/modules/nf-core/samtools/merge/test.yml
new file mode 100644
index 00000000000..e763f57a02a
--- /dev/null
+++ b/tests/modules/nf-core/samtools/merge/test.yml
@@ -0,0 +1,24 @@
+- name: samtools merge test_samtools_merge
+  command: nextflow run ./tests/modules/nf-core/samtools/merge -entry test_samtools_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/merge/nextflow.config
+  tags:
+    - samtools
+    - samtools/merge
+  files:
+    - path: output/samtools/test.bam
+
+- name: samtools merge test_samtools_merge_cram
+  command: nextflow run ./tests/modules/nf-core/samtools/merge -entry test_samtools_merge_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/merge/nextflow.config
+  tags:
+    - samtools
+    - samtools/merge
+  files:
+    - path: output/samtools/test.cram
+
+- name: samtools merge test_samtools_merge_single_file
+  command: nextflow run ./tests/modules/nf-core/samtools/merge -entry test_samtools_merge_single_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/merge/nextflow.config
+  tags:
+    - samtools
+    - samtools/merge
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 6e38ae132fadae4cb4915814d6f872b2
diff --git a/tests/modules/nf-core/samtools/mpileup/main.nf b/tests/modules/nf-core/samtools/mpileup/main.nf
new file mode 100644
index 00000000000..ce8540a06c2
--- /dev/null
+++ b/tests/modules/nf-core/samtools/mpileup/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_MPILEUP } from '../../../../../modules/nf-core/samtools/mpileup/main.nf'
+
+workflow test_samtools_mpileup {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                []
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    SAMTOOLS_MPILEUP ( input, fasta )
+}
+
+workflow test_samtools_mpileup_intervals {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    SAMTOOLS_MPILEUP ( input, fasta )
+}
diff --git a/tests/modules/samtools/mpileup/nextflow.config b/tests/modules/nf-core/samtools/mpileup/nextflow.config
similarity index 100%
rename from tests/modules/samtools/mpileup/nextflow.config
rename to tests/modules/nf-core/samtools/mpileup/nextflow.config
diff --git a/tests/modules/nf-core/samtools/mpileup/test.yml b/tests/modules/nf-core/samtools/mpileup/test.yml
new file mode 100644
index 00000000000..72a96def52d
--- /dev/null
+++ b/tests/modules/nf-core/samtools/mpileup/test.yml
@@ -0,0 +1,19 @@
+- name: samtools mpileup test_samtools_mpileup
+  command: nextflow run ./tests/modules/nf-core/samtools/mpileup -entry test_samtools_mpileup -c ./tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/mpileup
+  files:
+    - path: output/samtools/test.mpileup.gz
+      md5sum: 29455c36377196e8bc9cf831cf17b5dc
+    - path: output/samtools/versions.yml
+
+- name: samtools mpileup test_samtools_mpileup_intervals
+  command: nextflow run ./tests/modules/nf-core/samtools/mpileup -entry test_samtools_mpileup_intervals -c ./tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/mpileup
+  files:
+    - path: output/samtools/test.mpileup.gz
+      md5sum: d0538ec23b294245748ced92484b9a8d
+    - path: output/samtools/versions.yml
diff --git a/tests/modules/nf-core/samtools/sort/main.nf b/tests/modules/nf-core/samtools/sort/main.nf
new file mode 100644
index 00000000000..8811c00e4ae
--- /dev/null
+++ b/tests/modules/nf-core/samtools/sort/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_SORT } from '../../../../../modules/nf-core/samtools/sort/main.nf'
+
+workflow test_samtools_sort  {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_SORT ( input )
+}
diff --git a/tests/modules/samtools/sort/nextflow.config b/tests/modules/nf-core/samtools/sort/nextflow.config
similarity index 100%
rename from tests/modules/samtools/sort/nextflow.config
rename to tests/modules/nf-core/samtools/sort/nextflow.config
diff --git a/tests/modules/nf-core/samtools/sort/test.yml b/tests/modules/nf-core/samtools/sort/test.yml
new file mode 100644
index 00000000000..9e749635157
--- /dev/null
+++ b/tests/modules/nf-core/samtools/sort/test.yml
@@ -0,0 +1,8 @@
+- name: samtools sort
+  command: nextflow run ./tests/modules/nf-core/samtools/sort -entry test_samtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/sort/nextflow.config
+  tags:
+    - samtools
+    - samtools/sort
+  files:
+    - path: output/samtools/test.sorted.bam
+      md5sum: f00f5d392fd5c531e1fd528d9f57b32b
diff --git a/tests/modules/nf-core/samtools/stats/main.nf b/tests/modules/nf-core/samtools/stats/main.nf
new file mode 100644
index 00000000000..523056ae72c
--- /dev/null
+++ b/tests/modules/nf-core/samtools/stats/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_STATS } from '../../../../../modules/nf-core/samtools/stats/main.nf'
+
+workflow test_samtools_stats {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+            ]
+
+    SAMTOOLS_STATS ( input, [])
+}
+
+workflow test_samtools_stats_cram {
+   input = [ [ id: 'test', single_end:true ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
+            ]
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    SAMTOOLS_STATS ( input, fasta )
+}
diff --git a/tests/modules/samtools/stats/nextflow.config b/tests/modules/nf-core/samtools/stats/nextflow.config
similarity index 100%
rename from tests/modules/samtools/stats/nextflow.config
rename to tests/modules/nf-core/samtools/stats/nextflow.config
diff --git a/tests/modules/nf-core/samtools/stats/test.yml b/tests/modules/nf-core/samtools/stats/test.yml
new file mode 100644
index 00000000000..3372206ed6e
--- /dev/null
+++ b/tests/modules/nf-core/samtools/stats/test.yml
@@ -0,0 +1,17 @@
+- name: samtools stats test_samtools_stats
+  command: nextflow run ./tests/modules/nf-core/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/stats/nextflow.config
+  tags:
+    - samtools/stats
+    - samtools
+  files:
+    - path: output/samtools/test.stats
+      md5sum: 5e6fa3805f6d6b330262456746709239
+
+- name: samtools stats test_samtools_stats_cram
+  command: nextflow run ./tests/modules/nf-core/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/stats/nextflow.config
+  tags:
+    - samtools/stats
+    - samtools
+  files:
+    - path: output/samtools/test.stats
+      md5sum: 916a8e5bfd97a53f806e5a14565631bb
diff --git a/tests/modules/nf-core/samtools/view/main.nf b/tests/modules/nf-core/samtools/view/main.nf
new file mode 100644
index 00000000000..f30eeefe88c
--- /dev/null
+++ b/tests/modules/nf-core/samtools/view/main.nf
@@ -0,0 +1,65 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_VIEW } from '../../../../../modules/nf-core/samtools/view/main.nf'
+
+workflow test_samtools_view {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+                []
+            ]
+
+    SAMTOOLS_VIEW ( input, [], [] )
+}
+
+workflow test_samtools_view_cram {
+   input = [ [ id: 'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+            ]
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    SAMTOOLS_VIEW ( input, fasta, [] )
+}
+
+workflow test_samtools_view_convert {
+    input = [ [ id: 'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                []
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    SAMTOOLS_VIEW ( input, fasta, [] )
+}
+
+workflow test_samtools_view_index {
+    input = [ [ id: 'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                []
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    SAMTOOLS_VIEW ( input, fasta, [] )
+}
+
+workflow test_samtools_view_filter {
+    input = [ [ id: 'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                []
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    qname = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true)
+
+    SAMTOOLS_VIEW ( input, fasta, qname )
+}
+
+workflow test_samtools_view_stubs {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+                []
+            ]
+
+    SAMTOOLS_VIEW ( input, [], [] )
+}
diff --git a/tests/modules/samtools/view/nextflow.config b/tests/modules/nf-core/samtools/view/nextflow.config
similarity index 100%
rename from tests/modules/samtools/view/nextflow.config
rename to tests/modules/nf-core/samtools/view/nextflow.config
diff --git a/tests/modules/nf-core/samtools/view/test.yml b/tests/modules/nf-core/samtools/view/test.yml
new file mode 100644
index 00000000000..1959eb27ff5
--- /dev/null
+++ b/tests/modules/nf-core/samtools/view/test.yml
@@ -0,0 +1,56 @@
+- name: samtools view test_samtools_view
+  command: nextflow run ./tests/modules/nf-core/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/view/nextflow.config
+  tags:
+    - samtools/view
+    - samtools
+  files:
+    - path: output/samtools/test.bam
+      md5sum: e6a9285be7b1c616dc4e17679fce5f1e
+
+- name: samtools view test_samtools_view_cram
+  command: nextflow run ./tests/modules/nf-core/samtools/view -entry test_samtools_view_cram -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/view/nextflow.config
+  tags:
+    - samtools/view
+    - samtools
+  files:
+    - path: output/samtools/test.cram
+
+- name: samtools view test_samtools_view_convert
+  command: nextflow run ./tests/modules/nf-core/samtools/view -entry test_samtools_view_convert -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/view/nextflow.config
+  tags:
+    - samtools/view
+    - samtools
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 4f4a97da17db79c78b1912da3cdc1d8f
+
+- name: samtools view test_samtools_view_index
+  command: nextflow run ./tests/modules/nf-core/samtools/view -entry test_samtools_view_index -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/view/nextflow.config
+  tags:
+    - samtools/view
+    - samtools
+  files:
+    - path: output/samtools/test.bam
+      md5sum: b2d2482cea94adfc9628473792b0d215
+    - path: output/samtools/test.bam.csi
+      md5sum: 343a2085b436cab2123147dafd255607
+
+- name: samtools view test_samtools_view_filter
+  command: nextflow run ./tests/modules/nf-core/samtools/view -entry test_samtools_view_filter -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/view/nextflow.config
+  tags:
+    - samtools/view
+    - samtools
+  files:
+    - path: output/samtools/test.bam
+      md5sum: d8e20876423cb1123a559e4347115249
+    - path: output/samtools/test.bam.csi
+      md5sum: b1d688576e59529271333aa50b3ad3ae
+
+- name: samtools view test_samtools_view_stubs
+  command: nextflow run ./tests/modules/nf-core/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/samtools/view/nextflow.config
+  tags:
+    - samtools/view
+    - samtools
+  files:
+    - path: output/samtools/test.bam
+      md5sum: e6a9285be7b1c616dc4e17679fce5f1e
diff --git a/tests/modules/nf-core/scoary/main.nf b/tests/modules/nf-core/scoary/main.nf
new file mode 100644
index 00000000000..6d606eabcf6
--- /dev/null
+++ b/tests/modules/nf-core/scoary/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SCOARY } from '../../../../modules/nf-core/scoary/main.nf'
+
+workflow test_scoary {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://github.com/AdmiralenOla/Scoary/raw/master/scoary/exampledata/Gene_presence_absence.csv", checkIfExists: true),
+              file("https://github.com/AdmiralenOla/Scoary/raw/master/scoary/exampledata/Tetracycline_resistance.csv", checkIfExists: true) ]
+
+    tree = []
+    SCOARY ( input, tree)
+}
diff --git a/tests/modules/scoary/nextflow.config b/tests/modules/nf-core/scoary/nextflow.config
similarity index 100%
rename from tests/modules/scoary/nextflow.config
rename to tests/modules/nf-core/scoary/nextflow.config
diff --git a/tests/modules/nf-core/scoary/test.yml b/tests/modules/nf-core/scoary/test.yml
new file mode 100644
index 00000000000..2fd4edeadd5
--- /dev/null
+++ b/tests/modules/nf-core/scoary/test.yml
@@ -0,0 +1,9 @@
+- name: scoary test_scoary
+  command: nextflow run ./tests/modules/nf-core/scoary -entry test_scoary -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/scoary/nextflow.config
+  tags:
+    - scoary
+  files:
+    - path: output/scoary/Bogus_trait.results.csv
+      md5sum: 9550c692bbe6ff0ac844357bfabb809b
+    - path: output/scoary/Tetracycline_resistance.results.csv
+      md5sum: a87740818ab4de69a758fc75d7b879dd
diff --git a/tests/modules/nf-core/scramble/clusteranalysis/main.nf b/tests/modules/nf-core/scramble/clusteranalysis/main.nf
new file mode 100644
index 00000000000..58020321afb
--- /dev/null
+++ b/tests/modules/nf-core/scramble/clusteranalysis/main.nf
@@ -0,0 +1,54 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SCRAMBLE_CLUSTERANALYSIS   } from '../../../../../modules/nf-core/scramble/clusteranalysis/main.nf'
+include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../../modules/nf-core/scramble/clusteridentifier/main.nf'
+
+workflow test_scramble_clusteranalysis {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['scramble']['bam'], checkIfExists: true),   
+        file(params.test_data['homo_sapiens']['scramble']['bam_bai'], checkIfExists: true),   
+        []
+    ]
+
+    fasta = []
+    mei_ref = []
+
+    SCRAMBLE_CLUSTERIDENTIFIER(
+        input,
+        fasta
+    )
+
+    SCRAMBLE_CLUSTERANALYSIS (
+        SCRAMBLE_CLUSTERIDENTIFIER.out.clusters,
+        fasta,
+        mei_ref
+    )
+}
+
+workflow test_scramble_clusteranalysis_fasta {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['scramble']['cram'], checkIfExists: true),   
+        file(params.test_data['homo_sapiens']['scramble']['cram_crai'], checkIfExists: true),   
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['scramble']['fasta'], checkIfExists: true)
+    mei_ref = []
+
+    SCRAMBLE_CLUSTERIDENTIFIER(
+        input,
+        fasta
+    )
+
+    SCRAMBLE_CLUSTERANALYSIS (
+        SCRAMBLE_CLUSTERIDENTIFIER.out.clusters,
+        fasta,
+        mei_ref
+    )
+}
\ No newline at end of file
diff --git a/tests/modules/scramble/clusteranalysis/nextflow.config b/tests/modules/nf-core/scramble/clusteranalysis/nextflow.config
similarity index 100%
rename from tests/modules/scramble/clusteranalysis/nextflow.config
rename to tests/modules/nf-core/scramble/clusteranalysis/nextflow.config
diff --git a/tests/modules/nf-core/scramble/clusteranalysis/test.yml b/tests/modules/nf-core/scramble/clusteranalysis/test.yml
new file mode 100644
index 00000000000..a7eb3eec1e6
--- /dev/null
+++ b/tests/modules/nf-core/scramble/clusteranalysis/test.yml
@@ -0,0 +1,25 @@
+- name: scramble clusteranalysis test_scramble_clusteranalysis
+  command: nextflow run ./tests/modules/nf-core/scramble/clusteranalysis -entry test_scramble_clusteranalysis -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/scramble/clusteranalysis/nextflow.config
+  tags:
+    - scramble/clusteranalysis
+    - scramble
+  files:
+    - path: output/scramble/test.clusters.txt
+      md5sum: 9b2777a44bfbcff8fac1bf67c3985f1f
+    - path: output/scramble/test_MEIs.txt
+      md5sum: a14c40c7e5f3630defde68ae1de51bca
+
+- name: scramble clusteranalysis test_scramble_clusteranalysis_fasta
+  command: nextflow run ./tests/modules/nf-core/scramble/clusteranalysis -entry test_scramble_clusteranalysis_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/scramble/clusteranalysis/nextflow.config
+  tags:
+    - scramble/clusteranalysis
+    - scramble
+  files:
+    - path: output/scramble/test.clusters.txt
+      md5sum: 9b2777a44bfbcff8fac1bf67c3985f1f
+    - path: output/scramble/test.vcf
+      contains: [fileformat=VCFv4.2]
+    - path: output/scramble/test_MEIs.txt
+      md5sum: a14c40c7e5f3630defde68ae1de51bca
+    - path: output/scramble/test_PredictedDeletions.txt
+      md5sum: 1fa0d3d0a58fdf81bd259b3c71774ba8
diff --git a/tests/modules/nf-core/scramble/clusteridentifier/main.nf b/tests/modules/nf-core/scramble/clusteridentifier/main.nf
new file mode 100644
index 00000000000..2c2602652cd
--- /dev/null
+++ b/tests/modules/nf-core/scramble/clusteridentifier/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../../modules/nf-core/scramble/clusteridentifier/main.nf'
+
+workflow test_scramble_clusteridentifier_bam {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['scramble']['bam'], checkIfExists: true),   
+        file(params.test_data['homo_sapiens']['scramble']['bam_bai'], checkIfExists: true),   
+        []
+    ]
+
+    fasta = []
+
+    SCRAMBLE_CLUSTERIDENTIFIER ( input, fasta )
+}
+
+workflow test_scramble_clusteridentifier_cram {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['scramble']['cram'], checkIfExists: true),   
+        file(params.test_data['homo_sapiens']['scramble']['cram_crai'], checkIfExists: true),   
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['scramble']['fasta'], checkIfExists: true)
+
+    SCRAMBLE_CLUSTERIDENTIFIER ( input, fasta )
+}
diff --git a/tests/modules/scramble/clusteridentifier/nextflow.config b/tests/modules/nf-core/scramble/clusteridentifier/nextflow.config
similarity index 100%
rename from tests/modules/scramble/clusteridentifier/nextflow.config
rename to tests/modules/nf-core/scramble/clusteridentifier/nextflow.config
diff --git a/tests/modules/nf-core/scramble/clusteridentifier/test.yml b/tests/modules/nf-core/scramble/clusteridentifier/test.yml
new file mode 100644
index 00000000000..9e03d0b38ba
--- /dev/null
+++ b/tests/modules/nf-core/scramble/clusteridentifier/test.yml
@@ -0,0 +1,17 @@
+- name: scramble clusteridentifier test_scramble_clusteridentifier_bam
+  command: nextflow run ./tests/modules/nf-core/scramble/clusteridentifier -entry test_scramble_clusteridentifier_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/scramble/clusteridentifier/nextflow.config
+  tags:
+    - scramble/clusteridentifier
+    - scramble
+  files:
+    - path: output/scramble/test.clusters.txt
+      md5sum: 9b2777a44bfbcff8fac1bf67c3985f1f
+
+- name: scramble clusteridentifier test_scramble_clusteridentifier_cram
+  command: nextflow run ./tests/modules/nf-core/scramble/clusteridentifier -entry test_scramble_clusteridentifier_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/scramble/clusteridentifier/nextflow.config
+  tags:
+    - scramble/clusteridentifier
+    - scramble
+  files:
+    - path: output/scramble/test.clusters.txt
+      md5sum: 9b2777a44bfbcff8fac1bf67c3985f1f
diff --git a/tests/modules/nf-core/seacr/callpeak/main.nf b/tests/modules/nf-core/seacr/callpeak/main.nf
new file mode 100644
index 00000000000..002115c81b0
--- /dev/null
+++ b/tests/modules/nf-core/seacr/callpeak/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEACR_CALLPEAK } from '../../../../../modules/nf-core/seacr/callpeak/main.nf'
+
+workflow test_seacr_callpeak {
+    input = [ [ id:'test_1'],
+              file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_1'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_2'], checkIfExists: true) 
+            ]
+
+    SEACR_CALLPEAK ( input, 0.05 )
+}
+
+workflow test_seacr_callpeak_threshold {
+    input = [ [ id:'test_1'],
+              file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_1'], checkIfExists: true),
+              []
+            ]
+
+    SEACR_CALLPEAK ( input, 0.05 )
+}
\ No newline at end of file
diff --git a/tests/modules/seacr/callpeak/nextflow.config b/tests/modules/nf-core/seacr/callpeak/nextflow.config
similarity index 100%
rename from tests/modules/seacr/callpeak/nextflow.config
rename to tests/modules/nf-core/seacr/callpeak/nextflow.config
diff --git a/tests/modules/nf-core/seacr/callpeak/test.yml b/tests/modules/nf-core/seacr/callpeak/test.yml
new file mode 100644
index 00000000000..df591c7f13b
--- /dev/null
+++ b/tests/modules/nf-core/seacr/callpeak/test.yml
@@ -0,0 +1,17 @@
+- name: seacr callpeak
+  command: nextflow run ./tests/modules/nf-core/seacr/callpeak -entry test_seacr_callpeak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seacr/callpeak/nextflow.config
+  tags:
+    - seacr
+    - seacr/callpeak
+  files:
+    - path: output/seacr/test_1.stringent.bed
+      md5sum: a3cb0c7c4ffa895788da3f0d6371b7df
+
+- name: seacr callpeak threshold
+  command: nextflow run ./tests/modules/nf-core/seacr/callpeak -entry test_seacr_callpeak_threshold -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seacr/callpeak/nextflow.config
+  tags:
+    - seacr
+    - seacr/callpeak
+  files:
+    - path: output/seacr/test_1.stringent.bed
+      md5sum: 1d23015c7087f7b48cc3139d53fd3463
diff --git a/tests/modules/nf-core/seqkit/pair/main.nf b/tests/modules/nf-core/seqkit/pair/main.nf
new file mode 100644
index 00000000000..f8f57e37b1a
--- /dev/null
+++ b/tests/modules/nf-core/seqkit/pair/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQKIT_PAIR } from '../../../../../modules/nf-core/seqkit/pair/main.nf'
+
+workflow test_seqkit_pair {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    SEQKIT_PAIR ( input )
+}
diff --git a/tests/modules/seqkit/pair/nextflow.config b/tests/modules/nf-core/seqkit/pair/nextflow.config
similarity index 100%
rename from tests/modules/seqkit/pair/nextflow.config
rename to tests/modules/nf-core/seqkit/pair/nextflow.config
diff --git a/tests/modules/nf-core/seqkit/pair/test.yml b/tests/modules/nf-core/seqkit/pair/test.yml
new file mode 100644
index 00000000000..b27ed5443bc
--- /dev/null
+++ b/tests/modules/nf-core/seqkit/pair/test.yml
@@ -0,0 +1,12 @@
+- name: seqkit pair test_seqkit_pair
+  command: nextflow run ./tests/modules/nf-core/seqkit/pair -entry test_seqkit_pair -c ./tests/config/nextflow.config
+  tags:
+    - seqkit/pair
+    - seqkit
+  files:
+    - path: output/seqkit/test_1.paired.fastq.gz
+      md5sum: fbfe7e8bdbc29abaaf58b6f1a32448e5
+    - path: output/seqkit/test_2.paired.fastq.gz
+      md5sum: 7d3c0912e5adc2674e8ecc1e647381b3
+    - path: output/seqkit/versions.yml
+      md5sum: 3086293bc986fc2ece38b1951d090819
diff --git a/tests/modules/nf-core/seqkit/replace/main.nf b/tests/modules/nf-core/seqkit/replace/main.nf
new file mode 100644
index 00000000000..a066a33f10c
--- /dev/null
+++ b/tests/modules/nf-core/seqkit/replace/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQKIT_REPLACE } from '../../../../../modules/nf-core/seqkit/replace/main.nf'
+include { SEQKIT_REPLACE as SEQKIT_REPLACEUNCOMP } from '../../../../../modules/nf-core/seqkit/replace/main.nf'
+
+workflow test_seqkit_replace {
+
+    input = [ [ id:'test' ],   // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_REPLACE ( input )
+}
+
+workflow test_seqkit_replace_uncomp {
+
+    input = [ [ id:'test' ],   // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_REPLACEUNCOMP ( input )
+}
diff --git a/tests/modules/seqkit/replace/nextflow.config b/tests/modules/nf-core/seqkit/replace/nextflow.config
similarity index 100%
rename from tests/modules/seqkit/replace/nextflow.config
rename to tests/modules/nf-core/seqkit/replace/nextflow.config
diff --git a/tests/modules/nf-core/seqkit/replace/test.yml b/tests/modules/nf-core/seqkit/replace/test.yml
new file mode 100644
index 00000000000..a83b809b2f8
--- /dev/null
+++ b/tests/modules/nf-core/seqkit/replace/test.yml
@@ -0,0 +1,21 @@
+- name: seqkit replace test_seqkit_replace
+  command: nextflow run ./tests/modules/nf-core/seqkit/replace -entry test_seqkit_replace -c ./tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/replace
+  files:
+    - path: output/seqkit/test.fasta.gz
+      md5sum: 053847219695c0a923d02352442d7abf
+    - path: output/seqkit/versions.yml
+      md5sum: dc9d18b7836c9db00a3032fd191bd831
+
+- name: seqkit replace test_seqkit_replace_uncomp
+  command: nextflow run ./tests/modules/nf-core/seqkit/replace -entry test_seqkit_replace_uncomp -c ./tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/replace
+  files:
+    - path: output/seqkit/test..fasta
+      md5sum: 05d3294a62c72f5489f067c1da3c2f6c
+    - path: output/seqkit/versions.yml
+      md5sum: 3b88128487ec949f0bdeecebc375c407
diff --git a/tests/modules/nf-core/seqkit/split2/main.nf b/tests/modules/nf-core/seqkit/split2/main.nf
new file mode 100644
index 00000000000..39d6a76051c
--- /dev/null
+++ b/tests/modules/nf-core/seqkit/split2/main.nf
@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../../modules/nf-core/seqkit/split2/main.nf'
+include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE   } from '../../../../../modules/nf-core/seqkit/split2/main.nf'
+include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART   } from '../../../../../modules/nf-core/seqkit/split2/main.nf'
+
+workflow test_seqkit_split2_single_end_length {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_SPLIT2_LENGTH ( input )
+}
+
+workflow test_seqkit_split2_single_end_size {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_SPLIT2_SIZE ( input )
+}
+
+workflow test_seqkit_split2_single_end_part {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_SPLIT2_PART ( input )
+}
+
+workflow test_seqkit_split2_paired_end_length {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_SPLIT2_LENGTH ( input )
+}
+
+workflow test_seqkit_split2_paired_end_size {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_SPLIT2_SIZE ( input )
+}
+
+workflow test_seqkit_split2_paired_end_part {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQKIT_SPLIT2_PART ( input )
+}
diff --git a/tests/modules/seqkit/split2/nextflow.config b/tests/modules/nf-core/seqkit/split2/nextflow.config
similarity index 100%
rename from tests/modules/seqkit/split2/nextflow.config
rename to tests/modules/nf-core/seqkit/split2/nextflow.config
diff --git a/tests/modules/nf-core/seqkit/split2/test.yml b/tests/modules/nf-core/seqkit/split2/test.yml
new file mode 100644
index 00000000000..4bea4419b97
--- /dev/null
+++ b/tests/modules/nf-core/seqkit/split2/test.yml
@@ -0,0 +1,95 @@
+- name: seqkit split2 test_seqkit_split2_single_end_length
+  command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_single_end_length -c ./tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/split2
+  files:
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
+      md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
+      md5sum: 45cccacb4676bca33beb17064322a781
+    - path: output/seqkit/versions.yml
+      md5sum: 2d5a709d129be364687cc0b561efa532
+
+- name: seqkit split2 test_seqkit_split2_single_end_size
+  command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_single_end_size -c ./tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/split2
+  files:
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
+      md5sum: b09324606fb3636b51448d6a007d2c71
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
+      md5sum: f7873475d463e3b4d21dccbf8e859270
+    - path: output/seqkit/versions.yml
+      md5sum: 490d00accd1092a8eca4e83ed809bad3
+
+- name: seqkit split2 test_seqkit_split2_single_end_part
+  command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_single_end_part -c ./tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/split2
+  files:
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
+      md5sum: a9d29d08e27246b6d36e21e5def405e3
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
+      md5sum: 6d547a959adcd027dd1a8734e195dd7d
+    - path: output/seqkit/test/test_1.part_003.fastq.gz
+      md5sum: 6d63cc8400dd2a96d808514fb18278ee
+    - path: output/seqkit/versions.yml
+      md5sum: 90431cd3d28954f656988230d4481115
+
+- name: seqkit split2 test_seqkit_split2_paired_end_length
+  command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c ./tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/split2
+  files:
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
+      md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
+      md5sum: 45cccacb4676bca33beb17064322a781
+    - path: output/seqkit/test/test_2.part_001.fastq.gz
+      md5sum: 160b5fd363ff7cad8af9d914269d6426
+    - path: output/seqkit/test/test_2.part_002.fastq.gz
+      md5sum: 18bc5434cf55706394cccb44e6108561
+    - path: output/seqkit/versions.yml
+      md5sum: 9272afc1a126ae997a712edeef317f22
+
+- name: seqkit split2 test_seqkit_split2_paired_end_size
+  command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c ./tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/split2
+  files:
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
+      md5sum: b09324606fb3636b51448d6a007d2c71
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
+      md5sum: f7873475d463e3b4d21dccbf8e859270
+    - path: output/seqkit/test/test_2.part_001.fastq.gz
+      md5sum: c0602b62aae860dd284c0eb0062c24dd
+    - path: output/seqkit/test/test_2.part_002.fastq.gz
+      md5sum: 5bc7a98b618100b29910eb41c4c9ac0d
+    - path: output/seqkit/versions.yml
+      md5sum: af66912ae8abc493f77f70e3bf473144
+
+- name: seqkit split2 test_seqkit_split2_paired_end_part
+  command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c ./tests/config/nextflow.config
+  tags:
+    - seqkit
+    - seqkit/split2
+  files:
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
+      md5sum: a9d29d08e27246b6d36e21e5def405e3
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
+      md5sum: 6d547a959adcd027dd1a8734e195dd7d
+    - path: output/seqkit/test/test_1.part_003.fastq.gz
+      md5sum: 6d63cc8400dd2a96d808514fb18278ee
+    - path: output/seqkit/test/test_2.part_001.fastq.gz
+      md5sum: b51a1bed106e4ec0c9be7d9e224d0616
+    - path: output/seqkit/test/test_2.part_002.fastq.gz
+      md5sum: 079078a7f86114ae29cda8c00d5a7fc9
+    - path: output/seqkit/test/test_2.part_003.fastq.gz
+      md5sum: 6987941bf8c4a37565e333029ba41ca0
+    - path: output/seqkit/versions.yml
+      md5sum: 193bc5f0c429076f816ab0a529c4c1fc
diff --git a/tests/modules/nf-core/seqkit/stats/main.nf b/tests/modules/nf-core/seqkit/stats/main.nf
new file mode 100644
index 00000000000..5d6fc6eb2d4
--- /dev/null
+++ b/tests/modules/nf-core/seqkit/stats/main.nf
@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQKIT_STATS } from '../../../../../modules/nf-core/seqkit/stats/main.nf'
+
+workflow test_seqkit_stats_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_nanopore {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_genome_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_transcriptome_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true),
+    ]
+
+    SEQKIT_STATS ( input )
+}
diff --git a/tests/modules/seqkit/stats/nextflow.config b/tests/modules/nf-core/seqkit/stats/nextflow.config
similarity index 100%
rename from tests/modules/seqkit/stats/nextflow.config
rename to tests/modules/nf-core/seqkit/stats/nextflow.config
diff --git a/tests/modules/nf-core/seqkit/stats/test.yml b/tests/modules/nf-core/seqkit/stats/test.yml
new file mode 100644
index 00000000000..bf7b7b2331d
--- /dev/null
+++ b/tests/modules/nf-core/seqkit/stats/test.yml
@@ -0,0 +1,54 @@
+- name: seqkit stats test_seqkit_stats_single_end
+  command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_single_end -c ./tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: e23227d089a7e04b0ec0cb547c4aadff
+    - path: output/seqkit/versions.yml
+      md5sum: d67f0c16feb9df77b11f6c91bbdf9926
+
+- name: seqkit stats test_seqkit_stats_paired_end
+  command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: 9de20dc39fb01285e3f0c382fda9db52
+    - path: output/seqkit/versions.yml
+      md5sum: bd8881933b953d07f2600e2e6a88ebf3
+
+- name: seqkit stats test_seqkit_stats_nanopore
+  command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_nanopore -c ./tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: 5da1709eb5ae64fa3b2d624bffe2e7aa
+    - path: output/seqkit/versions.yml
+      md5sum: 565632701fbe048f7ba99f1865bd48ca
+
+- name: seqkit stats test_seqkit_stats_genome_fasta
+  command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_genome_fasta -c ./tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: f64489767a4e769539ef3faf83260184
+    - path: output/seqkit/versions.yml
+      md5sum: 782fcdeaa922c8bb532ffa5808849d87
+
+- name: seqkit stats test_seqkit_stats_transcriptome_fasta
+  command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_transcriptome_fasta -c ./tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: fbb975b665a08c8862fcd1268613a945
+    - path: output/seqkit/versions.yml
+      md5sum: db99b016d986d26102ec398264a58410
diff --git a/tests/modules/nf-core/seqsero2/main.nf b/tests/modules/nf-core/seqsero2/main.nf
new file mode 100644
index 00000000000..40908120995
--- /dev/null
+++ b/tests/modules/nf-core/seqsero2/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQSERO2 } from '../../../../modules/nf-core/seqsero2/main.nf'
+
+workflow test_seqsero2 {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    SEQSERO2 ( input )
+}
diff --git a/tests/modules/seqsero2/nextflow.config b/tests/modules/nf-core/seqsero2/nextflow.config
similarity index 100%
rename from tests/modules/seqsero2/nextflow.config
rename to tests/modules/nf-core/seqsero2/nextflow.config
diff --git a/tests/modules/nf-core/seqsero2/test.yml b/tests/modules/nf-core/seqsero2/test.yml
new file mode 100644
index 00000000000..23fd046e528
--- /dev/null
+++ b/tests/modules/nf-core/seqsero2/test.yml
@@ -0,0 +1,11 @@
+- name: seqsero2 test_seqsero2
+  command: nextflow run ./tests/modules/nf-core/seqsero2 -entry test_seqsero2 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqsero2/nextflow.config
+  tags:
+    - seqsero2
+  files:
+    - path: output/seqsero2/results/SeqSero_log.txt
+      md5sum: d00242dfa734b5abb3622a6048f0b4fb
+    - path: output/seqsero2/results/SeqSero_result.tsv
+      contains: ["Sample", "Predicted", "Note"]
+    - path: output/seqsero2/results/SeqSero_result.txt
+      contains: ["Sample", "Predicted", "Note"]
diff --git a/tests/modules/nf-core/seqtk/mergepe/main.nf b/tests/modules/nf-core/seqtk/mergepe/main.nf
new file mode 100644
index 00000000000..af82e367131
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/mergepe/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQTK_MERGEPE } from '../../../../../modules/nf-core/seqtk/mergepe/main.nf'
+
+//
+// Test with single-end data
+//
+
+workflow test_seqtk_mergepe_single_end {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+
+    SEQTK_MERGEPE ( input )
+}
+
+//
+// Test with paired-end data
+//
+
+workflow test_seqtk_mergepe_paired_end {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQTK_MERGEPE ( input )
+}
diff --git a/tests/modules/seqtk/mergepe/nextflow.config b/tests/modules/nf-core/seqtk/mergepe/nextflow.config
similarity index 100%
rename from tests/modules/seqtk/mergepe/nextflow.config
rename to tests/modules/nf-core/seqtk/mergepe/nextflow.config
diff --git a/tests/modules/nf-core/seqtk/mergepe/test.yml b/tests/modules/nf-core/seqtk/mergepe/test.yml
new file mode 100644
index 00000000000..4e2bf25251e
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/mergepe/test.yml
@@ -0,0 +1,21 @@
+- name: seqtk mergepe test_seqtk_mergepe_single_end
+  command: nextflow run ./tests/modules/nf-core/seqtk/mergepe -entry test_seqtk_mergepe_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqtk/mergepe/nextflow.config
+  tags:
+    - seqtk/mergepe
+    - seqtk
+  files:
+    - path: output/seqtk/test.processed.fastq.gz
+      contains:
+        - "@"
+        - "+"
+
+- name: seqtk mergepe test_seqtk_mergepe_paired_end
+  command: nextflow run ./tests/modules/nf-core/seqtk/mergepe -entry test_seqtk_mergepe_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqtk/mergepe/nextflow.config
+  tags:
+    - seqtk/mergepe
+    - seqtk
+  files:
+    - path: output/seqtk/test.processed.fastq.gz
+      contains:
+        - "@"
+        - "+"
diff --git a/tests/modules/nf-core/seqtk/rename/main.nf b/tests/modules/nf-core/seqtk/rename/main.nf
new file mode 100644
index 00000000000..eb225d3e759
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/rename/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQTK_RENAME } from '../../../../../modules/nf-core/seqtk/rename/main.nf'
+
+workflow test_seqtk_rename {
+    input = [ [ id:'test' ],   // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+            ]
+    SEQTK_RENAME ( input )
+}
+
+workflow test_seqtk_rename_fq {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    SEQTK_RENAME ( input )
+}
diff --git a/tests/modules/seqtk/rename/nextflow.config b/tests/modules/nf-core/seqtk/rename/nextflow.config
similarity index 100%
rename from tests/modules/seqtk/rename/nextflow.config
rename to tests/modules/nf-core/seqtk/rename/nextflow.config
diff --git a/tests/modules/nf-core/seqtk/rename/test.yml b/tests/modules/nf-core/seqtk/rename/test.yml
new file mode 100644
index 00000000000..4409a899000
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/rename/test.yml
@@ -0,0 +1,21 @@
+- name: seqtk rename test_seqtk_rename
+  command: nextflow run ./tests/modules/nf-core/seqtk/rename -entry test_seqtk_rename -c ./tests/config/nextflow.config
+  tags:
+    - seqtk
+    - seqtk/rename
+  files:
+    - path: output/seqtk/test.renamed.fasta.gz
+      contains:
+        - ">test1"
+
+- name: seqtk rename test_seqtk_rename_fq
+  command: nextflow run ./tests/modules/nf-core/seqtk/rename -entry test_seqtk_rename_fq -c ./tests/config/nextflow.config
+  tags:
+    - seqtk
+    - seqtk/rename
+  files:
+    - path: output/seqtk/test.renamed.fastq.gz
+      contains:
+        - "@test1"
+        - "@test2"
+        - "@test3"
diff --git a/tests/modules/nf-core/seqtk/sample/main.nf b/tests/modules/nf-core/seqtk/sample/main.nf
new file mode 100644
index 00000000000..5e0d30e1702
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/sample/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQTK_SAMPLE } from '../../../../../modules/nf-core/seqtk/sample/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_seqtk_sample_single_end {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+
+    SEQTK_SAMPLE ( input, 50 )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_seqtk_sample_paired_end {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SEQTK_SAMPLE ( input, 50 )
+}
diff --git a/tests/modules/seqtk/sample/nextflow.config b/tests/modules/nf-core/seqtk/sample/nextflow.config
similarity index 100%
rename from tests/modules/seqtk/sample/nextflow.config
rename to tests/modules/nf-core/seqtk/sample/nextflow.config
diff --git a/tests/modules/nf-core/seqtk/sample/test.yml b/tests/modules/nf-core/seqtk/sample/test.yml
new file mode 100644
index 00000000000..1f847ebe9c0
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/sample/test.yml
@@ -0,0 +1,22 @@
+- name: seqtk sample test_seqtk_sample_single_end
+  command: nextflow run ./tests/modules/nf-core/seqtk/sample -entry test_seqtk_sample_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqtk/sample/nextflow.config
+  tags:
+    - seqtk
+    - seqtk/sample
+  files:
+    - path: output/seqtk/test.sampled.fastq.gz
+      contains:
+        - "@ERR5069949"
+
+- name: seqtk sample test_seqtk_sample_paired_end
+  command: nextflow run ./tests/modules/nf-core/seqtk/sample -entry test_seqtk_sample_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqtk/sample/nextflow.config
+  tags:
+    - seqtk
+    - seqtk/sample
+  files:
+    - path: output/seqtk/test.sampled_1.fastq.gz
+      contains:
+        - "@ERR5069949"
+    - path: output/seqtk/test.sampled_2.fastq.gz
+      contains:
+        - "@ERR5069949"
diff --git a/tests/modules/nf-core/seqtk/seq/main.nf b/tests/modules/nf-core/seqtk/seq/main.nf
new file mode 100644
index 00000000000..4feff0d7e3e
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/seq/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQTK_SEQ } from '../../../../../modules/nf-core/seqtk/seq/main.nf'
+
+workflow test_seqtk_seq {
+    input = [ [ id:'test' ],   // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+            ]
+    SEQTK_SEQ ( input )
+}
+
+workflow test_seqtk_seq_fq {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    SEQTK_SEQ ( input )
+}
\ No newline at end of file
diff --git a/tests/modules/seqtk/seq/nextflow.config b/tests/modules/nf-core/seqtk/seq/nextflow.config
similarity index 100%
rename from tests/modules/seqtk/seq/nextflow.config
rename to tests/modules/nf-core/seqtk/seq/nextflow.config
diff --git a/tests/modules/nf-core/seqtk/seq/test.yml b/tests/modules/nf-core/seqtk/seq/test.yml
new file mode 100644
index 00000000000..ab1806daa1d
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/seq/test.yml
@@ -0,0 +1,18 @@
+- name: seqtk seq test_seqtk_seq
+  command: nextflow run ./tests/modules/nf-core/seqtk/seq -entry test_seqtk_seq -c ./tests/config/nextflow.config
+  tags:
+    - seqtk/seq
+    - seqtk
+  files:
+    - path: output/seqtk/test.seqtk-seq.fasta.gz
+      md5sum: 50d73992c8c7e56dc095ef47ec52a754
+
+- name: seqtk seq test_seqtk_seq_fq
+  command: nextflow run ./tests/modules/nf-core/seqtk/seq -entry test_seqtk_seq_fq -c ./tests/config/nextflow.config
+  tags:
+    - seqtk/seq
+    - seqtk
+  files:
+    - path: output/seqtk/test.seqtk-seq.fasta.gz
+      contains:
+        - ">ERR5069949"
diff --git a/tests/modules/nf-core/seqtk/subseq/main.nf b/tests/modules/nf-core/seqtk/subseq/main.nf
new file mode 100644
index 00000000000..f96fa9f8a4d
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/subseq/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQTK_SUBSEQ } from '../../../../../modules/nf-core/seqtk/subseq/main.nf'
+
+workflow test_seqtk_subseq {
+    
+    sequences = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    filter_list = file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true)
+
+    SEQTK_SUBSEQ ( sequences, filter_list )
+}
diff --git a/tests/modules/seqtk/subseq/nextflow.config b/tests/modules/nf-core/seqtk/subseq/nextflow.config
similarity index 100%
rename from tests/modules/seqtk/subseq/nextflow.config
rename to tests/modules/nf-core/seqtk/subseq/nextflow.config
diff --git a/tests/modules/nf-core/seqtk/subseq/test.yml b/tests/modules/nf-core/seqtk/subseq/test.yml
new file mode 100644
index 00000000000..9b9e0750647
--- /dev/null
+++ b/tests/modules/nf-core/seqtk/subseq/test.yml
@@ -0,0 +1,8 @@
+- name: seqtk subseq test_seqtk_subseq
+  command: nextflow run ./tests/modules/nf-core/seqtk/subseq -entry test_seqtk_subseq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqtk/subseq/nextflow.config
+  tags:
+    - seqtk
+    - seqtk/subseq
+  files:
+    - path: output/seqtk/genome.fasta.filtered.fa.gz
+      md5sum: 488001c0fbedabf24d3e10fe7f96c78a
diff --git a/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf b/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf
new file mode 100755
index 00000000000..9304d805314
--- /dev/null
+++ b/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../../modules/nf-core/sequenzautils/bam2seqz/main.nf'
+
+workflow test_sequenzautils_bam2seqz {
+
+    tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
+
+    input = [ [ id:'test' ], // meta map
+              tumourbam,
+              normalbam
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    wig   = file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true)
+
+    SEQUENZAUTILS_BAM2SEQZ ( input, fasta, wig )
+}
diff --git a/tests/modules/sequenzautils/bam2seqz/nextflow.config b/tests/modules/nf-core/sequenzautils/bam2seqz/nextflow.config
similarity index 100%
rename from tests/modules/sequenzautils/bam2seqz/nextflow.config
rename to tests/modules/nf-core/sequenzautils/bam2seqz/nextflow.config
diff --git a/tests/modules/nf-core/sequenzautils/bam2seqz/test.yml b/tests/modules/nf-core/sequenzautils/bam2seqz/test.yml
new file mode 100644
index 00000000000..3326aef5ff8
--- /dev/null
+++ b/tests/modules/nf-core/sequenzautils/bam2seqz/test.yml
@@ -0,0 +1,8 @@
+- name: sequenzautils bam2seqz
+  command: nextflow run ./tests/modules/nf-core/sequenzautils/bam2seqz -entry test_sequenzautils_bam2seqz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sequenzautils/bam2seqz/nextflow.config
+  tags:
+    - sequenzautils
+    - sequenzautils/bam2seqz
+  files:
+    - path: output/sequenzautils/test.gz
+      md5sum: 12b41979a498ac10c0aff162b12e6a6e
diff --git a/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf b/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf
new file mode 100644
index 00000000000..776e4f17f32
--- /dev/null
+++ b/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQUENZAUTILS_GCWIGGLE } from '../../../../../modules/nf-core/sequenzautils/gcwiggle/main.nf'
+
+workflow test_sequenzautils_gcwiggle {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            ]
+
+    SEQUENZAUTILS_GCWIGGLE ( input )
+}
diff --git a/tests/modules/sequenzautils/gcwiggle/nextflow.config b/tests/modules/nf-core/sequenzautils/gcwiggle/nextflow.config
similarity index 100%
rename from tests/modules/sequenzautils/gcwiggle/nextflow.config
rename to tests/modules/nf-core/sequenzautils/gcwiggle/nextflow.config
diff --git a/tests/modules/nf-core/sequenzautils/gcwiggle/test.yml b/tests/modules/nf-core/sequenzautils/gcwiggle/test.yml
new file mode 100644
index 00000000000..973adb44fe1
--- /dev/null
+++ b/tests/modules/nf-core/sequenzautils/gcwiggle/test.yml
@@ -0,0 +1,7 @@
+- name: sequenzautils gcwiggle
+  command: nextflow run ./tests/modules/nf-core/sequenzautils/gcwiggle -entry test_sequenzautils_gcwiggle -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sequenzautils/gcwiggle/nextflow.config
+  tags:
+    - sequenzautils
+    - sequenzautils/gcwiggle
+  files:
+    - path: output/sequenzautils/test.wig.gz
diff --git a/tests/modules/nf-core/seqwish/induce/main.nf b/tests/modules/nf-core/seqwish/induce/main.nf
new file mode 100644
index 00000000000..20aae22b07e
--- /dev/null
+++ b/tests/modules/nf-core/seqwish/induce/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQWISH_INDUCE } from '../../../../../modules/nf-core/seqwish/induce/main.nf'
+
+workflow test_seqwish_induce_transcriptome {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['transcriptome_paf'], checkIfExists: true)],
+              [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+            ]
+
+    SEQWISH_INDUCE ( input )
+}
+
+workflow test_seqwish_induce_pangenome {
+    input = [ [ id:'test' ], // meta map
+            [ file(params.test_data['homo_sapiens']['pangenome']['pangenome_paf'], checkIfExists: true)],
+            [ file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa'], checkIfExists: true) ]
+        ]
+
+    SEQWISH_INDUCE ( input )
+}
diff --git a/tests/modules/seqwish/induce/nextflow.config b/tests/modules/nf-core/seqwish/induce/nextflow.config
similarity index 100%
rename from tests/modules/seqwish/induce/nextflow.config
rename to tests/modules/nf-core/seqwish/induce/nextflow.config
diff --git a/tests/modules/nf-core/seqwish/induce/test.yml b/tests/modules/nf-core/seqwish/induce/test.yml
new file mode 100644
index 00000000000..20d17b794de
--- /dev/null
+++ b/tests/modules/nf-core/seqwish/induce/test.yml
@@ -0,0 +1,17 @@
+- name: seqwish induce transcriptome
+  command: nextflow run ./tests/modules/nf-core/seqwish/induce -entry test_seqwish_induce_transcriptome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqwish/induce/nextflow.config
+  tags:
+    - seqwish
+    - seqwish/induce
+  files:
+    - path: output/seqwish/test.gfa
+      md5sum: 216a02d3aca322a457c31a62c628548e
+
+- name: seqwish induce pangenome
+  command: nextflow run ./tests/modules/nf-core/seqwish/induce -entry test_seqwish_induce_pangenome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqwish/induce/nextflow.config
+  tags:
+    - seqwish
+    - seqwish/induce
+  files:
+    - path: output/seqwish/test.gfa
+      md5sum: a73e998dc13a75d86d4685b12625d784
diff --git a/tests/modules/nf-core/seroba/run/main.nf b/tests/modules/nf-core/seroba/run/main.nf
new file mode 100644
index 00000000000..0f58c610d2c
--- /dev/null
+++ b/tests/modules/nf-core/seroba/run/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEROBA_RUN } from '../../../../../modules/nf-core/seroba/run/main.nf'
+
+workflow test_seroba_run {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true),
+                file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ]
+            ]
+
+    SEROBA_RUN ( input )
+}
diff --git a/tests/modules/seroba/run/nextflow.config b/tests/modules/nf-core/seroba/run/nextflow.config
similarity index 100%
rename from tests/modules/seroba/run/nextflow.config
rename to tests/modules/nf-core/seroba/run/nextflow.config
diff --git a/tests/modules/nf-core/seroba/run/test.yml b/tests/modules/nf-core/seroba/run/test.yml
new file mode 100644
index 00000000000..adcc2a2e571
--- /dev/null
+++ b/tests/modules/nf-core/seroba/run/test.yml
@@ -0,0 +1,8 @@
+- name: seroba run test_seroba_run
+  command: nextflow run ./tests/modules/nf-core/seroba/run -entry test_seroba_run -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/seroba/run/nextflow.config
+  tags:
+    - seroba
+    - seroba/run
+  files:
+    - path: output/seroba/test/test.tsv
+      md5sum: 28b2ce33df270172e6a39db4429e684b
diff --git a/tests/modules/nf-core/sexdeterrmine/main.nf b/tests/modules/nf-core/sexdeterrmine/main.nf
new file mode 100644
index 00000000000..10d3e53f469
--- /dev/null
+++ b/tests/modules/nf-core/sexdeterrmine/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_DEPTH } from '../../../../modules/nf-core/samtools/depth/main.nf'
+include { SEXDETERRMINE } from '../../../../modules/nf-core/sexdeterrmine/main.nf'
+
+workflow test_sexdeterrmine {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test3_single_end_markduplicates_sorted_bam'], checkIfExists: true) ]
+
+    SAMTOOLS_DEPTH ( input )
+    SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )
+}
diff --git a/tests/modules/sexdeterrmine/nextflow.config b/tests/modules/nf-core/sexdeterrmine/nextflow.config
similarity index 100%
rename from tests/modules/sexdeterrmine/nextflow.config
rename to tests/modules/nf-core/sexdeterrmine/nextflow.config
diff --git a/tests/modules/nf-core/sexdeterrmine/test.yml b/tests/modules/nf-core/sexdeterrmine/test.yml
new file mode 100644
index 00000000000..7dd2542d12f
--- /dev/null
+++ b/tests/modules/nf-core/sexdeterrmine/test.yml
@@ -0,0 +1,15 @@
+- name: sexdeterrmine test_sexdeterrmine
+  command: nextflow run ./tests/modules/nf-core/sexdeterrmine -entry test_sexdeterrmine -c ./tests/config/nextflow.config
+  tags:
+    - sexdeterrmine
+  files:
+    - path: output/samtools/test.tsv
+      md5sum: fa2992ca1ea93a6e1b3e838476191935
+    - path: output/samtools/versions.yml
+      md5sum: dbd04b700335c8ad236bd667254c8dd8
+    - path: output/sexdeterrmine/sexdeterrmine.json
+      md5sum: bafb2419bb8630eda29a251c20e97166
+    - path: output/sexdeterrmine/test_sexdet.tsv
+      md5sum: 1cf8a2b97b38353eb97a96ab872dcca9
+    - path: output/sexdeterrmine/versions.yml
+      md5sum: 077361101e8e7997aec3da8a01e59eee
diff --git a/tests/modules/nf-core/shasta/main.nf b/tests/modules/nf-core/shasta/main.nf
new file mode 100644
index 00000000000..0bf5298a365
--- /dev/null
+++ b/tests/modules/nf-core/shasta/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SHASTA } from '../../../../modules/nf-core/shasta/main.nf'
+
+workflow test_shasta {
+    
+    input = [ 
+        [ id:'test', model:'Nanopore-Dec2019' ], // meta map
+        [ file(params.test_data['candidatus_portiera_aleyrodidarum']['nanopore']['test_fastq_gz']) ],
+    ]
+
+    SHASTA ( input )
+}
diff --git a/tests/modules/shasta/nextflow.config b/tests/modules/nf-core/shasta/nextflow.config
similarity index 100%
rename from tests/modules/shasta/nextflow.config
rename to tests/modules/nf-core/shasta/nextflow.config
diff --git a/tests/modules/nf-core/shasta/test.yml b/tests/modules/nf-core/shasta/test.yml
new file mode 100644
index 00000000000..356b0194ff6
--- /dev/null
+++ b/tests/modules/nf-core/shasta/test.yml
@@ -0,0 +1,35 @@
+- name: shasta test_shasta
+  command: nextflow run ./tests/modules/nf-core/shasta -entry test_shasta -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/shasta/nextflow.config
+  tags:
+    - shasta
+  files:
+    - path: output/shasta/ShastaRun/Assembly-BothStrands-NoSequence.gfa
+    - path: output/shasta/ShastaRun/Assembly-BothStrands.gfa
+    - path: output/shasta/ShastaRun/Assembly.fasta
+    - path: output/shasta/ShastaRun/Assembly.gfa
+    - path: output/shasta/ShastaRun/AssemblySummary.csv
+    - path: output/shasta/ShastaRun/AssemblySummary.html
+    - path: output/shasta/ShastaRun/AssemblySummary.json
+    - path: output/shasta/ShastaRun/Binned-ReadLengthHistogram.csv
+      md5sum: f7997650e6ff2b060c583c6fa796628e
+    - path: output/shasta/ShastaRun/DisjointSetsHistogram.csv
+      md5sum: eecb9fae34b719dad64952257e2398a6
+    - path: output/shasta/ShastaRun/LowHashBucketHistogram.csv
+      md5sum: e5eb4a0d28ade913de6584928f32b7aa
+    - path: output/shasta/ShastaRun/MarkerGraphEdgeCoverageHistogram.csv
+      md5sum: 37ecac444067fbf4e0d96dc2705a9ada
+    - path: output/shasta/ShastaRun/MarkerGraphVertexCoverageHistogram.csv
+      md5sum: ccb236ab97ab1b9964b4856aa47d3c94
+    - path: output/shasta/ShastaRun/ReadGraphComponents.csv
+    - path: output/shasta/ShastaRun/ReadLengthHistogram.csv
+      md5sum: ccb25c4850ba2682fd1d452d6596d7bc
+    - path: output/shasta/ShastaRun/ReadLowHashStatistics.csv
+      md5sum: 2431d47341b239cb6edf8e3a7a76021f
+    - path: output/shasta/ShastaRun/ReadSummary.csv
+      md5sum: 8e0bffccf7afae54a937266949d118af
+    - path: output/shasta/ShastaRun/index.html
+      md5sum: 2d067ccc873b94a73e7300fe597db135
+    - path: output/shasta/ShastaRun/shasta.conf
+      md5sum: cba4aebac8a74eb5868f4a20f04bc618
+    - path: output/shasta/test_Assembly.fasta.gz
+    - path: output/shasta/test_Assembly.gfa.gz
diff --git a/tests/modules/nf-core/shasum/main.nf b/tests/modules/nf-core/shasum/main.nf
new file mode 100644
index 00000000000..d7f3ce50680
--- /dev/null
+++ b/tests/modules/nf-core/shasum/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SHASUM } from '../../../../modules/nf-core/shasum/main.nf'
+
+workflow test_shasum {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    SHASUM ( input )
+}
diff --git a/tests/modules/shasum/nextflow.config b/tests/modules/nf-core/shasum/nextflow.config
similarity index 100%
rename from tests/modules/shasum/nextflow.config
rename to tests/modules/nf-core/shasum/nextflow.config
diff --git a/tests/modules/nf-core/shasum/test.yml b/tests/modules/nf-core/shasum/test.yml
new file mode 100644
index 00000000000..063844d0edd
--- /dev/null
+++ b/tests/modules/nf-core/shasum/test.yml
@@ -0,0 +1,8 @@
+- name: shasum test_shasum
+  command: nextflow run ./tests/modules/nf-core/shasum -entry test_shasum -c ./tests/config/nextflow.config
+  tags:
+    - shasum
+  files:
+    - path: output/shasum/test.paired_end.bam.sha256
+      md5sum: 138a19e100f09fc975ea1b717da9b6dd
+    - path: output/shasum/versions.yml
diff --git a/tests/modules/nf-core/shigatyper/main.nf b/tests/modules/nf-core/shigatyper/main.nf
new file mode 100644
index 00000000000..e04fd5ad2f7
--- /dev/null
+++ b/tests/modules/nf-core/shigatyper/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SHIGATYPER } from '../../../../modules/nf-core/shigatyper/main.nf'
+
+workflow test_shigatyper_pe {
+    
+    input = [ 
+        [ id:'test', single_end:false, is_ont:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    SHIGATYPER ( input )
+}
+
+workflow test_shigatyper_se {
+    
+    input = [ 
+        [ id:'test', single_end:true, is_ont:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    SHIGATYPER ( input )
+}
+
+workflow test_shigatyper_ont {
+    
+    input = [ 
+        [ id:'test', single_end:true, is_ont:true ], // meta map
+        [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    SHIGATYPER ( input )
+}
diff --git a/tests/modules/shigatyper/nextflow.config b/tests/modules/nf-core/shigatyper/nextflow.config
similarity index 100%
rename from tests/modules/shigatyper/nextflow.config
rename to tests/modules/nf-core/shigatyper/nextflow.config
diff --git a/tests/modules/nf-core/shigatyper/test.yml b/tests/modules/nf-core/shigatyper/test.yml
new file mode 100644
index 00000000000..407a7906427
--- /dev/null
+++ b/tests/modules/nf-core/shigatyper/test.yml
@@ -0,0 +1,29 @@
+- name: shigatyper test_shigatyper_pe
+  command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_pe -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config
+  tags:
+    - shigatyper
+  files:
+    - path: output/shigatyper/test.tsv
+      md5sum: 4f7d38c956993800546b9acb9881d717
+    - path: output/shigatyper/versions.yml
+      md5sum: d8ca45ed88dfba9bc570c01e4b49773b
+
+- name: shigatyper test_shigatyper_se
+  command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_se -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config
+  tags:
+    - shigatyper
+  files:
+    - path: output/shigatyper/test.tsv
+      md5sum: 4f7d38c956993800546b9acb9881d717
+    - path: output/shigatyper/versions.yml
+      md5sum: 8bbf165da5a5df3b7771a33aad197eec
+
+- name: shigatyper test_shigatyper_ont
+  command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_ont -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config
+  tags:
+    - shigatyper
+  files:
+    - path: output/shigatyper/test.tsv
+      md5sum: 4f7d38c956993800546b9acb9881d717
+    - path: output/shigatyper/versions.yml
+      md5sum: 0da333e1178e9e7e84a9116ad5a5ff71
diff --git a/tests/modules/nf-core/shovill/main.nf b/tests/modules/nf-core/shovill/main.nf
new file mode 100644
index 00000000000..5596c7cb78a
--- /dev/null
+++ b/tests/modules/nf-core/shovill/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SHOVILL                    } from '../../../../modules/nf-core/shovill/main.nf'
+include { SHOVILL as SHOVILL_SKESA   } from '../../../../modules/nf-core/shovill/main.nf'
+include { SHOVILL as SHOVILL_MEGAHIT } from '../../../../modules/nf-core/shovill/main.nf'
+include { SHOVILL as SHOVILL_VELVET  } from '../../../../modules/nf-core/shovill/main.nf'
+
+workflow test_shovill {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true),
+                file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ]
+            ]
+
+    SHOVILL ( input )
+}
+
+workflow test_shovill_megahit {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SHOVILL_MEGAHIT ( input )
+}
+
+workflow test_shovill_skesa {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SHOVILL_SKESA ( input )
+}
+
+workflow test_shovill_velvet {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SHOVILL_VELVET ( input )
+}
diff --git a/tests/modules/shovill/nextflow.config b/tests/modules/nf-core/shovill/nextflow.config
similarity index 100%
rename from tests/modules/shovill/nextflow.config
rename to tests/modules/nf-core/shovill/nextflow.config
diff --git a/tests/modules/nf-core/shovill/test.yml b/tests/modules/nf-core/shovill/test.yml
new file mode 100644
index 00000000000..755c384fb0e
--- /dev/null
+++ b/tests/modules/nf-core/shovill/test.yml
@@ -0,0 +1,51 @@
+- name: shovill with spades
+  command: nextflow run ./tests/modules/nf-core/shovill -entry test_shovill -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shovill/nextflow.config
+  tags:
+    - shovill
+  files:
+    - path: output/shovill/contigs.gfa
+      md5sum: 277af5d8ae8a0d2432db59a316226828
+    - path: output/shovill/spades.fasta
+      md5sum: 2506fc2af3a24397a3c5d3fbda0861fb
+    # MD5sum not reproducible (timestamp)
+    - path: output/shovill/contigs.fa
+    - path: output/shovill/shovill.corrections
+    - path: output/shovill/shovill.log
+
+- name: shovill with megahit
+  command: nextflow run ./tests/modules/nf-core/shovill -entry test_shovill_megahit -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shovill/nextflow.config
+  tags:
+    - shovill
+  files:
+    - path: output/shovill/shovill.corrections
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    # MD5sum not reproducible (timestamp, contig order)
+    - path: output/shovill/contigs.fa
+    - path: output/shovill/contigs.fastg
+    - path: output/shovill/megahit.fasta
+    - path: output/shovill/shovill.log
+
+- name: shovill with skesa
+  command: nextflow run ./tests/modules/nf-core/shovill -entry test_shovill_skesa -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shovill/nextflow.config
+  tags:
+    - shovill
+  files:
+    - path: output/shovill/shovill.corrections
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/shovill/skesa.fasta
+      md5sum: 8157837dbe8315922f588dafa7af5ef8
+    # MD5sum not reproducible (timestamp)
+    - path: output/shovill/contigs.fa
+    - path: output/shovill/shovill.log
+
+- name: shovill with velvet
+  command: nextflow run ./tests/modules/nf-core/shovill -entry test_shovill_velvet -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shovill/nextflow.config
+  tags:
+    - shovill
+  files:
+    # MD5sum not reproducible (timestamp, contig order)
+    - path: output/shovill/contigs.fa
+    - path: output/shovill/contigs.LastGraph
+    - path: output/shovill/shovill.corrections
+    - path: output/shovill/shovill.log
+    - path: output/shovill/velvet.fasta
diff --git a/tests/modules/nf-core/sistr/main.nf b/tests/modules/nf-core/sistr/main.nf
new file mode 100644
index 00000000000..4b8948d23f3
--- /dev/null
+++ b/tests/modules/nf-core/sistr/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SISTR } from '../../../../modules/nf-core/sistr/main.nf'
+
+workflow test_sistr {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    SISTR ( input )
+}
diff --git a/tests/modules/sistr/nextflow.config b/tests/modules/nf-core/sistr/nextflow.config
similarity index 100%
rename from tests/modules/sistr/nextflow.config
rename to tests/modules/nf-core/sistr/nextflow.config
diff --git a/tests/modules/nf-core/sistr/test.yml b/tests/modules/nf-core/sistr/test.yml
new file mode 100644
index 00000000000..5ec8ac00f26
--- /dev/null
+++ b/tests/modules/nf-core/sistr/test.yml
@@ -0,0 +1,15 @@
+- name: sistr test_sistr
+  command: nextflow run ./tests/modules/nf-core/sistr -entry test_sistr -c ./tests/config/nextflow.config
+  tags:
+    - sistr
+  files:
+    - path: output/sistr/test-allele.fasta
+      md5sum: 144a74999eb9dd01520be5c61e8bd210
+    - path: output/sistr/test-allele.json
+      md5sum: 3eb993c9489904621f539a93ff9a90ec
+    - path: output/sistr/test-cgmlst.csv
+      md5sum: c50a2144955fe1b98a6d5792bf295088
+    - path: output/sistr/test.tab
+      contains: ["cgmlst_ST", "serovar", "matched"]
+    - path: output/sistr/versions.yml
+      md5sum: 8b852f002c3ce67e3f6498da15b28296
diff --git a/tests/modules/nf-core/slimfastq/main.nf b/tests/modules/nf-core/slimfastq/main.nf
new file mode 100644
index 00000000000..2993eb981f9
--- /dev/null
+++ b/tests/modules/nf-core/slimfastq/main.nf
@@ -0,0 +1,46 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SLIMFASTQ } from '../../../../modules/nf-core/slimfastq/main.nf'
+
+workflow test_slimfastq_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    SLIMFASTQ ( input )
+}
+
+workflow test_slimfastq_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+         file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
+    ]
+
+    SLIMFASTQ ( input )
+}
+
+workflow test_slimfastq_nanopore {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+    ]
+
+    SLIMFASTQ ( input )
+}
+
+workflow test_slimfastq_pacbio {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true)
+    ]
+
+    SLIMFASTQ ( input )
+}
diff --git a/tests/modules/slimfastq/nextflow.config b/tests/modules/nf-core/slimfastq/nextflow.config
similarity index 100%
rename from tests/modules/slimfastq/nextflow.config
rename to tests/modules/nf-core/slimfastq/nextflow.config
diff --git a/tests/modules/nf-core/slimfastq/test.yml b/tests/modules/nf-core/slimfastq/test.yml
new file mode 100644
index 00000000000..6010f2c6ce0
--- /dev/null
+++ b/tests/modules/nf-core/slimfastq/test.yml
@@ -0,0 +1,41 @@
+- name: slimfastq test_slimfastq_single_end
+  command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_single_end -c ./tests/config/nextflow.config
+  tags:
+    - slimfastq
+  files:
+    - path: output/slimfastq/test.sfq
+      md5sum: 6a942eeca6c99ee9a9a0cedab5d246f1
+    - path: output/slimfastq/versions.yml
+      md5sum: f52351f5c9e6259af02745c8eae5c780
+
+- name: slimfastq test_slimfastq_paired_end
+  command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - slimfastq
+  files:
+    - path: output/slimfastq/test_1.sfq
+      md5sum: 6a942eeca6c99ee9a9a0cedab5d246f1
+    - path: output/slimfastq/test_2.sfq
+      md5sum: 0d2c60b52a39f7c2cb7843e848d90afd
+    - path: output/slimfastq/versions.yml
+      md5sum: 6239853705877651a4851c4cb6d62da4
+
+- name: slimfastq test_slimfastq_nanopore
+  command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_nanopore -c ./tests/config/nextflow.config
+  tags:
+    - slimfastq
+  files:
+    - path: output/slimfastq/test.sfq
+      md5sum: e17f14d64d3a75356b03ff2f9e8881f7
+    - path: output/slimfastq/versions.yml
+      md5sum: 33153f1103482a2bd35cb2f4c337c5e8
+
+- name: slimfastq test_slimfastq_pacbio
+  command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_pacbio -c ./tests/config/nextflow.config
+  tags:
+    - slimfastq
+  files:
+    - path: output/slimfastq/test.sfq
+      md5sum: 9e8389e47e6ddf8c25e92412dd628339
+    - path: output/slimfastq/versions.yml
+      md5sum: 1982789c3d5c7de37c0a9351e4ae63f7
diff --git a/tests/modules/nf-core/snapaligner/align/main.nf b/tests/modules/nf-core/snapaligner/align/main.nf
new file mode 100644
index 00000000000..8f30888369d
--- /dev/null
+++ b/tests/modules/nf-core/snapaligner/align/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNAPALIGNER_INDEX } from '../../../../../modules/nf-core/snapaligner/index/main.nf'
+include { SNAPALIGNER_ALIGN } from '../../../../../modules/nf-core/snapaligner/align/main.nf'
+
+workflow test_snapaligner_single {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+    ]
+
+    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
+    SNAPALIGNER_ALIGN ( input, SNAPALIGNER_INDEX.out.index )
+}
+
+workflow test_snapaligner_paired {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
+    ]
+
+    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
+    SNAPALIGNER_ALIGN ( input, SNAPALIGNER_INDEX.out.index )
+}
diff --git a/tests/modules/snapaligner/align/nextflow.config b/tests/modules/nf-core/snapaligner/align/nextflow.config
similarity index 100%
rename from tests/modules/snapaligner/align/nextflow.config
rename to tests/modules/nf-core/snapaligner/align/nextflow.config
diff --git a/tests/modules/nf-core/snapaligner/align/test.yml b/tests/modules/nf-core/snapaligner/align/test.yml
new file mode 100644
index 00000000000..1acf9af5985
--- /dev/null
+++ b/tests/modules/nf-core/snapaligner/align/test.yml
@@ -0,0 +1,21 @@
+- name: snapaligner align test_snapaligner_single
+  command: nextflow run ./tests/modules/nf-core/snapaligner/align -entry test_snapaligner_single -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/snapaligner/align/nextflow.config
+  tags:
+    - snapaligner/align
+    - snapaligner
+  files:
+    - path: output/snapaligner/test.bam
+      md5sum: 9958e511fe759012cd11b7ef1f097639
+    - path: output/snapaligner/test.bam.bai
+      md5sum: f180c68a77445b317a22e3f1d6e6e114
+
+- name: snapaligner align test_snapaligner_paired
+  command: nextflow run ./tests/modules/nf-core/snapaligner/align -entry test_snapaligner_paired -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/snapaligner/align/nextflow.config
+  tags:
+    - snapaligner/align
+    - snapaligner
+  files:
+    - path: output/snapaligner/test.bam
+      md5sum: cf656d5f18afa6a97825a685e1b2b141
+    - path: output/snapaligner/test.bam.bai
+      md5sum: fa2226d7f5b0b4b15d014332f94a8b84
diff --git a/tests/modules/nf-core/snapaligner/index/main.nf b/tests/modules/nf-core/snapaligner/index/main.nf
new file mode 100644
index 00000000000..a1b01c36f9c
--- /dev/null
+++ b/tests/modules/nf-core/snapaligner/index/main.nf
@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNAPALIGNER_INDEX } from '../../../../../modules/nf-core/snapaligner/index/main.nf'
+
+workflow test_snapaligner_index {
+    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
+}
diff --git a/tests/modules/snapaligner/index/nextflow.config b/tests/modules/nf-core/snapaligner/index/nextflow.config
similarity index 100%
rename from tests/modules/snapaligner/index/nextflow.config
rename to tests/modules/nf-core/snapaligner/index/nextflow.config
diff --git a/tests/modules/nf-core/snapaligner/index/test.yml b/tests/modules/nf-core/snapaligner/index/test.yml
new file mode 100644
index 00000000000..43898e069c8
--- /dev/null
+++ b/tests/modules/nf-core/snapaligner/index/test.yml
@@ -0,0 +1,13 @@
+- name: snapaligner index test_snapaligner_index
+  command: nextflow run ./tests/modules/nf-core/snapaligner/index -entry test_snapaligner_index -c ./tests/config/nextflow.config
+  tags:
+    - snapaligner/index
+    - snapaligner
+  files:
+    - path: output/snapaligner/snap/Genome
+      md5sum: 7e189c954142ba37460332b467e34ed4
+    - path: output/snapaligner/snap/GenomeIndex
+      md5sum: 298da8bcb1134f7b24379a792a7a46f8
+    - path: output/snapaligner/snap/GenomeIndexHash
+    - path: output/snapaligner/snap/OverflowTable
+    - path: output/snapaligner/versions.yml
diff --git a/tests/modules/nf-core/snippy/core/main.nf b/tests/modules/nf-core/snippy/core/main.nf
new file mode 100644
index 00000000000..3f786c371f4
--- /dev/null
+++ b/tests/modules/nf-core/snippy/core/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNIPPY_RUN } from '../../../../../modules/nf-core/snippy/run/main.nf'
+include { SNIPPY_CORE } from '../../../../../modules/nf-core/snippy/core/main.nf'
+
+workflow test_snippy_core {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['candidatus_portiera_aleyrodidarum']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['candidatus_portiera_aleyrodidarum']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    reference = file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
+
+    SNIPPY_RUN ( input, reference )
+    SNIPPY_RUN.out.vcf.collect{meta, vcf -> vcf}.map{ vcf -> [[id:'snippy-core'], vcf]}.set{ ch_merge_vcf }
+    SNIPPY_RUN.out.aligned_fa.collect{meta, aligned_fa -> aligned_fa}.map{ aligned_fa -> [[id:'snippy-core'], aligned_fa]}.set{ ch_merge_aligned_fa }
+    ch_merge_vcf.join( ch_merge_aligned_fa ).set{ ch_snippy_core }
+    SNIPPY_CORE( ch_snippy_core, reference )
+
+}
diff --git a/tests/modules/snippy/core/nextflow.config b/tests/modules/nf-core/snippy/core/nextflow.config
similarity index 100%
rename from tests/modules/snippy/core/nextflow.config
rename to tests/modules/nf-core/snippy/core/nextflow.config
diff --git a/tests/modules/nf-core/snippy/core/test.yml b/tests/modules/nf-core/snippy/core/test.yml
new file mode 100644
index 00000000000..d6147d9fe2f
--- /dev/null
+++ b/tests/modules/nf-core/snippy/core/test.yml
@@ -0,0 +1,16 @@
+- name: snippy core test_snippy_core
+  command: nextflow run ./tests/modules/nf-core/snippy/core -entry test_snippy_core -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/snippy/core/nextflow.config
+  tags:
+    - snippy
+    - snippy/core
+  files:
+    - path: output/snippy/snippy-core.aln
+      md5sum: 23cf80454a83849977aeb7193a5eab8e
+    - path: output/snippy/snippy-core.full.aln
+      md5sum: fcadf17c2c8109fe4491ab7e7df6e261
+    - path: output/snippy/snippy-core.tab
+      md5sum: 1eb437b4d82d8dbc93649b0edf94abc8
+    - path: output/snippy/snippy-core.txt
+      md5sum: 243961814f44b9a6cac48b69f02b4349
+    - path: output/snippy/snippy-core.vcf
+      md5sum: 8b4ff1f2e7f1cef9d168dad5d70e642a
diff --git a/tests/modules/nf-core/snippy/run/main.nf b/tests/modules/nf-core/snippy/run/main.nf
new file mode 100644
index 00000000000..1150c893701
--- /dev/null
+++ b/tests/modules/nf-core/snippy/run/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNIPPY_RUN } from '../../../../../modules/nf-core/snippy/run/main.nf'
+
+workflow test_snippy_run {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    SNIPPY_RUN ( input, reference )
+}
diff --git a/tests/modules/snippy/run/nextflow.config b/tests/modules/nf-core/snippy/run/nextflow.config
similarity index 100%
rename from tests/modules/snippy/run/nextflow.config
rename to tests/modules/nf-core/snippy/run/nextflow.config
diff --git a/tests/modules/nf-core/snippy/run/test.yml b/tests/modules/nf-core/snippy/run/test.yml
new file mode 100644
index 00000000000..dcdf41b84e0
--- /dev/null
+++ b/tests/modules/nf-core/snippy/run/test.yml
@@ -0,0 +1,39 @@
+- name: snippy run test_snippy_run
+  command: |
+    nextflow run ./tests/modules/nf-core/snippy/run -entry test_snippy_run -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snippy/run/nextflow.config
+  tags:
+    - snippy/run
+    - snippy
+  files:
+    - path: output/snippy/test/test.aligned.fa
+      md5sum: 47e3390d4167edf1955d162d37aca5e3
+    - path: output/snippy/test/test.bam
+    - path: output/snippy/test/test.bam.bai
+    - path: output/snippy/test/test.bed
+    - path: output/snippy/test/test.consensus.fa
+      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
+    - path: output/snippy/test/test.consensus.subs.fa
+      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
+    - path: output/snippy/test/test.csv
+      md5sum: 322f942115e5945c2041a88246166703
+    - path: output/snippy/test/test.filt.vcf
+      contains: ["fileformat", "freebayes", "CHROM"]
+    - path: output/snippy/test/test.gff
+      md5sum: df19e1b84ba6f691d20c72b397c88abf
+    - path: output/snippy/test/test.html
+      md5sum: 1ccbf0ffcadae1a6b2e11681d24c9938
+    - path: output/snippy/test/test.log
+      contains: ["snippy", "consensus", "subs"]
+    - path: output/snippy/test/test.raw.vcf
+      contains: ["fileformat", "freebayes", "CHROM"]
+    - path: output/snippy/test/test.tab
+      md5sum: beb9bde3bce985e53e8feba9ec5b136e
+    - path: output/snippy/test/test.txt
+      contains: ["DateTime", "ReadFiles", "VariantTotal"]
+    - path: output/snippy/test/test.vcf
+      contains: ["fileformat", "freebayes", "CHROM"]
+    - path: output/snippy/test/test.vcf.gz
+    - path: output/snippy/test/test.vcf.gz.csi
+      md5sum: bed9fa291c220a1ba04eb2d448932ffc
+    - path: output/snippy/versions.yml
+      md5sum: 518aad56c4dbefb6cbcde5ab38cf7b5d
diff --git a/tests/modules/nf-core/snpdists/main.nf b/tests/modules/nf-core/snpdists/main.nf
new file mode 100644
index 00000000000..3cbf0e12cd0
--- /dev/null
+++ b/tests/modules/nf-core/snpdists/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNPDISTS } from '../../../../modules/nf-core/snpdists/main.nf'
+
+workflow test_snpdists {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
+
+    SNPDISTS ( input )
+}
diff --git a/tests/modules/snpdists/nextflow.config b/tests/modules/nf-core/snpdists/nextflow.config
similarity index 100%
rename from tests/modules/snpdists/nextflow.config
rename to tests/modules/nf-core/snpdists/nextflow.config
diff --git a/tests/modules/nf-core/snpdists/test.yml b/tests/modules/nf-core/snpdists/test.yml
new file mode 100644
index 00000000000..784abb6a7f2
--- /dev/null
+++ b/tests/modules/nf-core/snpdists/test.yml
@@ -0,0 +1,7 @@
+- name: snpdists
+  command: nextflow run ./tests/modules/nf-core/snpdists -entry test_snpdists -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snpdists/nextflow.config
+  tags:
+    - snpdists
+  files:
+    - path: output/snpdists/test.tsv
+      md5sum: 0018e5ec43990eb16abe2411fff4e47e
diff --git a/tests/modules/nf-core/snpeff/main.nf b/tests/modules/nf-core/snpeff/main.nf
new file mode 100644
index 00000000000..1670076a249
--- /dev/null
+++ b/tests/modules/nf-core/snpeff/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNPEFF } from '../../../../modules/nf-core/snpeff/main.nf'
+
+workflow test_snpeff {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    SNPEFF ( input, "WBcel235.105", [] )
+}
diff --git a/tests/modules/snpeff/nextflow.config b/tests/modules/nf-core/snpeff/nextflow.config
similarity index 100%
rename from tests/modules/snpeff/nextflow.config
rename to tests/modules/nf-core/snpeff/nextflow.config
diff --git a/tests/modules/nf-core/snpeff/test.yml b/tests/modules/nf-core/snpeff/test.yml
new file mode 100644
index 00000000000..b2043ba032e
--- /dev/null
+++ b/tests/modules/nf-core/snpeff/test.yml
@@ -0,0 +1,11 @@
+- name: snpeff test_snpeff
+  command: nextflow run ./tests/modules/nf-core/snpeff -entry test_snpeff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snpeff/nextflow.config
+  tags:
+    - snpeff
+  files:
+    - path: output/snpeff/test.ann.vcf
+      md5sum: e933384e572fc5ed0cce0faf1c0b2cc9
+    - path: output/snpeff/test.csv
+    - path: output/snpeff/test.genes.txt
+      md5sum: 130536bf0237d7f3f746d32aaa32840a
+    - path: output/snpeff/snpEff_summary.html
diff --git a/tests/modules/nf-core/snpsift/split/main.nf b/tests/modules/nf-core/snpsift/split/main.nf
new file mode 100644
index 00000000000..11cee60d860
--- /dev/null
+++ b/tests/modules/nf-core/snpsift/split/main.nf
@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNPSIFT_SPLIT } from '../../../../../modules/nf-core/snpsift/split/main.nf'
+
+workflow test_snpsift_split_base {
+
+    input = [ [ id:'test', split:true], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true) ]
+
+    SNPSIFT_SPLIT ( input )
+}
+
+workflow test_snpsift_split_gz {
+
+    input = [ [ id:'test', split:true ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+
+    SNPSIFT_SPLIT ( input )
+}
+
+workflow test_snpsift_join {
+
+    input = [   [ id:'test', split:false ], // meta map
+                [   file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+
+    SNPSIFT_SPLIT ( input )
+
+}
diff --git a/tests/modules/snpsift/split/nextflow.config b/tests/modules/nf-core/snpsift/split/nextflow.config
similarity index 100%
rename from tests/modules/snpsift/split/nextflow.config
rename to tests/modules/nf-core/snpsift/split/nextflow.config
diff --git a/tests/modules/nf-core/snpsift/split/test.yml b/tests/modules/nf-core/snpsift/split/test.yml
new file mode 100644
index 00000000000..30fe340fd7b
--- /dev/null
+++ b/tests/modules/nf-core/snpsift/split/test.yml
@@ -0,0 +1,32 @@
+- name: snpsift split test_snpsift_split_base
+  command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_split_base -c ./tests/config/nextflow.config
+  tags:
+    - snpsift/split
+    - snpsift
+  files:
+    - path: output/snpsift/test.rnaseq.chr22.vcf
+      md5sum: 1bb8724dcbe6fa3101a814c0be51d1ea
+    - path: output/snpsift/versions.yml
+      md5sum: 2b9f6b788db6c4fcbf258db763d8fab7
+
+- name: snpsift split test_snpsift_split_gz
+  command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_split_gz -c ./tests/config/nextflow.config
+  tags:
+    - snpsift/split
+    - snpsift
+  files:
+    - path: output/snpsift/test.MT192765.1.vcf
+      md5sum: 9d491cfa84067450342ba8e66c75e5b8
+    - path: output/snpsift/versions.yml
+      md5sum: 6bd63376670d6c1445caea2f31a3f579
+
+- name: snpsift split test_snpsift_join
+  command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_join -c ./tests/config/nextflow.config
+  tags:
+    - snpsift/split
+    - snpsift
+  files:
+    - path: output/snpsift/test.joined.vcf
+      md5sum: c400c7458524d889e0967b06ed72534f
+    - path: output/snpsift/versions.yml
+      md5sum: be54682a73d3b91a17eacc0e533448f5
diff --git a/tests/modules/nf-core/snpsites/main.nf b/tests/modules/nf-core/snpsites/main.nf
new file mode 100644
index 00000000000..a6a43095212
--- /dev/null
+++ b/tests/modules/nf-core/snpsites/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNPSITES } from '../../../../modules/nf-core/snpsites/main.nf'
+
+workflow test_snpsites {
+    
+    input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
+
+    SNPSITES ( input )
+}
diff --git a/tests/modules/snpsites/nextflow.config b/tests/modules/nf-core/snpsites/nextflow.config
similarity index 100%
rename from tests/modules/snpsites/nextflow.config
rename to tests/modules/nf-core/snpsites/nextflow.config
diff --git a/tests/modules/nf-core/snpsites/test.yml b/tests/modules/nf-core/snpsites/test.yml
new file mode 100644
index 00000000000..e8e071e499f
--- /dev/null
+++ b/tests/modules/nf-core/snpsites/test.yml
@@ -0,0 +1,9 @@
+- name: snpsites
+  command: nextflow run ./tests/modules/nf-core/snpsites -entry test_snpsites -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snpsites/nextflow.config
+  tags:
+    - snpsites
+  files:
+    - path: output/snpsites/filtered_alignment.fas
+      md5sum: f96c7513003e878e16fa9eac9fcda0f4
+    - path: output/snpsites/constant.sites.txt
+      md5sum: 8b9b226e3787f7baaefce07405af22c9
diff --git a/tests/modules/nf-core/somalier/extract/main.nf b/tests/modules/nf-core/somalier/extract/main.nf
new file mode 100644
index 00000000000..68847626e83
--- /dev/null
+++ b/tests/modules/nf-core/somalier/extract/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SOMALIER_EXTRACT } from '../../../../../modules/nf-core/somalier/extract/main.nf'
+
+fasta       = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+
+fasta_fai   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+sites       = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/sites_chr21.hg38.vcf.gz", checkIfExists: true)
+
+
+workflow test_somalier_extract {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    SOMALIER_EXTRACT ( input, [fasta, fasta_fai], sites )
+}
diff --git a/tests/modules/somalier/extract/nextflow.config b/tests/modules/nf-core/somalier/extract/nextflow.config
similarity index 100%
rename from tests/modules/somalier/extract/nextflow.config
rename to tests/modules/nf-core/somalier/extract/nextflow.config
diff --git a/tests/modules/nf-core/somalier/extract/test.yml b/tests/modules/nf-core/somalier/extract/test.yml
new file mode 100644
index 00000000000..23c6861866d
--- /dev/null
+++ b/tests/modules/nf-core/somalier/extract/test.yml
@@ -0,0 +1,8 @@
+- name: somalier extract test_somalier_extract
+  command: nextflow run ./tests/modules/nf-core/somalier/extract/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/somalier/extract/nextflow.config -entry test_somalier_extract
+  tags:
+    - somalier/extract
+    - somalier
+  files:
+    - path: output/somalier/normal.somalier
+      md5sum: 21f0b980edd42ddaa8ab964959c1de02
diff --git a/tests/modules/nf-core/somalier/relate/main.nf b/tests/modules/nf-core/somalier/relate/main.nf
new file mode 100644
index 00000000000..14b1977e635
--- /dev/null
+++ b/tests/modules/nf-core/somalier/relate/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SOMALIER_RELATE } from '../../../../../modules/nf-core/somalier/relate/main.nf'
+
+
+workflow test_somalier_relate {
+
+    input = [ [ id:'cohort', single_end:false ], // meta map
+        [ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/normal.somalier", checkIfExists: true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/tumour.somalier", checkIfExists: true) ]
+    ]
+
+    SOMALIER_RELATE (input,[],[])
+}
+
+
+workflow test_somalier_relate_ped_groups {
+
+input = [ [ id:'cohort', single_end:false ], // meta map
+    [ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/normal.somalier", checkIfExists: true),
+    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/tumour.somalier", checkIfExists: true) ]
+]
+
+    groups = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/groups.txt", checkIfExists: true)
+    ped = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/family.ped", checkIfExists: true)
+
+    SOMALIER_RELATE (input,groups,ped)
+}
diff --git a/tests/modules/somalier/relate/nextflow.config b/tests/modules/nf-core/somalier/relate/nextflow.config
similarity index 100%
rename from tests/modules/somalier/relate/nextflow.config
rename to tests/modules/nf-core/somalier/relate/nextflow.config
diff --git a/tests/modules/nf-core/somalier/relate/test.yml b/tests/modules/nf-core/somalier/relate/test.yml
new file mode 100644
index 00000000000..604a4e3ba17
--- /dev/null
+++ b/tests/modules/nf-core/somalier/relate/test.yml
@@ -0,0 +1,25 @@
+- name: somalier relate test_somalier_relate
+  command: nextflow run ./tests/modules/nf-core/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/somalier/relate/nextflow.config -entry test_somalier_relate
+  tags:
+    - somalier/relate
+    - somalier
+  files:
+    - path: output/somalier/cohort.html
+      md5sum: 03cac9b2c67a8a06f63e07f83ee11e18
+    - path: output/somalier/cohort.pairs.tsv
+      md5sum: 54d1e9fca1bf9d747d4254c6fa98edcf
+    - path: output/somalier/cohort.samples.tsv
+      md5sum: 97257d88886db1325c4d7d10cefa7169
+
+- name: somalier relate test_somalier_relate_ped_groups
+  command: nextflow run ./tests/modules/nf-core/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/somalier/relate/nextflow.config -entry test_somalier_relate_ped_groups
+  tags:
+    - somalier/relate
+    - somalier
+  files:
+    - path: output/somalier/cohort.html
+      md5sum: 0d573016c9279ccdfdcfd4eb01d73b89
+    - path: output/somalier/cohort.pairs.tsv
+      md5sum: 8655714f1e5359329188e9f501168131
+    - path: output/somalier/cohort.samples.tsv
+      md5sum: 38ef93340e55fbeef47640abda9e48b0
diff --git a/tests/modules/nf-core/sourmash/sketch/main.nf b/tests/modules/nf-core/sourmash/sketch/main.nf
new file mode 100644
index 00000000000..bb398d9a893
--- /dev/null
+++ b/tests/modules/nf-core/sourmash/sketch/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SOURMASH_SKETCH } from '../../../../../modules/nf-core/sourmash/sketch/main.nf'
+
+workflow test_sourmash_sketch {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    SOURMASH_SKETCH ( input )
+}
diff --git a/tests/modules/sourmash/sketch/nextflow.config b/tests/modules/nf-core/sourmash/sketch/nextflow.config
similarity index 100%
rename from tests/modules/sourmash/sketch/nextflow.config
rename to tests/modules/nf-core/sourmash/sketch/nextflow.config
diff --git a/tests/modules/nf-core/sourmash/sketch/test.yml b/tests/modules/nf-core/sourmash/sketch/test.yml
new file mode 100644
index 00000000000..2497236b645
--- /dev/null
+++ b/tests/modules/nf-core/sourmash/sketch/test.yml
@@ -0,0 +1,10 @@
+- name: sourmash sketch test_sourmash_sketch
+  command: nextflow run ./tests/modules/nf-core/sourmash/sketch -entry test_sourmash_sketch -c ./tests/config/nextflow.config
+  tags:
+    - sourmash
+    - sourmash/sketch
+  files:
+    - path: output/sourmash/test.sig
+      md5sum: 4b0dee307e35fc670cd0d416321e4961
+    - path: output/sourmash/versions.yml
+      md5sum: ec70dabc3e4b3bf11d39c17a99ca4bc6
diff --git a/tests/modules/nf-core/spades/main.nf b/tests/modules/nf-core/spades/main.nf
new file mode 100644
index 00000000000..9305112956a
--- /dev/null
+++ b/tests/modules/nf-core/spades/main.nf
@@ -0,0 +1,48 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SPADES } from '../../../../modules/nf-core/spades/main.nf'
+
+workflow test_spades_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
+              [],
+              []
+            ]
+    SPADES ( input, [] )
+}
+
+workflow test_spades_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
+              [],
+              []
+            ]
+
+    SPADES ( input, [] )
+}
+
+workflow test_spades_illumina_nanopore {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
+              [],
+              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    SPADES ( input, [] )
+}
+
+// that isnt perfect, because CCS reads should rather be used with -s instead of --pacbio
+workflow test_spades_illumina_pacbio {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
+              [ file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true) ],
+              []
+            ]
+
+    SPADES ( input, [] )
+}
diff --git a/tests/modules/spades/nextflow.config b/tests/modules/nf-core/spades/nextflow.config
similarity index 100%
rename from tests/modules/spades/nextflow.config
rename to tests/modules/nf-core/spades/nextflow.config
diff --git a/tests/modules/nf-core/spades/test.yml b/tests/modules/nf-core/spades/test.yml
new file mode 100644
index 00000000000..b4850b50b0f
--- /dev/null
+++ b/tests/modules/nf-core/spades/test.yml
@@ -0,0 +1,52 @@
+- name: spades test_spades_single_end
+  command: nextflow run ./tests/modules/nf-core/spades -entry test_spades_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spades/nextflow.config
+  tags:
+    - spades
+  files:
+    - path: output/spades/test.assembly.gfa.gz
+      md5sum: e5eab229363a906954a07df00e2495a6
+    - path: output/spades/test.contigs.fa.gz
+      md5sum: 64f6b339872b934138c6efd6baa445f4
+    - path: output/spades/test.scaffolds.fa.gz
+      md5sum: 64f6b339872b934138c6efd6baa445f4
+    - path: output/spades/test.spades.log
+
+- name: spades test_spades_paired_end
+  command: nextflow run ./tests/modules/nf-core/spades -entry test_spades_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spades/nextflow.config
+  tags:
+    - spades
+  files:
+    - path: output/spades/test.assembly.gfa.gz
+      md5sum: c8614fb69907ae832a1359a054af240f
+    - path: output/spades/test.contigs.fa.gz
+      md5sum: eab5165b3cda96c235aaa1388010cb27
+    - path: output/spades/test.spades.log
+    - path: output/spades/warnings.log
+
+- name: spades test_spades_illumina_nanopore
+  command: nextflow run ./tests/modules/nf-core/spades -entry test_spades_illumina_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spades/nextflow.config
+  tags:
+    - spades
+  files:
+    - path: output/spades/test.assembly.gfa.gz
+      md5sum: e438534f14e107f005efdd659adeba6a
+    - path: output/spades/test.contigs.fa.gz
+      md5sum: 027b0e54bfd8f4bc359e751e094133ef
+    - path: output/spades/test.scaffolds.fa.gz
+      md5sum: 027b0e54bfd8f4bc359e751e094133ef
+    - path: output/spades/test.spades.log
+    - path: output/spades/warnings.log
+
+- name: spades test_spades_illumina_pacbio
+  command: nextflow run ./tests/modules/nf-core/spades -entry test_spades_illumina_pacbio -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spades/nextflow.config
+  tags:
+    - spades
+  files:
+    - path: output/spades/test.assembly.gfa.gz
+      md5sum: 22f92cbade8f25be3ac170eaf09f4c7b
+    - path: output/spades/test.contigs.fa.gz
+      md5sum: bb2d294a5752a6f3a208834b8799ec98
+    - path: output/spades/test.scaffolds.fa.gz
+      md5sum: 65aa6e3364925ec617fffda3e84b4cbc
+    - path: output/spades/test.spades.log
+    - path: output/spades/warnings.log
diff --git a/tests/modules/nf-core/spatyper/main.nf b/tests/modules/nf-core/spatyper/main.nf
new file mode 100644
index 00000000000..5f6ced1d393
--- /dev/null
+++ b/tests/modules/nf-core/spatyper/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SPATYPER } from '../../../../modules/nf-core/spatyper/main.nf'
+include { SPATYPER as SPATYPER_ENRICH } from '../../../../modules/nf-core/spatyper/main.nf'
+
+workflow test_spatyper {
+    input = [ [ id:'test' ],
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    repeats = []
+    repeat_order = []
+
+    SPATYPER ( input, repeats, repeat_order )
+}
+
+workflow test_spatyper_enrich {
+    input = [ [ id:'test' ],
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    repeats = []
+    repeat_order = []
+
+    SPATYPER_ENRICH ( input, repeats, repeat_order )
+}
diff --git a/tests/modules/spatyper/nextflow.config b/tests/modules/nf-core/spatyper/nextflow.config
similarity index 100%
rename from tests/modules/spatyper/nextflow.config
rename to tests/modules/nf-core/spatyper/nextflow.config
diff --git a/tests/modules/nf-core/spatyper/test.yml b/tests/modules/nf-core/spatyper/test.yml
new file mode 100644
index 00000000000..4b998739a6e
--- /dev/null
+++ b/tests/modules/nf-core/spatyper/test.yml
@@ -0,0 +1,15 @@
+- name: spatyper test_spatyper
+  command: nextflow run ./tests/modules/nf-core/spatyper -entry test_spatyper -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spatyper/nextflow.config
+  tags:
+    - spatyper
+  files:
+    - path: output/spatyper/test.tsv
+      md5sum: a698352823875171696e5e7ed7015c13
+
+- name: spatyper test_spatyper_enrich
+  command: nextflow run ./tests/modules/nf-core/spatyper -entry test_spatyper_enrich -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spatyper/nextflow.config
+  tags:
+    - spatyper
+  files:
+    - path: output/spatyper/test.tsv
+      md5sum: a698352823875171696e5e7ed7015c13
diff --git a/tests/modules/nf-core/sratools/fasterqdump/main.nf b/tests/modules/nf-core/sratools/fasterqdump/main.nf
new file mode 100644
index 00000000000..922387069a0
--- /dev/null
+++ b/tests/modules/nf-core/sratools/fasterqdump/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf'
+include { SRATOOLS_FASTERQDUMP } from '../../../../../modules/nf-core/sratools/fasterqdump/main.nf'
+
+workflow test_sratools_fasterqdump_single_end {
+
+    archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]
+    UNTAR ( archive )
+
+    def input = Channel.of([ id:'test_single_end', single_end:true ])
+        .combine(UNTAR.out.untar.map{ it[1] })
+
+    SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
+}
+
+workflow test_sratools_fasterqdump_paired_end {
+
+    archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]
+    UNTAR ( archive )
+
+    def input = Channel.of([ id:'test_paired_end', single_end:false ])
+        .combine(UNTAR.out.untar.map{ it[1] })
+
+    SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
+}
diff --git a/tests/modules/sratools/fasterqdump/nextflow.config b/tests/modules/nf-core/sratools/fasterqdump/nextflow.config
similarity index 100%
rename from tests/modules/sratools/fasterqdump/nextflow.config
rename to tests/modules/nf-core/sratools/fasterqdump/nextflow.config
diff --git a/tests/modules/nf-core/sratools/fasterqdump/test.yml b/tests/modules/nf-core/sratools/fasterqdump/test.yml
new file mode 100644
index 00000000000..dcccb204b2d
--- /dev/null
+++ b/tests/modules/nf-core/sratools/fasterqdump/test.yml
@@ -0,0 +1,29 @@
+- name: sratools fasterqdump test_sratools_fasterqdump_single_end
+  command: nextflow run ./tests/modules/nf-core/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sratools/fasterqdump/nextflow.config
+  tags:
+    - sratools
+    - sratools/fasterqdump
+  files:
+    - path: output/sratools/SRR13255544.fastq.gz
+      md5sum: 1054c7b71884acdb5eed8a378f18be82
+    - path: output/untar/SRR13255544/SRR13255544.sra
+      md5sum: 466d05dafb2eec672150754168010b4d
+    - path: output/sratools/versions.yml
+      contains:
+        - "sratools: 2.11.0"
+
+- name: sratools fasterqdump test_sratools_fasterqdump_paired_end
+  command: nextflow run ./tests/modules/nf-core/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sratools/fasterqdump/nextflow.config
+  tags:
+    - sratools
+    - sratools/fasterqdump
+  files:
+    - path: output/sratools/SRR11140744_1.fastq.gz
+      md5sum: 193809c784a4ea132ab2a253fa4f55b6
+    - path: output/sratools/SRR11140744_2.fastq.gz
+      md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
+    - path: output/untar/SRR11140744/SRR11140744.sra
+      md5sum: 065666caf5b2d5dfb0cb25d5f3abe659
+    - path: output/sratools/versions.yml
+      contains:
+        - "sratools: 2.11.0"
diff --git a/tests/modules/nf-core/sratools/prefetch/main.nf b/tests/modules/nf-core/sratools/prefetch/main.nf
new file mode 100644
index 00000000000..be20bbc1bce
--- /dev/null
+++ b/tests/modules/nf-core/sratools/prefetch/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SRATOOLS_PREFETCH } from '../../../../../modules/nf-core/sratools/prefetch/main.nf'
+
+workflow test_sratools_prefetch {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        'DRR000774'
+    ]
+
+    SRATOOLS_PREFETCH(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
+}
diff --git a/tests/modules/sratools/prefetch/nextflow.config b/tests/modules/nf-core/sratools/prefetch/nextflow.config
similarity index 100%
rename from tests/modules/sratools/prefetch/nextflow.config
rename to tests/modules/nf-core/sratools/prefetch/nextflow.config
diff --git a/tests/modules/nf-core/sratools/prefetch/test.yml b/tests/modules/nf-core/sratools/prefetch/test.yml
new file mode 100644
index 00000000000..538b30a166e
--- /dev/null
+++ b/tests/modules/nf-core/sratools/prefetch/test.yml
@@ -0,0 +1,11 @@
+- name: sratools prefetch test_sratools_prefetch
+  command: nextflow run ./tests/modules/nf-core/sratools/prefetch -entry test_sratools_prefetch -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sratools/prefetch/nextflow.config
+  tags:
+    - sratools/prefetch
+    - sratools
+  files:
+    - path: output/sratools/DRR000774/DRR000774.sra
+      md5sum: 7647dba20c89c0e3d7ad13842f060eb0
+    - path: output/sratools/versions.yml
+      contains:
+        - "sratools: 2.11.0"
diff --git a/tests/modules/nf-core/srst2/srst2/main.nf b/tests/modules/nf-core/srst2/srst2/main.nf
new file mode 100644
index 00000000000..e82f603943e
--- /dev/null
+++ b/tests/modules/nf-core/srst2/srst2/main.nf
@@ -0,0 +1,53 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SRST2_SRST2 } from '../../../../../modules/nf-core/srst2/srst2/main.nf'
+
+workflow test_srst2_srst2_exit {
+
+    input = [
+        [ id:'test', single_end:false, db:"test"], // meta map
+        [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
+//        [("")]
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_mlst {
+
+    input = [
+        [ id:'test', single_end:false, db:"mlst"], // meta map
+        [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_1.fastq.gz", checkIfExists: true),
+          file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_2.fastq.gz", checkIfExists: true) ],
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/MLST_DB.fas')
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_paired_end {
+
+    input = [
+        [ id:'test', single_end:false, db:"gene"], // meta map
+        [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')  // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_single_end {
+
+    input = [
+        [ id:'test', single_end:true, db:"gene" ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')  // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
+    ]
+
+    SRST2_SRST2(input)
+}
diff --git a/tests/modules/srst2/srst2/nextflow.config b/tests/modules/nf-core/srst2/srst2/nextflow.config
similarity index 100%
rename from tests/modules/srst2/srst2/nextflow.config
rename to tests/modules/nf-core/srst2/srst2/nextflow.config
diff --git a/tests/modules/nf-core/srst2/srst2/test.yml b/tests/modules/nf-core/srst2/srst2/test.yml
new file mode 100644
index 00000000000..7d8a6cba546
--- /dev/null
+++ b/tests/modules/nf-core/srst2/srst2/test.yml
@@ -0,0 +1,51 @@
+- name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db
+  command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_exit -c ./tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  exit_code: 1
+
+- name: srst2 srst2 test_srst2_srst2_mlst
+  command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_mlst -c ./tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__SRR9067271.MLST_DB.pileup
+      contains:
+        - "dnaJ-1	2	C	17	.........,.......	FFFFFFFFFFFFFFFFF"
+    - path: output/srst2/test__SRR9067271.MLST_DB.sorted.bam
+    - path: output/srst2/test__mlst__MLST_DB__results.txt
+      md5sum: ec1b1f69933401d67c57f64cad11a098
+    - path: output/srst2/versions.yml
+      md5sum: a0c256a2fd3636069710b8ef22ee5ea7
+
+- name: srst2 srst2 test_srst2_srst2_paired_end
+  command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
+      md5sum: 099aa6cacec5524b311f606debdfb3a9
+    - path: output/srst2/test__test1.resFinder_20180221_srst2.pileup
+      md5sum: 64b512ff495b828c456405ec7b676ad1
+    - path: output/srst2/test__test1.resFinder_20180221_srst2.sorted.bam
+    - path: output/srst2/versions.yml
+      md5sum: b446a70f1a2b4f60757829bcd744a214
+
+- name: srst2 srst2 test_srst2_srst2_single_end
+  command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_single_end -c ./tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__fullgenes__resFinder_20180221_srst2__results.txt
+      md5sum: d0762ef8c38afd0e0a34cce52ed1a3db
+    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
+      md5sum: b8850c6644406d8b131e471ecc3f9013
+    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.pileup
+      md5sum: 5f6279dc8124aa762a9dfe3d7a871277
+    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.sorted.bam
+    - path: output/srst2/versions.yml
+      md5sum: 790fe00493c6634d17801a930073218b
diff --git a/tests/modules/nf-core/ssuissero/main.nf b/tests/modules/nf-core/ssuissero/main.nf
new file mode 100644
index 00000000000..9613bc71011
--- /dev/null
+++ b/tests/modules/nf-core/ssuissero/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SSUISSERO } from '../../../../modules/nf-core/ssuissero/main.nf'
+
+workflow test_ssuissero {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    SSUISSERO ( input )
+}
diff --git a/tests/modules/ssuissero/nextflow.config b/tests/modules/nf-core/ssuissero/nextflow.config
similarity index 100%
rename from tests/modules/ssuissero/nextflow.config
rename to tests/modules/nf-core/ssuissero/nextflow.config
diff --git a/tests/modules/nf-core/ssuissero/test.yml b/tests/modules/nf-core/ssuissero/test.yml
new file mode 100644
index 00000000000..4fa8af5d71a
--- /dev/null
+++ b/tests/modules/nf-core/ssuissero/test.yml
@@ -0,0 +1,9 @@
+- name: ssuissero test_ssuissero
+  command: nextflow run ./tests/modules/nf-core/ssuissero -entry test_ssuissero -c ./tests/config/nextflow.config
+  tags:
+    - ssuissero
+  files:
+    - path: output/ssuissero/test_serotyping_res.tsv
+      md5sum: 559dd2ca386eeb58f3975e3204ce9d43
+    - path: output/ssuissero/versions.yml
+      md5sum: be29b478690b2047e0413ffe01c85e1e
diff --git a/tests/modules/nf-core/stadeniolib/scramble/main.nf b/tests/modules/nf-core/stadeniolib/scramble/main.nf
new file mode 100644
index 00000000000..9ff96fe1cde
--- /dev/null
+++ b/tests/modules/nf-core/stadeniolib/scramble/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STADENIOLIB_SCRAMBLE } from '../../../../../modules/nf-core/stadeniolib/scramble/main.nf'
+
+workflow test_stadeniolib {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    STADENIOLIB_SCRAMBLE ( input, file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true), [])
+}
diff --git a/tests/modules/stadeniolib/scramble/nextflow.config b/tests/modules/nf-core/stadeniolib/scramble/nextflow.config
similarity index 100%
rename from tests/modules/stadeniolib/scramble/nextflow.config
rename to tests/modules/nf-core/stadeniolib/scramble/nextflow.config
diff --git a/tests/modules/nf-core/stadeniolib/scramble/test.yml b/tests/modules/nf-core/stadeniolib/scramble/test.yml
new file mode 100644
index 00000000000..d208a67b769
--- /dev/null
+++ b/tests/modules/nf-core/stadeniolib/scramble/test.yml
@@ -0,0 +1,7 @@
+- name: stadeniolib test_stadeniolib
+  command: nextflow run ./tests/modules/nf-core/stadeniolib -entry test_stadeniolib -c ./tests/config/nextflow.config
+  tags:
+    - stadeniolib
+  files:
+    - path: output/stadeniolib/test.cram
+    - path: output/stadeniolib/versions.yml
diff --git a/tests/modules/nf-core/staphopiasccmec/main.nf b/tests/modules/nf-core/staphopiasccmec/main.nf
new file mode 100644
index 00000000000..63afbcec129
--- /dev/null
+++ b/tests/modules/nf-core/staphopiasccmec/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STAPHOPIASCCMEC } from '../../../../modules/nf-core/staphopiasccmec/main.nf'
+include { STAPHOPIASCCMEC as STAPHOPIASCCMEC_HAMMING } from '../../../../modules/nf-core/staphopiasccmec/main.nf'
+
+workflow test_staphopiasccmec {
+    
+    input = [ [ id:'test' ],
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    STAPHOPIASCCMEC ( input )
+}
+
+workflow test_staphopiasccmec_hamming {
+    
+    input = [ [ id:'test' ],
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    STAPHOPIASCCMEC_HAMMING ( input )
+}
diff --git a/tests/modules/staphopiasccmec/nextflow.config b/tests/modules/nf-core/staphopiasccmec/nextflow.config
similarity index 100%
rename from tests/modules/staphopiasccmec/nextflow.config
rename to tests/modules/nf-core/staphopiasccmec/nextflow.config
diff --git a/tests/modules/nf-core/staphopiasccmec/test.yml b/tests/modules/nf-core/staphopiasccmec/test.yml
new file mode 100644
index 00000000000..332138a09af
--- /dev/null
+++ b/tests/modules/nf-core/staphopiasccmec/test.yml
@@ -0,0 +1,15 @@
+- name: staphopiasccmec test_staphopiasccmec
+  command: nextflow run ./tests/modules/nf-core/staphopiasccmec -entry test_staphopiasccmec -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/staphopiasccmec/nextflow.config
+  tags:
+    - staphopiasccmec
+  files:
+    - path: output/staphopiasccmec/test.tsv
+      md5sum: e6460d4164f3af5b290c5ccdb11343bf
+
+- name: staphopiasccmec test_staphopiasccmec_hamming
+  command: nextflow run ./tests/modules/nf-core/staphopiasccmec -entry test_staphopiasccmec_hamming -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/staphopiasccmec/nextflow.config
+  tags:
+    - staphopiasccmec
+  files:
+    - path: output/staphopiasccmec/test.tsv
+      md5sum: 164cda1b05b3b6814c1f0786d93ca070
diff --git a/tests/modules/nf-core/star/align/main.nf b/tests/modules/nf-core/star/align/main.nf
new file mode 100644
index 00000000000..adafa76eeb6
--- /dev/null
+++ b/tests/modules/nf-core/star/align/main.nf
@@ -0,0 +1,78 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STAR_GENOMEGENERATE               } from '../../../../../modules/nf-core/star/genomegenerate/main.nf'
+include { STAR_ALIGN                        } from '../../../../../modules/nf-core/star/align/main.nf'
+include { STAR_ALIGN as STAR_FOR_ARRIBA     } from '../../../../../modules/nf-core/star/align/main.nf'
+include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../../modules/nf-core/star/align/main.nf'
+
+workflow test_star_alignment_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
+    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    star_ignore_sjdbgtf = false
+    seq_platform = 'illumina'
+    seq_center = false
+
+    STAR_GENOMEGENERATE ( fasta, gtf )
+    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
+}
+
+workflow test_star_alignment_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    star_ignore_sjdbgtf = false
+    seq_platform = 'illumina'
+    seq_center = false
+
+    STAR_GENOMEGENERATE ( fasta, gtf )
+    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
+}
+
+
+workflow test_star_alignment_paired_end_for_fusion {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    star_ignore_sjdbgtf = false
+    seq_platform = 'illumina'
+    seq_center = false
+
+    STAR_GENOMEGENERATE ( fasta, gtf )
+    STAR_FOR_ARRIBA ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
+}
+
+workflow test_star_alignment_paired_end_for_starfusion {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+    star_ignore_sjdbgtf = false
+    seq_platform = false
+    seq_center = false
+
+    STAR_GENOMEGENERATE ( fasta, gtf )
+    STAR_FOR_STARFUSION ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
+}
diff --git a/tests/modules/star/align/nextflow.config b/tests/modules/nf-core/star/align/nextflow.config
similarity index 100%
rename from tests/modules/star/align/nextflow.config
rename to tests/modules/nf-core/star/align/nextflow.config
diff --git a/tests/modules/nf-core/star/align/test.yml b/tests/modules/nf-core/star/align/test.yml
new file mode 100644
index 00000000000..a90c903941e
--- /dev/null
+++ b/tests/modules/nf-core/star/align/test.yml
@@ -0,0 +1,193 @@
+- name: star align test_star_alignment_single_end
+  command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config
+  tags:
+    - star/align
+    - star
+  files:
+    - path: output/star/star/Genome
+      md5sum: a654229fbca6071dcb6b01ce7df704da
+    - path: output/star/star/Log.out
+    - path: output/star/star/SA
+      md5sum: 8c3edc46697b72c9e92440d4cf43506c
+    - path: output/star/star/SAindex
+      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
+    - path: output/star/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/star/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/star/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/star/star/chrStart.txt
+      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: d04497f69d6ef889efd4d34fe63edcc4
+    - path: output/star/star/exonInfo.tab
+      md5sum: 0d560290fab688b7268d88d5494bf9fe
+    - path: output/star/star/geneInfo.tab
+      md5sum: 8b608537307443ffaee4927d2b428805
+    - path: output/star/star/genomeParameters.txt
+      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: 8760c33e966dad0b39f440301ebbdee4
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
+    - path: output/star/test.Aligned.out.bam
+      md5sum: 63de6af2210e138b49d7b4d570c6e67f
+    - path: output/star/test.Log.final.out
+    - path: output/star/test.Log.out
+    - path: output/star/test.Log.progress.out
+    - path: output/star/test.SJ.out.tab
+
+- name: star align test_star_alignment_paired_end
+  command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config
+  tags:
+    - star/align
+    - star
+  files:
+    - path: output/star/star/Genome
+      md5sum: a654229fbca6071dcb6b01ce7df704da
+    - path: output/star/star/Log.out
+    - path: output/star/star/SA
+      md5sum: 8c3edc46697b72c9e92440d4cf43506c
+    - path: output/star/star/SAindex
+      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
+    - path: output/star/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/star/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/star/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/star/star/chrStart.txt
+      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: d04497f69d6ef889efd4d34fe63edcc4
+    - path: output/star/star/exonInfo.tab
+      md5sum: 0d560290fab688b7268d88d5494bf9fe
+    - path: output/star/star/geneInfo.tab
+      md5sum: 8b608537307443ffaee4927d2b428805
+    - path: output/star/star/genomeParameters.txt
+      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: 8760c33e966dad0b39f440301ebbdee4
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
+    - path: output/star/test.Aligned.out.bam
+      md5sum: 7cdef439bc8092bfefb4d091bf8ee6ab
+    - path: output/star/test.Log.final.out
+    - path: output/star/test.Log.out
+    - path: output/star/test.Log.progress.out
+    - path: output/star/test.SJ.out.tab
+
+- name: star align test_star_alignment_paired_end_for_fusion
+  command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_paired_end_for_fusion -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config
+  tags:
+    - star/align
+    - star
+  files:
+    - path: output/star/star/Genome
+      md5sum: a654229fbca6071dcb6b01ce7df704da
+    - path: output/star/star/Log.out
+    - path: output/star/star/SA
+      md5sum: 8c3edc46697b72c9e92440d4cf43506c
+    - path: output/star/star/SAindex
+      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
+    - path: output/star/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/star/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/star/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/star/star/chrStart.txt
+      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: d04497f69d6ef889efd4d34fe63edcc4
+    - path: output/star/star/exonInfo.tab
+      md5sum: 0d560290fab688b7268d88d5494bf9fe
+    - path: output/star/star/geneInfo.tab
+      md5sum: 8b608537307443ffaee4927d2b428805
+    - path: output/star/star/genomeParameters.txt
+      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: 8760c33e966dad0b39f440301ebbdee4
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
+    - path: output/star/test.Aligned.out.bam
+      md5sum: 5dbc36fce7b72628c809bbc7d3d67973
+    - path: output/star/test.Log.final.out
+    - path: output/star/test.Log.out
+    - path: output/star/test.Log.progress.out
+    - path: output/star/test.SJ.out.tab
+
+- name: star align test_star_alignment_paired_end_for_starfusion
+  command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_paired_end_for_starfusion -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config
+  tags:
+    - star/align
+    - star
+  files:
+    - path: output/star/star/Genome
+      md5sum: a654229fbca6071dcb6b01ce7df704da
+    - path: output/star/star/Log.out
+    - path: output/star/star/SA
+      md5sum: 8c3edc46697b72c9e92440d4cf43506c
+    - path: output/star/star/SAindex
+      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
+    - path: output/star/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/star/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/star/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/star/star/chrStart.txt
+      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: d04497f69d6ef889efd4d34fe63edcc4
+    - path: output/star/star/exonInfo.tab
+      md5sum: 0d560290fab688b7268d88d5494bf9fe
+    - path: output/star/star/geneInfo.tab
+      md5sum: 8b608537307443ffaee4927d2b428805
+    - path: output/star/star/genomeParameters.txt
+      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: 8760c33e966dad0b39f440301ebbdee4
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
+    - path: output/star/test.Aligned.out.bam
+      md5sum: d85858bf55a523121dde762046a34c5c
+    - path: output/star/test.Chimeric.out.junction
+      md5sum: ae87d1a24180f5a35cf6b47fdfdd0539
+    - path: output/star/test.Log.final.out
+    - path: output/star/test.Log.out
+    - path: output/star/test.Log.progress.out
+    - path: output/star/test.SJ.out.tab
+
+- name: star align test_star_alignment_single_end stub
+  command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config -stub-run
+  tags:
+    - star/align
+    - star
+  files:
+    - path: output/star/test.Aligned.unsort.out.bam
+    - path: output/star/test.Log.final.out
+    - path: output/star/test.Log.out
+    - path: output/star/test.Log.progress.out
+    - path: output/star/test.Chimeric.out.junction
+    - path: output/star/test.unmapped_1.fastq.gz
+    - path: output/star/test.unmapped_2.fastq.gz
+    - path: output/star/test.tab
+    - path: output/star/test.out.sam
diff --git a/tests/modules/nf-core/star/genomegenerate/main.nf b/tests/modules/nf-core/star/genomegenerate/main.nf
new file mode 100644
index 00000000000..b11d32ac679
--- /dev/null
+++ b/tests/modules/nf-core/star/genomegenerate/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STAR_GENOMEGENERATE } from '../../../../../modules/nf-core/star/genomegenerate/main.nf'
+
+workflow test_star_genomegenerate {
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+
+    STAR_GENOMEGENERATE ( fasta, gtf )
+}
diff --git a/tests/modules/star/genomegenerate/nextflow.config b/tests/modules/nf-core/star/genomegenerate/nextflow.config
similarity index 100%
rename from tests/modules/star/genomegenerate/nextflow.config
rename to tests/modules/nf-core/star/genomegenerate/nextflow.config
diff --git a/tests/modules/nf-core/star/genomegenerate/test.yml b/tests/modules/nf-core/star/genomegenerate/test.yml
new file mode 100644
index 00000000000..55fd4999970
--- /dev/null
+++ b/tests/modules/nf-core/star/genomegenerate/test.yml
@@ -0,0 +1,60 @@
+- name: star genomegenerate test_star_genomegenerate
+  command: nextflow run ./tests/modules/nf-core/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/genomegenerate/nextflow.config
+  tags:
+    - star
+    - star/genomegenerate
+  files:
+    - path: output/star/star/Genome
+      md5sum: a654229fbca6071dcb6b01ce7df704da
+    - path: output/star/star/Log.out
+    - path: output/star/star/SA
+      md5sum: 8c3edc46697b72c9e92440d4cf43506c
+    - path: output/star/star/SAindex
+      md5sum: d0fbf2789ee1e9f60c352ba3655d9de4
+    - path: output/star/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/star/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/star/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/star/star/chrStart.txt
+      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: d04497f69d6ef889efd4d34fe63edcc4
+    - path: output/star/star/exonInfo.tab
+      md5sum: 0d560290fab688b7268d88d5494bf9fe
+    - path: output/star/star/geneInfo.tab
+      md5sum: 8b608537307443ffaee4927d2b428805
+    - path: output/star/star/genomeParameters.txt
+      md5sum: 5a1ec027e575c3d7c1851e6b80fb8c5d
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: 8760c33e966dad0b39f440301ebbdee4
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
+
+- name: star genomegenerate test_star_genomegenerate stub
+  command: nextflow run ./tests/modules/nf-core/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/genomegenerate/nextflow.config -stub-run
+  tags:
+    - star
+    - star/genomegenerate
+  files:
+    - path: output/star/star/Genome
+    - path: output/star/star/Log.out
+    - path: output/star/star/SA
+    - path: output/star/star/SAindex
+    - path: output/star/star/chrLength.txt
+    - path: output/star/star/chrName.txt
+    - path: output/star/star/chrNameLength.txt
+    - path: output/star/star/chrStart.txt
+    - path: output/star/star/exonGeTrInfo.tab
+    - path: output/star/star/exonInfo.tab
+    - path: output/star/star/geneInfo.tab
+    - path: output/star/star/genomeParameters.txt
+    - path: output/star/star/sjdbInfo.txt
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+    - path: output/star/star/sjdbList.out.tab
+    - path: output/star/star/transcriptInfo.tab
diff --git a/tests/modules/nf-core/stranger/main.nf b/tests/modules/nf-core/stranger/main.nf
new file mode 100644
index 00000000000..492c886990d
--- /dev/null
+++ b/tests/modules/nf-core/stranger/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EXPANSIONHUNTER } from '../../../../modules/nf-core/expansionhunter/main.nf'
+include { STRANGER } from '../../../../modules/nf-core/stranger/main.nf'
+
+
+input = [ [ id:'test', gender:'male' ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        ]
+fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
+
+
+workflow test_stranger {
+    EXPANSIONHUNTER ( input, fasta, variant_catalog )
+    STRANGER ( EXPANSIONHUNTER.out.vcf, variant_catalog )
+}
+
+workflow test_stranger_without_optional_variant_catalog {
+    EXPANSIONHUNTER ( input, fasta, variant_catalog )
+    STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
+}
+
+workflow test_stranger_without_optional_variant_catalog_stubs {
+    EXPANSIONHUNTER ( input, fasta, variant_catalog )
+    STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
+}
diff --git a/tests/modules/stranger/nextflow.config b/tests/modules/nf-core/stranger/nextflow.config
similarity index 100%
rename from tests/modules/stranger/nextflow.config
rename to tests/modules/nf-core/stranger/nextflow.config
diff --git a/tests/modules/nf-core/stranger/test.yml b/tests/modules/nf-core/stranger/test.yml
new file mode 100644
index 00000000000..6a8721cc6d6
--- /dev/null
+++ b/tests/modules/nf-core/stranger/test.yml
@@ -0,0 +1,37 @@
+- name: stranger test_stranger
+  command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger -c ./tests/config/nextflow.config
+  tags:
+    - stranger
+  files:
+    - path: output/expansionhunter/test.vcf
+      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
+    - path: output/expansionhunter/versions.yml
+      md5sum: f3962a6eecfddf9682414c0f605a885a
+    - path: output/stranger/test.vcf.gz
+      md5sum: 68b0ca1319851134ffa8793a4704dc11
+    - path: output/stranger/versions.yml
+      md5sum: 5ec35fd835fb1be50bc3e7c004310fc0
+
+- name: stranger test_stranger_without_optional_variant_catalog
+  command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger_without_optional_variant_catalog -c ./tests/config/nextflow.config
+  tags:
+    - stranger
+  files:
+    - path: output/expansionhunter/test.vcf
+      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
+    - path: output/expansionhunter/versions.yml
+      md5sum: c95af9e6d8cd9bd2ce1090ca4e7a6020
+    - path: output/stranger/test.vcf.gz
+      md5sum: bbe15159195681d5c18596d3ad85c78f
+    - path: output/stranger/versions.yml
+      md5sum: 8558542a007e90ea5dcdceed3f12585d
+
+- name: stranger test_stranger_without_optional_variant_catalog_stubs
+  command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger_without_optional_variant_catalog -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - stranger
+  files:
+    - path: output/expansionhunter/test.vcf
+    - path: output/expansionhunter/versions.yml
+    - path: output/stranger/test.vcf.gz
+    - path: output/stranger/versions.yml
diff --git a/tests/modules/nf-core/strelka/germline/main.nf b/tests/modules/nf-core/strelka/germline/main.nf
new file mode 100644
index 00000000000..7337bc6f2fc
--- /dev/null
+++ b/tests/modules/nf-core/strelka/germline/main.nf
@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STRELKA_GERMLINE } from '../../../../../modules/nf-core/strelka/germline/main.nf'
+
+workflow test_strelka_germline {
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        [],
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    STRELKA_GERMLINE ( input, fasta, fai)
+}
+
+workflow test_strelka_germline_target_bed {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    STRELKA_GERMLINE ( input, fasta, fai)
+}
+
diff --git a/tests/modules/strelka/germline/nextflow.config b/tests/modules/nf-core/strelka/germline/nextflow.config
similarity index 100%
rename from tests/modules/strelka/germline/nextflow.config
rename to tests/modules/nf-core/strelka/germline/nextflow.config
diff --git a/tests/modules/nf-core/strelka/germline/test.yml b/tests/modules/nf-core/strelka/germline/test.yml
new file mode 100644
index 00000000000..989ff3e8d77
--- /dev/null
+++ b/tests/modules/nf-core/strelka/germline/test.yml
@@ -0,0 +1,21 @@
+- name: strelka germline test_strelka_germline
+  command: nextflow run ./tests/modules/nf-core/strelka/germline -entry test_strelka_germline -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/strelka/germline/nextflow.config
+  tags:
+    - strelka
+    - strelka/germline
+  files:
+    - path: output/strelka/test.genome.vcf.gz
+    - path: output/strelka/test.genome.vcf.gz.tbi
+    - path: output/strelka/test.variants.vcf.gz
+    - path: output/strelka/test.variants.vcf.gz.tbi
+
+- name: strelka germline test_strelka_germline_target_bed
+  command: nextflow run ./tests/modules/nf-core/strelka/germline -entry test_strelka_germline_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/strelka/germline/nextflow.config
+  tags:
+    - strelka
+    - strelka/germline
+  files:
+    - path: output/strelka/test.genome.vcf.gz
+    - path: output/strelka/test.genome.vcf.gz.tbi
+    - path: output/strelka/test.variants.vcf.gz
+    - path: output/strelka/test.variants.vcf.gz.tbi
diff --git a/tests/modules/nf-core/strelka/somatic/main.nf b/tests/modules/nf-core/strelka/somatic/main.nf
new file mode 100644
index 00000000000..d11e372f9aa
--- /dev/null
+++ b/tests/modules/nf-core/strelka/somatic/main.nf
@@ -0,0 +1,45 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STRELKA_SOMATIC } from '../../../../../modules/nf-core/strelka/somatic/main.nf'
+
+workflow test_strelka_somatic {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        [],[],
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    STRELKA_SOMATIC (input, fasta, fai )
+}
+
+workflow test_strelka_best_practices_somatic {
+
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    STRELKA_SOMATIC ( input, fasta, fai )
+}
diff --git a/tests/modules/strelka/somatic/nextflow.config b/tests/modules/nf-core/strelka/somatic/nextflow.config
similarity index 100%
rename from tests/modules/strelka/somatic/nextflow.config
rename to tests/modules/nf-core/strelka/somatic/nextflow.config
diff --git a/tests/modules/nf-core/strelka/somatic/test.yml b/tests/modules/nf-core/strelka/somatic/test.yml
new file mode 100644
index 00000000000..07e5306f02d
--- /dev/null
+++ b/tests/modules/nf-core/strelka/somatic/test.yml
@@ -0,0 +1,21 @@
+- name: strelka somatic test_strelka_somatic
+  command: nextflow run ./tests/modules/nf-core/strelka/somatic -entry test_strelka_somatic -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/strelka/somatic/nextflow.config
+  tags:
+    - strelka
+    - strelka/somatic
+  files:
+    - path: output/strelka/test.somatic_indels.vcf.gz
+    - path: output/strelka/test.somatic_indels.vcf.gz.tbi
+    - path: output/strelka/test.somatic_snvs.vcf.gz
+    - path: output/strelka/test.somatic_snvs.vcf.gz.tbi
+
+- name: strelka somatic test_strelka_best_practices_somatic
+  command: nextflow run ./tests/modules/nf-core/strelka/somatic -entry test_strelka_best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/strelka/somatic/nextflow.config
+  tags:
+    - strelka
+    - strelka/somatic
+  files:
+    - path: output/strelka/test.somatic_indels.vcf.gz
+    - path: output/strelka/test.somatic_indels.vcf.gz.tbi
+    - path: output/strelka/test.somatic_snvs.vcf.gz
+    - path: output/strelka/test.somatic_snvs.vcf.gz.tbi
diff --git a/tests/modules/nf-core/stringtie/merge/main.nf b/tests/modules/nf-core/stringtie/merge/main.nf
new file mode 100644
index 00000000000..1395bc8b148
--- /dev/null
+++ b/tests/modules/nf-core/stringtie/merge/main.nf
@@ -0,0 +1,46 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STRINGTIE_STRINGTIE } from '../../../../../modules/nf-core/stringtie/stringtie/main.nf'
+include { STRINGTIE_MERGE     } from '../../../../../modules/nf-core/stringtie/merge/main.nf'
+
+/*
+ * Test with forward strandedness
+ */
+workflow test_stringtie_forward_merge {
+    input = [
+        [ id:'test', strandedness:'forward' ], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
+        .out
+        .transcript_gtf
+        .map { it -> it[1] }
+        .set { stringtie_gtf }
+
+    STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
+}
+
+/*
+ * Test with reverse strandedness
+ */
+workflow test_stringtie_reverse_merge {
+    input = [
+        [ id:'test', strandedness:'reverse' ], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
+        .out
+        .transcript_gtf
+        .map { it -> it[1] }
+        .set { stringtie_gtf }
+
+    STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
+}
diff --git a/tests/modules/stringtie/merge/nextflow.config b/tests/modules/nf-core/stringtie/merge/nextflow.config
similarity index 100%
rename from tests/modules/stringtie/merge/nextflow.config
rename to tests/modules/nf-core/stringtie/merge/nextflow.config
diff --git a/tests/modules/nf-core/stringtie/merge/test.yml b/tests/modules/nf-core/stringtie/merge/test.yml
new file mode 100644
index 00000000000..89e0a90a350
--- /dev/null
+++ b/tests/modules/nf-core/stringtie/merge/test.yml
@@ -0,0 +1,69 @@
+- name: stringtie merge forward-strand
+  command: nextflow run ./tests/modules/nf-core/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/merge/nextflow.config
+  tags:
+    - stringtie
+    - stringtie/merge
+  files:
+    - path: output/stringtie/stringtie.merged.gtf
+      md5sum: d959eb2fab0db48ded7275e0a2e83c05
+    - path: output/stringtie/test.ballgown/e2t.ctab
+      md5sum: 9ae42e056c955a88a883e5e917840d77
+    - path: output/stringtie/test.ballgown/e_data.ctab
+      md5sum: adbedee7b2f84c70362ad6dfa57442b7
+    - path: output/stringtie/test.ballgown/i2t.ctab
+      md5sum: 658131af118cfb416939044fdb5411de
+    - path: output/stringtie/test.ballgown/i_data.ctab
+      md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
+    - path: output/stringtie/test.ballgown/t_data.ctab
+      md5sum: 92a98902784e7406ffe054d2adbabc7c
+    - path: output/stringtie/test.coverage.gtf
+    - path: output/stringtie/test.gene.abundance.txt
+      md5sum: 8bcd8e2730ed3337e2730186dbc184f3
+    - path: output/stringtie/test.transcripts.gtf
+      md5sum: a914bd55b68a4b5f607738b17861e362
+
+- name: stringtie merge test_stringtie_reverse_merge
+  command: nextflow run ./tests/modules/nf-core/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/merge/nextflow.config
+  tags:
+    - stringtie
+    - stringtie/merge
+  files:
+    - path: output/stringtie/stringtie.merged.gtf
+      md5sum: 6da479298d73d5b3216d4e1576a2bdf4
+    - path: output/stringtie/test.ballgown/e2t.ctab
+      md5sum: 9ae42e056c955a88a883e5e917840d77
+    - path: output/stringtie/test.ballgown/e_data.ctab
+      md5sum: fd8496d3957ade3b2c0853155f9a67da
+    - path: output/stringtie/test.ballgown/i2t.ctab
+      md5sum: 658131af118cfb416939044fdb5411de
+    - path: output/stringtie/test.ballgown/i_data.ctab
+      md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
+    - path: output/stringtie/test.ballgown/t_data.ctab
+      md5sum: 92a98902784e7406ffe054d2adbabc7c
+    - path: output/stringtie/test.coverage.gtf
+    - path: output/stringtie/test.gene.abundance.txt
+      md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
+    - path: output/stringtie/test.transcripts.gtf
+      md5sum: 9dcdc9577c0fdbb25089eda210267546
+
+- name: stringtie merge forward-strand stub
+  command: nextflow run ./tests/modules/nf-core/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/merge/nextflow.config -stub-run
+  tags:
+    - stringtie
+    - stringtie/merge
+  files:
+    - path: output/stringtie/stringtie.merged.gtf
+    - path: output/stringtie/test.coverage.gtf
+    - path: output/stringtie/test.gene.abundance.txt
+    - path: output/stringtie/test.transcripts.gtf
+
+- name: stringtie merge test_stringtie_reverse_merge stub
+  command: nextflow run ./tests/modules/nf-core/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/merge/nextflow.config -stub-run
+  tags:
+    - stringtie
+    - stringtie/merge
+  files:
+    - path: output/stringtie/stringtie.merged.gtf
+    - path: output/stringtie/test.coverage.gtf
+    - path: output/stringtie/test.gene.abundance.txt
+    - path: output/stringtie/test.transcripts.gtf
diff --git a/tests/modules/nf-core/stringtie/stringtie/main.nf b/tests/modules/nf-core/stringtie/stringtie/main.nf
new file mode 100644
index 00000000000..b95ddfca0e3
--- /dev/null
+++ b/tests/modules/nf-core/stringtie/stringtie/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STRINGTIE_STRINGTIE } from '../../../../../modules/nf-core/stringtie/stringtie/main.nf'
+//
+// Test with forward strandedness
+//
+workflow test_stringtie_forward {
+    input = [
+        [ id:'test', strandedness:'forward' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+}
+
+//
+// Test with reverse strandedness
+//
+workflow test_stringtie_reverse {
+    input = [
+        [ id:'test', strandedness:'reverse' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+}
diff --git a/tests/modules/stringtie/stringtie/nextflow.config b/tests/modules/nf-core/stringtie/stringtie/nextflow.config
similarity index 100%
rename from tests/modules/stringtie/stringtie/nextflow.config
rename to tests/modules/nf-core/stringtie/stringtie/nextflow.config
diff --git a/tests/modules/nf-core/stringtie/stringtie/test.yml b/tests/modules/nf-core/stringtie/stringtie/test.yml
new file mode 100644
index 00000000000..8d0ba91ea1f
--- /dev/null
+++ b/tests/modules/nf-core/stringtie/stringtie/test.yml
@@ -0,0 +1,63 @@
+- name: stringtie stringtie forward
+  command: nextflow run ./tests/modules/nf-core/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/stringtie/nextflow.config
+  tags:
+    - stringtie
+    - stringtie/stringtie
+  files:
+    - path: ./output/stringtie/test.transcripts.gtf
+    - path: ./output/stringtie/test.gene.abundance.txt
+      md5sum: 7d8bce7f2a922e367cedccae7267c22e
+    - path: ./output/stringtie/test.coverage.gtf
+    - path: ./output/stringtie/test.ballgown/e_data.ctab
+      md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
+    - path: ./output/stringtie/test.ballgown/i_data.ctab
+      md5sum: be3abe09740603213f83d50dcf81427f
+    - path: ./output/stringtie/test.ballgown/t_data.ctab
+      md5sum: 3b66c065da73ae0dd41cc332eff6a818
+    - path: ./output/stringtie/test.ballgown/i2t.ctab
+      md5sum: 8a117c8aa4334b4c2d4711932b006fb4
+    - path: ./output/stringtie/test.ballgown/e2t.ctab
+      md5sum: e981c0038295ae54b63cedb1083f1540
+
+- name: stringtie stringtie reverse
+  command: nextflow run ./tests/modules/nf-core/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/stringtie/nextflow.config
+  tags:
+    - stringtie
+    - stringtie/stringtie
+  files:
+    - path: ./output/stringtie/test.transcripts.gtf
+    - path: ./output/stringtie/test.gene.abundance.txt
+      md5sum: 7385b870b955dae2c2ab78a70cf05cce
+    - path: ./output/stringtie/test.coverage.gtf
+    - path: ./output/stringtie/test.ballgown/e_data.ctab
+      md5sum: 879b6696029d19c4737b562e9d149218
+    - path: ./output/stringtie/test.ballgown/i_data.ctab
+      md5sum: be3abe09740603213f83d50dcf81427f
+    - path: ./output/stringtie/test.ballgown/t_data.ctab
+      md5sum: 3b66c065da73ae0dd41cc332eff6a818
+    - path: ./output/stringtie/test.ballgown/i2t.ctab
+      md5sum: 8a117c8aa4334b4c2d4711932b006fb4
+    - path: ./output/stringtie/test.ballgown/e2t.ctab
+      md5sum: e981c0038295ae54b63cedb1083f1540
+
+- name: stringtie stringtie forward stub
+  command: nextflow run ./tests/modules/nf-core/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/stringtie/nextflow.config -stub-run
+  tags:
+    - stringtie
+    - stringtie/stringtie
+  files:
+    - path: ./output/stringtie/test.transcripts.gtf
+    - path: ./output/stringtie/test.gene.abundance.txt
+    - path: ./output/stringtie/test.coverage.gtf
+    - path: ./output/stringtie/test.ballgown
+
+- name: stringtie stringtie reverse stub
+  command: nextflow run ./tests/modules/nf-core/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/stringtie/nextflow.config -stub-run
+  tags:
+    - stringtie
+    - stringtie/stringtie
+  files:
+    - path: ./output/stringtie/test.transcripts.gtf
+    - path: ./output/stringtie/test.gene.abundance.txt
+    - path: ./output/stringtie/test.coverage.gtf
+    - path: ./output/stringtie/test.ballgown
diff --git a/tests/modules/nf-core/subread/featurecounts/main.nf b/tests/modules/nf-core/subread/featurecounts/main.nf
new file mode 100644
index 00000000000..1cc38b1115f
--- /dev/null
+++ b/tests/modules/nf-core/subread/featurecounts/main.nf
@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SUBREAD_FEATURECOUNTS } from '../../../../../modules/nf-core/subread/featurecounts/main.nf'
+
+workflow test_subread_featurecounts_forward {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
+
+    SUBREAD_FEATURECOUNTS ( input )
+}
+
+workflow test_subread_featurecounts_reverse {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
+
+    SUBREAD_FEATURECOUNTS ( input )
+}
+
+workflow test_subread_featurecounts_unstranded {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
+
+    SUBREAD_FEATURECOUNTS ( input )
+}
\ No newline at end of file
diff --git a/tests/modules/subread/featurecounts/nextflow.config b/tests/modules/nf-core/subread/featurecounts/nextflow.config
similarity index 100%
rename from tests/modules/subread/featurecounts/nextflow.config
rename to tests/modules/nf-core/subread/featurecounts/nextflow.config
diff --git a/tests/modules/nf-core/subread/featurecounts/test.yml b/tests/modules/nf-core/subread/featurecounts/test.yml
new file mode 100644
index 00000000000..b6ec04f4c22
--- /dev/null
+++ b/tests/modules/nf-core/subread/featurecounts/test.yml
@@ -0,0 +1,32 @@
+- name: subread featurecounts test_subread_featurecounts_forward
+  command: nextflow run ./tests/modules/nf-core/subread/featurecounts -entry test_subread_featurecounts_forward -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/subread/featurecounts/nextflow.config
+  tags:
+    - subread
+    - subread/featurecounts
+  files:
+    - path: output/subread/test.featureCounts.txt
+      md5sum: 0012df4c0a0e47eec1440017ab34f75f
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: 8f602ff9a8ef467af43294e80b367cdf
+
+- name: subread featurecounts test_subread_featurecounts_reverse
+  command: nextflow run ./tests/modules/nf-core/subread/featurecounts -entry test_subread_featurecounts_reverse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/subread/featurecounts/nextflow.config
+  tags:
+    - subread
+    - subread/featurecounts
+  files:
+    - path: output/subread/test.featureCounts.txt
+      md5sum: 8175816b8260ed444d59232bd7e7120b
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: 7cfa30ad678b9bc1bc63afbb0281547b
+
+- name: subread featurecounts test_subread_featurecounts_unstranded
+  command: nextflow run ./tests/modules/nf-core/subread/featurecounts -entry test_subread_featurecounts_unstranded -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/subread/featurecounts/nextflow.config
+  tags:
+    - subread
+    - subread/featurecounts
+  files:
+    - path: output/subread/test.featureCounts.txt
+      md5sum: 3307d31b44a5d6bb3389786bb8f4e91f
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: 23164b79f9f23f11c82820db61a35560
diff --git a/tests/modules/nf-core/svdb/merge/main.nf b/tests/modules/nf-core/svdb/merge/main.nf
new file mode 100644
index 00000000000..ddf64479a6e
--- /dev/null
+++ b/tests/modules/nf-core/svdb/merge/main.nf
@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SVDB_MERGE } from '../../../../../modules/nf-core/svdb/merge/main.nf'
+
+workflow test_svdb_merge {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+    priority = [ 'tiddit', 'cnvnator']
+
+    SVDB_MERGE ( input, priority )
+}
+
+workflow test_svdb_merge_noprio {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+
+    SVDB_MERGE ( input, [] )
+}
diff --git a/tests/modules/svdb/merge/nextflow.config b/tests/modules/nf-core/svdb/merge/nextflow.config
similarity index 100%
rename from tests/modules/svdb/merge/nextflow.config
rename to tests/modules/nf-core/svdb/merge/nextflow.config
diff --git a/tests/modules/nf-core/svdb/merge/test.yml b/tests/modules/nf-core/svdb/merge/test.yml
new file mode 100644
index 00000000000..88e61469e4c
--- /dev/null
+++ b/tests/modules/nf-core/svdb/merge/test.yml
@@ -0,0 +1,21 @@
+- name: svdb merge test_svdb_merge
+  command: nextflow run ./tests/modules/nf-core/svdb/merge -entry test_svdb_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/merge/nextflow.config
+  tags:
+    - svdb
+    - svdb/merge
+  files:
+    - path: output/svdb/test_sv_merge.vcf.gz
+- name: svdb merge test_svdb_merge_noprio
+  command: nextflow run ./tests/modules/nf-core/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/merge/nextflow.config
+  tags:
+    - svdb
+    - svdb/merge
+  files:
+    - path: output/svdb/test_sv_merge.vcf.gz
+- name: svdb merge test_svdb_merge_noprio stub
+  command: nextflow run ./tests/modules/nf-core/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/merge/nextflow.config -stub
+  tags:
+    - svdb
+    - svdb/merge
+  files:
+    - path: output/svdb/test_sv_merge.vcf.gz
diff --git a/tests/modules/nf-core/svdb/query/main.nf b/tests/modules/nf-core/svdb/query/main.nf
new file mode 100644
index 00000000000..136dd5e0395
--- /dev/null
+++ b/tests/modules/nf-core/svdb/query/main.nf
@@ -0,0 +1,42 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SVDB_QUERY } from '../../../../../modules/nf-core/svdb/query/main.nf'
+
+workflow test_svdb_query {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_sv_vcf'], checkIfExists: true) ]
+            ]
+
+    vcf_db = [
+                file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_sv_vcf_gz'], checkIfExists: true)
+            ]
+
+    in_occs = ['AC']
+    in_frqs = ['AF']
+    out_occs = ['gnomad_svAC']
+    out_frqs = ['gnomad_svAF']
+
+    SVDB_QUERY ( input, in_occs, in_frqs, out_occs, out_frqs, vcf_db )
+}
+
+workflow test_svdb_query_multiple {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_sv_vcf'], checkIfExists: true) ]
+            ]
+
+    vcf_db = [
+                file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_sv_vcf_gz'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['genome']['gnomad2_r2_1_1_sv_vcf_gz'], checkIfExists: true)
+            ]
+
+    in_occs = ['AC','AC']
+    in_frqs = ['AF','AF']
+    out_occs = ['gnomad_svAC','gnomad_svAC']
+    out_frqs = ['gnomad_svAF','gnomad_svAF']
+
+    SVDB_QUERY ( input, in_occs, in_frqs, out_occs, out_frqs, vcf_db )
+}
diff --git a/tests/modules/svdb/query/nextflow.config b/tests/modules/nf-core/svdb/query/nextflow.config
similarity index 100%
rename from tests/modules/svdb/query/nextflow.config
rename to tests/modules/nf-core/svdb/query/nextflow.config
diff --git a/tests/modules/nf-core/svdb/query/test.yml b/tests/modules/nf-core/svdb/query/test.yml
new file mode 100644
index 00000000000..7f683efe6bf
--- /dev/null
+++ b/tests/modules/nf-core/svdb/query/test.yml
@@ -0,0 +1,15 @@
+- name: svdb query
+  command: nextflow run ./tests/modules/nf-core/svdb/query -entry test_svdb_query -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/query/nextflow.config
+  tags:
+    - svdb
+    - svdb/query
+  files:
+    - path: output/svdb/test_query.vcf
+
+- name: svdb query multiple
+  command: nextflow run ./tests/modules/nf-core/svdb/query -entry test_svdb_query_multiple -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/query/nextflow.config
+  tags:
+    - svdb
+    - svdb/query
+  files:
+    - path: output/svdb/test_query.vcf
diff --git a/tests/modules/nf-core/svtk/standardize/main.nf b/tests/modules/nf-core/svtk/standardize/main.nf
new file mode 100644
index 00000000000..0964ace0684
--- /dev/null
+++ b/tests/modules/nf-core/svtk/standardize/main.nf
@@ -0,0 +1,56 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SVTK_STANDARDIZE } from '../../../../../modules/nf-core/svtk/standardize/main.nf'
+include { MANTA_GERMLINE   } from '../../../../../modules/nf-core/manta/germline/main.nf'
+
+workflow test_svtk_standardize {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    MANTA_GERMLINE(
+        input,
+        fasta,
+        fasta_fai
+    )
+
+    SVTK_STANDARDIZE ( 
+        MANTA_GERMLINE.out.diploid_sv_vcf,
+        fasta_fai
+    )
+}
+
+workflow test_svtk_standardize_no_contigs {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    MANTA_GERMLINE(
+        input,
+        fasta,
+        fasta_fai
+    )
+
+    SVTK_STANDARDIZE ( 
+        MANTA_GERMLINE.out.diploid_sv_vcf,
+        []
+    )
+}
diff --git a/tests/modules/svtk/standardize/nextflow.config b/tests/modules/nf-core/svtk/standardize/nextflow.config
similarity index 100%
rename from tests/modules/svtk/standardize/nextflow.config
rename to tests/modules/nf-core/svtk/standardize/nextflow.config
diff --git a/tests/modules/nf-core/svtk/standardize/test.yml b/tests/modules/nf-core/svtk/standardize/test.yml
new file mode 100644
index 00000000000..cd0e9ea2ab7
--- /dev/null
+++ b/tests/modules/nf-core/svtk/standardize/test.yml
@@ -0,0 +1,35 @@
+- name: svtk standardize test_svtk_standardize
+  command: nextflow run ./tests/modules/nf-core/svtk/standardize -entry test_svtk_standardize -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svtk/standardize/nextflow.config
+  tags:
+    - svtk
+    - svtk/standardize
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.diploid_sv.vcf.gz
+    - path: output/manta/test.diploid_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/svtk/test.std.vcf.gz
+      md5sum: f7530f3bc7e6020e758cc996adc8ae35
+
+- name: svtk standardize test_svtk_standardize_no_contigs
+  command: nextflow run ./tests/modules/nf-core/svtk/standardize -entry test_svtk_standardize_no_contigs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svtk/standardize/nextflow.config
+  tags:
+    - svtk
+    - svtk/standardize
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.diploid_sv.vcf.gz
+    - path: output/manta/test.diploid_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/svtk/test.std.vcf.gz
+      md5sum: ea67be7438a0fb72db8096e1bc1bb957
diff --git a/tests/modules/nf-core/tabix/bgzip/main.nf b/tests/modules/nf-core/tabix/bgzip/main.nf
new file mode 100644
index 00000000000..2e407090fc0
--- /dev/null
+++ b/tests/modules/nf-core/tabix/bgzip/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TABIX_BGZIP } from '../../../../../modules/nf-core/tabix/bgzip/main.nf'
+include { TABIX_BGZIP as TABIX_BGZIP_WITH_GZI } from '../../../../../modules/nf-core/tabix/bgzip/main.nf'
+
+workflow test_tabix_bgzip_compress {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+            ]
+
+    TABIX_BGZIP ( input )
+}
+
+workflow test_tabix_bgzip_compress_gzi {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+            ]
+
+    TABIX_BGZIP_WITH_GZI ( input )
+}
+
+workflow test_tabix_bgzip_decompress {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ]
+            ]
+
+    TABIX_BGZIP ( input )
+}
diff --git a/tests/modules/tabix/bgzip/nextflow.config b/tests/modules/nf-core/tabix/bgzip/nextflow.config
similarity index 100%
rename from tests/modules/tabix/bgzip/nextflow.config
rename to tests/modules/nf-core/tabix/bgzip/nextflow.config
diff --git a/tests/modules/nf-core/tabix/bgzip/test.yml b/tests/modules/nf-core/tabix/bgzip/test.yml
new file mode 100644
index 00000000000..906e509ecb2
--- /dev/null
+++ b/tests/modules/nf-core/tabix/bgzip/test.yml
@@ -0,0 +1,28 @@
+- name: tabix bgzip compress
+  command: nextflow run ./tests/modules/nf-core/tabix/bgzip -entry test_tabix_bgzip_compress -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/bgzip/nextflow.config
+  tags:
+    - tabix
+    - tabix/bgzip
+  files:
+    - path: ./output/tabix/test.vcf.gz
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+    - path: ./output/tabix/test.vcf.gz.gzi
+      should_exist: false
+- name: tabix bgzip compress gzi
+  command: nextflow run ./tests/modules/nf-core/tabix/bgzip -entry test_tabix_bgzip_compress_gzi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/bgzip/nextflow.config
+  tags:
+    - tabix
+    - tabix/bgzip
+  files:
+    - path: ./output/tabix/test.vcf.gz
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+    - path: ./output/tabix/test.vcf.gz.gzi
+      md5sum: 7dea362b3fac8e00956a4952a3d4f474
+- name: tabix bgzip decompress
+  command: nextflow run ./tests/modules/nf-core/tabix/bgzip -entry test_tabix_bgzip_decompress -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/bgzip/nextflow.config
+  tags:
+    - tabix
+    - tabix/bgzip
+  files:
+    - path: ./output/tabix/test.bed
+      md5sum: fe4053cf4de3aebbdfc3be2efb125a74
diff --git a/tests/modules/nf-core/tabix/bgziptabix/main.nf b/tests/modules/nf-core/tabix/bgziptabix/main.nf
new file mode 100644
index 00000000000..26e17101f8b
--- /dev/null
+++ b/tests/modules/nf-core/tabix/bgziptabix/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TABIX_BGZIPTABIX } from '../../../../../modules/nf-core/tabix/bgziptabix/main.nf'
+
+workflow test_tabix_bgziptabix {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+            ]
+
+    TABIX_BGZIPTABIX ( input )
+}
diff --git a/tests/modules/tabix/bgziptabix/nextflow.config b/tests/modules/nf-core/tabix/bgziptabix/nextflow.config
similarity index 100%
rename from tests/modules/tabix/bgziptabix/nextflow.config
rename to tests/modules/nf-core/tabix/bgziptabix/nextflow.config
diff --git a/tests/modules/nf-core/tabix/bgziptabix/test.yml b/tests/modules/nf-core/tabix/bgziptabix/test.yml
new file mode 100644
index 00000000000..78ce288b321
--- /dev/null
+++ b/tests/modules/nf-core/tabix/bgziptabix/test.yml
@@ -0,0 +1,10 @@
+- name: tabix bgziptabix test_tabix_bgziptabix
+  command: nextflow run ./tests/modules/nf-core/tabix/bgziptabix -entry test_tabix_bgziptabix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/bgziptabix/nextflow.config
+  tags:
+    - tabix/bgziptabix
+    - tabix
+  files:
+    - path: output/tabix/test.vcf.gz
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+    - path: output/tabix/test.vcf.gz.tbi
+      md5sum: 36e11bf96ed0af4a92caa91a68612d64
diff --git a/tests/modules/nf-core/tabix/tabix/main.nf b/tests/modules/nf-core/tabix/tabix/main.nf
new file mode 100644
index 00000000000..1eb7bacff9d
--- /dev/null
+++ b/tests/modules/nf-core/tabix/tabix/main.nf
@@ -0,0 +1,40 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TABIX_TABIX as TABIX_BED     } from '../../../../../modules/nf-core/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_GFF     } from '../../../../../modules/nf-core/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../../modules/nf-core/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../../modules/nf-core/tabix/tabix/main.nf'
+
+workflow test_tabix_tabix_bed {
+    input = [ [ id:'B.bed' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ] 
+            ]
+
+    TABIX_BED ( input )
+}
+
+workflow test_tabix_tabix_gff {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ] 
+            ]
+
+    TABIX_GFF ( input )
+}
+
+workflow test_tabix_tabix_vcf_tbi {
+    input = [ [ id:'test.vcf' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] 
+            ]
+
+    TABIX_VCF_TBI ( input )
+}
+
+workflow test_tabix_tabix_vcf_csi {
+    input = [ [ id:'test.vcf' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+            ]
+
+    TABIX_VCF_CSI ( input )
+}
diff --git a/tests/modules/tabix/tabix/nextflow.config b/tests/modules/nf-core/tabix/tabix/nextflow.config
similarity index 100%
rename from tests/modules/tabix/tabix/nextflow.config
rename to tests/modules/nf-core/tabix/tabix/nextflow.config
diff --git a/tests/modules/nf-core/tabix/tabix/test.yml b/tests/modules/nf-core/tabix/tabix/test.yml
new file mode 100644
index 00000000000..9457790b178
--- /dev/null
+++ b/tests/modules/nf-core/tabix/tabix/test.yml
@@ -0,0 +1,32 @@
+- name: tabix tabix bed
+  command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - path: ./output/tabix/test.bed.gz.tbi
+      md5sum: 5b40851ab6b8ccf7946313c86481c0df
+- name: tabix tabix gff
+  command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_gff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - path: ./output/tabix/genome.gff3.gz.tbi
+      md5sum: f79a67d95a98076e04fbe0455d825926
+- name: tabix tabix vcf
+  command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - path: output/tabix/test.vcf.gz.tbi
+      md5sum: 36e11bf96ed0af4a92caa91a68612d64
+- name: tabix tabix vcf csi
+  command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - path: output/tabix/test.vcf.gz.csi
+      md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd
diff --git a/tests/modules/nf-core/tailfindr/main.nf b/tests/modules/nf-core/tailfindr/main.nf
new file mode 100644
index 00000000000..c9e109cba71
--- /dev/null
+++ b/tests/modules/nf-core/tailfindr/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TAILFINDR } from '../../../../modules/nf-core/tailfindr/main.nf'
+
+workflow test_tailfindr {
+    
+    input = [
+        [ id: 'test' ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/tailfindr/test.fast5', checkIfExists: true)
+    ]
+
+    TAILFINDR ( input )
+}
diff --git a/tests/modules/tailfindr/nextflow.config b/tests/modules/nf-core/tailfindr/nextflow.config
similarity index 100%
rename from tests/modules/tailfindr/nextflow.config
rename to tests/modules/nf-core/tailfindr/nextflow.config
diff --git a/tests/modules/nf-core/tailfindr/test.yml b/tests/modules/nf-core/tailfindr/test.yml
new file mode 100644
index 00000000000..ac4f13d492d
--- /dev/null
+++ b/tests/modules/nf-core/tailfindr/test.yml
@@ -0,0 +1,9 @@
+- name: "tailfindr"
+  command: nextflow run ./tests/modules/nf-core/tailfindr -entry test_tailfindr -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tailfindr/nextflow.config
+  tags:
+    - "tailfindr"
+  files:
+    - path: "output/tailfindr/test.csv.gz"
+      md5sum: 329e856d529dfd1ab31b0dedffc71f3c
+    - path: output/tailfindr/versions.yml
+      md5sum: 3a4e99bd95d9489da261b12a0ad740bb
diff --git a/tests/modules/nf-core/tbprofiler/profile/main.nf b/tests/modules/nf-core/tbprofiler/profile/main.nf
new file mode 100644
index 00000000000..00b1feb4ee1
--- /dev/null
+++ b/tests/modules/nf-core/tbprofiler/profile/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TBPROFILER_PROFILE } from '../../../../../modules/nf-core/tbprofiler/profile/main.nf'
+
+workflow test_tbprofiler_profile_illumina {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    TBPROFILER_PROFILE ( input )
+}
+
+workflow test_tbprofiler_profile_nanopore {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+    ]
+
+    TBPROFILER_PROFILE ( input )
+}
diff --git a/tests/modules/tbprofiler/profile/nextflow.config b/tests/modules/nf-core/tbprofiler/profile/nextflow.config
similarity index 100%
rename from tests/modules/tbprofiler/profile/nextflow.config
rename to tests/modules/nf-core/tbprofiler/profile/nextflow.config
diff --git a/tests/modules/nf-core/tbprofiler/profile/test.yml b/tests/modules/nf-core/tbprofiler/profile/test.yml
new file mode 100644
index 00000000000..24eaa37e511
--- /dev/null
+++ b/tests/modules/nf-core/tbprofiler/profile/test.yml
@@ -0,0 +1,21 @@
+- name: tbprofiler profile illumina
+  command: nextflow run ./tests/modules/nf-core/tbprofiler/profile -entry test_tbprofiler_profile_illumina -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tbprofiler/profile/nextflow.config
+  tags:
+    - tbprofiler
+    - tbprofiler/profile
+  files:
+    - path: output/tbprofiler/bam/test.bam
+    - path: output/tbprofiler/results/test.results.json
+      contains: ["genome_positions", "locus_tag", "tbprofiler_version"]
+    - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz
+
+- name: tbprofiler profile nanopore
+  command: nextflow run ./tests/modules/nf-core/tbprofiler/profile -entry test_tbprofiler_profile_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tbprofiler/profile/nextflow.config
+  tags:
+    - tbprofiler
+    - tbprofiler/profile
+  files:
+    - path: output/tbprofiler/bam/test.bam
+    - path: output/tbprofiler/results/test.results.json
+      contains: ["genome_positions", "locus_tag", "tbprofiler_version"]
+    - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz
diff --git a/tests/modules/nf-core/tiddit/cov/main.nf b/tests/modules/nf-core/tiddit/cov/main.nf
new file mode 100644
index 00000000000..fccb515d64b
--- /dev/null
+++ b/tests/modules/nf-core/tiddit/cov/main.nf
@@ -0,0 +1,42 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TIDDIT_COV as TIDDIT_COV_BED } from '../../../../../modules/nf-core/tiddit/cov/main.nf'
+include { TIDDIT_COV as TIDDIT_COV_WIG } from '../../../../../modules/nf-core/tiddit/cov/main.nf'
+
+workflow test_tiddit_cov_cram_bed {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    TIDDIT_COV_BED ( input, fasta )
+}
+
+workflow test_tiddit_cov_bam_bed {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+
+    TIDDIT_COV_BED ( input, [] )
+}
+
+workflow test_tiddit_cov_cram_wig {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    TIDDIT_COV_WIG ( input, fasta )
+}
+
+workflow test_tiddit_cov_bam_wig {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+
+    TIDDIT_COV_WIG ( input, [] )
+}
diff --git a/tests/modules/tiddit/cov/nextflow.config b/tests/modules/nf-core/tiddit/cov/nextflow.config
similarity index 100%
rename from tests/modules/tiddit/cov/nextflow.config
rename to tests/modules/nf-core/tiddit/cov/nextflow.config
diff --git a/tests/modules/nf-core/tiddit/cov/test.yml b/tests/modules/nf-core/tiddit/cov/test.yml
new file mode 100644
index 00000000000..5bbdbda16f4
--- /dev/null
+++ b/tests/modules/nf-core/tiddit/cov/test.yml
@@ -0,0 +1,35 @@
+- name: tiddit cov test_tiddit_cov_cram_bed
+  command: nextflow run ./tests/modules/nf-core/tiddit/cov -entry test_tiddit_cov_cram_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/cov/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/cov
+  files:
+    - path: output/tiddit/test.bed
+      md5sum: 3b1a28c62a5f25bbba77c1042e9abdf7
+
+- name: tiddit cov test_tiddit_cov_bam_bed
+  command: nextflow run ./tests/modules/nf-core/tiddit/cov -entry test_tiddit_cov_bam_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/cov/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/cov
+  files:
+    - path: output/tiddit/test.bed
+      md5sum: 9d1474f1c7c6516205254077087bb026
+
+- name: tiddit cov test_tiddit_cov_cram_wig
+  command: nextflow run ./tests/modules/nf-core/tiddit/cov -entry test_tiddit_cov_cram_wig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/cov/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/cov
+  files:
+    - path: output/tiddit/test.wig
+      md5sum: ca3645fd0c3491c86c075c91d16d57c4
+
+- name: tiddit cov test_tiddit_cov_bam_wig
+  command: nextflow run ./tests/modules/nf-core/tiddit/cov -entry test_tiddit_cov_bam_wig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/cov/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/cov
+  files:
+    - path: output/tiddit/test.wig
+      md5sum: 44bea2ac6a56774738e65773065da670
diff --git a/tests/modules/nf-core/tiddit/sv/main.nf b/tests/modules/nf-core/tiddit/sv/main.nf
new file mode 100644
index 00000000000..04d88c9dd10
--- /dev/null
+++ b/tests/modules/nf-core/tiddit/sv/main.nf
@@ -0,0 +1,59 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX                    } from '../../../../../modules/nf-core/bwa/index/main.nf'
+include { TIDDIT_SV                    } from '../../../../../modules/nf-core/tiddit/sv/main.nf'
+include { TIDDIT_SV as TIDDIT_SV_NOBWA } from '../../../../../modules/nf-core/tiddit/sv/main.nf'
+
+workflow test_tiddit_sv_bam {
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX( fasta )
+
+    TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
+}
+
+workflow test_tiddit_sv_cram {
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX( fasta )
+
+    TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
+}
+
+workflow test_tiddit_sv_nobwa_bam {
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    TIDDIT_SV_NOBWA ( input, fasta, [])
+}
+
+workflow test_tiddit_sv_nobwa_cram {
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    TIDDIT_SV_NOBWA ( input, fasta, [])
+}
diff --git a/tests/modules/tiddit/sv/nextflow.config b/tests/modules/nf-core/tiddit/sv/nextflow.config
similarity index 100%
rename from tests/modules/tiddit/sv/nextflow.config
rename to tests/modules/nf-core/tiddit/sv/nextflow.config
diff --git a/tests/modules/nf-core/tiddit/sv/test.yml b/tests/modules/nf-core/tiddit/sv/test.yml
new file mode 100644
index 00000000000..e8a0974065e
--- /dev/null
+++ b/tests/modules/nf-core/tiddit/sv/test.yml
@@ -0,0 +1,43 @@
+- name: tiddit sv test_tiddit_sv_bam
+  command: nextflow run ./tests/modules/nf-core/tiddit/sv -entry test_tiddit_sv_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/sv/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/sv
+  files:
+    - path: output/tiddit/test.ploidies.tab
+      md5sum: 6319d3611f7b6b94425a184d274b3dfc
+    - path: output/tiddit/test.vcf
+      md5sum: 157907671297c34bacfd3e73eff9bbdf
+
+- name: tiddit sv test_tiddit_sv_cram
+  command: nextflow run ./tests/modules/nf-core/tiddit/sv -entry test_tiddit_sv_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/sv/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/sv
+  files:
+    - path: output/tiddit/test.ploidies.tab
+      md5sum: f1162a940ddc8b963f6e0e506bb5c136
+    - path: output/tiddit/test.vcf
+      md5sum: 56687eeffa452f78f18d54a69dd17c78
+
+- name: tiddit sv test_tiddit_sv_nobwa_bam
+  command: nextflow run ./tests/modules/nf-core/tiddit/sv -entry test_tiddit_sv_nobwa_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/sv/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/sv
+  files:
+    - path: output/tiddit/test.ploidies.tab
+      md5sum: 6319d3611f7b6b94425a184d274b3dfc
+    - path: output/tiddit/test.vcf
+      md5sum: ddac94f9cd4f991b6ce2052d7f78a525
+
+- name: tiddit sv test_tiddit_sv_nobwa_cram
+  command: nextflow run ./tests/modules/nf-core/tiddit/sv -entry test_tiddit_sv_nobwa_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/sv/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/sv
+  files:
+    - path: output/tiddit/test.ploidies.tab
+      md5sum: f1162a940ddc8b963f6e0e506bb5c136
+    - path: output/tiddit/test.vcf
+      md5sum: 680e60574cc28d38c9673a916ecd675c
diff --git a/tests/modules/nf-core/transdecoder/longorf/main.nf b/tests/modules/nf-core/transdecoder/longorf/main.nf
new file mode 100644
index 00000000000..1877d9ee8fd
--- /dev/null
+++ b/tests/modules/nf-core/transdecoder/longorf/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TRANSDECODER_LONGORF } from '../../../../../modules/nf-core/transdecoder/longorf/main.nf'
+
+workflow test_transdecoder_longorf {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
+    ]
+
+    TRANSDECODER_LONGORF ( input )
+}
diff --git a/tests/modules/transdecoder/longorf/nextflow.config b/tests/modules/nf-core/transdecoder/longorf/nextflow.config
similarity index 100%
rename from tests/modules/transdecoder/longorf/nextflow.config
rename to tests/modules/nf-core/transdecoder/longorf/nextflow.config
diff --git a/tests/modules/nf-core/transdecoder/longorf/test.yml b/tests/modules/nf-core/transdecoder/longorf/test.yml
new file mode 100644
index 00000000000..3a06da79103
--- /dev/null
+++ b/tests/modules/nf-core/transdecoder/longorf/test.yml
@@ -0,0 +1,16 @@
+- name: transdecoder longorf test_transdecoder_longorf
+  command: nextflow run ./tests/modules/nf-core/transdecoder/longorf -entry test_transdecoder_longorf -c ./tests/config/nextflow.config
+  tags:
+    - transdecoder
+    - transdecoder/longorf
+  files:
+    - path: output/transdecoder/versions.yml
+      md5sum: 15cffd5b1119e63d52dc754caf0f2d3c
+    - path: output/transdecoder/test/base_freqs.dat
+      md5sum: 5226ef383532e9b16c16b03e35ce181e
+    - path: output/transdecoder/test/longest_orfs.cds
+      md5sum: 041ac609e4c4ffb38676b1f88365be0f
+    - path: output/transdecoder/test/longest_orfs.gff3
+      md5sum: 96062ef88364f6bf1368d65cd1aad350
+    - path: output/transdecoder/test/longest_orfs.pep
+      md5sum: 0b903d36040676efeb2c50ab5ba46bbd
diff --git a/tests/modules/nf-core/transdecoder/predict/main.nf b/tests/modules/nf-core/transdecoder/predict/main.nf
new file mode 100644
index 00000000000..2a085151e74
--- /dev/null
+++ b/tests/modules/nf-core/transdecoder/predict/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TRANSDECODER_PREDICT } from '../../../../../modules/nf-core/transdecoder/predict/main.nf'
+include { TRANSDECODER_LONGORF } from '../../../../../modules/nf-core/transdecoder/longorf/main.nf'
+
+workflow test_transdecoder_predict {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+    
+    TRANSDECODER_LONGORF ( input )
+    TRANSDECODER_PREDICT ( input, TRANSDECODER_LONGORF.out.folder )
+
+}
+
diff --git a/tests/modules/transdecoder/predict/nextflow.config b/tests/modules/nf-core/transdecoder/predict/nextflow.config
similarity index 100%
rename from tests/modules/transdecoder/predict/nextflow.config
rename to tests/modules/nf-core/transdecoder/predict/nextflow.config
diff --git a/tests/modules/nf-core/transdecoder/predict/test.yml b/tests/modules/nf-core/transdecoder/predict/test.yml
new file mode 100644
index 00000000000..31cf06b4987
--- /dev/null
+++ b/tests/modules/nf-core/transdecoder/predict/test.yml
@@ -0,0 +1,12 @@
+- name: transdecoder predict test_transdecoder_predict
+  command: nextflow run ./tests/modules/nf-core/transdecoder/predict -entry test_transdecoder_predict -c ./tests/config/nextflow.config
+  tags:
+    - transdecoder
+    - transdecoder/predict
+  files:
+    - path: output/transdecoder/genome.fasta.transdecoder.bed
+    - path: output/transdecoder/genome.fasta.transdecoder.cds
+    - path: output/transdecoder/genome.fasta.transdecoder.gff3
+    - path: output/transdecoder/genome.fasta.transdecoder.pep
+    - path: output/transdecoder/versions.yml
+      md5sum: 2847cc159dc93e9014b57d76987623ea
diff --git a/tests/modules/nf-core/trimgalore/main.nf b/tests/modules/nf-core/trimgalore/main.nf
new file mode 100644
index 00000000000..6c09dcb7f1a
--- /dev/null
+++ b/tests/modules/nf-core/trimgalore/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { TRIMGALORE } from '../../../../modules/nf-core/trimgalore/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_trimgalore_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    TRIMGALORE ( input )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_trimgalore_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    TRIMGALORE ( input )
+}
diff --git a/tests/modules/trimgalore/nextflow.config b/tests/modules/nf-core/trimgalore/nextflow.config
similarity index 100%
rename from tests/modules/trimgalore/nextflow.config
rename to tests/modules/nf-core/trimgalore/nextflow.config
diff --git a/tests/modules/nf-core/trimgalore/test.yml b/tests/modules/nf-core/trimgalore/test.yml
new file mode 100644
index 00000000000..5351d273c10
--- /dev/null
+++ b/tests/modules/nf-core/trimgalore/test.yml
@@ -0,0 +1,21 @@
+- name: trimgalore single-end
+  command: nextflow run ./tests/modules/nf-core/trimgalore/ -entry test_trimgalore_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimgalore/nextflow.config
+  tags:
+    - trimgalore
+  files:
+    # These can't be md5'd reliably
+    # TODO Test for includes
+    - path: ./output/trimgalore/test.fastq.gz_trimming_report.txt
+    - path: ./output/trimgalore/test_trimmed.fq.gz
+
+- name: trimgalore paired-end
+  command: nextflow run ./tests/modules/nf-core/trimgalore/ -entry test_trimgalore_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimgalore/nextflow.config
+  tags:
+    - trimgalore
+  files:
+    # These can't be md5'd reliably
+    # TODO Test for includes
+    - path: ./output/trimgalore/test_2_val_2.fq.gz
+    - path: ./output/trimgalore/test_1_val_1.fq.gz
+    - path: ./output/trimgalore/test_1.fastq.gz_trimming_report.txt
+    - path: ./output/trimgalore/test_2.fastq.gz_trimming_report.txt
diff --git a/tests/modules/nf-core/trimmomatic/main.nf b/tests/modules/nf-core/trimmomatic/main.nf
new file mode 100644
index 00000000000..0114743e225
--- /dev/null
+++ b/tests/modules/nf-core/trimmomatic/main.nf
@@ -0,0 +1,42 @@
+nextflow.enable.dsl = 2
+
+include {
+    TRIMMOMATIC as TRIMMOMATIC_SE
+    TRIMMOMATIC as TRIMMOMATIC_PE
+    TRIMMOMATIC
+} from '../../../../modules/nf-core/trimmomatic/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_trimmomatic_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    TRIMMOMATIC_SE ( input )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_trimmomatic_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    TRIMMOMATIC_PE ( input )
+}
+
+//
+// Failing test with no adaptor
+//
+workflow test_trimmomatic_no_adaptor {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    TRIMMOMATIC ( input )
+}
diff --git a/tests/modules/trimmomatic/nextflow.config b/tests/modules/nf-core/trimmomatic/nextflow.config
similarity index 100%
rename from tests/modules/trimmomatic/nextflow.config
rename to tests/modules/nf-core/trimmomatic/nextflow.config
diff --git a/tests/modules/nf-core/trimmomatic/test.yml b/tests/modules/nf-core/trimmomatic/test.yml
new file mode 100644
index 00000000000..b2813597d9b
--- /dev/null
+++ b/tests/modules/nf-core/trimmomatic/test.yml
@@ -0,0 +1,26 @@
+- name: trimmomatic single-end
+  command: nextflow run ./tests/modules/nf-core/trimmomatic -entry test_trimmomatic_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimmomatic/nextflow.config
+  tags:
+    - "trimmomatic"
+  files:
+    - path: "output/trimmomatic/test.SE.paired.trim.fastq.gz"
+    - path: "output/trimmomatic/test.log"
+      md5sum: e4c3f619e9b0e26847f8f3e3d9af319b
+
+- name: trimmomatic paired-end
+  command: nextflow run ./tests/modules/nf-core/trimmomatic -entry test_trimmomatic_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimmomatic/nextflow.config
+  tags:
+    - "trimmomatic"
+  files:
+    - path: "output/trimmomatic/test.log"
+      md5sum: 9629761761a34576b3484bf4174f681f
+    - path: "output/trimmomatic/test.paired.trim_1.fastq.gz"
+    - path: "output/trimmomatic/test.unpaired.trim_1.fastq.gz"
+    - path: "output/trimmomatic/test.paired.trim_2.fastq.gz"
+    - path: "output/trimmomatic/test.unpaired.trim_2.fastq.gz"
+
+- name: trimmomatic no adapter specified
+  command: nextflow run ./tests/modules/nf-core/trimmomatic -entry test_trimmomatic_no_adaptor -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimmomatic/nextflow.config
+  tags:
+    - "trimmomatic"
+  exit_code: 1
diff --git a/tests/modules/nf-core/ucsc/bedclip/main.nf b/tests/modules/nf-core/ucsc/bedclip/main.nf
new file mode 100755
index 00000000000..df0dabe28a7
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/bedclip/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_BEDCLIP } from '../../../../../modules/nf-core/ucsc/bedclip/main.nf'
+
+workflow test_ucsc_bedclip {
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_bedgraph'], checkIfExists: true)
+            ]
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+
+    UCSC_BEDCLIP ( input, sizes )
+}
diff --git a/tests/modules/ucsc/bedclip/nextflow.config b/tests/modules/nf-core/ucsc/bedclip/nextflow.config
similarity index 100%
rename from tests/modules/ucsc/bedclip/nextflow.config
rename to tests/modules/nf-core/ucsc/bedclip/nextflow.config
diff --git a/tests/modules/nf-core/ucsc/bedclip/test.yml b/tests/modules/nf-core/ucsc/bedclip/test.yml
new file mode 100755
index 00000000000..55da06df78b
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/bedclip/test.yml
@@ -0,0 +1,8 @@
+- name: ucsc bedclip
+  command: nextflow run ./tests/modules/nf-core/ucsc/bedclip -entry test_ucsc_bedclip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bedclip/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/bedclip
+  files:
+    - path: output/ucsc/test.clip.bedGraph
+      md5sum: e02395e1f7c593b3f79563067159ebc2
diff --git a/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
new file mode 100644
index 00000000000..de7efec6f06
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_BEDGRAPHTOBIGWIG  } from '../../../../../modules/nf-core/ucsc/bedgraphtobigwig/main.nf'
+
+workflow test_ucsc_bedgraphtobigwig {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_bedgraph'], checkIfExists: true) ]
+            ]
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+
+    UCSC_BEDGRAPHTOBIGWIG ( input, sizes )
+}
diff --git a/tests/modules/ucsc/bedgraphtobigwig/nextflow.config b/tests/modules/nf-core/ucsc/bedgraphtobigwig/nextflow.config
similarity index 100%
rename from tests/modules/ucsc/bedgraphtobigwig/nextflow.config
rename to tests/modules/nf-core/ucsc/bedgraphtobigwig/nextflow.config
diff --git a/tests/modules/nf-core/ucsc/bedgraphtobigwig/test.yml b/tests/modules/nf-core/ucsc/bedgraphtobigwig/test.yml
new file mode 100644
index 00000000000..34b28baa2fa
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/bedgraphtobigwig/test.yml
@@ -0,0 +1,8 @@
+- name: ucsc bedgraphtobigwig
+  command: nextflow run ./tests/modules/nf-core/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bedgraphtobigwig/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/bedgraphtobigwig
+  files:
+    - path: output/ucsc/test.bigWig
+      md5sum: 910ecc7f57e3bbd5fac5a8edba4f615d
diff --git a/tests/modules/nf-core/ucsc/bedtobigbed/main.nf b/tests/modules/nf-core/ucsc/bedtobigbed/main.nf
new file mode 100644
index 00000000000..07708297697
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/bedtobigbed/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_BEDTOBIGBED } from '../../../../../modules/nf-core/ucsc/bedtobigbed/main.nf'
+include { UCSC_BEDTOBIGBED as UCSC_BEDTOBIGBED_AS } from '../../../../../modules/nf-core/ucsc/bedtobigbed/main.nf'
+
+workflow test_ucsc_bedtobigbed {
+    input = [ [ id: 'test' ], // meta map 
+              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
+            ]
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+
+    UCSC_BEDTOBIGBED ( input, sizes, [] )
+}
+
+workflow test_ucsc_bedtobigbed_autosql {
+    input = [ [ id: 'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
+            ]
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+    autosql = file(params.test_data['sarscov2']['genome']['bed_autosql'], checkIfExists: true)
+
+    UCSC_BEDTOBIGBED_AS ( input, sizes, autosql )
+}
diff --git a/tests/modules/ucsc/bedtobigbed/nextflow.config b/tests/modules/nf-core/ucsc/bedtobigbed/nextflow.config
similarity index 100%
rename from tests/modules/ucsc/bedtobigbed/nextflow.config
rename to tests/modules/nf-core/ucsc/bedtobigbed/nextflow.config
diff --git a/tests/modules/nf-core/ucsc/bedtobigbed/test.yml b/tests/modules/nf-core/ucsc/bedtobigbed/test.yml
new file mode 100644
index 00000000000..e17777359b7
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/bedtobigbed/test.yml
@@ -0,0 +1,16 @@
+- name: ucsc bedtobigbed
+  command: nextflow run ./tests/modules/nf-core/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bedtobigbed/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/bedtobigbed
+  files:
+    - path: output/ucsc/test.bigBed
+      md5sum: 3c2400aab8f7a3ac333905c7484d9a24
+- name: ucsc bedtobigbed autosql
+  command: nextflow run ./tests/modules/nf-core/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed_autosql -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bedtobigbed/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/bedtobigbed
+  files:
+    - path: output/ucsc/test.bigBed
+      md5sum: 6dc69a14b95bcceee98e9e6b3c3def09
diff --git a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf
new file mode 100644
index 00000000000..771bf066e8e
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../../modules/nf-core/ucsc/bigwigaverageoverbed/main.nf'
+
+workflow test_ucsc_bigwigaverageoverbed {
+    input = [
+        [ id: 'test' ], // meta map
+        [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
+    ]
+    bigwig = file(params.test_data['sarscov2']['illumina']['test_bigwig'], checkIfExists: true)
+
+    UCSC_BIGWIGAVERAGEOVERBED ( input, bigwig )
+}
diff --git a/tests/modules/ucsc/bigwigaverageoverbed/nextflow.config b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/nextflow.config
similarity index 100%
rename from tests/modules/ucsc/bigwigaverageoverbed/nextflow.config
rename to tests/modules/nf-core/ucsc/bigwigaverageoverbed/nextflow.config
diff --git a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml
new file mode 100644
index 00000000000..07661349ef2
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml
@@ -0,0 +1,8 @@
+- name: ucsc bigwigaverageoverbed test_ucsc_bigwigaverageoverbed
+  command: nextflow run ./tests/modules/nf-core/ucsc/bigwigaverageoverbed -entry test_ucsc_bigwigaverageoverbed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bigwigaverageoverbed/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/bigwigaverageoverbed
+  files:
+    - path: output/ucsc/test.tab
+      md5sum: d92334d90353577571eaf777933dce9b
diff --git a/tests/modules/nf-core/ucsc/liftover/main.nf b/tests/modules/nf-core/ucsc/liftover/main.nf
new file mode 100644
index 00000000000..87b4f6d47cb
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/liftover/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_LIFTOVER } from '../../../../../modules/nf-core/ucsc/liftover/main.nf'
+
+workflow test_ucsc_liftover {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]
+    chain =  file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
+
+    UCSC_LIFTOVER ( input, chain )
+}
diff --git a/tests/modules/ucsc/liftover/nextflow.config b/tests/modules/nf-core/ucsc/liftover/nextflow.config
similarity index 100%
rename from tests/modules/ucsc/liftover/nextflow.config
rename to tests/modules/nf-core/ucsc/liftover/nextflow.config
diff --git a/tests/modules/nf-core/ucsc/liftover/test.yml b/tests/modules/nf-core/ucsc/liftover/test.yml
new file mode 100644
index 00000000000..16f20b5e2b8
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/liftover/test.yml
@@ -0,0 +1,10 @@
+- name: ucsc liftover test_ucsc_liftover
+  command: nextflow run ./tests/modules/nf-core/ucsc/liftover -entry test_ucsc_liftover -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/liftover/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/liftover
+  files:
+    - path: output/ucsc/test.lifted.bed
+      md5sum: fd5878470257a8a0edeaa8b9374bd520
+    - path: output/ucsc/test.unlifted.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/nf-core/ucsc/wigtobigwig/main.nf b/tests/modules/nf-core/ucsc/wigtobigwig/main.nf
new file mode 100644
index 00000000000..2f5558987bc
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/wigtobigwig/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_WIGTOBIGWIG } from '../../../../../modules/nf-core/ucsc/wigtobigwig/main.nf'
+
+workflow test_ucsc_wigtobigwig {
+
+    input = [ [ id:'test', single_end:false ], // meta map,
+                file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true) ]
+
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+
+    UCSC_WIGTOBIGWIG ( input, sizes )
+}
diff --git a/tests/modules/ucsc/wigtobigwig/nextflow.config b/tests/modules/nf-core/ucsc/wigtobigwig/nextflow.config
similarity index 100%
rename from tests/modules/ucsc/wigtobigwig/nextflow.config
rename to tests/modules/nf-core/ucsc/wigtobigwig/nextflow.config
diff --git a/tests/modules/nf-core/ucsc/wigtobigwig/test.yml b/tests/modules/nf-core/ucsc/wigtobigwig/test.yml
new file mode 100644
index 00000000000..79decdbc64a
--- /dev/null
+++ b/tests/modules/nf-core/ucsc/wigtobigwig/test.yml
@@ -0,0 +1,19 @@
+- name: ucsc wigtobigwig test_ucsc_wigtobigwig
+  command: nextflow run ./tests/modules/nf-core/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/wigtobigwig/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/wigtobigwig
+  files:
+    - path: output/ucsc/test.bw
+      md5sum: b64af7003665dc51fae958216b06ed95
+    - path: output/ucsc/versions.yml
+      md5sum: 7e14421c65faf5165389f34806acdb12
+
+- name: ucsc wigtobigwig test_ucsc_wigtobigwig stub
+  command: nextflow run ./tests/modules/nf-core/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/wigtobigwig/nextflow.config -stub
+  tags:
+    - ucsc
+    - ucsc/wigtobigwig
+  files:
+    - path: output/ucsc/test.bw
+    - path: output/ucsc/versions.yml
diff --git a/tests/modules/nf-core/ultra/align/main.nf b/tests/modules/nf-core/ultra/align/main.nf
new file mode 100644
index 00000000000..ff40ed1acdf
--- /dev/null
+++ b/tests/modules/nf-core/ultra/align/main.nf
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP        } from '../../../../../modules/nf-core/gunzip/main.nf'
+include { GFFREAD       } from '../../../../../modules/nf-core/gffread/main.nf'
+include { ULTRA_INDEX   } from '../../../../../modules/nf-core/ultra/index/main.nf'
+include { ULTRA_ALIGN   } from '../../../../../modules/nf-core/ultra/align/main.nf'
+
+workflow test_ultra_align {
+
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
+    ]
+
+    genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf    = file(params.test_data['homo_sapiens']['genome']['genome_gtf']  , checkIfExists: true)
+
+    GUNZIP ( input )
+    GFFREAD ( gtf )
+    ULTRA_INDEX ( genome, GFFREAD.out.gtf )
+    ULTRA_ALIGN ( GUNZIP.out.gunzip, genome, ULTRA_INDEX.out.index )
+}
diff --git a/tests/modules/ultra/align/nextflow.config b/tests/modules/nf-core/ultra/align/nextflow.config
similarity index 100%
rename from tests/modules/ultra/align/nextflow.config
rename to tests/modules/nf-core/ultra/align/nextflow.config
diff --git a/tests/modules/nf-core/ultra/align/test.yml b/tests/modules/nf-core/ultra/align/test.yml
new file mode 100644
index 00000000000..1eafd64295e
--- /dev/null
+++ b/tests/modules/nf-core/ultra/align/test.yml
@@ -0,0 +1,33 @@
+- name: ultra align test_ultra_align
+  command: nextflow run ./tests/modules/nf-core/ultra/align -entry test_ultra_align -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ultra/align/nextflow.config
+  tags:
+    - ultra/align
+    - ultra
+  files:
+    - path: output/gffread/genome_sorted.gtf
+      md5sum: c0b034860c679a354cd093109ed90437
+    - path: output/gunzip/test_hifi.fastq
+      md5sum: 20e41c569d5828c1e87337e13a5185d3
+    - path: output/ultra/all_splice_pairs_annotations.pickle
+    - path: output/ultra/all_splice_sites_annotations.pickle
+    - path: output/ultra/chr_to_id.pickle
+    - path: output/ultra/database.db
+    - path: output/ultra/exon_choordinates_to_id.pickle
+    - path: output/ultra/flank_choordinates.pickle
+    - path: output/ultra/gene_to_small_segments.pickle
+    - path: output/ultra/id_to_chr.pickle
+    - path: output/ultra/max_intron_chr.pickle
+    - path: output/ultra/parts_to_segments.pickle
+    - path: output/ultra/ref_exon_sequences.pickle
+    - path: output/ultra/ref_flank_sequences.pickle
+    - path: output/ultra/ref_part_sequences.pickle
+    - path: output/ultra/ref_segment_sequences.pickle
+    - path: output/ultra/refs_id_lengths.pickle
+    - path: output/ultra/refs_lengths.pickle
+    - path: output/ultra/segment_id_to_choordinates.pickle
+    - path: output/ultra/segment_to_gene.pickle
+    - path: output/ultra/segment_to_ref.pickle
+    - path: output/ultra/splices_to_transcripts.pickle
+    - path: output/ultra/test.bam
+      md5sum: b34c3631a899ba800602ff07b8183f87
+    - path: output/ultra/transcripts_to_splices.pickle
diff --git a/tests/modules/nf-core/ultra/index/main.nf b/tests/modules/nf-core/ultra/index/main.nf
new file mode 100644
index 00000000000..e5df61e6c44
--- /dev/null
+++ b/tests/modules/nf-core/ultra/index/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ULTRA_INDEX } from '../../../../../modules/nf-core/ultra/index/main.nf'
+include { GFFREAD     } from '../../../../../modules/nf-core/gffread/main.nf'
+
+workflow test_ultra_index {
+
+    genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf    = file(params.test_data['homo_sapiens']['genome']['genome_gtf']  , checkIfExists: true)
+    GFFREAD ( gtf )
+
+    ULTRA_INDEX ( genome, GFFREAD.out.gtf )
+}
diff --git a/tests/modules/ultra/index/nextflow.config b/tests/modules/nf-core/ultra/index/nextflow.config
similarity index 100%
rename from tests/modules/ultra/index/nextflow.config
rename to tests/modules/nf-core/ultra/index/nextflow.config
diff --git a/tests/modules/nf-core/ultra/index/test.yml b/tests/modules/nf-core/ultra/index/test.yml
new file mode 100644
index 00000000000..2e192ea684b
--- /dev/null
+++ b/tests/modules/nf-core/ultra/index/test.yml
@@ -0,0 +1,29 @@
+- name: ultra index test_ultra_index
+  command: nextflow run ./tests/modules/nf-core/ultra/index -entry test_ultra_index -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/ultra/index/nextflow.config
+  tags:
+    - ultra
+    - ultra/index
+  files:
+    - path: output/gffread/genome_sorted.gtf
+      md5sum: c0b034860c679a354cd093109ed90437
+    - path: output/ultra/all_splice_pairs_annotations.pickle
+    - path: output/ultra/all_splice_sites_annotations.pickle
+    - path: output/ultra/chr_to_id.pickle
+    - path: output/ultra/database.db
+    - path: output/ultra/exon_choordinates_to_id.pickle
+    - path: output/ultra/flank_choordinates.pickle
+    - path: output/ultra/gene_to_small_segments.pickle
+    - path: output/ultra/id_to_chr.pickle
+    - path: output/ultra/max_intron_chr.pickle
+    - path: output/ultra/parts_to_segments.pickle
+    - path: output/ultra/ref_exon_sequences.pickle
+    - path: output/ultra/ref_flank_sequences.pickle
+    - path: output/ultra/ref_part_sequences.pickle
+    - path: output/ultra/ref_segment_sequences.pickle
+    - path: output/ultra/refs_id_lengths.pickle
+    - path: output/ultra/refs_lengths.pickle
+    - path: output/ultra/segment_id_to_choordinates.pickle
+    - path: output/ultra/segment_to_gene.pickle
+    - path: output/ultra/segment_to_ref.pickle
+    - path: output/ultra/splices_to_transcripts.pickle
+    - path: output/ultra/transcripts_to_splices.pickle
diff --git a/tests/modules/nf-core/ultra/pipeline/main.nf b/tests/modules/nf-core/ultra/pipeline/main.nf
new file mode 100644
index 00000000000..fe0487e4417
--- /dev/null
+++ b/tests/modules/nf-core/ultra/pipeline/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ULTRA_PIPELINE } from '../../../../../modules/nf-core/ultra/pipeline/main.nf'
+include { GUNZIP         } from '../../../../../modules/nf-core/gunzip/main.nf'
+include { GFFREAD        } from '../../../../../modules/nf-core/gffread/main.nf'
+
+workflow test_ultra_pipeline {
+
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
+    ]
+    GUNZIP ( input )
+
+    gtf    = file(params.test_data['homo_sapiens']['genome']['genome_gtf']  , checkIfExists: true)
+    genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    GFFREAD ( gtf )
+
+    ULTRA_PIPELINE ( GUNZIP.out.gunzip, genome, GFFREAD.out.gtf )
+}
diff --git a/tests/modules/ultra/pipeline/nextflow.config b/tests/modules/nf-core/ultra/pipeline/nextflow.config
similarity index 100%
rename from tests/modules/ultra/pipeline/nextflow.config
rename to tests/modules/nf-core/ultra/pipeline/nextflow.config
diff --git a/tests/modules/nf-core/ultra/pipeline/test.yml b/tests/modules/nf-core/ultra/pipeline/test.yml
new file mode 100644
index 00000000000..4abfbcf2182
--- /dev/null
+++ b/tests/modules/nf-core/ultra/pipeline/test.yml
@@ -0,0 +1,12 @@
+- name: ultra pipeline test_ultra_pipeline
+  command: nextflow run ./tests/modules/nf-core/ultra/pipeline -entry test_ultra_pipeline -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ultra/pipeline/nextflow.config
+  tags:
+    - ultra
+    - ultra/pipeline
+  files:
+    - path: output/gffread/genome_sorted.gtf
+      md5sum: c0b034860c679a354cd093109ed90437
+    - path: output/gunzip/test_hifi.fastq
+      md5sum: 20e41c569d5828c1e87337e13a5185d3
+    - path: output/ultra/test.sam
+      md5sum: a37a1f9594a3099522dc1f6a903b2b12
diff --git a/tests/modules/nf-core/umitools/dedup/main.nf b/tests/modules/nf-core/umitools/dedup/main.nf
new file mode 100644
index 00000000000..2a9b6af1ba4
--- /dev/null
+++ b/tests/modules/nf-core/umitools/dedup/main.nf
@@ -0,0 +1,83 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UMITOOLS_EXTRACT } from '../../../../../modules/nf-core/umitools/extract/main.nf'
+include { BWA_INDEX        } from '../../../../../modules/nf-core/bwa/index/main.nf'
+include { BWA_MEM          } from '../../../../../modules/nf-core/bwa/mem/main.nf'
+include { SAMTOOLS_INDEX   } from '../../../../../modules/nf-core/samtools/index/main.nf'
+include { UMITOOLS_DEDUP   } from '../../../../../modules/nf-core/umitools/dedup/main.nf'
+
+//
+// Test with no UMI
+//
+workflow test_umitools_dedup_no_umi {
+    input = [ 
+        [ id:'test'], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+    get_output_stats = false
+
+    UMITOOLS_DEDUP ( input, get_output_stats )
+}
+
+//
+// Test with single-end data without --output-stats
+//
+workflow test_umitools_dedup_single_end_no_stats {
+    input = [ 
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    get_output_stats = false
+
+    UMITOOLS_EXTRACT ( input )
+    BWA_INDEX ( fasta )
+    BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
+    SAMTOOLS_INDEX ( BWA_MEM.out.bam )
+    UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
+}
+
+//
+// Test with paired-end data without --output-stats
+//
+workflow test_umitools_dedup_paired_end_no_stats {
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [ 
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    get_output_stats = false
+
+    UMITOOLS_EXTRACT ( input )
+    BWA_INDEX ( fasta )
+    BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
+    SAMTOOLS_INDEX ( BWA_MEM.out.bam )
+    UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
+}
+
+//
+// Test with paired-end data with --output-stats
+//
+workflow test_umitools_dedup_paired_end_stats {
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [ 
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    get_output_stats = true
+
+    UMITOOLS_EXTRACT ( input )
+    BWA_INDEX ( fasta )
+    BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
+    SAMTOOLS_INDEX ( BWA_MEM.out.bam )
+    UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
+}
diff --git a/tests/modules/umitools/dedup/nextflow.config b/tests/modules/nf-core/umitools/dedup/nextflow.config
similarity index 100%
rename from tests/modules/umitools/dedup/nextflow.config
rename to tests/modules/nf-core/umitools/dedup/nextflow.config
diff --git a/tests/modules/nf-core/umitools/dedup/test.yml b/tests/modules/nf-core/umitools/dedup/test.yml
new file mode 100644
index 00000000000..157c67cabb4
--- /dev/null
+++ b/tests/modules/nf-core/umitools/dedup/test.yml
@@ -0,0 +1,87 @@
+- name: umitools dedup test_umitools_dedup_no_umi
+  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_no_umi -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
+  tags:
+    - umitools/dedup
+    - umitools
+  files:
+    - path: output/umitools/test.dedup.bam
+
+- name: umitools dedup test_umitools_dedup_single_end_no_stats
+  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_single_end_no_stats -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
+  tags:
+    - umitools/dedup
+    - umitools
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+    - path: output/bwa/test.bam
+      md5sum: 3ecbe569cadb9b6c881917ce60779f75
+    - path: output/samtools/test.bam.bai
+      md5sum: 095af0ad3921212597ffd7c342ecd5a0
+    - path: output/umitools/test.dedup.bam
+    - path: output/umitools/test.umi_extract.fastq.gz
+    - path: output/umitools/test.umi_extract.log
+
+- name: umitools dedup test_umitools_dedup_paired_end_no_stats
+  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
+  tags:
+    - umitools/dedup
+    - umitools
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+    - path: output/bwa/test.bam
+      md5sum: e7dcbac1825bf210409b762dbb4fec8f
+    - path: output/samtools/test.bam.bai
+      md5sum: f75780d1de7860329b7fb4afeadc4bed
+    - path: output/umitools/test.dedup.bam
+    - path: output/umitools/test.umi_extract.log
+    - path: output/umitools/test.umi_extract_1.fastq.gz
+    - path: output/umitools/test.umi_extract_2.fastq.gz
+
+- name: umitools dedup test_umitools_dedup_paired_end_stats
+  command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/umitools/dedup/nextflow.config
+  tags:
+    - umitools/dedup
+    - umitools
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+    - path: output/bwa/test.bam
+      md5sum: e7dcbac1825bf210409b762dbb4fec8f
+    - path: output/samtools/test.bam.bai
+      md5sum: f75780d1de7860329b7fb4afeadc4bed
+    - path: output/umitools/test.dedup.bam
+    - path: output/umitools/test.dedup_edit_distance.tsv
+      md5sum: c247a49b58768e6e2e86a6c08483e612
+    - path: output/umitools/test.dedup_per_umi.tsv
+      md5sum: 10e35ca37f2bfb521ac6dd7314951a68
+    - path: output/umitools/test.dedup_per_umi_per_position.tsv
+      md5sum: 2e1a12e6f720510880068deddeefe063
+    - path: output/umitools/test.umi_extract.log
+    - path: output/umitools/test.umi_extract_1.fastq.gz
+    - path: output/umitools/test.umi_extract_2.fastq.gz
diff --git a/tests/modules/nf-core/umitools/extract/main.nf b/tests/modules/nf-core/umitools/extract/main.nf
new file mode 100644
index 00000000000..417cc70f077
--- /dev/null
+++ b/tests/modules/nf-core/umitools/extract/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UMITOOLS_EXTRACT } from '../../../../../modules/nf-core/umitools/extract/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_umitools_extract_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    UMITOOLS_EXTRACT ( input )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_umitools_extract_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    UMITOOLS_EXTRACT ( input )
+}
+
diff --git a/tests/modules/umitools/extract/nextflow.config b/tests/modules/nf-core/umitools/extract/nextflow.config
similarity index 100%
rename from tests/modules/umitools/extract/nextflow.config
rename to tests/modules/nf-core/umitools/extract/nextflow.config
diff --git a/tests/modules/nf-core/umitools/extract/test.yml b/tests/modules/nf-core/umitools/extract/test.yml
new file mode 100644
index 00000000000..0355061afae
--- /dev/null
+++ b/tests/modules/nf-core/umitools/extract/test.yml
@@ -0,0 +1,27 @@
+- name: umitools extract test_umitools_extract_single_end
+  command: nextflow run ./tests/modules/nf-core/umitools/extract -entry test_umitools_extract_single_end -c ./tests/config/nextflow.config
+  tags:
+    - umitools/extract
+    - umitools
+  files:
+    - path: output/umitools/test.umi_extract.fastq.gz
+      should_exist: true
+    - path: output/umitools/test.umi_extract.log
+      contains: ["job finished in"]
+    - path: output/umitools/versions.yml
+      md5sum: 397e6972343f9d7b8eae387fc18c12c7
+
+- name: umitools extract test_umitools_extract_paired_end
+  command: nextflow run ./tests/modules/nf-core/umitools/extract -entry test_umitools_extract_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - umitools/extract
+    - umitools
+  files:
+    - path: output/umitools/test.umi_extract.log
+      contains: ["job finished in"]
+    - path: output/umitools/test.umi_extract_1.fastq.gz
+      should_exist: true
+    - path: output/umitools/test.umi_extract_2.fastq.gz
+      should_exist: true
+    - path: output/umitools/versions.yml
+      md5sum: 0aec6f919d62b7b79f6d0c5d79411464
diff --git a/tests/modules/nf-core/unicycler/main.nf b/tests/modules/nf-core/unicycler/main.nf
new file mode 100644
index 00000000000..0c7c037b6d0
--- /dev/null
+++ b/tests/modules/nf-core/unicycler/main.nf
@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNICYCLER } from '../../../../modules/nf-core/unicycler/main.nf'
+
+workflow test_unicycler_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true) ],
+              []
+            ]
+
+    UNICYCLER ( input )
+}
+
+workflow test_unicycler_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
+              []
+            ]
+
+    UNICYCLER ( input )
+}
+
+workflow test_unicycler_shortreads_longreads {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
+              [ file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    UNICYCLER ( input )
+}
diff --git a/tests/modules/unicycler/nextflow.config b/tests/modules/nf-core/unicycler/nextflow.config
similarity index 100%
rename from tests/modules/unicycler/nextflow.config
rename to tests/modules/nf-core/unicycler/nextflow.config
diff --git a/tests/modules/nf-core/unicycler/test.yml b/tests/modules/nf-core/unicycler/test.yml
new file mode 100644
index 00000000000..61bb0d9c692
--- /dev/null
+++ b/tests/modules/nf-core/unicycler/test.yml
@@ -0,0 +1,32 @@
+- name: unicycler test_unicycler_single_end
+  command: nextflow run ./tests/modules/nf-core/unicycler -entry test_unicycler_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/unicycler/nextflow.config
+  tags:
+    - unicycler
+  files:
+    - path: output/unicycler/test.assembly.gfa.gz
+    - path: output/unicycler/test.scaffolds.fa.gz
+    - path: output/unicycler/test.unicycler.log
+      contains:
+        - "Assembly complete"
+
+- name: unicycler test_unicycler_paired_end
+  command: nextflow run ./tests/modules/nf-core/unicycler -entry test_unicycler_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/unicycler/nextflow.config
+  tags:
+    - unicycler
+  files:
+    - path: output/unicycler/test.assembly.gfa.gz
+    - path: output/unicycler/test.scaffolds.fa.gz
+    - path: output/unicycler/test.unicycler.log
+      contains:
+        - "Assembly complete"
+
+- name: unicycler test_unicycler_shortreads_longreads
+  command: nextflow run ./tests/modules/nf-core/unicycler -entry test_unicycler_shortreads_longreads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/unicycler/nextflow.config
+  tags:
+    - unicycler
+  files:
+    - path: output/unicycler/test.assembly.gfa.gz
+    - path: output/unicycler/test.scaffolds.fa.gz
+    - path: output/unicycler/test.unicycler.log
+      contains:
+        - "Assembly complete"
diff --git a/tests/modules/nf-core/untar/main.nf b/tests/modules/nf-core/untar/main.nf
new file mode 100644
index 00000000000..3d92298bc0f
--- /dev/null
+++ b/tests/modules/nf-core/untar/main.nf
@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR } from '../../../../modules/nf-core/untar/main.nf'
+
+workflow test_untar {
+    input = [
+        [],
+        file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
+    ]
+
+    UNTAR ( input )
+}
+
+
+workflow test_untar_different_output_path {
+    input = [
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
+    ]
+
+    UNTAR ( input )
+}
+
+
+workflow test_untar_onlyfiles {
+    input = [
+        [],
+        file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true)
+    ]
+
+    UNTAR ( input )
+}
diff --git a/tests/modules/untar/nextflow.config b/tests/modules/nf-core/untar/nextflow.config
similarity index 100%
rename from tests/modules/untar/nextflow.config
rename to tests/modules/nf-core/untar/nextflow.config
diff --git a/tests/modules/nf-core/untar/test.yml b/tests/modules/nf-core/untar/test.yml
new file mode 100644
index 00000000000..a314e167b12
--- /dev/null
+++ b/tests/modules/nf-core/untar/test.yml
@@ -0,0 +1,27 @@
+- name: untar test_untar
+  command: nextflow run ./tests/modules/nf-core/untar -entry test_untar -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/untar/nextflow.config
+  tags:
+    - untar
+  files:
+    - path: output/untar/kraken2/hash.k2d
+      md5sum: 8b8598468f54a7087c203ad0190555d9
+    - path: output/untar/kraken2/opts.k2d
+      md5sum: a033d00cf6759407010b21700938f543
+    - path: output/untar/kraken2/taxo.k2d
+      md5sum: 094d5891cdccf2f1468088855c214b2c
+
+- name: untar test_untar_different_output_path
+  command: nextflow run ./tests/modules/nf-core/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/untar/nextflow.config
+  tags:
+    - untar
+  files:
+    - path: output/untar/flowcell/RunInfo.xml
+      md5sum: 03038959f4dd181c86bc97ae71fe270a
+
+- name: untar test_untar_onlyfiles
+  command: nextflow run ./tests/modules/nf-core/untar -entry test_untar_onlyfiles -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/untar/nextflow.config
+  tags:
+    - untar
+  files:
+    - path: output/untar/hello/hello.txt
+      md5sum: e59ff97941044f85df5297e1c302d260
diff --git a/tests/modules/nf-core/unzip/main.nf b/tests/modules/nf-core/unzip/main.nf
new file mode 100644
index 00000000000..7992797b59e
--- /dev/null
+++ b/tests/modules/nf-core/unzip/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNZIP } from '../../../../modules/nf-core/unzip/main.nf'
+
+workflow test_unzip {
+
+    archive = [
+        [],
+        file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
+    ]
+
+    UNZIP ( archive )
+}
diff --git a/tests/modules/unzip/nextflow.config b/tests/modules/nf-core/unzip/nextflow.config
similarity index 100%
rename from tests/modules/unzip/nextflow.config
rename to tests/modules/nf-core/unzip/nextflow.config
diff --git a/tests/modules/nf-core/unzip/test.yml b/tests/modules/nf-core/unzip/test.yml
new file mode 100644
index 00000000000..0e02cbe07ee
--- /dev/null
+++ b/tests/modules/nf-core/unzip/test.yml
@@ -0,0 +1,10 @@
+- name: unzip
+  command: nextflow run ./tests/modules/nf-core/unzip -entry test_unzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/unzip/nextflow.config
+  tags:
+    - unzip
+  files:
+    - path: output/unzip/ncbi_taxmap/
+    - path: output/unzip/ncbi_taxmap/ncbi.map
+      md5sum: de30dbba85f9070612b632e2a5a95952
+    - path: output/unzip/ncbi_taxmap/ncbi.tre
+      md5sum: 4029dd2091c685b9a86ddd9d0d870db0
diff --git a/tests/modules/nf-core/vardictjava/main.nf b/tests/modules/nf-core/vardictjava/main.nf
new file mode 100644
index 00000000000..5c199a844e1
--- /dev/null
+++ b/tests/modules/nf-core/vardictjava/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VARDICTJAVA } from '../../../../modules/nf-core/vardictjava/main.nf'
+
+workflow test_vardictjava_bam {
+    
+    bam_input_ch = Channel.value([
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+    ])
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)   
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    VARDICTJAVA ( bam_input_ch, fasta, fasta_fai )
+}
diff --git a/tests/modules/vardictjava/nextflow.config b/tests/modules/nf-core/vardictjava/nextflow.config
similarity index 100%
rename from tests/modules/vardictjava/nextflow.config
rename to tests/modules/nf-core/vardictjava/nextflow.config
diff --git a/tests/modules/nf-core/vardictjava/test.yml b/tests/modules/nf-core/vardictjava/test.yml
new file mode 100644
index 00000000000..1f516da1d9e
--- /dev/null
+++ b/tests/modules/nf-core/vardictjava/test.yml
@@ -0,0 +1,7 @@
+- name: vardictjava test_vardictjava_bam
+  command: nextflow run ./tests/modules/nf-core/vardictjava -entry test_vardictjava_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vardictjava/nextflow.config
+  tags:
+    - vardictjava
+  files:
+    - path: output/vardictjava/test.vcf.gz
+      md5sum: 3f1f227afc532bddeb58f16fd3013fc8
diff --git a/tests/modules/nf-core/variantbam/main.nf b/tests/modules/nf-core/variantbam/main.nf
new file mode 100644
index 00000000000..8adbee3fac9
--- /dev/null
+++ b/tests/modules/nf-core/variantbam/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VARIANTBAM } from '../../../../modules/nf-core/variantbam/main.nf'
+
+workflow test_variantbam {
+
+    input = [ [ id:'test', single_end:false ],
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+
+    VARIANTBAM ( input )
+}
diff --git a/tests/modules/variantbam/nextflow.config b/tests/modules/nf-core/variantbam/nextflow.config
similarity index 100%
rename from tests/modules/variantbam/nextflow.config
rename to tests/modules/nf-core/variantbam/nextflow.config
diff --git a/tests/modules/nf-core/variantbam/test.yml b/tests/modules/nf-core/variantbam/test.yml
new file mode 100644
index 00000000000..60ec26a6b97
--- /dev/null
+++ b/tests/modules/nf-core/variantbam/test.yml
@@ -0,0 +1,7 @@
+- name: variantbam test_variantbam
+  command: nextflow run ./tests/modules/nf-core/variantbam -entry test_variantbam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/variantbam/nextflow.config
+  tags:
+    - variantbam
+  files:
+    - path: output/variantbam/test.bam
+      md5sum: fc08f065475d60b3b06ee32920564d4b
diff --git a/tests/modules/nf-core/vcf2db/main.nf b/tests/modules/nf-core/vcf2db/main.nf
new file mode 100644
index 00000000000..6ea67bbbfa3
--- /dev/null
+++ b/tests/modules/nf-core/vcf2db/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VCF2DB } from '../../../../modules/nf-core/vcf2db/main.nf'
+
+workflow test_vcf2db {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+    ]
+
+    VCF2DB ( input )
+}
diff --git a/tests/modules/vcf2db/nextflow.config b/tests/modules/nf-core/vcf2db/nextflow.config
similarity index 100%
rename from tests/modules/vcf2db/nextflow.config
rename to tests/modules/nf-core/vcf2db/nextflow.config
diff --git a/tests/modules/nf-core/vcf2db/test.yml b/tests/modules/nf-core/vcf2db/test.yml
new file mode 100644
index 00000000000..5b37f4218d8
--- /dev/null
+++ b/tests/modules/nf-core/vcf2db/test.yml
@@ -0,0 +1,6 @@
+- name: vcf2db test_vcf2db
+  command: nextflow run ./tests/modules/nf-core/vcf2db -entry test_vcf2db -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcf2db/nextflow.config
+  tags:
+    - vcf2db
+  files:
+    - path: output/vcf2db/test.db
diff --git a/tests/modules/nf-core/vcf2maf/main.nf b/tests/modules/nf-core/vcf2maf/main.nf
new file mode 100644
index 00000000000..8deed5cf74a
--- /dev/null
+++ b/tests/modules/nf-core/vcf2maf/main.nf
@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VCF2MAF } from '../../../../modules/nf-core/vcf2maf/main.nf'
+include { UNTAR   } from '../../../../modules/nf-core/untar/main.nf'
+
+workflow test_vcf2maf_no_vep {
+
+    input_vcf = [
+        [ id:'test' ],
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
+    ]
+    fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    VCF2MAF ( input_vcf, fasta, [] )
+}
+
+workflow test_vcf2maf_vep {
+
+    input_vcf = [
+        [ id:'test' ],
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
+    ]
+    fasta     = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+    vep_cache = [ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['vep_cache'], checkIfExists: true) ]
+
+    vep_cache_unpacked = UNTAR(vep_cache).untar.map { it[1] }
+    VCF2MAF ( input_vcf, fasta, vep_cache_unpacked)
+}
diff --git a/tests/modules/vcf2maf/nextflow.config b/tests/modules/nf-core/vcf2maf/nextflow.config
similarity index 100%
rename from tests/modules/vcf2maf/nextflow.config
rename to tests/modules/nf-core/vcf2maf/nextflow.config
diff --git a/tests/modules/nf-core/vcf2maf/test.yml b/tests/modules/nf-core/vcf2maf/test.yml
new file mode 100644
index 00000000000..e62e39f8e43
--- /dev/null
+++ b/tests/modules/nf-core/vcf2maf/test.yml
@@ -0,0 +1,15 @@
+- name: vcf2maf test_vcf2maf_no_vep
+  command: nextflow run ./tests/modules/nf-core/vcf2maf -entry test_vcf2maf_no_vep -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/vcf2maf/nextflow.config
+  tags:
+    - vcf2maf
+  files:
+    - path: output/vcf2maf/test.maf
+      md5sum: c7f357efa774fd5c4003d84f05212ed0
+
+- name: vcf2maf test_vcf2maf_vep
+  command: nextflow run ./tests/modules/nf-core/vcf2maf -entry test_vcf2maf_vep -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/vcf2maf/nextflow.config
+  tags:
+    - vcf2maf
+  files:
+    - path: output/vcf2maf/test.maf
+      md5sum: bf114692a2f421225926c9b651eff161
diff --git a/tests/modules/nf-core/vcfanno/main.nf b/tests/modules/nf-core/vcfanno/main.nf
new file mode 100644
index 00000000000..3fdfe71eb8b
--- /dev/null
+++ b/tests/modules/nf-core/vcfanno/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR } from '../../../../modules/nf-core/untar/main.nf'
+include { VCFANNO } from '../../../../modules/nf-core/vcfanno/main.nf'
+
+workflow test_vcfanno {
+
+    input = [
+        [ id:'test_compressed', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
+    resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( resource_dir )
+    VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
+}
+
+workflow test_vcfanno_uncompressed {
+
+    input = [ 
+        [ id:'test_uncompressed', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+        [] 
+    ]
+
+    toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
+    resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( resource_dir )
+    VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
+}
diff --git a/tests/modules/vcfanno/nextflow.config b/tests/modules/nf-core/vcfanno/nextflow.config
similarity index 100%
rename from tests/modules/vcfanno/nextflow.config
rename to tests/modules/nf-core/vcfanno/nextflow.config
diff --git a/tests/modules/nf-core/vcfanno/test.yml b/tests/modules/nf-core/vcfanno/test.yml
new file mode 100644
index 00000000000..fe1d8cf9a05
--- /dev/null
+++ b/tests/modules/nf-core/vcfanno/test.yml
@@ -0,0 +1,23 @@
+- name: vcfanno test_vcfanno
+  command: nextflow run ./tests/modules/nf-core/vcfanno -entry test_vcfanno -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/vcfanno/nextflow.config
+  tags:
+    - vcfanno
+  files:
+    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz
+      md5sum: eba4b55d81148d9c316cda68a5c0ad6d
+    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz.tbi
+      md5sum: ec47aa09f0248f4f32ae12fb7ba03f34
+    - path: output/vcfanno/test_compressed_annotated.vcf
+      md5sum: 90ceb2fd2e06e781846d69c3981db665
+
+- name: vcfanno test_vcfanno_uncompressed
+  command: nextflow run ./tests/modules/nf-core/vcfanno -entry test_vcfanno_uncompressed -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/vcfanno/nextflow.config
+  tags:
+    - vcfanno
+  files:
+    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz
+      md5sum: eba4b55d81148d9c316cda68a5c0ad6d
+    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz.tbi
+      md5sum: ec47aa09f0248f4f32ae12fb7ba03f34
+    - path: output/vcfanno/test_uncompressed_annotated.vcf
+      md5sum: 90ceb2fd2e06e781846d69c3981db665
diff --git a/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf
new file mode 100644
index 00000000000..1f8cd39f07b
--- /dev/null
+++ b/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VCFLIB_VCFBREAKMULTI } from '../../../../../modules/nf-core/vcflib/vcfbreakmulti/main.nf'
+
+workflow test_vcflib_vcfbreakmulti {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    VCFLIB_VCFBREAKMULTI ( input )
+}
diff --git a/tests/modules/vcflib/vcfbreakmulti/nextflow.config b/tests/modules/nf-core/vcflib/vcfbreakmulti/nextflow.config
similarity index 100%
rename from tests/modules/vcflib/vcfbreakmulti/nextflow.config
rename to tests/modules/nf-core/vcflib/vcfbreakmulti/nextflow.config
diff --git a/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml b/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml
new file mode 100644
index 00000000000..3a2a51c5999
--- /dev/null
+++ b/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml
@@ -0,0 +1,16 @@
+- name: vcflib vcfbreakmulti
+  command: nextflow run ./tests/modules/nf-core/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c ./tests/config/nextflow.config
+  tags:
+    - vcflib/vcfbreakmulti
+    - vcflib
+  files:
+    - path: output/vcflib/test.breakmulti.vcf.gz
+      md5sum: 666d2d970399cf219dc1dc1eadff9170
+
+- name: vcflib vcfbreakmulti stub
+  command: nextflow run ./tests/modules/nf-core/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c ./tests/config/nextflow.config -stub
+  tags:
+    - vcflib/vcfbreakmulti
+    - vcflib
+  files:
+    - path: output/vcflib/test.breakmulti.vcf.gz
diff --git a/tests/modules/nf-core/vcflib/vcfuniq/main.nf b/tests/modules/nf-core/vcflib/vcfuniq/main.nf
new file mode 100644
index 00000000000..b355301e5a1
--- /dev/null
+++ b/tests/modules/nf-core/vcflib/vcfuniq/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VCFLIB_VCFUNIQ } from '../../../../../modules/nf-core/vcflib/vcfuniq/main.nf'
+
+workflow test_vcflib_vcfuniq {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    VCFLIB_VCFUNIQ ( input )
+}
diff --git a/tests/modules/vcflib/vcfuniq/nextflow.config b/tests/modules/nf-core/vcflib/vcfuniq/nextflow.config
similarity index 100%
rename from tests/modules/vcflib/vcfuniq/nextflow.config
rename to tests/modules/nf-core/vcflib/vcfuniq/nextflow.config
diff --git a/tests/modules/nf-core/vcflib/vcfuniq/test.yml b/tests/modules/nf-core/vcflib/vcfuniq/test.yml
new file mode 100644
index 00000000000..f51c7b0c7f3
--- /dev/null
+++ b/tests/modules/nf-core/vcflib/vcfuniq/test.yml
@@ -0,0 +1,8 @@
+- name: vcflib vcfuniq
+  command: nextflow run ./tests/modules/nf-core/vcflib/vcfuniq -entry test_vcflib_vcfuniq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcflib/vcfuniq/nextflow.config
+  tags:
+    - vcflib
+    - vcflib/vcfuniq
+  files:
+    - path: output/vcflib/test.uniq.vcf.gz
+      md5sum: c5f2a6a912964c45e8231140420561f9
diff --git a/tests/modules/nf-core/vcftools/main.nf b/tests/modules/nf-core/vcftools/main.nf
new file mode 100644
index 00000000000..d1e49cb3618
--- /dev/null
+++ b/tests/modules/nf-core/vcftools/main.nf
@@ -0,0 +1,40 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VCFTOOLS as VCFTOOLS_BASE     } from '../../../../modules/nf-core/vcftools/main.nf'
+include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../../modules/nf-core/vcftools/main.nf'
+
+workflow test_vcftools_vcf_base {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+            ]
+
+    VCFTOOLS_BASE ( input, [], [] )
+}
+
+workflow test_vcftools_vcfgz_base {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
+            ]
+
+    VCFTOOLS_BASE ( input, [], [] )
+}
+
+workflow test_vcftools_vcf_optional {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+            ]
+    bed   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+
+    VCFTOOLS_OPTIONAL ( input, bed, [] )
+}
+
+workflow test_vcftools_vcfgz_optional {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
+            ]
+    bed   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+
+    VCFTOOLS_OPTIONAL ( input, bed, [] )
+}
diff --git a/tests/modules/vcftools/nextflow.config b/tests/modules/nf-core/vcftools/nextflow.config
similarity index 100%
rename from tests/modules/vcftools/nextflow.config
rename to tests/modules/nf-core/vcftools/nextflow.config
diff --git a/tests/modules/nf-core/vcftools/test.yml b/tests/modules/nf-core/vcftools/test.yml
new file mode 100644
index 00000000000..e0a1e31f1a2
--- /dev/null
+++ b/tests/modules/nf-core/vcftools/test.yml
@@ -0,0 +1,31 @@
+- name: vcftools test_vcftools_vcf_base
+  command: nextflow run ./tests/modules/nf-core/vcftools -entry test_vcftools_vcf_base -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcftools/nextflow.config
+  tags:
+    - vcftools
+  files:
+    - path: output/vcftools/test.frq
+      md5sum: 7f126655f17268fd1a338734f62868e9
+
+- name: vcftools test_vcftools_vcfgz_base
+  command: nextflow run ./tests/modules/nf-core/vcftools -entry test_vcftools_vcfgz_base -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcftools/nextflow.config
+  tags:
+    - vcftools
+  files:
+    - path: output/vcftools/test.frq
+      md5sum: 7f126655f17268fd1a338734f62868e9
+
+- name: vcftools test_vcftools_vcf_optional
+  command: nextflow run ./tests/modules/nf-core/vcftools -entry test_vcftools_vcf_optional -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcftools/nextflow.config
+  tags:
+    - vcftools
+  files:
+    - path: output/vcftools/test.frq
+      md5sum: 7f126655f17268fd1a338734f62868e9
+
+- name: vcftools test_vcftools_vcfgz_optional
+  command: nextflow run ./tests/modules/nf-core/vcftools -entry test_vcftools_vcfgz_optional -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcftools/nextflow.config
+  tags:
+    - vcftools
+  files:
+    - path: output/vcftools/test.frq
+      md5sum: 7f126655f17268fd1a338734f62868e9
diff --git a/tests/modules/nf-core/vsearch/sintax/main.nf b/tests/modules/nf-core/vsearch/sintax/main.nf
new file mode 100644
index 00000000000..59e551bca79
--- /dev/null
+++ b/tests/modules/nf-core/vsearch/sintax/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VSEARCH_SINTAX } from '../../../../../modules/nf-core/vsearch/sintax/main.nf'
+
+workflow test_vsearch_sintax {
+    
+    query = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    db = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+
+    VSEARCH_SINTAX ( [[id:'test'], query], db )
+}
diff --git a/tests/modules/vsearch/sintax/nextflow.config b/tests/modules/nf-core/vsearch/sintax/nextflow.config
similarity index 100%
rename from tests/modules/vsearch/sintax/nextflow.config
rename to tests/modules/nf-core/vsearch/sintax/nextflow.config
diff --git a/tests/modules/nf-core/vsearch/sintax/test.yml b/tests/modules/nf-core/vsearch/sintax/test.yml
new file mode 100644
index 00000000000..70f6d1bbaa3
--- /dev/null
+++ b/tests/modules/nf-core/vsearch/sintax/test.yml
@@ -0,0 +1,8 @@
+- name: vsearch sintax test_vsearch_sintax
+  command: nextflow run ./tests/modules/nf-core/vsearch/sintax -entry test_vsearch_sintax -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/vsearch/sintax/nextflow.config
+  tags:
+    - vsearch
+    - vsearch/sintax
+  files:
+    - path: output/vsearch/test.tsv
+      md5sum: 93bc75fb89343e23fbae971df157b14a
diff --git a/tests/modules/nf-core/vsearch/usearchglobal/main.nf b/tests/modules/nf-core/vsearch/usearchglobal/main.nf
new file mode 100644
index 00000000000..925f0cb2ac3
--- /dev/null
+++ b/tests/modules/nf-core/vsearch/usearchglobal/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VSEARCH_USEARCHGLOBAL } from '../../../../../modules/nf-core/vsearch/usearchglobal/main.nf'
+
+workflow test_vsearch_usearchglobal {
+    
+    query = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    idcutoff = 0.985
+    outoption = "xcfert"  // Nonsense text to check default case.
+    columns = "" 
+    VSEARCH_USEARCHGLOBAL ( [[id:'test'], query], db, idcutoff, outoption, columns )
+}
+
+workflow test_vsearch_usearchglobal_userout {
+    
+    query = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    idcutoff = 0.985
+    outoption = "userout"
+    columns = "query+target+id" 
+    VSEARCH_USEARCHGLOBAL ( [[id:'test'], query], db, idcutoff, outoption, columns )
+}
diff --git a/tests/modules/vsearch/usearchglobal/nextflow.config b/tests/modules/nf-core/vsearch/usearchglobal/nextflow.config
similarity index 100%
rename from tests/modules/vsearch/usearchglobal/nextflow.config
rename to tests/modules/nf-core/vsearch/usearchglobal/nextflow.config
diff --git a/tests/modules/nf-core/vsearch/usearchglobal/test.yml b/tests/modules/nf-core/vsearch/usearchglobal/test.yml
new file mode 100644
index 00000000000..9dcc8db45df
--- /dev/null
+++ b/tests/modules/nf-core/vsearch/usearchglobal/test.yml
@@ -0,0 +1,26 @@
+- name: vsearch usearchglobal test_vsearch_usearchglobal
+  command: nextflow run ./tests/modules/nf-core/vsearch/usearchglobal -entry test_vsearch_usearchglobal -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/vsearch/usearchglobal/nextflow.config
+  tags:
+    - vsearch/usearchglobal
+    - vsearch
+  files:
+    - path: output/vsearch/test.aln
+      contains:
+        - "vsearch --usearch_global transcriptome.fasta --db genome.fasta --id 0.985 --threads 2 --alnout test.aln"
+        - "Query >lcl|MT192765.1_cds_QIK50427.1_2"
+        - "%Id   TLen  Target"
+        - "100%  29829  MT192765.1"
+        - "Query  3822nt >lcl|MT192765.1_cds_QIK50427.1_2"
+        - "Target 29829nt >MT192765.1"
+        - "Qry 21249 + CAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAA 21291"
+        - "Tgt 21506 + CAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAA 21548"
+        - "21291 cols, 21290 ids (100.0%), 1 gaps (0.0%)"
+
+- name: vsearch usearchglobal test_vsearch_usearchglobal_userout
+  command: nextflow run ./tests/modules/nf-core/vsearch/usearchglobal -entry test_vsearch_usearchglobal_userout -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/vsearch/usearchglobal/nextflow.config
+  tags:
+    - vsearch/usearchglobal
+    - vsearch
+  files:
+    - path: output/vsearch/test.tsv
+      md5sum: b6cc50f7c8d18cb82e74dab70ed4baab
diff --git a/tests/modules/nf-core/whamg/main.nf b/tests/modules/nf-core/whamg/main.nf
new file mode 100644
index 00000000000..3301b194d43
--- /dev/null
+++ b/tests/modules/nf-core/whamg/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { WHAMG } from '../../../../modules/nf-core/whamg/main.nf'
+
+workflow test_whamg_bam {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    WHAMG ( input, fasta )
+}
diff --git a/tests/modules/whamg/nextflow.config b/tests/modules/nf-core/whamg/nextflow.config
similarity index 100%
rename from tests/modules/whamg/nextflow.config
rename to tests/modules/nf-core/whamg/nextflow.config
diff --git a/tests/modules/nf-core/whamg/test.yml b/tests/modules/nf-core/whamg/test.yml
new file mode 100644
index 00000000000..2e1323a22b9
--- /dev/null
+++ b/tests/modules/nf-core/whamg/test.yml
@@ -0,0 +1,6 @@
+- name: whamg test_whamg_bam
+  command: nextflow run ./tests/modules/nf-core/whamg -entry test_whamg_bam -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/whamg/nextflow.config
+  tags:
+    - whamg
+  files:
+    - path: output/whamg/test.vcf.gz
diff --git a/tests/modules/nf-core/yara/index/main.nf b/tests/modules/nf-core/yara/index/main.nf
new file mode 100644
index 00000000000..32a8efef899
--- /dev/null
+++ b/tests/modules/nf-core/yara/index/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { YARA_INDEX } from '../../../../../modules/nf-core/yara/index/main.nf'
+
+workflow test_yara_index {
+
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    YARA_INDEX ( input )
+}
diff --git a/tests/modules/yara/index/nextflow.config b/tests/modules/nf-core/yara/index/nextflow.config
similarity index 100%
rename from tests/modules/yara/index/nextflow.config
rename to tests/modules/nf-core/yara/index/nextflow.config
diff --git a/tests/modules/nf-core/yara/index/test.yml b/tests/modules/nf-core/yara/index/test.yml
new file mode 100644
index 00000000000..973e08d441a
--- /dev/null
+++ b/tests/modules/nf-core/yara/index/test.yml
@@ -0,0 +1,30 @@
+- name: yara index test_yara_index
+  command: nextflow run ./tests/modules/nf-core/yara/index -entry test_yara_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/yara/index/nextflow.config
+  tags:
+    - yara/index
+    - yara
+  files:
+    - path: output/yara/yara/yara.rid.limits
+      md5sum: 8b814661f30a0c9e350bfbcb454930ce
+    - path: output/yara/yara/yara.sa.len
+      md5sum: 45677f66c28c79c02250ceb8b58645e8
+    - path: output/yara/yara/yara.sa.ind
+      md5sum: 464314583efb5f07260b0efecc29a1ce
+    - path: output/yara/yara/yara.lf.drp
+      md5sum: 3ef99a87a4e44513f46d42f4261f7842
+    - path: output/yara/yara/yara.txt.size
+      md5sum: 063987b3c3f747be7d2b8043c9d91000
+    - path: output/yara/yara/yara.rid.concat
+      md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
+    - path: output/yara/yara/yara.txt.concat
+      md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
+    - path: output/yara/yara/yara.lf.drs
+      md5sum: 55a54008ad1ba589aa210d2629c1df41
+    - path: output/yara/yara/yara.txt.limits
+      md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
+    - path: output/yara/yara/yara.sa.val
+      md5sum: ce57cc82e2d3ae7b9824210f54168ce9
+    - path: output/yara/yara/yara.lf.pst
+      md5sum: e8daba34298e99e42942435286f9b3f0
+    - path: output/yara/yara/yara.lf.drv
+      md5sum: cf6408307fe9fd7f99c33f521bf95550
diff --git a/tests/modules/nf-core/yara/mapper/main.nf b/tests/modules/nf-core/yara/mapper/main.nf
new file mode 100644
index 00000000000..a6c502d3881
--- /dev/null
+++ b/tests/modules/nf-core/yara/mapper/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+
+include { YARA_INDEX  } from '../../../../../modules/nf-core/yara/index/main.nf'
+include { YARA_MAPPER } from '../../../../../modules/nf-core/yara/mapper/main.nf'
+
+workflow test_yara_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    YARA_INDEX ( fasta )
+    YARA_MAPPER ( input, YARA_INDEX.out.index )
+}
+
+workflow test_yara_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    YARA_INDEX ( fasta )
+    YARA_MAPPER ( input, YARA_INDEX.out.index )
+}
diff --git a/tests/modules/yara/mapper/nextflow.config b/tests/modules/nf-core/yara/mapper/nextflow.config
similarity index 100%
rename from tests/modules/yara/mapper/nextflow.config
rename to tests/modules/nf-core/yara/mapper/nextflow.config
diff --git a/tests/modules/nf-core/yara/mapper/test.yml b/tests/modules/nf-core/yara/mapper/test.yml
new file mode 100644
index 00000000000..93e4f39b709
--- /dev/null
+++ b/tests/modules/nf-core/yara/mapper/test.yml
@@ -0,0 +1,71 @@
+- name: yara mapper test_yara_single_end
+  command: nextflow run ./tests/modules/nf-core/yara/mapper -entry test_yara_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/yara/mapper/nextflow.config
+  tags:
+    - yara/mapper
+    - yara
+  files:
+    - path: output/yara/test.mapped.bam
+    - path: output/yara/test.mapped.bam.bai
+    - path: output/yara/yara/yara.txt.size
+      md5sum: 063987b3c3f747be7d2b8043c9d91000
+    - path: output/yara/yara/yara.lf.drs
+      md5sum: 55a54008ad1ba589aa210d2629c1df41
+    - path: output/yara/yara/yara.lf.pst
+      md5sum: e8daba34298e99e42942435286f9b3f0
+    - path: output/yara/yara/yara.sa.len
+      md5sum: 45677f66c28c79c02250ceb8b58645e8
+    - path: output/yara/yara/yara.rid.concat
+      md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
+    - path: output/yara/yara/yara.txt.concat
+      md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
+    - path: output/yara/yara/yara.sa.val
+      md5sum: ce57cc82e2d3ae7b9824210f54168ce9
+    - path: output/yara/yara/yara.sa.ind
+      md5sum: 464314583efb5f07260b0efecc29a1ce
+    - path: output/yara/yara/yara.rid.limits
+      md5sum: 8b814661f30a0c9e350bfbcb454930ce
+    - path: output/yara/yara/yara.lf.drp
+      md5sum: 3ef99a87a4e44513f46d42f4261f7842
+    - path: output/yara/yara/yara.txt.limits
+      md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
+    - path: output/yara/yara/yara.lf.drv
+      md5sum: cf6408307fe9fd7f99c33f521bf95550
+    - path: output/yara/yara/yara.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+
+- name: yara mapper test_yara_paired_end
+  command: nextflow run ./tests/modules/nf-core/yara/mapper -entry test_yara_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/yara/mapper/nextflow.config
+  tags:
+    - yara/mapper
+    - yara
+  files:
+    - path: output/yara/test_2.mapped.bam
+    - path: output/yara/test_2.mapped.bam.bai
+    - path: output/yara/test_1.mapped.bam
+    - path: output/yara/test_1.mapped.bam.bai
+    - path: output/yara/yara/yara.txt.size
+      md5sum: 063987b3c3f747be7d2b8043c9d91000
+    - path: output/yara/yara/yara.lf.drs
+      md5sum: 55a54008ad1ba589aa210d2629c1df41
+    - path: output/yara/yara/yara.lf.pst
+      md5sum: e8daba34298e99e42942435286f9b3f0
+    - path: output/yara/yara/yara.sa.len
+      md5sum: 45677f66c28c79c02250ceb8b58645e8
+    - path: output/yara/yara/yara.rid.concat
+      md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
+    - path: output/yara/yara/yara.txt.concat
+      md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
+    - path: output/yara/yara/yara.sa.val
+      md5sum: ce57cc82e2d3ae7b9824210f54168ce9
+    - path: output/yara/yara/yara.sa.ind
+      md5sum: 464314583efb5f07260b0efecc29a1ce
+    - path: output/yara/yara/yara.rid.limits
+      md5sum: 8b814661f30a0c9e350bfbcb454930ce
+    - path: output/yara/yara/yara.lf.drp
+      md5sum: 3ef99a87a4e44513f46d42f4261f7842
+    - path: output/yara/yara/yara.txt.limits
+      md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
+    - path: output/yara/yara/yara.lf.drv
+      md5sum: cf6408307fe9fd7f99c33f521bf95550
+    - path: output/yara/yara/yara.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
diff --git a/tests/modules/ngmaster/main.nf b/tests/modules/ngmaster/main.nf
deleted file mode 100644
index b23530bccab..00000000000
--- a/tests/modules/ngmaster/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NGMASTER } from '../../../modules/ngmaster/main.nf'
-
-workflow test_ngmaster {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    NGMASTER ( input )
-}
diff --git a/tests/modules/ngmaster/test.yml b/tests/modules/ngmaster/test.yml
deleted file mode 100644
index fb8dec827b4..00000000000
--- a/tests/modules/ngmaster/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: ngmaster test_ngmaster
-  command: nextflow run ./tests/modules/ngmaster -entry test_ngmaster -c ./tests/config/nextflow.config -c ./tests/modules/ngmaster/nextflow.config
-  tags:
-    - ngmaster
-  files:
-    - path: output/ngmaster/test.tsv
-      md5sum: cf674474eaf8ac6abfcebce0af0226cf
diff --git a/tests/modules/ngscheckmate/ncm/main.nf b/tests/modules/ngscheckmate/ncm/main.nf
deleted file mode 100644
index ab6a46392ba..00000000000
--- a/tests/modules/ngscheckmate/ncm/main.nf
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_BAM} from '../../../../modules/ngscheckmate/ncm/main.nf'
-include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_VCF} from '../../../../modules/ngscheckmate/ncm/main.nf'
-
-include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf'
-
-include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf'
-include { BCFTOOLS_MPILEUP as BCFTOOLS_MPILEUP2 } from '../../../../modules/bcftools/mpileup/main.nf'
-
-workflow test_ngscheckmate_ncm_bam {
-    input    = [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
-
-    fasta    = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    inputBed = [ [ id:'test'],
-                 file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
-
-    BEDTOOLS_MAKEWINDOWS(inputBed, true).
-    tab.
-    map{it[1]}.
-    view().
-    set{snp_channel}
-
-    NGSCHECKMATE_NCM_BAM(input, snp_channel, fasta)
-}
-
-workflow test_ngscheckmate_ncm_vcf {
-    input1   = [ [ id:'test1' ], // meta map
-                 [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-               ]
-
-    input2   = [ [ id:'test2' ], // meta map
-                 [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-               ]
-
-    fasta    = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    inputBed = [ [ id:'test'],
-                 file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
-
-    BCFTOOLS_MPILEUP ( input1, fasta, false )
-    BCFTOOLS_MPILEUP2 ( input2, fasta, false )
-
-    BCFTOOLS_MPILEUP2.out.vcf.
-        combine( BCFTOOLS_MPILEUP.out.vcf ).
-        map { [ it[1], it[3] ] }.
-        set { vcf_channel }
-
-    BEDTOOLS_MAKEWINDOWS( inputBed, true ).tab.
-        map { it[1] }.
-        view().
-        set { snp_channel }
-
-    NGSCHECKMATE_NCM_VCF(vcf_channel, snp_channel, fasta)
-}
-
-
diff --git a/tests/modules/ngscheckmate/ncm/test.yml b/tests/modules/ngscheckmate/ncm/test.yml
deleted file mode 100644
index c0c8bc00c60..00000000000
--- a/tests/modules/ngscheckmate/ncm/test.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-- name: ngscheckmate ncm test_ngscheckmate_ncm_bam
-  command: nextflow run tests/modules/ngscheckmate/ncm -entry test_ngscheckmate_ncm_bam -c tests/config/nextflow.config
-  tags:
-    - ngscheckmate/ncm
-    - ngscheckmate
-  files:
-    - path: output/ngscheckmate/output_all.txt
-      md5sum: f71a712c3f6ecf64dd526365212f1b7c
-    - path: output/ngscheckmate/output_corr_matrix.txt
-      md5sum: 6777377aa9ae3d57f841b12896318db0
-    - path: output/ngscheckmate/output_matched.txt
-      md5sum: f71a712c3f6ecf64dd526365212f1b7c
-    - path: output/ngscheckmate/versions.yml
-      md5sum: fbb2bebd65b4f4e1e93c6bf5c08a6829
-
-- name: ngscheckmate ncm test_ngscheckmate_ncm_vcf
-  command: nextflow run tests/modules/ngscheckmate/ncm -entry test_ngscheckmate_ncm_vcf -c tests/config/nextflow.config
-  tags:
-    - ngscheckmate/ncm
-    - ngscheckmate
-  files:
-    - path: output/ngscheckmate/output_all.txt
-      md5sum: fd74956dcac279b6f58e82ea73e344f8
-    - path: output/ngscheckmate/output_corr_matrix.txt
-      md5sum: 0c86bdad2721c470fe6be119f291c8e5
-    - path: output/ngscheckmate/output_matched.txt
-      md5sum: fd74956dcac279b6f58e82ea73e344f8
-    - path: output/ngscheckmate/versions.yml
-      md5sum: f06910b83dde194a47870c553cefe193
diff --git a/tests/modules/nucmer/main.nf b/tests/modules/nucmer/main.nf
deleted file mode 100644
index 98e74b07d19..00000000000
--- a/tests/modules/nucmer/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NUCMER } from '../../../modules/nucmer/main.nf'
-
-workflow test_nucmer {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-
-    NUCMER ( input )
-}
diff --git a/tests/modules/nucmer/test.yml b/tests/modules/nucmer/test.yml
deleted file mode 100644
index cebd0d4e6fc..00000000000
--- a/tests/modules/nucmer/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: nucmer test_nucmer
-  command: nextflow run ./tests/modules/nucmer -entry test_nucmer -c ./tests/config/nextflow.config -c ./tests/modules/nucmer/nextflow.config
-  tags:
-    - nucmer
-  files:
-    - path: output/nucmer/test.coords
-      contains: ["MT192765.1"]
-    - path: output/nucmer/test.delta
-      contains: ["MT192765.1"]
diff --git a/tests/modules/optitype/main.nf b/tests/modules/optitype/main.nf
deleted file mode 100644
index 6ed14d96dcb..00000000000
--- a/tests/modules/optitype/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { OPTITYPE } from '../../../modules/optitype/main.nf'
-
-workflow test_optitype {
-    input = [ [ id:'test', seq_type:'dna' ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam_bai'], checkIfExists: true)
-            ]
-
-    OPTITYPE ( input )
-}
diff --git a/tests/modules/optitype/test.yml b/tests/modules/optitype/test.yml
deleted file mode 100644
index 0cbb99cbad7..00000000000
--- a/tests/modules/optitype/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: optitype test_optitype
-  command: nextflow run ./tests/modules/optitype -entry test_optitype -c ./tests/config/nextflow.config -c ./tests/modules/optitype/nextflow.config
-  tags:
-    - optitype
-  files:
-    - path: output/optitype/test/test_coverage_plot.pdf
-    - path: output/optitype/test/test_result.tsv
-      contains:
-        - "1439"
diff --git a/tests/modules/pairix/main.nf b/tests/modules/pairix/main.nf
deleted file mode 100644
index 474bacbbf47..00000000000
--- a/tests/modules/pairix/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PAIRIX } from '../../../modules/pairix/main.nf'
-
-workflow test_pairix {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("https://raw.githubusercontent.com/4dn-dcic/pairix/master/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz", checkIfExists: true) ]
-
-    PAIRIX ( input )
-}
diff --git a/tests/modules/pairix/test.yml b/tests/modules/pairix/test.yml
deleted file mode 100644
index 4cd9d37d325..00000000000
--- a/tests/modules/pairix/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: pairix test_pairix
-  command: nextflow run ./tests/modules/pairix -entry test_pairix -c ./tests/config/nextflow.config -c ./tests/modules/pairix/nextflow.config
-  tags:
-    - pairix
-  files:
-    - path: output/pairix/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz
-      md5sum: a0165859d0151f45fe6fb206f2f4814b
-    - path: output/pairix/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2
-      md5sum: a6e41cc7cff16fd15b5ee505549ec99a
diff --git a/tests/modules/pairtools/dedup/main.nf b/tests/modules/pairtools/dedup/main.nf
deleted file mode 100644
index 28121526d83..00000000000
--- a/tests/modules/pairtools/dedup/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PAIRTOOLS_DEDUP } from '../../../../modules/pairtools/dedup/main.nf'
-
-workflow test_pairtools_dedup {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.4dedup.pairsam", checkIfExists: true) ]
-
-    PAIRTOOLS_DEDUP ( input )
-}
diff --git a/tests/modules/pairtools/dedup/test.yml b/tests/modules/pairtools/dedup/test.yml
deleted file mode 100644
index 6d7f99f4896..00000000000
--- a/tests/modules/pairtools/dedup/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: pairtools dedup test_pairtools_dedup
-  command: nextflow run ./tests/modules/pairtools/dedup -entry test_pairtools_dedup -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/dedup/nextflow.config
-  tags:
-    - pairtools/dedup
-    - pairtools
-  files:
-    - path: output/pairtools/test.dedup.pairs.gz
-      md5sum: 785ffc9495731fd3d0f6f679a0a0e988
-    - path: output/pairtools/test.dedup.pairs.stat
-      md5sum: a554a846567cbcda66f070c76a9173bc
diff --git a/tests/modules/pairtools/flip/main.nf b/tests/modules/pairtools/flip/main.nf
deleted file mode 100644
index e4d740e2077..00000000000
--- a/tests/modules/pairtools/flip/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PAIRTOOLS_FLIP } from '../../../../modules/pairtools/flip/main.nf'
-
-workflow test_pairtools_flip {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.4flip.pairs", checkIfExists: true) ]
-    sizes = file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.chrom.sizes", checkIfExists:true)
-
-    PAIRTOOLS_FLIP ( input, sizes )
-}
diff --git a/tests/modules/pairtools/flip/test.yml b/tests/modules/pairtools/flip/test.yml
deleted file mode 100644
index cec549760d7..00000000000
--- a/tests/modules/pairtools/flip/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: pairtools flip test_pairtools_flip
-  command: nextflow run ./tests/modules/pairtools/flip -entry test_pairtools_flip -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/flip/nextflow.config
-  tags:
-    - pairtools/flip
-    - pairtools
-  files:
-    - path: output/pairtools/test.flip.gz
diff --git a/tests/modules/pairtools/parse/main.nf b/tests/modules/pairtools/parse/main.nf
deleted file mode 100644
index f006fd6aef1..00000000000
--- a/tests/modules/pairtools/parse/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PAIRTOOLS_PARSE } from '../../../../modules/pairtools/parse/main.nf'
-
-workflow test_pairtools_parse {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.sam", checkIfExists: true) ]
-    sizes = file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.chrom.sizes", checkIfExists:true)
-
-    PAIRTOOLS_PARSE ( input, sizes )
-}
diff --git a/tests/modules/pairtools/parse/test.yml b/tests/modules/pairtools/parse/test.yml
deleted file mode 100644
index cf01038c0d8..00000000000
--- a/tests/modules/pairtools/parse/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: pairtools parse test_pairtools_parse
-  command: nextflow run ./tests/modules/pairtools/parse -entry test_pairtools_parse -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/parse/nextflow.config
-  tags:
-    - pairtools
-    - pairtools/parse
-  files:
-    - path: output/pairtools/test.raw.pairsam.gz
-    - path: output/pairtools/test.raw.pairsam.stat
-      md5sum: 11e90f346f855ffd750c7c348ac1d456
diff --git a/tests/modules/pairtools/restrict/main.nf b/tests/modules/pairtools/restrict/main.nf
deleted file mode 100644
index ae7e328b62f..00000000000
--- a/tests/modules/pairtools/restrict/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PAIRTOOLS_RESTRICT } from '../../../../modules/pairtools/restrict/main.nf'
-
-workflow test_pairtools_restrict {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.4flip.pairs", checkIfExists: true) ]
-    File dig  = new File("${workflow.workDir}/frag.bed")
-    dig.write("chr1\t0\t50\r\nchr1\t50\t100\r\nchr2\t0\t50\r\nchr2\t50\t100\r\n!\t0\t1\r\n")
-    frag  = file(dig)
-
-    PAIRTOOLS_RESTRICT ( input, frag )
-}
diff --git a/tests/modules/pairtools/restrict/test.yml b/tests/modules/pairtools/restrict/test.yml
deleted file mode 100644
index 484b37390b4..00000000000
--- a/tests/modules/pairtools/restrict/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: pairtools restrict test_pairtools_restrict
-  command: nextflow run ./tests/modules/pairtools/restrict -entry test_pairtools_restrict -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/restrict/nextflow.config
-  tags:
-    - pairtools/restrict
-    - pairtools
-  files:
-    - path: output/pairtools/test.restrict.pairs.gz
diff --git a/tests/modules/pairtools/select/main.nf b/tests/modules/pairtools/select/main.nf
deleted file mode 100644
index ff65cd95262..00000000000
--- a/tests/modules/pairtools/select/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PAIRTOOLS_SELECT } from '../../../../modules/pairtools/select/main.nf'
-
-workflow test_pairtools_select {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.pairsam", checkIfExists: true) ]
-
-    PAIRTOOLS_SELECT ( input )
-}
diff --git a/tests/modules/pairtools/select/test.yml b/tests/modules/pairtools/select/test.yml
deleted file mode 100644
index 431e8366d6f..00000000000
--- a/tests/modules/pairtools/select/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: pairtools select test_pairtools_select
-  command: nextflow run ./tests/modules/pairtools/select -entry test_pairtools_select -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/select/nextflow.config
-  tags:
-    - pairtools/select
-    - pairtools
-  files:
-    - path: output/pairtools/test.selected.pairs.gz
-    - path: output/pairtools/test.unselected.pairs.gz
diff --git a/tests/modules/pairtools/sort/main.nf b/tests/modules/pairtools/sort/main.nf
deleted file mode 100644
index 0e484c76f0e..00000000000
--- a/tests/modules/pairtools/sort/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PAIRTOOLS_SORT } from '../../../../modules/pairtools/sort/main.nf'
-
-workflow test_pairtools_sort {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("https://raw.githubusercontent.com/open2c/pairtools/master/tests/data/mock.pairsam", checkIfExists: true) ]
-
-    PAIRTOOLS_SORT ( input )
-}
diff --git a/tests/modules/pairtools/sort/test.yml b/tests/modules/pairtools/sort/test.yml
deleted file mode 100644
index 4d4866aac6b..00000000000
--- a/tests/modules/pairtools/sort/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: pairtools sort test_pairtools_sort
-  command: nextflow run ./tests/modules/pairtools/sort -entry test_pairtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/sort/nextflow.config
-  tags:
-    - pairtools/sort
-    - pairtools
-  files:
-    - path: output/pairtools/test.sorted.pairs.gz
diff --git a/tests/modules/panaroo/run/main.nf b/tests/modules/panaroo/run/main.nf
deleted file mode 100644
index 1fab62eddf6..00000000000
--- a/tests/modules/panaroo/run/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PANAROO_RUN } from '../../../../modules/panaroo/run/main.nf'
-
-workflow test_panaroo_run {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
-        ]
-    ]
-
-    PANAROO_RUN ( input )
-}
diff --git a/tests/modules/panaroo/run/test.yml b/tests/modules/panaroo/run/test.yml
deleted file mode 100644
index 20f0b814af9..00000000000
--- a/tests/modules/panaroo/run/test.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-- name: panaroo run test_panaroo_run
-  command: nextflow run tests/modules/panaroo/run -entry test_panaroo_run -c tests/config/nextflow.config
-  tags:
-    - panaroo/run
-    - panaroo
-  files:
-    - path: output/panaroo/results/combined_DNA_CDS.fasta
-      md5sum: 92bd4f6b9c84c84c0989d77d2558b7d1
-    - path: output/panaroo/results/combined_protein_CDS.fasta
-      md5sum: 7a5636c4f2abc190f5dd4dfbb1da7034
-    - path: output/panaroo/results/combined_protein_cdhit_out.txt
-      md5sum: 2164b81606712b53af2198b4d50eed08
-    - path: output/panaroo/results/combined_protein_cdhit_out.txt.clstr
-      md5sum: aaa9fc2b797c932b6d9ff2df640113f1
-    - path: output/panaroo/results/core_alignment_header.embl
-      contains: ["DNA", "feature", "locus_tag"]
-    - path: output/panaroo/results/core_gene_alignment.aln
-      contains: ["test1", "test2", "test3"]
-    - path: output/panaroo/results/final_graph.gml
-      contains: ["graph", "isolateNames", "test3"]
-    - path: output/panaroo/results/gene_data.csv
-      md5sum: 45df2d26ac81754b858c0e4757e834b2
-    - path: output/panaroo/results/gene_presence_absence.Rtab
-      md5sum: 9efbed5df121dc0c4fbb58869b65c3e4
-    - path: output/panaroo/results/gene_presence_absence.csv
-      contains: ["Gene", "unique", "test3"]
-    - path: output/panaroo/results/gene_presence_absence_roary.csv
-      contains: ["Gene", "Max", "Fragment"]
-    - path: output/panaroo/results/pan_genome_reference.fa
-      md5sum: d0b03cdfaab8965d86cb1045db3c2d20
-    - path: output/panaroo/results/pre_filt_graph.gml
-      contains: ["graph", "node", "id"]
-    - path: output/panaroo/results/struct_presence_absence.Rtab
-      md5sum: 246017db1175f9b1683dfe60cb2e9b5b
-    - path: output/panaroo/results/summary_statistics.txt
-      md5sum: 9c73c416e1758bea06c67b4ec9fd0720
-    - path: output/panaroo/versions.yml
-      md5sum: 909e7b046a8a87319986d34b7328641c
diff --git a/tests/modules/pangolin/main.nf b/tests/modules/pangolin/main.nf
deleted file mode 100644
index ab4aa4af4da..00000000000
--- a/tests/modules/pangolin/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PANGOLIN } from '../../../modules/pangolin/main.nf'
-
-workflow test_pangolin {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ]
-
-    PANGOLIN ( input )
-}
diff --git a/tests/modules/pangolin/test.yml b/tests/modules/pangolin/test.yml
deleted file mode 100644
index 0ddb2195042..00000000000
--- a/tests/modules/pangolin/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: pangolin
-  command: nextflow run ./tests/modules/pangolin -entry test_pangolin -c ./tests/config/nextflow.config -c ./tests/modules/pangolin/nextflow.config
-  tags:
-    - pangolin
-  files:
-    - path: ./output/pangolin/test.pangolin.csv
-      md5sum: 3484156c2f2e2e638431be7934cfc5b7
diff --git a/tests/modules/paraclu/main.nf b/tests/modules/paraclu/main.nf
deleted file mode 100644
index 3bd75dc066c..00000000000
--- a/tests/modules/paraclu/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PARACLU } from '../../../modules/paraclu/main.nf'
-
-workflow test_paraclu {
-
-    input = [[  id:'test' ], // meta map
-                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-                ]
-    min_cluster = 30
-
-    PARACLU ( input, min_cluster )
-}
diff --git a/tests/modules/paraclu/test.yml b/tests/modules/paraclu/test.yml
deleted file mode 100644
index 36b37df5a76..00000000000
--- a/tests/modules/paraclu/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: paraclu test_paraclu
-  command: nextflow run ./tests/modules/paraclu -entry test_paraclu -c ./tests/config/nextflow.config -c ./tests/modules/paraclu/nextflow.config
-  tags:
-    - paraclu
-  files:
-    - path: output/paraclu/test.clustered.simplified.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/pasty/main.nf b/tests/modules/pasty/main.nf
deleted file mode 100644
index 2dc5ea98f49..00000000000
--- a/tests/modules/pasty/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PASTY } from '../../../modules/pasty/main.nf'
-
-workflow test_pasty {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    PASTY ( input )
-}
diff --git a/tests/modules/pasty/test.yml b/tests/modules/pasty/test.yml
deleted file mode 100644
index 3a4e9b12ab9..00000000000
--- a/tests/modules/pasty/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: pasty test_pasty
-  command: nextflow run ./tests/modules/pasty -entry test_pasty -c ./tests/config/nextflow.config  -c ./tests/modules/pasty/nextflow.config
-  tags:
-    - pasty
-  files:
-    - path: output/pasty/test.blastn.tsv
-      md5sum: 45de2825f0bb3cc8fe9f2b7c419f66f2
-    - path: output/pasty/test.details.tsv
-      md5sum: d6822beea048a27af839087dfc14a536
-    - path: output/pasty/test.tsv
-      md5sum: edbae35d3edc17283ea73f7f3eb22087
diff --git a/tests/modules/pbbam/pbmerge/main.nf b/tests/modules/pbbam/pbmerge/main.nf
deleted file mode 100644
index 34ed33a622e..00000000000
--- a/tests/modules/pbbam/pbmerge/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PBBAM_PBMERGE } from '../../../../modules/pbbam/pbmerge/main.nf'
-
-workflow test_pbbam_pbmerge {
-
-    input = [
-        [ id:'test' ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['pacbio']['cluster']   , checkIfExists: true),
-            file(params.test_data['homo_sapiens']['pacbio']['singletons'], checkIfExists: true)
-        ]
-    ]
-
-    PBBAM_PBMERGE ( input )
-}
diff --git a/tests/modules/pbbam/pbmerge/test.yml b/tests/modules/pbbam/pbmerge/test.yml
deleted file mode 100644
index 0a6d7da3a0a..00000000000
--- a/tests/modules/pbbam/pbmerge/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: pbbam pbmerge test_pbbam_pbmerge
-  command: nextflow run ./tests/modules/pbbam/pbmerge -entry test_pbbam_pbmerge -c ./tests/config/nextflow.config -c ./tests/modules/pbbam/pbmerge/nextflow.config
-  tags:
-    - pbbam/pbmerge
-    - pbbam
-  files:
-    - path: output/pbbam/test.merged.bam
-      md5sum: 727c7ba1289192085c06890dda70f973
-    - path: output/pbbam/test.merged.bam.pbi
-      md5sum: edfadd3a81c598d1ee051899792db75d
diff --git a/tests/modules/pbccs/main.nf b/tests/modules/pbccs/main.nf
deleted file mode 100644
index 91a2ab30113..00000000000
--- a/tests/modules/pbccs/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PBCCS } from '../../../modules/pbccs/main.nf'
-
-workflow test_pbccs {
-
-    input = [
-        [ id:'alz' ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['alz'],    checkIfExists: true),
-        file(params.test_data['homo_sapiens']['pacbio']['alzpbi'], checkIfExists: true)
-    ]
-
-    chunk_num = 2
-    chunk_on  = 3
-
-    PBCCS ( input, chunk_num, chunk_on )
-}
diff --git a/tests/modules/pbccs/test.yml b/tests/modules/pbccs/test.yml
deleted file mode 100644
index 7154945856f..00000000000
--- a/tests/modules/pbccs/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: pbccs test_pbccs
-  command: nextflow run ./tests/modules/pbccs -entry test_pbccs -c ./tests/config/nextflow.config -c ./tests/modules/pbccs/nextflow.config
-  tags:
-    - pbccs
-  files:
-    - path: output/pbccs/alz.chunk2.bam
-      md5sum: 2b6451f2d0454eb08359cb84e2e4069c
-    - path: output/pbccs/alz.chunk2.bam.pbi
-      md5sum: 3112cda9744e3facbf38245d41aaf080
-    - path: output/pbccs/alz.chunk2.metrics.json.gz
-      contains: ["zmws"]
-    - path: output/pbccs/alz.chunk2.report.json
-      contains: ["Created by pbcopper"]
-    - path: output/pbccs/alz.chunk2.report.txt
-      md5sum: bbc5bd7a1269345cf7a7f3d4c746024b
diff --git a/tests/modules/pbptyper/main.nf b/tests/modules/pbptyper/main.nf
deleted file mode 100644
index ba4854301ff..00000000000
--- a/tests/modules/pbptyper/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PBPTYPER } from '../../../modules/pbptyper/main.nf'
-
-workflow test_pbptyper {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    PBPTYPER ( input, [] )
-}
diff --git a/tests/modules/pbptyper/test.yml b/tests/modules/pbptyper/test.yml
deleted file mode 100644
index 98ea0c1ceca..00000000000
--- a/tests/modules/pbptyper/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: pbptyper test_pbptyper
-  command: nextflow run ./tests/modules/pbptyper -entry test_pbptyper -c ./tests/config/nextflow.config  -c ./tests/modules/pbptyper/nextflow.config
-  tags:
-    - pbptyper
-  files:
-    - path: output/pbptyper/test-1A.tblastn.tsv
-      md5sum: 16bb26284bd7bf2327337fc95c055429
-    - path: output/pbptyper/test-2B.tblastn.tsv
-      md5sum: 16bb26284bd7bf2327337fc95c055429
-    - path: output/pbptyper/test-2X.tblastn.tsv
-      md5sum: 16bb26284bd7bf2327337fc95c055429
-    - path: output/pbptyper/test.tsv
-      md5sum: 7115fb3533ee30f0a7dde61a42f69185
diff --git a/tests/modules/pear/main.nf b/tests/modules/pear/main.nf
deleted file mode 100644
index 3646740d301..00000000000
--- a/tests/modules/pear/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PEAR } from '../../../modules/pear/main.nf'
-
-workflow test_pear {
-
-    input = [
-        [ id:'test' ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    PEAR ( input )
-}
diff --git a/tests/modules/pear/test.yml b/tests/modules/pear/test.yml
deleted file mode 100644
index 6e77e6e5eb0..00000000000
--- a/tests/modules/pear/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: pear test_pear
-  command: nextflow run ./tests/modules/pear -entry test_pear -c ./tests/config/nextflow.config  -c ./tests/modules/pear/nextflow.config
-  tags:
-    - pear
-  files:
-    - path: output/pear/test.assembled.fastq.gz
-      md5sum: d02799ee04909655e7be5c9161c876b2
-    - path: output/pear/test.discarded.fastq.gz # Known empty file
-    - path: output/pear/test.unassembled.forward.fastq.gz
-      md5sum: 2e35f09a6abbb4559127c512f5652e7e
-    - path: output/pear/test.unassembled.reverse.fastq.gz
-      md5sum: 6e1c73c502230869c21b03a41faddafb
diff --git a/tests/modules/peddy/main.nf b/tests/modules/peddy/main.nf
deleted file mode 100644
index e53e8152122..00000000000
--- a/tests/modules/peddy/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PEDDY } from '../../../modules/peddy/main.nf'
-
-workflow test_peddy {
-
-    input = [
-        [ id:'test', single_end:false ],
-        file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz_tbi'], checkIfExists: true)
-    ]
-    ped = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
-
-    PEDDY ( input, ped )
-}
diff --git a/tests/modules/peddy/test.yml b/tests/modules/peddy/test.yml
deleted file mode 100644
index 0ed6dc9440c..00000000000
--- a/tests/modules/peddy/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: peddy test_peddy
-  command: nextflow run ./tests/modules/peddy -entry test_peddy -c ./tests/config/nextflow.config ./tests/modules/peddy/nextflow.config
-  tags:
-    - peddy
-  files:
-    - path: output/peddy/justhusky_minimal.het_check.csv
-      md5sum: f4006d47355f2a760e40215b403926c3
-    - path: output/peddy/justhusky_minimal.html
-      md5sum: 4f189cdbe8f03fe5c32d343c183506a5
-    - path: output/peddy/justhusky_minimal.ped_check.csv
-      md5sum: d79a98558e280afe794d1374d2b985d4
-    - path: output/peddy/justhusky_minimal.ped_check.rel-difference.csv
-      md5sum: 9de7e287cb30c742db2ff3622b0e63b1
-    - path: output/peddy/justhusky_minimal.sex_check.csv
-      md5sum: 60848489bc697490da6a53b5170baf3b
-    - path: output/peddy/justhusky_minimal.vs.html
-      md5sum: 20f5f3a97fa781057c876ac79e044010
diff --git a/tests/modules/phantompeakqualtools/main.nf b/tests/modules/phantompeakqualtools/main.nf
deleted file mode 100644
index 3b995d68083..00000000000
--- a/tests/modules/phantompeakqualtools/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PHANTOMPEAKQUALTOOLS } from '../../../modules/phantompeakqualtools/main.nf'
-
-workflow test_phantompeakqualtools_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
-    ]
-
-    PHANTOMPEAKQUALTOOLS ( input )
-}
-
-workflow test_phantompeakqualtools_paired_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    PHANTOMPEAKQUALTOOLS ( input )
-}
diff --git a/tests/modules/phantompeakqualtools/test.yml b/tests/modules/phantompeakqualtools/test.yml
deleted file mode 100644
index 3ab612bd37b..00000000000
--- a/tests/modules/phantompeakqualtools/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: phantompeakqualtools test_phantompeakqualtools_single_end
-  command: nextflow run tests/modules/phantompeakqualtools -entry test_phantompeakqualtools_single_end -c tests/config/nextflow.config
-  tags:
-    - phantompeakqualtools
-  files:
-    - path: output/phantompeakqualtools/test.spp.Rdata
-    - path: output/phantompeakqualtools/test.spp.out
-      md5sum: b01d976506b6fe45b66c821b1e8a1d15
-    - path: output/phantompeakqualtools/test.spp.pdf
-    - path: output/phantompeakqualtools/versions.yml
-      md5sum: 6c2ede1aac4c574e3c72fbe09f15c03f
-
-- name: phantompeakqualtools test_phantompeakqualtools_paired_end
-  command: nextflow run tests/modules/phantompeakqualtools -entry test_phantompeakqualtools_paired_end -c tests/config/nextflow.config
-  tags:
-    - phantompeakqualtools
-  files:
-    - path: output/phantompeakqualtools/test.spp.Rdata
-    - path: output/phantompeakqualtools/test.spp.out
-      md5sum: eed46e75eab119224f397a7a8b5924e6
-    - path: output/phantompeakqualtools/test.spp.pdf
-    - path: output/phantompeakqualtools/versions.yml
-      md5sum: 383d2dd583fcb40451bde0d3840bdb72
diff --git a/tests/modules/phyloflash/main.nf b/tests/modules/phyloflash/main.nf
deleted file mode 100644
index 412e0321fd7..00000000000
--- a/tests/modules/phyloflash/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PHYLOFLASH } from '../../../modules/phyloflash/main.nf'
-
-process STUB_PHYLOFLASH_DATABASE {
-    output:
-    path "ref"    , emit: silva_db
-    path "UniVec" , emit: univec_db
-
-    stub:
-    """
-    mkdir ref
-    touch UniVec
-    """
-}
-
-workflow test_phyloflash_single_end {
-
-    STUB_PHYLOFLASH_DATABASE ()
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db, STUB_PHYLOFLASH_DATABASE.out.univec_db )
-}
-
-workflow test_phyloflash_paired_end {
-
-    STUB_PHYLOFLASH_DATABASE ()
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db,  STUB_PHYLOFLASH_DATABASE.out.univec_db )
-}
diff --git a/tests/modules/phyloflash/test.yml b/tests/modules/phyloflash/test.yml
deleted file mode 100644
index 81eac2f2061..00000000000
--- a/tests/modules/phyloflash/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: phyloflash single-end
-  command: nextflow run ./tests/modules/phyloflash -entry test_phyloflash_single_end -c ./tests/config/nextflow.config -c ./tests/modules/phyloflash/nextflow.config -stub-run
-  tags:
-    - phyloflash
-  files:
-    - path: output/phyloflash/test/test.SSU.collection.fasta
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-
-- name: phyloflash paired-end
-  command: nextflow run ./tests/modules/phyloflash -entry test_phyloflash_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/phyloflash/nextflow.config -stub-run
-  tags:
-    - phyloflash
-  files:
-    - path: output/phyloflash/test/test.SSU.collection.fasta
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/picard/addorreplacereadgroups/main.nf b/tests/modules/picard/addorreplacereadgroups/main.nf
deleted file mode 100644
index d5148c36817..00000000000
--- a/tests/modules/picard/addorreplacereadgroups/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_ADDORREPLACEREADGROUPS } from '../../../../modules/picard/addorreplacereadgroups/main.nf'
-
-workflow test_picard_addorreplacereadgroups {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
-    ]
-
-    PICARD_ADDORREPLACEREADGROUPS ( input )
-}
diff --git a/tests/modules/picard/addorreplacereadgroups/test.yml b/tests/modules/picard/addorreplacereadgroups/test.yml
deleted file mode 100644
index 3478d166206..00000000000
--- a/tests/modules/picard/addorreplacereadgroups/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: picard addorreplacereadgroups test_picard_addorreplacereadgroups
-  command: nextflow run tests/modules/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c tests/config/nextflow.config
-  tags:
-    - picard
-    - picard/addorreplacereadgroups
-  files:
-    - path: output/picard/test.bam
-      md5sum: 7b82f3461c2d80fc6a10385e78c9427f
-    - path: output/picard/versions.yml
-- name: picard addorreplacereadgroups test_picard_addorreplacereadgroups stub
-  command: nextflow run tests/modules/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c tests/config/nextflow.config -stub
-  tags:
-    - picard
-    - picard/addorreplacereadgroups
-  files:
-    - path: output/picard/test.bam
-    - path: output/picard/versions.yml
diff --git a/tests/modules/picard/cleansam/main.nf b/tests/modules/picard/cleansam/main.nf
deleted file mode 100644
index f189b0f3d20..00000000000
--- a/tests/modules/picard/cleansam/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_CLEANSAM } from '../../../../modules/picard/cleansam/main.nf'
-
-workflow test_picard_cleansam {
-    
-    input = [ 
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) 
-    ]
-
-    PICARD_CLEANSAM ( input )
-}
diff --git a/tests/modules/picard/cleansam/test.yml b/tests/modules/picard/cleansam/test.yml
deleted file mode 100644
index 08dcd84d00f..00000000000
--- a/tests/modules/picard/cleansam/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: picard cleansam test_picard_cleansam
-  command: nextflow run tests/modules/picard/cleansam -entry test_picard_cleansam -c tests/config/nextflow.config
-  tags:
-    - picard/cleansam
-    - picard
-  files:
-    - path: output/picard/test.bam
-      md5sum: a48f8e77a1480445efc57570c3a38a68
-    - path: output/picard/versions.yml
diff --git a/tests/modules/picard/collecthsmetrics/main.nf b/tests/modules/picard/collecthsmetrics/main.nf
deleted file mode 100644
index b25f3bf576e..00000000000
--- a/tests/modules/picard/collecthsmetrics/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_COLLECTHSMETRICS } from '../../../../modules/picard/collecthsmetrics/main.nf'
-
-workflow test_picard_collecthsmetrics {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
-    target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
-
-    PICARD_COLLECTHSMETRICS ( input, fasta, fai, bait_intervals, target_intervals )
-}
-
-workflow test_picard_collecthsmetrics_nofasta {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
-
-    bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
-    target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
-
-    PICARD_COLLECTHSMETRICS ( input, [], [], bait_intervals, target_intervals )
-}
diff --git a/tests/modules/picard/collecthsmetrics/test.yml b/tests/modules/picard/collecthsmetrics/test.yml
deleted file mode 100644
index 61069b5555a..00000000000
--- a/tests/modules/picard/collecthsmetrics/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: picard collecthsmetrics test_picard_collecthsmetrics
-  command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collecthsmetrics/nextflow.config
-  tags:
-    - picard/collecthsmetrics
-    - picard
-  files:
-    - path: output/picard/test.CollectHsMetrics.coverage_metrics
-
-- name: picard collecthsmetrics test_picard_collecthsmetrics_nofasta
-  command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collecthsmetrics/nextflow.config
-  tags:
-    - picard/collecthsmetrics
-    - picard
-  files:
-    - path: output/picard/test.CollectHsMetrics.coverage_metrics
diff --git a/tests/modules/picard/collectmultiplemetrics/main.nf b/tests/modules/picard/collectmultiplemetrics/main.nf
deleted file mode 100644
index 3a103f65829..00000000000
--- a/tests/modules/picard/collectmultiplemetrics/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf'
-
-workflow test_picard_collectmultiplemetrics {
-    input = [
-                [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, [] )
-}
-
-workflow test_picard_collectmultiplemetrics_nofasta {
-    input = [
-                [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    PICARD_COLLECTMULTIPLEMETRICS ( input, [], [] )
-}
-
-workflow test_picard_collectmultiplemetrics_cram {
-    input = [
-                [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, fai )
-}
diff --git a/tests/modules/picard/collectmultiplemetrics/test.yml b/tests/modules/picard/collectmultiplemetrics/test.yml
deleted file mode 100644
index 4f3cecc4bff..00000000000
--- a/tests/modules/picard/collectmultiplemetrics/test.yml
+++ /dev/null
@@ -1,96 +0,0 @@
-- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics
-  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
-  tags:
-    - picard
-    - picard/collectmultiplemetrics
-  files:
-    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
-      contains:
-        - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
-    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
-    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
-      contains:
-        - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
-        - "1\t1\t20\t26\t32\t22\t0"
-    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
-    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
-      contains:
-        - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
-        - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311"
-    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
-    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
-      contains:
-        - "CYCLE\tMEAN_QUALITY"
-        - "1\t32"
-        - "2\t31.35"
-    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
-    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
-      contains:
-        - "QUALITY\tCOUNT_OF_Q"
-        - "14\t1926"
-    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
-
-- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta
-  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
-  tags:
-    - picard
-    - picard/collectmultiplemetrics
-  files:
-    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
-      contains:
-        - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
-    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
-    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
-      contains:
-        - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
-        - "1\t1\t20\t26\t32\t22\t0"
-    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
-    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
-      contains:
-        - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
-        - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311"
-    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
-    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
-      contains:
-        - "CYCLE\tMEAN_QUALITY"
-        - "1\t32"
-        - "2\t31.35"
-    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
-    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
-      contains:
-        - "QUALITY\tCOUNT_OF_Q"
-        - "14\t1926"
-    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
-
-- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_cram
-  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_cram -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
-  tags:
-    - picard
-    - picard/collectmultiplemetrics
-  files:
-    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
-      contains:
-        - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
-    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
-    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
-      contains:
-        - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
-        - "1\t1\t34.065934\t15.242822\t16.093584\t34.526764\t0.070897"
-    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
-    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
-      contains:
-        - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
-        - "123\t96\t23\t32\t300\t125.684397\t32.447863\t2820\tFR\t11\t17\t27\t37\t47\t57\t69\t83\t103\t125\t169"
-    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
-    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
-      contains:
-        - "CYCLE\tMEAN_QUALITY"
-        - "1\t41.018079"
-        - "2\t40.981921"
-    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
-    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
-      contains:
-        - "QUALITY\tCOUNT_OF_Q"
-        - "3\t2"
-        - "4\t44"
-    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
diff --git a/tests/modules/picard/collectwgsmetrics/main.nf b/tests/modules/picard/collectwgsmetrics/main.nf
deleted file mode 100644
index eddf56031fe..00000000000
--- a/tests/modules/picard/collectwgsmetrics/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgsmetrics/main.nf'
-
-workflow test_picard_collectwgsmetrics {
-    input = [ [ id:'test', single_end:false ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    PICARD_COLLECTWGSMETRICS ( input, fasta )
-}
diff --git a/tests/modules/picard/collectwgsmetrics/test.yml b/tests/modules/picard/collectwgsmetrics/test.yml
deleted file mode 100644
index 9abba0159ab..00000000000
--- a/tests/modules/picard/collectwgsmetrics/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: picard collectwgsmetrics test_picard_collectwgsmetrics
-  command: nextflow run ./tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectwgsmetrics/nextflow.config
-  tags:
-    - picard/collectwgsmetrics
-    - picard
-  files:
-    - path: output/picard/test.CollectWgsMetrics.coverage_metrics
-
-- name: picard collectwgsmetrics test_picard_collectwgsmetrics stub
-  command: nextflow run ./tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectwgsmetrics/nextflow.config -stub-run
-  tags:
-    - picard/collectwgsmetrics
-    - picard
-  files:
-    - path: output/picard/test.CollectWgsMetrics.coverage_metrics
diff --git a/tests/modules/picard/createsequencedictionary/main.nf b/tests/modules/picard/createsequencedictionary/main.nf
deleted file mode 100644
index 4dc24c8a423..00000000000
--- a/tests/modules/picard/createsequencedictionary/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../../modules/picard/createsequencedictionary/main.nf'
-
-workflow test_picard_createsequencedictionary {
-    
-    input = [ 
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
-    ]
-
-    PICARD_CREATESEQUENCEDICTIONARY ( input )
-}
diff --git a/tests/modules/picard/createsequencedictionary/test.yml b/tests/modules/picard/createsequencedictionary/test.yml
deleted file mode 100644
index 59f2dd44262..00000000000
--- a/tests/modules/picard/createsequencedictionary/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: picard createsequencedictionary test_picard_createsequencedictionary
-  command: nextflow run tests/modules/picard/createsequencedictionary -entry test_picard_createsequencedictionary -c tests/config/nextflow.config
-  tags:
-    - picard/createsequencedictionary
-    - picard
-  files:
-    - path: output/picard/test.dict
-      contains: ["SN:MT192765.1"]
-    - path: output/picard/versions.yml
diff --git a/tests/modules/picard/crosscheckfingerprints/main.nf b/tests/modules/picard/crosscheckfingerprints/main.nf
deleted file mode 100644
index 55ddb5c5966..00000000000
--- a/tests/modules/picard/crosscheckfingerprints/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_CROSSCHECKFINGERPRINTS } from '../../../../modules/picard/crosscheckfingerprints/main.nf'
-
-workflow test_picard_crosscheckfingerprints {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
-    ]
-    PICARD_CROSSCHECKFINGERPRINTS ( input,[], file(params.test_data['homo_sapiens']['genome']['haplotype_map'], checkIfExists: true))
-}
diff --git a/tests/modules/picard/crosscheckfingerprints/test.yml b/tests/modules/picard/crosscheckfingerprints/test.yml
deleted file mode 100644
index 534c206d62b..00000000000
--- a/tests/modules/picard/crosscheckfingerprints/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: "picard crosscheckfingerprints"
-  command: nextflow run ./tests/modules/picard/crosscheckfingerprints -entry test_picard_crosscheckfingerprints -c ./tests/config/nextflow.config -c ./tests/modules/picard/crosscheckfingerprints/nextflow.config
-  tags:
-    - "picard"
-    - "picard/crosscheckfingerprints"
-  files:
-    - path: "output/picard/test.crosscheck_metrics.txt"
-    - path: output/picard/versions.yml
diff --git a/tests/modules/picard/fastqtosam/main.nf b/tests/modules/picard/fastqtosam/main.nf
deleted file mode 100644
index 2eb55e63995..00000000000
--- a/tests/modules/picard/fastqtosam/main.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_FASTQTOSAM } from '../../../../modules/picard/fastqtosam/main.nf'
-
-workflow test_picard_fastqtosam_single {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    PICARD_FASTQTOSAM ( input )
-}
-
-workflow test_picard_fastqtosam_paired {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    PICARD_FASTQTOSAM ( input )
-}
-
-workflow test_picard_fastqtosam_paired_custom_samplename {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    PICARD_FASTQTOSAM ( input )
-}
diff --git a/tests/modules/picard/fastqtosam/test.yml b/tests/modules/picard/fastqtosam/test.yml
deleted file mode 100644
index 929af92a18f..00000000000
--- a/tests/modules/picard/fastqtosam/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: picard fastqtosam test_picard_fastqtosam_single
-  command: nextflow run ./tests/modules/picard/fastqtosam -entry test_picard_fastqtosam_single -c ./tests/config/nextflow.config  -c ./tests/modules/picard/fastqtosam/nextflow.config
-  tags:
-    - picard
-    - picard/fastqtosam
-  files:
-    - path: output/picard/test.bam
-      md5sum: fe2882efe8f13a8da20fcc63469ed0aa
-
-- name: picard fastqtosam test_picard_fastqtosam_paired
-  command: nextflow run ./tests/modules/picard/fastqtosam -entry test_picard_fastqtosam_paired -c ./tests/config/nextflow.config  -c ./tests/modules/picard/fastqtosam/nextflow.config
-  tags:
-    - picard
-    - picard/fastqtosam
-  files:
-    - path: output/picard/test.bam
-      md5sum: 90e4f59f9d942f96c3f3c41160f3fd5d
-
-- name: picard fastqtosam test_picard_fastqtosam_paired_custom_samplename
-  command: nextflow run ./tests/modules/picard/fastqtosam -entry test_picard_fastqtosam_paired_custom_samplename -c ./tests/config/nextflow.config  -c ./tests/modules/picard/fastqtosam/nextflow.config
-  tags:
-    - picard
-    - picard/fastqtosam
-  files:
-    - path: output/picard/test.bam
-      md5sum: 69d35ee2b5dc263d022eaf59a9e383d3
diff --git a/tests/modules/picard/filtersamreads/main.nf b/tests/modules/picard/filtersamreads/main.nf
deleted file mode 100644
index 847bee57dec..00000000000
--- a/tests/modules/picard/filtersamreads/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_SORTSAM        } from '../../../../modules/picard/sortsam/main.nf'
-include { PICARD_FILTERSAMREADS } from '../../../../modules/picard/filtersamreads/main.nf'
-
-workflow test_picard_filtersamreads {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
-    sort_order = 'queryname'
-    filter = 'includeAligned'
-
-    PICARD_SORTSAM ( input, sort_order )
-    PICARD_SORTSAM.out.bam
-        .map {
-            [ it[0], it[1], [] ]
-        }
-        .set{ ch_sorted_for_filtersamreads }
-    PICARD_FILTERSAMREADS ( ch_sorted_for_filtersamreads, filter )
-}
-
-workflow test_picard_filtersamreads_readlist {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_single_end_bam_readlist_txt'], checkIfExists: true) ]
-    filter = 'includeReadList'
-
-    PICARD_FILTERSAMREADS ( input, filter )
-}
diff --git a/tests/modules/picard/filtersamreads/test.yml b/tests/modules/picard/filtersamreads/test.yml
deleted file mode 100644
index af30d6d2ce0..00000000000
--- a/tests/modules/picard/filtersamreads/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: picard filtersamreads
-  command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads -c ./tests/config/nextflow.config -c ./tests/modules/picard/filtersamreads/nextflow.config
-  tags:
-    - picard
-    - picard/filtersamreads
-  files:
-    - path: output/picard/test.filtered.bam
-      md5sum: b44a6ca04811a9470c7813c3c9465fd5
-
-- name: picard filtersamreads readlist
-  command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c ./tests/config/nextflow.config -c ./tests/modules/picard/filtersamreads/nextflow.config
-  tags:
-    - picard
-    - picard/filtersamreads
-  files:
-    - path: output/picard/test.filtered.bam
-      md5sum: 1e86b738b56f2c2b09f4cab52baf05c7
diff --git a/tests/modules/picard/fixmateinformation/main.nf b/tests/modules/picard/fixmateinformation/main.nf
deleted file mode 100644
index 46b4248b91f..00000000000
--- a/tests/modules/picard/fixmateinformation/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_FIXMATEINFORMATION } from '../../../../modules/picard/fixmateinformation/main.nf'
-
-workflow test_picard_fixmateinformation {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
-    ]
-
-    PICARD_FIXMATEINFORMATION ( input )
-}
diff --git a/tests/modules/picard/fixmateinformation/test.yml b/tests/modules/picard/fixmateinformation/test.yml
deleted file mode 100644
index f2f9c4916c0..00000000000
--- a/tests/modules/picard/fixmateinformation/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: picard fixmateinformation test_picard_fixmateinformation
-  command: nextflow run tests/modules/picard/fixmateinformation -entry test_picard_fixmateinformation -c tests/config/nextflow.config
-  tags:
-    - picard
-    - picard/fixmateinformation
-  files:
-    - path: output/picard/test.bam
-      md5sum: 746102e8c242c0ef42e045c49d320030
-    - path: output/picard/versions.yml
diff --git a/tests/modules/picard/liftovervcf/main.nf b/tests/modules/picard/liftovervcf/main.nf
deleted file mode 100644
index 08181a8a723..00000000000
--- a/tests/modules/picard/liftovervcf/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_LIFTOVERVCF } from '../../../../modules/picard/liftovervcf/main.nf'
-
-workflow test_picard_liftovervcf {
-
-    input_vcf = [ [ id:'test' ],
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
-            ]
-    dict =  file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-    chain =  file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
-    fasta  = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
-}
-
-workflow test_picard_liftovervcf_stubs {
-
-    input_vcf = [ [ id:'test' ],
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
-            ]
-    dict =  file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-    chain =  file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
-    fasta  = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
-}
diff --git a/tests/modules/picard/liftovervcf/test.yml b/tests/modules/picard/liftovervcf/test.yml
deleted file mode 100644
index 436fcf21838..00000000000
--- a/tests/modules/picard/liftovervcf/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: picard liftovervcf test_picard_liftovervcf
-  command: nextflow run tests/modules/picard/liftovervcf -entry test_picard_liftovervcf -c tests/config/nextflow.config
-  tags:
-    - picard/liftovervcf
-    - picard
-  files:
-    - path: output/picard/test.lifted.vcf.gz
-      contains:
-        - "chr22"
-    - path: output/picard/test.unlifted.vcf.gz
-    - path: output/picard/versions.yml
-
-- name: picard liftovervcf test_picard_liftovervcf_stubs
-  command: nextflow run tests/modules/picard/liftovervcf -entry test_picard_liftovervcf_stubs -c tests/config/nextflow.config -stub-run
-  tags:
-    - picard/liftovervcf
-    - picard
-  files:
-    - path: output/picard/test.lifted.vcf.gz
-    - path: output/picard/test.unlifted.vcf.gz
-    - path: output/picard/versions.yml
diff --git a/tests/modules/picard/markduplicates/main.nf b/tests/modules/picard/markduplicates/main.nf
deleted file mode 100644
index 12f3ac26afc..00000000000
--- a/tests/modules/picard/markduplicates/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf'
-include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED}  from '../../../../modules/picard/markduplicates/main.nf'
-
-workflow test_picard_markduplicates_sorted_bam  {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    PICARD_MARKDUPLICATES ( input )
-}
-
-workflow test_picard_markduplicates_unsorted_bam  {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-            ]
-
-    PICARD_MARKDUPLICATES_UNSORTED ( input )
-}
diff --git a/tests/modules/picard/markduplicates/test.yml b/tests/modules/picard/markduplicates/test.yml
deleted file mode 100644
index cfb5b5de290..00000000000
--- a/tests/modules/picard/markduplicates/test.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-- name: picard markduplicates sorted bam
-  command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/picard/markduplicates/nextflow.config
-  tags:
-    - picard
-    - picard/markduplicates
-  files:
-    - path: ./output/picard/test.MarkDuplicates.metrics.txt
-      contains:
-        - "1.0	97	97"
-    - path: ./output/picard/test.bam
-- name: picard markduplicates unsorted bam
-  command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/picard/markduplicates/nextflow.config
-  tags:
-    - picard
-    - picard/markduplicates
-  files:
-    - path: ./output/picard/test.MarkDuplicates.metrics.txt
-      contains:
-        - "1.0	97	97"
-    - path: ./output/picard/test.bam
diff --git a/tests/modules/picard/mergesamfiles/main.nf b/tests/modules/picard/mergesamfiles/main.nf
deleted file mode 100644
index 51c070b645c..00000000000
--- a/tests/modules/picard/mergesamfiles/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_MERGESAMFILES } from '../../../../modules/picard/mergesamfiles/main.nf'
-
-workflow test_picard_mergesamfiles {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true), ]
-            ]
-
-    PICARD_MERGESAMFILES ( input )
-}
diff --git a/tests/modules/picard/mergesamfiles/test.yml b/tests/modules/picard/mergesamfiles/test.yml
deleted file mode 100644
index 1cf59cb7ca8..00000000000
--- a/tests/modules/picard/mergesamfiles/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: picard mergesamfiles
-  command: nextflow run ./tests/modules/picard/mergesamfiles -entry test_picard_mergesamfiles -c ./tests/config/nextflow.config -c ./tests/modules/picard/mergesamfiles/nextflow.config
-  tags:
-    - picard
-    - picard/mergesamfiles
-  files:
-    - path: ./output/picard/test.bam
diff --git a/tests/modules/picard/sortsam/main.nf b/tests/modules/picard/sortsam/main.nf
deleted file mode 100644
index 1516682cf27..00000000000
--- a/tests/modules/picard/sortsam/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf'
-
-workflow test_picard_sortsam {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
-    sort_order = "queryname"
-
-    PICARD_SORTSAM ( input, sort_order )
-}
diff --git a/tests/modules/picard/sortsam/test.yml b/tests/modules/picard/sortsam/test.yml
deleted file mode 100644
index 61521850e2d..00000000000
--- a/tests/modules/picard/sortsam/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: picard sortsam
-  command: nextflow run ./tests/modules/picard/sortsam -entry test_picard_sortsam -c ./tests/config/nextflow.config -c ./tests/modules/picard/sortsam/nextflow.config
-  tags:
-    - picard
-    - picard/sortsam
-  files:
-    - path: output/picard/test.sorted.bam
-      md5sum: b44a6ca04811a9470c7813c3c9465fd5
diff --git a/tests/modules/picard/sortvcf/main.nf b/tests/modules/picard/sortvcf/main.nf
deleted file mode 100644
index a88c69fc768..00000000000
--- a/tests/modules/picard/sortvcf/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_SORTVCF } from '../../../../modules/picard/sortvcf/main.nf'
-
-workflow test_picard_sortvcf {
-
-    input = [ [ id:'test' ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-            ]
-
-    fasta  = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    dict  = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
-
-    PICARD_SORTVCF ( input, fasta, dict )
-}
diff --git a/tests/modules/picard/sortvcf/test.yml b/tests/modules/picard/sortvcf/test.yml
deleted file mode 100644
index 26271077cba..00000000000
--- a/tests/modules/picard/sortvcf/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: picard sortvcf
-  command: nextflow run ./tests/modules/picard/sortvcf -entry test_picard_sortvcf -c ./tests/config/nextflow.config -c ./tests/modules/picard/sortvcf/nextflow.config
-  tags:
-    - picard
-    - picard/sortvcf
-  files:
-    - path: output/picard/test_sorted.vcf.gz
diff --git a/tests/modules/pints/caller/main.nf b/tests/modules/pints/caller/main.nf
deleted file mode 100644
index 6dd7938dda7..00000000000
--- a/tests/modules/pints/caller/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PINTS_CALLER } from '../../../../modules/pints/caller/main.nf'
-
-workflow test_pints_caller {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        // FIXME Fails if it doesn't find any signals
-        [file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S0mR1.bam", checkIfExists: true),
-         file("https://raw.githubusercontent.com/Kraus-Lab/groHMM/master/inst/extdata/S40mR1.bam", checkIfExists: true)]
-    ]
-
-    PINTS_CALLER ( input )
-}
-
-// TODO Test single bam input
-// TODO Test single bigwig input
-// TODO Test multiple bigwig input
diff --git a/tests/modules/pints/caller/test.yml b/tests/modules/pints/caller/test.yml
deleted file mode 100644
index 296fdb903fe..00000000000
--- a/tests/modules/pints/caller/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: "pints caller"
-  command: nextflow run ./tests/modules/pints/caller -entry test_pints_caller -c ./tests/config/nextflow.config -c ./tests/modules/pints/caller/nextflow.config
-  tags:
-    - "pints"
-    - "pints/caller"
-  files:
-    - path: output/pints/test_1_bidirectional_peaks.bed
-      md5sum: 8c69305ab896bd772e450e938ddf45f0
-    - path: output/pints/test_1_divergent_peaks.bed
-      md5sum: 2078c643951071f5836d365e5dc7ba1c
-    - path: output/pints/test_1_unidirectional_peaks.bed
-    - path: output/pints/test_2_bidirectional_peaks.bed
-      md5sum: c4efa0f297ba4cdb00659c5e6700ebe5
-    - path: output/pints/test_2_divergent_peaks.bed
-      md5sum: 213a2ba5d9930768d76bf2a7d8c3f7fb
-    - path: output/pints/test_2_unidirectional_peaks.bed
diff --git a/tests/modules/pirate/main.nf b/tests/modules/pirate/main.nf
deleted file mode 100644
index 45c60713af4..00000000000
--- a/tests/modules/pirate/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PIRATE } from '../../../modules/pirate/main.nf'
-
-workflow test_pirate {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
-        ]
-    ]
-
-    PIRATE ( input )
-}
diff --git a/tests/modules/pirate/test.yml b/tests/modules/pirate/test.yml
deleted file mode 100644
index ffee5552326..00000000000
--- a/tests/modules/pirate/test.yml
+++ /dev/null
@@ -1,98 +0,0 @@
-- name: pirate test_pirate
-  command: nextflow run ./tests/modules/pirate -entry test_pirate -c ./tests/config/nextflow.config -c ./tests/modules/pirate/nextflow.config
-  tags:
-    - pirate
-  files:
-    - path: output/pirate/results/PIRATE.gene_families.ordered.tsv
-      contains: ["allele_name"]
-    - path: output/pirate/results/PIRATE.gene_families.tsv
-      contains: ["allele_name"]
-    - path: output/pirate/results/PIRATE.genomes_per_allele.tsv
-      contains: ["g0197"]
-    - path: output/pirate/results/PIRATE.log
-      contains: ["PIRATE input options"]
-    - path: output/pirate/results/PIRATE.pangenome_summary.txt
-      md5sum: 4551c291bc06b21f984f25c09329ed7d
-    - path: output/pirate/results/PIRATE.unique_alleles.tsv
-      contains: ["allele_name"]
-    - path: output/pirate/results/binary_presence_absence.fasta
-      contains: ["test1"]
-    - path: output/pirate/results/binary_presence_absence.nwk
-      md5sum: 1fcf7434911bbab39b74791259f1f989
-    - path: output/pirate/results/cluster_alleles.tab
-      contains: ["g0001"]
-    - path: output/pirate/results/co-ords/test1.co-ords.tab
-      md5sum: f1e75c045b35bae260dadb1a2f000dfa
-    - path: output/pirate/results/co-ords/test2.co-ords.tab
-      md5sum: 953b0d2f1dfd4c3a6a6dd246c9174703
-    - path: output/pirate/results/co-ords/test3.co-ords.tab
-      md5sum: 61f2c52ef77dc9a97a200c57b89b7d69
-    - path: output/pirate/results/genome2loci.tab
-      md5sum: 2d9cdefd5b1a7f5e20b0a70a6e5fa588
-    - path: output/pirate/results/genome_list.txt
-      md5sum: c19ac63da7949b15179f42093cbf95b8
-    - path: output/pirate/results/link_clusters.log
-      contains: ["parsing paralog file"]
-    - path: output/pirate/results/loci_list.tab
-      contains: ["test1_00242"]
-    - path: output/pirate/results/loci_paralog_categories.tab
-      md5sum: f8c3d31f445c3cb66bd95ba77be0a7b8
-    - path: output/pirate/results/modified_gffs/test1.gff
-      md5sum: 5dc220e472165c3b693e1017f38fc0e3
-    - path: output/pirate/results/modified_gffs/test2.gff
-      md5sum: 975f5c7fb363caf1be9c53e5e237bb5d
-    - path: output/pirate/results/modified_gffs/test3.gff
-      md5sum: a4735a5ac75ce82aadba8a3de6cabc2e
-    - path: output/pirate/results/pan_sequences.fasta
-      md5sum: 0492833706f0f969b49a3555c16ec40d
-    - path: output/pirate/results/pangenome.connected_blocks.tsv
-      contains: ["block_number"]
-    - path: output/pirate/results/pangenome.edges
-      contains: ["g0259"]
-    - path: output/pirate/results/pangenome.gfa
-      contains: ["g0001"]
-    - path: output/pirate/results/pangenome.order.tsv
-      contains: ["g0172"]
-    - path: output/pirate/results/pangenome.reversed.tsv
-      md5sum: b2396ce09a6e4178761eca6dc7f4434f
-    - path: output/pirate/results/pangenome.syntenic_blocks.tsv
-      contains: ["g0091"]
-    - path: output/pirate/results/pangenome.temp
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
-      contains: ["test1_00242"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
-      contains: ["test1_00242"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
-      contains: ["test1_00242"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
-      contains: ["test1_00242"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
-      contains: ["test1_00242"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
-      contains: ["test1_00242"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
-      contains: ["test1_00242"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
-      md5sum: ffb3b5bf1ba24bf2bd0be677500139a2
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
-      contains: ["test1_00081"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
-      contains: ["test1_00242"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
-      contains: ["chaos"]
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
-      md5sum: 6e483c773ed90bd50b33f2bd569343e4
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
-    - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pto
-    - path: output/pirate/results/pangenome_log.txt
-      contains: ["Creating pangenome on amino acid"]
-    - path: output/pirate/results/paralog_clusters.tab
-      contains: ["g0216"]
-    - path: output/pirate/results/representative_sequences.faa
-      contains: ["representative_genome"]
-    - path: output/pirate/results/representative_sequences.ffn
-      contains: ["representative_genome"]
-    - path: output/pirate/results/split_groups.log
-      contains: ["g0"]
diff --git a/tests/modules/plasmidfinder/main.nf b/tests/modules/plasmidfinder/main.nf
deleted file mode 100644
index 518d135e940..00000000000
--- a/tests/modules/plasmidfinder/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PLASMIDFINDER } from '../../../modules/plasmidfinder/main.nf'
-
-workflow test_plasmidfinder {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    PLASMIDFINDER ( input )
-}
diff --git a/tests/modules/plasmidfinder/test.yml b/tests/modules/plasmidfinder/test.yml
deleted file mode 100644
index 91e90c75d90..00000000000
--- a/tests/modules/plasmidfinder/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: plasmidfinder test_plasmidfinder
-  command: nextflow run ./tests/modules/plasmidfinder -entry test_plasmidfinder -c ./tests/config/nextflow.config  -c ./tests/modules/plasmidfinder/nextflow.config
-  tags:
-    - plasmidfinder
-  files:
-    - path: output/plasmidfinder/test-hit_in_genome_seq.fsa
-    - path: output/plasmidfinder/test-plasmid_seqs.fsa
-    - path: output/plasmidfinder/test.json
-      contains: ["plasmidfinder", "filename", "results", "Rep_trans"]
-    - path: output/plasmidfinder/test.tsv
-      contains: ["Database", "Accession", "Query"]
-    - path: output/plasmidfinder/test.txt
-      contains: ["plasmidfinder", "Results", "Contig", "found"]
diff --git a/tests/modules/plasmidid/main.nf b/tests/modules/plasmidid/main.nf
deleted file mode 100644
index 52d25a91014..00000000000
--- a/tests/modules/plasmidid/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PLASMIDID } from '../../../modules/plasmidid/main.nf'
-
-workflow test_plasmidid {
-
-    contigs = [ [ id:'test' ], // meta map
-                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
-              ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    PLASMIDID ( contigs, fasta )
-}
diff --git a/tests/modules/plasmidid/test.yml b/tests/modules/plasmidid/test.yml
deleted file mode 100644
index cd0528cb1b6..00000000000
--- a/tests/modules/plasmidid/test.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-- name: plasmidid
-  command: nextflow run ./tests/modules/plasmidid -entry test_plasmidid -c ./tests/config/nextflow.config -c ./tests/modules/plasmidid/nextflow.config
-  tags:
-    - plasmidid
-  files:
-    - path: output/plasmidid/test/data/database_reconstruct_test.length
-      md5sum: a57c401f27ae5133823fb09fb21c8a3c
-    - path: output/plasmidid/test/data/test.coverage_adapted_clustered_ac
-      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
-    - path: output/plasmidid/test/data/test.err
-      md5sum: 011108fd8b0bb4a4c0b5b2cf46452a90
-    - path: output/plasmidid/test/data/test.fna
-      md5sum: 503a5e1d4654bb2df19420e211070db3
-    - path: output/plasmidid/test/data/test.gbk
-    - path: output/plasmidid/test/data/test.gff
-      md5sum: 3ed8912ee9b0712ca491fa78ff5f4da1
-    - path: output/plasmidid/test/data/test.karyotype_individual.txt
-      md5sum: aaf0f5bfe297fb9846ace761ff018d22
-    - path: output/plasmidid/test/data/test.karyotype_summary.txt
-      md5sum: aaf0f5bfe297fb9846ace761ff018d22
-    - path: output/plasmidid/test/data/test.plasmids.blast
-      md5sum: 241045ea62156c1ca9bc1eb734ac9526
-    - path: output/plasmidid/test/data/test.plasmids.blast.links
-      md5sum: a44d6aa388b582da8ad53c5b49467b8f
-    - path: output/plasmidid/test/data/test.plasmids.complete
-      md5sum: fbc7235285dbb963b07561dd6972a883
-    - path: output/plasmidid/test/database/test.fna
-      md5sum: 6b843fe652b4369addb382f61952c3dd
-    - path: output/plasmidid/test/database/test.gbk
-    - path: output/plasmidid/test/database/test.gff
-      md5sum: 7e65da147d0a413020b0d92b7b03ffcd
-    - path: output/plasmidid/test/fasta_files/MT192765.1_term.fasta
-      md5sum: 8a8537dd3b21e6905f9367b51c3b3074
-    - path: output/plasmidid/test/images/test_individual.circos.conf
-      md5sum: f74467ab77232e2b342e2bd408897b12
-    - path: output/plasmidid/test/images/test_MT192765.1_individual.circos.conf
-      md5sum: 548443ba0a68065a69383fe32b226780
-    - path: output/plasmidid/test/images/test_summary.circos.conf
-      md5sum: e59dc3b77ee610a48b79230da705aba0
-    - path: output/plasmidid/test/images/test_MT192765.1.png
-    - path: output/plasmidid/test/images/test_summary.png
-    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.clusters.tab
-      md5sum: cf75e4418631796bb4675129b575915d
-    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.representative.fasta
-      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
-    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.representative.fasta.blast.tmp.ndb
-      md5sum: f67f8be1e00eb7d3512869071fb4c2c2
-    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.fasta
-      md5sum: c7fe0e9e9a94d98d7f85a7be99c032fd
-    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.mash.distances.tab
-      md5sum: fd5408c3c2f8f68dc01e0123bb6a9079
-    - path: output/plasmidid/test/logs/draw_circos_images.log
-    - path: output/plasmidid/test/logs/plasmidID.log
-    - path: output/plasmidid/test/test_final_results.html
-    - path: output/plasmidid/test/test_final_results.tab
diff --git a/tests/modules/plink/extract/main.nf b/tests/modules/plink/extract/main.nf
deleted file mode 100644
index 6beb0469284..00000000000
--- a/tests/modules/plink/extract/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PLINK_VCF     } from '../../../../modules/plink/vcf/main.nf'
-include { PLINK_EXTRACT } from '../../../../modules/plink/extract/main.nf'
-
-workflow test_plink_extract {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true) 
-    ]
-
-    PLINK_VCF ( input )
-    
-    PLINK_VCF.out.bim
-        .splitText(file: 'variants.keep', keepHeader: false, by: 10)
-        .first()
-        .set { ch_variants }
-
-    PLINK_VCF.out.bed
-        .concat(PLINK_VCF.out.bim, PLINK_VCF.out.fam.concat(ch_variants))
-        .groupTuple()
-        .map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
-        .set { ch_extract }
-
-    PLINK_EXTRACT ( ch_extract )
-}
diff --git a/tests/modules/plink/extract/test.yml b/tests/modules/plink/extract/test.yml
deleted file mode 100644
index 87cf82ccf19..00000000000
--- a/tests/modules/plink/extract/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: plink extract test_plink_extract
-  command: nextflow run ./tests/modules/plink/extract -entry test_plink_extract -c ./tests/config/nextflow.config -c ./tests/modules/plink/extract/nextflow.config
-  tags:
-    - plink
-    - plink/extract
-  files:
-    - path: output/plink/test.bed
-      md5sum: 9121010aba9905eee965e96bc983611d
-    - path: output/plink/test.bim
-      md5sum: 510ec606219ee5daaf5c207cb01554bf
-    - path: output/plink/test.extract.bed
-      md5sum: 9e02f7143bcc756a51f20d50ca7f8032
-    - path: output/plink/test.extract.bim
-      md5sum: 63d190aea4094aa5d042aacd63397f94
-    - path: output/plink/test.extract.fam
-      md5sum: c499456df4da78792ef29934ef3cd47d
-    - path: output/plink/test.fam
-      md5sum: c499456df4da78792ef29934ef3cd47d
diff --git a/tests/modules/plink/vcf/main.nf b/tests/modules/plink/vcf/main.nf
deleted file mode 100644
index 4dac8978247..00000000000
--- a/tests/modules/plink/vcf/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf'
-
-workflow test_plink_vcf {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
-
-    PLINK_VCF ( input )
-}
diff --git a/tests/modules/plink/vcf/test.yml b/tests/modules/plink/vcf/test.yml
deleted file mode 100644
index 9042d14a161..00000000000
--- a/tests/modules/plink/vcf/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: plink vcf test_plink_vcf
-  command: nextflow run ./tests/modules/plink/vcf -entry test_plink_vcf -c ./tests/config/nextflow.config -c ./tests/modules/plink/vcf/nextflow.config
-  tags:
-    - plink
-    - plink/vcf
-  files:
-    - path: output/plink/test.bed
-      md5sum: 55c3ab2636212911b5f952ef6f5d855c
-    - path: output/plink/test.bim
-      md5sum: 54164b6f103e152de05712c6bb317db8
-    - path: output/plink/test.fam
-      md5sum: 22d32d7daa3ae6b819a24895e82b2a70
diff --git a/tests/modules/plink2/extract/main.nf b/tests/modules/plink2/extract/main.nf
deleted file mode 100644
index a72e153c9cc..00000000000
--- a/tests/modules/plink2/extract/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PLINK2_VCF     } from '../../../../modules/plink2/vcf/main.nf'
-include { PLINK2_EXTRACT } from '../../../../modules/plink2/extract/main.nf'
-
-workflow test_plink2_extract {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
-    ]
-    PLINK2_VCF ( input )
-
-    PLINK2_VCF.out.pvar
-        .splitText(file: 'variants.keep', keepHeader: false, by: 10)
-        .last()
-        .set { ch_variants }
-
-    ch_variants.view()
-
-    PLINK2_VCF.out.pgen
-        .concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar.concat(ch_variants))
-        .groupTuple()
-        .map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
-        .set { ch_extract }
-
-    PLINK2_EXTRACT ( ch_extract )
-}
diff --git a/tests/modules/plink2/extract/test.yml b/tests/modules/plink2/extract/test.yml
deleted file mode 100644
index 737ca215cd8..00000000000
--- a/tests/modules/plink2/extract/test.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-- name: plink2 extract test_plink2_extract
-  command: nextflow run tests/modules/plink2/extract -entry test_plink2_extract -c tests/config/nextflow.config
-  tags:
-    - plink2/extract
-    - plink2
-  files:
-    - path: output/plink2/test.extract.pgen
-      md5sum: 785e729a293ecabb0d39394865316bda
-    - path: output/plink2/test.extract.psam
-      md5sum: e6c714488754cb8448c3dfda08c4c0ea
-    - path: output/plink2/test.extract.pvar.zst
-      md5sum: 076767e6695e681115eabb924a447ee9
-    - path: output/plink2/test.pgen
-      md5sum: fac12ca9041d6950f6b7d60ac2120721
-    - path: output/plink2/test.psam
-      md5sum: e6c714488754cb8448c3dfda08c4c0ea
-    - path: output/plink2/test.pvar
-      md5sum: ff9e44f8e5f4035d8cf2bfe7be6755b3
-    - path: output/plink2/versions.yml
-      md5sum: c477b7c9f6e39b89710fe1a0bceee50d
diff --git a/tests/modules/plink2/score/main.nf b/tests/modules/plink2/score/main.nf
deleted file mode 100644
index 6a09e8294b9..00000000000
--- a/tests/modules/plink2/score/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
-include { PLINK2_SCORE } from '../../../../modules/plink2/score/main.nf'
-
-workflow test_plink2_score {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
-    ]
-    PLINK2_VCF ( input )
-
-    scorefile = file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_score'], checkIfExists: true)
-
-    PLINK2_VCF.out.pgen
-        .concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar)
-        .groupTuple()
-        .map { it.flatten() }
-        .set { ch_target_genome }
-
-    PLINK2_SCORE ( ch_target_genome, scorefile )
-}
diff --git a/tests/modules/plink2/score/test.yml b/tests/modules/plink2/score/test.yml
deleted file mode 100644
index 7993cb3406d..00000000000
--- a/tests/modules/plink2/score/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: plink2 score test_plink2_score
-  command: nextflow run tests/modules/plink2/score -entry test_plink2_score -c tests/config/nextflow.config
-  tags:
-    - plink2
-    - plink2/score
-  files:
-    - path: output/plink2/test.pgen
-      md5sum: fac12ca9041d6950f6b7d60ac2120721
-    - path: output/plink2/test.psam
-      md5sum: e6c714488754cb8448c3dfda08c4c0ea
-    - path: output/plink2/test.pvar.zst
-      md5sum: 98d59e9779a8b62d5032cd98b642a63b
-    - path: output/plink2/test.sscore
-      md5sum: 97bde840f69febd65f2c00e9243126e9
-    - path: output/plink2/versions.yml
-      md5sum: 71499ab14e1583c88ced3a7a4f05bfa7
diff --git a/tests/modules/plink2/vcf/main.nf b/tests/modules/plink2/vcf/main.nf
deleted file mode 100644
index 08d7dc611ae..00000000000
--- a/tests/modules/plink2/vcf/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
-
-workflow test_plink2_vcf {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
-
-    PLINK2_VCF ( input )
-}
diff --git a/tests/modules/plink2/vcf/test.yml b/tests/modules/plink2/vcf/test.yml
deleted file mode 100644
index d354af482b0..00000000000
--- a/tests/modules/plink2/vcf/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: plink2 vcf test_plink2_vcf
-  command: nextflow run tests/modules/plink2/vcf -entry test_plink2_vcf -c tests/config/nextflow.config
-  tags:
-    - plink2
-    - plink2/vcf
-  files:
-    - path: output/plink2/test.pgen
-      md5sum: d66d3cd4a6c9cca1a4073d7f4b277041
-    - path: output/plink2/test.psam
-      md5sum: dc3b77d7753a7bed41734323e3549b10
-    - path: output/plink2/test.pvar.zst
-      md5sum: b53cccb83e024a39789af5eab8de1c28
-    - path: output/plink2/versions.yml
-      md5sum: 82ada74bc81473b7cba377f696acf54c
diff --git a/tests/modules/pmdtools/filter/main.nf b/tests/modules/pmdtools/filter/main.nf
deleted file mode 100644
index f1b2b4d3fb1..00000000000
--- a/tests/modules/pmdtools/filter/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PMDTOOLS_FILTER } from '../../../../modules/pmdtools/filter/main.nf'
-
-workflow test_pmdtools_filter {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
-              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]]
-    threshold = 3
-    reference = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
-    PMDTOOLS_FILTER ( input, threshold, reference )
-}
diff --git a/tests/modules/pmdtools/filter/test.yml b/tests/modules/pmdtools/filter/test.yml
deleted file mode 100644
index a7ebefbec57..00000000000
--- a/tests/modules/pmdtools/filter/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: pmdtools filter
-  command: nextflow run ./tests/modules/pmdtools/filter -entry test_pmdtools_filter -c ./tests/config/nextflow.config -c ./tests/modules/pmdtools/filter/nextflow.config
-  tags:
-    - pmdtools
-    - pmdtools/filter
-  files:
-    - path: output/pmdtools/test.bam
-      md5sum: 0fa64cb87d0439d4482938a4b6990b9d
diff --git a/tests/modules/porechop/main.nf b/tests/modules/porechop/main.nf
deleted file mode 100644
index f20b7a6efd5..00000000000
--- a/tests/modules/porechop/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PORECHOP } from '../../../modules/porechop/main.nf'
-
-workflow test_porechop {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-                file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
-
-    PORECHOP ( input )
-}
diff --git a/tests/modules/porechop/test.yml b/tests/modules/porechop/test.yml
deleted file mode 100644
index fe2e2733bbc..00000000000
--- a/tests/modules/porechop/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: porechop test_porechop
-  command: nextflow run ./tests/modules/porechop -entry test_porechop -c ./tests/config/nextflow.config  -c ./tests/modules/porechop/nextflow.config
-  tags:
-    - porechop
-  files:
-    - path: output/porechop/test_porechop.fastq.gz
-      md5sum: 08f314ae9f162c8dcc27e5b513d2064d
-    - path: output/porechop/test_porechop.log
-      contains: ["Saving trimmed reads to file"]
diff --git a/tests/modules/preseq/ccurve/main.nf b/tests/modules/preseq/ccurve/main.nf
deleted file mode 100644
index 59149563c4f..00000000000
--- a/tests/modules/preseq/ccurve/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PRESEQ_CCURVE } from '../../../../modules/preseq/ccurve/main.nf'
-
-workflow test_preseq_ccurve_single_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
-    ]
-
-    PRESEQ_CCURVE ( input )
-}
-
-workflow test_preseq_ccurve_paired_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    PRESEQ_CCURVE ( input )
-}
diff --git a/tests/modules/preseq/ccurve/test.yml b/tests/modules/preseq/ccurve/test.yml
deleted file mode 100644
index c94dc978445..00000000000
--- a/tests/modules/preseq/ccurve/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: preseq ccurve single-end
-  command: nextflow run ./tests/modules/preseq/ccurve -entry test_preseq_ccurve_single_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/ccurve/nextflow.config
-  tags:
-    - preseq
-    - preseq/ccurve
-  files:
-    - path: output/preseq/test.c_curve.txt
-      md5sum: cf4743abdd355595d6ec1fb3f38e66e5
-    - path: output/preseq/test.command.log
-
-- name: preseq ccurve paired-end
-  command: nextflow run ./tests/modules/preseq/ccurve -entry test_preseq_ccurve_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/ccurve/nextflow.config
-  tags:
-    - preseq
-    - preseq/ccurve
-  files:
-    - path: output/preseq/test.c_curve.txt
-      md5sum: cf4743abdd355595d6ec1fb3f38e66e5
-    - path: output/preseq/test.command.log
diff --git a/tests/modules/preseq/lcextrap/main.nf b/tests/modules/preseq/lcextrap/main.nf
deleted file mode 100644
index 4bbbd146c24..00000000000
--- a/tests/modules/preseq/lcextrap/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PRESEQ_LCEXTRAP } from '../../../../modules/preseq/lcextrap/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_preseq_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true) ]
-            ]
-    PRESEQ_LCEXTRAP ( input )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_preseq_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true) ]
-            ]
-
-    PRESEQ_LCEXTRAP ( input )
-}
-
diff --git a/tests/modules/preseq/lcextrap/test.yml b/tests/modules/preseq/lcextrap/test.yml
deleted file mode 100644
index f5b5aea4779..00000000000
--- a/tests/modules/preseq/lcextrap/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: preseq lcextrap single-end
-  command: nextflow run ./tests/modules/preseq/lcextrap -entry test_preseq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/lcextrap/nextflow.config
-  tags:
-    - preseq
-    - preseq/lcextrap
-  files:
-    - path: output/preseq/test.lc_extrap.txt
-      md5sum: 1fa5cdd601079329618f61660bee00de
-    - path: output/preseq/test.command.log
-
-- name: preseq lcextrap paired-end
-  command: nextflow run ./tests/modules/preseq/lcextrap -entry test_preseq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/lcextrap/nextflow.config
-  tags:
-    - preseq
-    - preseq/lcextrap
-  files:
-    - path: output/preseq/test.lc_extrap.txt
-      md5sum: 10e5ea860e87fb6f5dc10f4f20c62040
-    - path: output/preseq/test.command.log
diff --git a/tests/modules/prinseqplusplus/main.nf b/tests/modules/prinseqplusplus/main.nf
deleted file mode 100644
index d6ee3be9e59..00000000000
--- a/tests/modules/prinseqplusplus/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PRINSEQPLUSPLUS } from '../../../modules/prinseqplusplus/main.nf'
-
-workflow test_prinseqplusplus_single_end {
-
-        input = [ [ id:'test', single_end:true ], // meta map
-            [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-        ]
-
-    PRINSEQPLUSPLUS ( input )
-}
-
-workflow test_prinseqplusplus_paired_end {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-            [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-        ]
-
-    PRINSEQPLUSPLUS ( input )
-}
diff --git a/tests/modules/prinseqplusplus/test.yml b/tests/modules/prinseqplusplus/test.yml
deleted file mode 100644
index e034febb3ac..00000000000
--- a/tests/modules/prinseqplusplus/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: prinseqplusplus test_prinseqplusplus_single_end
-  command: nextflow run tests/modules/prinseqplusplus -entry test_prinseqplusplus_single_end -c tests/config/nextflow.config
-  tags:
-    - prinseqplusplus
-  files:
-    - path: output/prinseqplusplus/test.log
-      contains:
-        - "reads removed by -lc_entropy"
-    - path: output/prinseqplusplus/test_bad_out.fastq.gz
-    - path: output/prinseqplusplus/test_good_out.fastq.gz
-    - path: output/prinseqplusplus/versions.yml
-
-- name: prinseqplusplus test_prinseqplusplus_paired_end
-  command: nextflow run tests/modules/prinseqplusplus -entry test_prinseqplusplus_paired_end -c tests/config/nextflow.config
-  tags:
-    - prinseqplusplus
-  files:
-    - path: output/prinseqplusplus/test.log
-      contains:
-        - "reads removed by -lc_entropy"
-    - path: output/prinseqplusplus/test_bad_out_R1.fastq.gz
-    - path: output/prinseqplusplus/test_bad_out_R2.fastq.gz
-    - path: output/prinseqplusplus/test_good_out_R1.fastq.gz
-    - path: output/prinseqplusplus/test_good_out_R2.fastq.gz
-    - path: output/prinseqplusplus/test_single_out_R1.fastq.gz
-    - path: output/prinseqplusplus/test_single_out_R2.fastq.gz
-    - path: output/prinseqplusplus/versions.yml
diff --git a/tests/modules/prodigal/main.nf b/tests/modules/prodigal/main.nf
deleted file mode 100644
index 6e2820151a3..00000000000
--- a/tests/modules/prodigal/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PRODIGAL } from '../../../modules/prodigal/main.nf'
-
-workflow test_prodigal {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
-            ]
-
-    PRODIGAL ( input , "gff")
-}
diff --git a/tests/modules/prodigal/test.yml b/tests/modules/prodigal/test.yml
deleted file mode 100644
index 7f0ab88c32e..00000000000
--- a/tests/modules/prodigal/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: prodigal test_prodigal
-  command: nextflow run ./tests/modules/prodigal -entry test_prodigal -c ./tests/config/nextflow.config -c ./tests/modules/prodigal/nextflow.config
-  tags:
-    - prodigal
-  files:
-    - path: output/prodigal/test.fna
-      md5sum: 1bc8a05bcb72a3c324f5e4ffaa716d3b
-    - path: output/prodigal/test.gff
-      md5sum: 612c2724c2891c63350f171f74165757
-    - path: output/prodigal/test.faa
-      md5sum: 7168b854103f3586ccfdb71a44c389f7
-    - path: output/prodigal/test_all.txt
-      md5sum: e6d6c50f0c39e5169f84ae3c90837fa9
diff --git a/tests/modules/prokka/main.nf b/tests/modules/prokka/main.nf
deleted file mode 100644
index 97e94ca8beb..00000000000
--- a/tests/modules/prokka/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PROKKA } from '../../../modules/prokka/main.nf'
-
-workflow test_prokka {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-            ]
-    
-    PROKKA ( input, [], [] )
-}
diff --git a/tests/modules/prokka/test.yml b/tests/modules/prokka/test.yml
deleted file mode 100644
index 92f813a71ed..00000000000
--- a/tests/modules/prokka/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: prokka
-  command: nextflow run ./tests/modules/prokka -entry test_prokka -c ./tests/config/nextflow.config -c ./tests/modules/prokka/nextflow.config
-  tags:
-    - prokka
-  files:
-    - path: output/prokka/test/test.err
-      md5sum: b3daedc646fddd422824e2b3e5e9229d
-    - path: output/prokka/test/test.faa
-      md5sum: a4ceda83262b3c222a6b1f508fb9e24b
-    - path: output/prokka/test/test.ffn
-      md5sum: 80f474b5367b7ea5ed23791935f65e34
-    - path: output/prokka/test/test.fna
-      md5sum: 787307f29a263e5657cc276ebbf7e2b3
-    - path: output/prokka/test/test.fsa
-      md5sum: 71bbefcb7f12046bcd3263f58cfd5404
-    - path: output/prokka/test/test.gff
-      md5sum: 5dbfb8fcf2db020564c16045976a0933
-    - path: output/prokka/test/test.tbl
-      md5sum: d8f816a066ced94b62d9618b13fb8add
-    - path: output/prokka/test/test.tsv
-      md5sum: da7c720c3018c5081d6a70b517b7d450
-    - path: output/prokka/test/test.txt
-      md5sum: b40e485ffc8eaf1feacf8d79d9751a33
-    # Contain time stamps
-    - path: output/prokka/test/test.gbk
-    - path: output/prokka/test/test.log
-    - path: output/prokka/test/test.sqn
diff --git a/tests/modules/pycoqc/main.nf b/tests/modules/pycoqc/main.nf
deleted file mode 100644
index c8a8ee2c15f..00000000000
--- a/tests/modules/pycoqc/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PYCOQC } from '../../../modules/pycoqc/main.nf'
-
-workflow test_pycoqc {
-
-    input = [ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ]
-
-    PYCOQC ( input )
-}
diff --git a/tests/modules/pycoqc/test.yml b/tests/modules/pycoqc/test.yml
deleted file mode 100644
index becd911bf2b..00000000000
--- a/tests/modules/pycoqc/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: pycoqc
-  command: nextflow run ./tests/modules/pycoqc -entry test_pycoqc -c ./tests/config/nextflow.config -c ./tests/modules/pycoqc/nextflow.config
-  tags:
-    - pycoqc
-  files:
-    - path: output/pycoqc/pycoqc.json
-      contains:
-        - '"reads_number": 100,'
-        - '"bases_number": 1160,'
-        - '"N50": 12,'
-    - path: output/pycoqc/pycoqc.html
diff --git a/tests/modules/pydamage/analyze/main.nf b/tests/modules/pydamage/analyze/main.nf
deleted file mode 100644
index 920a4201953..00000000000
--- a/tests/modules/pydamage/analyze/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PYDAMAGE_ANALYZE } from '../../../../modules/pydamage/analyze/main.nf'
-
-workflow test_pydamage {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-    PYDAMAGE_ANALYZE ( input )
-}
diff --git a/tests/modules/pydamage/analyze/test.yml b/tests/modules/pydamage/analyze/test.yml
deleted file mode 100644
index 9d22f20e391..00000000000
--- a/tests/modules/pydamage/analyze/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: pydamage analyze test workflow
-  command: nextflow run ./tests/modules/pydamage/analyze -entry test_pydamage -c ./tests/config/nextflow.config -c ./tests/modules/pydamage/analyze/nextflow.config
-  tags:
-    - pydamage
-    - pydamage/analyze
-  files:
-    - path: output/pydamage/pydamage_results/pydamage_results.csv
-      md5sum: 37ee6b4dee6890fd2ec8550337f21ac9
diff --git a/tests/modules/pydamage/filter/main.nf b/tests/modules/pydamage/filter/main.nf
deleted file mode 100644
index dac03e7879a..00000000000
--- a/tests/modules/pydamage/filter/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PYDAMAGE_ANALYZE } from '../../../../modules/pydamage/analyze/main.nf'
-include { PYDAMAGE_FILTER } from '../../../../modules/pydamage/filter/main.nf'
-
-workflow test_pydamage {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-
-    PYDAMAGE_ANALYZE ( input )
-    PYDAMAGE_FILTER (PYDAMAGE_ANALYZE.out.csv)
-}
diff --git a/tests/modules/pydamage/filter/test.yml b/tests/modules/pydamage/filter/test.yml
deleted file mode 100644
index b6738e3dae2..00000000000
--- a/tests/modules/pydamage/filter/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: pydamage filter test workflow
-  command: nextflow run ./tests/modules/pydamage/filter -entry test_pydamage -c ./tests/config/nextflow.config -c ./tests/modules/pydamage/filter/nextflow.config
-  tags:
-    - pydamage
-    - pydamage/filter
-  files:
-    - path: output/pydamage/pydamage_results/pydamage_filtered_results.csv
-      md5sum: 9f297233cf4932d7d7e52cc72d4727dc
-    - path: output/pydamage/pydamage_results/pydamage_results.csv
-      md5sum: 37ee6b4dee6890fd2ec8550337f21ac9
diff --git a/tests/modules/qcat/main.nf b/tests/modules/qcat/main.nf
deleted file mode 100644
index 8a5cdd6d8fd..00000000000
--- a/tests/modules/qcat/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { QCAT } from '../../../modules/qcat/main.nf'
-
-workflow test_qcat {
-    input = [ [ id:'test' ], // meta map
-              [ file("https://github.com/nf-core/test-datasets/raw/nanoseq/fastq/nondemultiplexed/sample_nobc_dx.fastq.gz", checkIfExists: true) ]
-            ]
-    barcode_kit = 'NBD103/NBD104'
-
-    QCAT ( input, barcode_kit )
-}
diff --git a/tests/modules/qcat/test.yml b/tests/modules/qcat/test.yml
deleted file mode 100644
index 04ddacff015..00000000000
--- a/tests/modules/qcat/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: qcat
-  command: nextflow run ./tests/modules/qcat -entry test_qcat -c ./tests/config/nextflow.config -c ./tests/modules/qcat/nextflow.config
-  tags:
-    - qcat
-  files:
-    - path: ./output/qcat/fastq/barcode06.fastq.gz
-    - path: ./output/qcat/fastq/barcode12.fastq.gz
-    - path: ./output/qcat/fastq/none.fastq.gz
diff --git a/tests/modules/qualimap/bamqc/main.nf b/tests/modules/qualimap/bamqc/main.nf
deleted file mode 100644
index 623634e4737..00000000000
--- a/tests/modules/qualimap/bamqc/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { QUALIMAP_BAMQC } from '../../../../modules/qualimap/bamqc/main.nf'
-
-workflow test_qualimap_bamqc {
-    input   = [ [ id:'test', single_end:false ], // meta map
-                [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-              ]
-    gff     = []
-
-    QUALIMAP_BAMQC ( input, gff )
-}
diff --git a/tests/modules/qualimap/bamqc/test.yml b/tests/modules/qualimap/bamqc/test.yml
deleted file mode 100644
index 41c4199e2c6..00000000000
--- a/tests/modules/qualimap/bamqc/test.yml
+++ /dev/null
@@ -1,81 +0,0 @@
-- name: qualimap bamqc test workflow
-  command: nextflow run ./tests/modules/qualimap/bamqc -entry test_qualimap_bamqc -c ./tests/config/nextflow.config -c ./tests/modules/qualimap/bamqc/nextflow.config
-  tags:
-    - qualimap
-    - qualimap/bamqc
-  files:
-    - path: ./output/qualimap/test/qualimapReport.html
-    - path: ./output/qualimap/test/genome_results.txt
-      md5sum: 5ec87ea86ad734d512c8c76fe8eb37b1
-    - path: ./output/qualimap/test/css/plus.png
-      md5sum: 0125e6faa04e2cf0141a2d599d3bb220
-    - path: ./output/qualimap/test/css/down-pressed.png
-      md5sum: ebe8979581eda700fb234a73c661a4b9
-    - path: ./output/qualimap/test/css/underscore.js
-      md5sum: db5ba047a66617d4cd3e8c5099cc51db
-    - path: ./output/qualimap/test/css/ajax-loader.gif
-      md5sum: ae6667053ad118020b8e68ccf307b519
-    - path: ./output/qualimap/test/css/searchtools.js
-      md5sum: d550841adeedc8ed47c40ee607620937
-    - path: ./output/qualimap/test/css/up.png
-    - path: ./output/qualimap/test/css/file.png
-    - path: ./output/qualimap/test/css/up-pressed.png
-    - path: ./output/qualimap/test/css/down.png
-    - path: ./output/qualimap/test/css/minus.png
-    - path: ./output/qualimap/test/css/bgtop.png
-    - path: ./output/qualimap/test/css/comment.png
-    - path: ./output/qualimap/test/css/basic.css
-      md5sum: 25b2823342c0604924a2870eeb4e7e94
-    - path: ./output/qualimap/test/css/report.css
-      md5sum: 7a5f09eaf7c176f966f4e8854168b812
-    - path: ./output/qualimap/test/css/pygments.css
-      md5sum: d625a0adb949f181bd0d3f1432b0fa7f
-    - path: ./output/qualimap/test/css/comment-close.png
-    - path: ./output/qualimap/test/css/doctools.js
-      md5sum: 5ff571aa60e63f69c1890283e240ff8d
-    - path: ./output/qualimap/test/css/comment-bright.png
-    - path: ./output/qualimap/test/css/qualimap_logo_small.png
-    - path: ./output/qualimap/test/css/websupport.js
-      md5sum: 9e61e1e8a7433c56bd7e5a615affcf85
-    - path: ./output/qualimap/test/css/agogo.css
-      md5sum: bd757b1a7ce6fdc0288ba148680f4583
-    - path: ./output/qualimap/test/css/bgfooter.png
-    - path: ./output/qualimap/test/css/jquery.js
-      md5sum: 10092eee563dec2dca82b77d2cf5a1ae
-    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_histogram.txt
-      md5sum: 749630484c5b24b4973ad613d85a2341
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt
-      md5sum: dbcb28c1ab2f0c78f6e803a24a2a695f
-    - path: ./output/qualimap/test/raw_data_qualimapReport/genome_fraction_coverage.txt
-      md5sum: d5ba8feb5418091d6e00e4ad0c865cf1
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_histogram.txt
-      md5sum: 8b638330338758c156200a37602c53d5
-    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_across_reference.txt
-      md5sum: dc553f58b5e361b9e5c894f118347bc1
-    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_histogram.txt
-      md5sum: f57a631c72f2373ca4d3f6c8deb1ad6d
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_across_reference.txt
-      md5sum: 42223637499a2221cf99b4dd08badb6f
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
-      md5sum: c7c7db9fa3febd58b27e95cff857df90
-    - path: ./output/qualimap/test/raw_data_qualimapReport/homopolymer_indels.txt
-      md5sum: ba7484d97ab505ab8642d73074afef04
-    - path: ./output/qualimap/test/raw_data_qualimapReport/duplication_rate_histogram.txt
-      md5sum: 7875c892eb75a6da5115b10e3b2b767e
-    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_across_reference.txt
-      md5sum: fbabd3fea386712fa453e7c9825107af
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_clipping_profile.txt
-      md5sum: e199f6930d4bda5f9e871cb5c628a69a
-    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_content_per_read_position.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_gc_content_per_window.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_0to50_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_uniq_read_starts_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_across_reference.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_across_reference.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_homopolymer_indels.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_across_reference.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_clipping_profile.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_quotes.png
diff --git a/tests/modules/qualimap/bamqccram/main.nf b/tests/modules/qualimap/bamqccram/main.nf
deleted file mode 100644
index e4d8433e59b..00000000000
--- a/tests/modules/qualimap/bamqccram/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { QUALIMAP_BAMQCCRAM } from '../../../../modules/qualimap/bamqccram/main.nf'
-
-workflow test_qualimap_bamqc {
-    input   = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
-              ]
-    gff     = []
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    QUALIMAP_BAMQCCRAM ( input, gff, fasta, fai )
-}
diff --git a/tests/modules/qualimap/bamqccram/test.yml b/tests/modules/qualimap/bamqccram/test.yml
deleted file mode 100644
index 49cf9b24db5..00000000000
--- a/tests/modules/qualimap/bamqccram/test.yml
+++ /dev/null
@@ -1,80 +0,0 @@
-- name: qualimap bamqccram test_qualimap_bamqc
-  command: nextflow run tests/modules/qualimap/bamqccram -entry test_qualimap_bamqc -c tests/config/nextflow.config
-  tags:
-    - qualimap/bamqccram
-    - qualimap
-  files:
-    - path: ./output/qualimap/test/qualimapReport.html
-    - path: ./output/qualimap/test/genome_results.txt
-      md5sum: 61d8b36507652fd7d7db9583de708161
-    - path: ./output/qualimap/test/css/plus.png
-      md5sum: 0125e6faa04e2cf0141a2d599d3bb220
-    - path: ./output/qualimap/test/css/down-pressed.png
-      md5sum: ebe8979581eda700fb234a73c661a4b9
-    - path: ./output/qualimap/test/css/underscore.js
-      md5sum: db5ba047a66617d4cd3e8c5099cc51db
-    - path: ./output/qualimap/test/css/ajax-loader.gif
-      md5sum: ae6667053ad118020b8e68ccf307b519
-    - path: ./output/qualimap/test/css/searchtools.js
-      md5sum: d550841adeedc8ed47c40ee607620937
-    - path: ./output/qualimap/test/css/up.png
-    - path: ./output/qualimap/test/css/file.png
-    - path: ./output/qualimap/test/css/up-pressed.png
-    - path: ./output/qualimap/test/css/down.png
-    - path: ./output/qualimap/test/css/minus.png
-    - path: ./output/qualimap/test/css/bgtop.png
-    - path: ./output/qualimap/test/css/comment.png
-    - path: ./output/qualimap/test/css/basic.css
-      md5sum: 25b2823342c0604924a2870eeb4e7e94
-    - path: ./output/qualimap/test/css/report.css
-      md5sum: 7a5f09eaf7c176f966f4e8854168b812
-    - path: ./output/qualimap/test/css/pygments.css
-      md5sum: d625a0adb949f181bd0d3f1432b0fa7f
-    - path: ./output/qualimap/test/css/comment-close.png
-    - path: ./output/qualimap/test/css/doctools.js
-      md5sum: 5ff571aa60e63f69c1890283e240ff8d
-    - path: ./output/qualimap/test/css/comment-bright.png
-    - path: ./output/qualimap/test/css/qualimap_logo_small.png
-    - path: ./output/qualimap/test/css/websupport.js
-      md5sum: 9e61e1e8a7433c56bd7e5a615affcf85
-    - path: ./output/qualimap/test/css/agogo.css
-      md5sum: bd757b1a7ce6fdc0288ba148680f4583
-    - path: ./output/qualimap/test/css/bgfooter.png
-    - path: ./output/qualimap/test/css/jquery.js
-      md5sum: 10092eee563dec2dca82b77d2cf5a1ae
-    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_histogram.txt
-      md5sum: b7aeda7558e9b31f027f7dc530df90b8
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt
-      md5sum: 42774c6edd6e36538acbdb6ffbd019c2
-    - path: ./output/qualimap/test/raw_data_qualimapReport/genome_fraction_coverage.txt
-      md5sum: 972a19d4846bf4e93ba32ae3dff5289c
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_histogram.txt
-      md5sum: 4e3918da81202b52395a576f99c1a50f
-    - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_across_reference.txt
-    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_histogram.txt
-      md5sum: 353e74d2a6c4281686c9063de570a64d
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_across_reference.txt
-      md5sum: 9bf33149528be9a0e154e4ba7cb89420
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
-      md5sum: be36d9346a402ba580718497d5075d06
-    - path: ./output/qualimap/test/raw_data_qualimapReport/homopolymer_indels.txt
-      md5sum: b0e19fcfb60e5f039eb0986ef61ab3ed
-    - path: ./output/qualimap/test/raw_data_qualimapReport/duplication_rate_histogram.txt
-      md5sum: 76e80e4ce8d0e01bbd65f1c28f5a92e7
-    - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_across_reference.txt
-      md5sum: b609d33a1f98d24aa84a04e60513cbee
-    - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_clipping_profile.txt
-      md5sum: 7c86f7b225b99bc60008d7e4e55d6adb
-    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_content_per_read_position.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_gc_content_per_window.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_0to50_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_uniq_read_starts_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_across_reference.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_across_reference.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_homopolymer_indels.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_histogram.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_across_reference.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_reads_clipping_profile.png
-    - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_quotes.png
diff --git a/tests/modules/quast/main.nf b/tests/modules/quast/main.nf
deleted file mode 100644
index c879a8a97e1..00000000000
--- a/tests/modules/quast/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { QUAST }   from '../../../modules/quast/main.nf'
-
-workflow test_quast_ref {
-    fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff       = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-    consensus = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
-    use_fasta = true
-    use_gtf   = true
-
-    QUAST ( consensus, fasta, gff, use_fasta, use_gtf )
-}
-
-workflow test_quast_noref {
-    fasta     = file('fasta_dummy')
-    gff       = file('gff_dummy')
-    consensus = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    use_fasta = false
-    use_gtf   = false
-
-    QUAST ( consensus, fasta, gff, use_fasta, use_gtf )
-}
diff --git a/tests/modules/quast/test.yml b/tests/modules/quast/test.yml
deleted file mode 100644
index beb895f3c66..00000000000
--- a/tests/modules/quast/test.yml
+++ /dev/null
@@ -1,107 +0,0 @@
-- name: quast with reference
-  command: nextflow run ./tests/modules/quast -entry test_quast_ref -c ./tests/config/nextflow.config -c ./tests/modules/quast/nextflow.config
-  tags:
-    - quast
-  files:
-    - path: ./output/quast/report.tsv
-    - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 1dacbc04dfea073cbd74488d8b3cf821
-    - path: ./output/quast/quast/transposed_report.tex
-      md5sum: 8d74e5b3d7967820b0e61acdeeee6dcb
-    - path: ./output/quast/quast/icarus.html
-    - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: c0a0d2f998087b307f1a372ed31f5cde
-    - path: ./output/quast/quast/report.tex
-      md5sum: 881df38fdcd5ce2a7b78ac3cbfebbde1
-    - path: ./output/quast/quast/report.txt
-      md5sum: dd24fa9b6f95676006dc0928130d7d0b
-    - path: ./output/quast/quast/report.tsv
-      md5sum: f9b9f817bde917c1672a17ad1d072d6c
-    - path: ./output/quast/quast/report.html
-    - path: ./output/quast/quast/report.pdf
-    - path: ./output/quast/quast/quast.log
-    - path: ./output/quast/quast/genome_stats/transcriptome_genomic_features_any.txt
-      md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
-    - path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
-    - path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
-    - path: ./output/quast/quast/genome_stats/genome_info.txt
-      md5sum: d0193b322079565dc78608291e9c44d1
-    - path: ./output/quast/quast/genome_stats/transcriptome_gaps.txt
-      md5sum: c52381f09ea40b6141be5232494727b6
-    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
-    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
-    - path: ./output/quast/quast/basic_stats/transcriptome_GC_content_plot.pdf
-    - path: ./output/quast/quast/basic_stats/gc.icarus.txt
-      md5sum: bdf3e7481880ee7dafbd53add5291da1
-    - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
-    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
-    - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
-    - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
-    - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.mis_contigs.info
-    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.unaligned.info
-      md5sum: a8505cf206bf53ca369f7e3073fee587
-    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
-      md5sum: d778f337899736cc62ed837b739b375c
-    - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
-      md5sum: 8b9a6d675a41bab6bf344dde2a20a939
-    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stdout
-    - path: ./output/quast/quast/contigs_reports/all_alignments_transcriptome.tsv
-      md5sum: c247152eb82b361106492642fd796e2c
-    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
-      md5sum: ec1f7a1d1fb4a1b465057cf897b90b51
-    - path: ./output/quast/quast/contigs_reports/transcriptome.mis_contigs.fa
-    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
-      md5sum: fdb440c653e2f0306286798cacceaadb
-    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
-      md5sum: 81d9597314356363a6b4e0d67027345a
-    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
-      md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3
-    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
-    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
-      md5sum: a32a09a0df811d1a75fbfe124081d1ca
-    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stderr
-    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
-    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
-      md5sum: e8e3bcb86da2cbd8eded980de80fa45c
-    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords.filtered
-      md5sum: ec9191d0acb5d5bce56b4842551a8598
-    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords
-      md5sum: dda3fc0addc41ecc0d5183dee6f95886
-    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.sf
-    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.unaligned
-    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords_tmp
-      md5sum: e5e26685b36489cbcff906fb07320cde
-    - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
-    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
-
-- name: quast without reference
-  command: nextflow run ./tests/modules/quast -entry test_quast_noref -c ./tests/config/nextflow.config -c ./tests/modules/quast/nextflow.config
-  tags:
-    - quast
-  files:
-    - path: ./output/quast/report.tsv
-      md5sum: 40e321250db460120563bd0449d76fe3
-    - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 28d6c8051278e9fe4e2facef69329b67
-    - path: ./output/quast/quast/transposed_report.tex
-      md5sum: 1cb47c314d9b0c1759375e88f7f91018
-    - path: ./output/quast/quast/icarus.html
-      md5sum: ecc0b67f3d4ff54568dfb83d8ac5911b
-    - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: 5de57a794763ced1015c1e81eaa0b32b
-    - path: ./output/quast/quast/report.tex
-      md5sum: a2c8b9b1811fa948b0ccad1907f8d21b
-    - path: ./output/quast/quast/report.txt
-      md5sum: 97f0306d20056e0efd213de88488b895
-    - path: ./output/quast/quast/report.tsv
-      md5sum: 40e321250db460120563bd0449d76fe3
-    - path: ./output/quast/quast/report.html
-    - path: ./output/quast/quast/report.pdf
-    - path: ./output/quast/quast/quast.log
-    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
-    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
-    - path: ./output/quast/quast/basic_stats/genome_GC_content_plot.pdf
-    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
-    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
diff --git a/tests/modules/racon/main.nf b/tests/modules/racon/main.nf
deleted file mode 100644
index 507d8d8d95d..00000000000
--- a/tests/modules/racon/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RACON } from '../../../modules/racon/main.nf'
-
-workflow test_racon {
-    input = [ [ id:'test', single_end:true ], // meta map
-              file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true),
-              file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
-              file(params.test_data['bacteroides_fragilis']['genome']['genome_paf'], checkIfExists: true)
-            ]
-
-    RACON ( input )
-}
\ No newline at end of file
diff --git a/tests/modules/racon/test.yml b/tests/modules/racon/test.yml
deleted file mode 100644
index 0250fa363a2..00000000000
--- a/tests/modules/racon/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: racon test_racon
-  command: nextflow run ./tests/modules/racon -entry test_racon -c ./tests/config/nextflow.config -c ./tests/modules/racon/nextflow.config
-  tags:
-    - racon
-  files:
-    - path: output/racon/test_assembly_consensus.fasta.gz
-      md5sum: 96a0ba94c6154f6f37b5a76a0207eb6f
diff --git a/tests/modules/rapidnj/main.nf b/tests/modules/rapidnj/main.nf
deleted file mode 100644
index 66d19c3c74e..00000000000
--- a/tests/modules/rapidnj/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RAPIDNJ } from '../../../modules/rapidnj/main.nf'
-
-workflow test_rapidnj {
-    
-    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
-
-    RAPIDNJ ( input )
-}
diff --git a/tests/modules/rapidnj/test.yml b/tests/modules/rapidnj/test.yml
deleted file mode 100644
index 21f6ead97af..00000000000
--- a/tests/modules/rapidnj/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: rapidnj
-  command: nextflow run ./tests/modules/rapidnj -entry test_rapidnj -c ./tests/config/nextflow.config -c ./tests/modules/rapidnj/nextflow.config
-  tags:
-    - rapidnj
-  files:
-    - path: output/rapidnj/alignment.sth
-      md5sum: d2e995c5dd3e3a8212a98414ae5b5de7
-    - path: output/rapidnj/rapidnj_phylogeny.tre
-      md5sum: 775909ea40138101976592cfa1814a1d
diff --git a/tests/modules/rasusa/main.nf b/tests/modules/rasusa/main.nf
deleted file mode 100644
index 8a11627c986..00000000000
--- a/tests/modules/rasusa/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RASUSA } from '../../../modules/rasusa/main.nf'
-
-workflow test_rasusa {
-    input = [ [ id:'test', single_end:false], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-              ],
-              "1000000b"
-            ]
-
-    depth_cutoff = 100
-
-    RASUSA ( input, depth_cutoff )
-}
diff --git a/tests/modules/rasusa/test.yml b/tests/modules/rasusa/test.yml
deleted file mode 100644
index 41c56b67111..00000000000
--- a/tests/modules/rasusa/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: rasusa test_rasusa
-  command: nextflow run ./tests/modules/rasusa -entry test_rasusa -c ./tests/config/nextflow.config -c ./tests/modules/rasusa/nextflow.config
-  tags:
-    - rasusa
-  files:
-    - path: output/rasusa/test_100X_1.fastq.gz
-      md5sum: b9d6f0bef1ef0c21576330d882a7edbb
-    - path: output/rasusa/test_100X_2.fastq.gz
-      md5sum: 479bc4cdce2511a9af219e6c39db8d30
diff --git a/tests/modules/raven/main.nf b/tests/modules/raven/main.nf
deleted file mode 100644
index 01b0451999b..00000000000
--- a/tests/modules/raven/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RAVEN } from '../../../modules/raven/main.nf'
-
-workflow test_raven {
-    
-    input = [ 
-              [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true) ] 
-            ]
-
-    RAVEN ( input )
-}
diff --git a/tests/modules/raven/test.yml b/tests/modules/raven/test.yml
deleted file mode 100644
index bbede6428ad..00000000000
--- a/tests/modules/raven/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: raven test_raven
-  command: nextflow run ./tests/modules/raven -entry test_raven -c ./tests/config/nextflow.config -c ./tests/modules/raven/nextflow.config
-  tags:
-    - raven
-  files:
-    - path: output/raven/test.fasta.gz
-      md5sum: b026b6aba793a9f2bbfb17f732c91926
-    - path: output/raven/test.gfa.gz
-      md5sum: 09053490495f6deb7a3941e559cda626
diff --git a/tests/modules/raxmlng/main.nf b/tests/modules/raxmlng/main.nf
deleted file mode 100644
index 5fad6953b56..00000000000
--- a/tests/modules/raxmlng/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RAXMLNG as RAXMLNG_NO_BOOTSTRAP } from '../../../modules/raxmlng/main.nf'
-include { RAXMLNG as RAXMLNG_BOOTSTRAP    } from '../../../modules/raxmlng/main.nf'
-
-//
-// Test without bootstrapping
-//
-workflow test_raxmlng_no_bootstrap {
-
-    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
-
-    RAXMLNG_NO_BOOTSTRAP ( input )
-}
-
-//
-// Test with bootstrapping
-//
-workflow test_raxmlng_bootstrap {
-
-    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
-
-    RAXMLNG_BOOTSTRAP ( input )
-}
diff --git a/tests/modules/raxmlng/test.yml b/tests/modules/raxmlng/test.yml
deleted file mode 100644
index 8054adac858..00000000000
--- a/tests/modules/raxmlng/test.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- name: raxmlng no_bootstrap
-  command: nextflow run ./tests/modules/raxmlng -entry test_raxmlng_no_bootstrap -c ./tests/config/nextflow.config -c ./tests/modules/raxmlng/nextflow.config
-  tags:
-    - raxmlng
-  files:
-    - path: output/raxmlng/output.raxml.bestTree
-      contains:
-        - "sample1:0.359"
-        - "sample2:1.50"
-        - "sample3:0.000001"
-        - "sample4:0.111"
-
-- name: raxmlng bootstrap
-  command: nextflow run ./tests/modules/raxmlng -entry test_raxmlng_bootstrap -c ./tests/config/nextflow.config -c ./tests/modules/raxmlng/nextflow.config
-  tags:
-    - raxmlng
-  files:
-    - path: output/raxmlng/output.raxml.bestTree
-      contains:
-        - "sample1:0.359"
-        - "sample2:1.50"
-        - "sample3:0.000001"
-        - "sample4:0.111"
-    - path: output/raxmlng/output.raxml.support
-      contains:
-        - "sample1:0.359"
-        - "sample2:1.50"
-        - "sample3:0.000001"
-        - "sample4:0.111"
-      contains_regex:
-        - '\)[89]\d:'
diff --git a/tests/modules/rgi/main/main.nf b/tests/modules/rgi/main/main.nf
deleted file mode 100644
index 9182a1548d5..00000000000
--- a/tests/modules/rgi/main/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RGI_MAIN } from '../../../../modules/rgi/main/main.nf'
-
-workflow test_rgi_main {
-
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
-    ]
-
-    RGI_MAIN ( input )
-}
diff --git a/tests/modules/rgi/main/test.yml b/tests/modules/rgi/main/test.yml
deleted file mode 100644
index b3941895065..00000000000
--- a/tests/modules/rgi/main/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: rgi main
-  command: nextflow run ./tests/modules/rgi/main -entry test_rgi_main -c ./tests/config/nextflow.config -c ./tests/modules/rgi/main/nextflow.config
-  tags:
-    - rgi
-    - rgi/main
-  files:
-    - path: output/rgi/test.json
-      contains: ["NZ_LS483480", "orf_end", "perc_identity", "Pulvomycin"]
-    - path: output/rgi/test.txt
-      contains: ["NZ_LS483480", "ORF_ID", "Model_type", "Pulvomycin"]
diff --git a/tests/modules/rhocall/annotate/main.nf b/tests/modules/rhocall/annotate/main.nf
deleted file mode 100644
index 9cca1520f3c..00000000000
--- a/tests/modules/rhocall/annotate/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RHOCALL_ANNOTATE } from '../../../../modules/rhocall/annotate/main.nf'
-include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf'
-
-workflow test_rhocall_annotate {
-
-    input = [ [ id:'test' ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-
-    af_file = [[],[]]
-    gen_map = []
-    regions = []
-    targets = []
-    samples = []
-
-    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
-    RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
-
-}
-
-workflow test_rhocall_annotate_stub {
-
-    input = [ [ id:'test' ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-
-    af_file = [[],[]]
-    gen_map = []
-    regions = []
-    targets = []
-    samples = []
-
-    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
-    RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
-
-}
diff --git a/tests/modules/rhocall/annotate/test.yml b/tests/modules/rhocall/annotate/test.yml
deleted file mode 100644
index 77c9f8ecc66..00000000000
--- a/tests/modules/rhocall/annotate/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: "rhocall annotate"
-  command: nextflow run ./tests/modules/rhocall/annotate -entry test_rhocall_annotate -c ./tests/config/nextflow.config -c ./tests/modules/rhocall/annotate/nextflow.config
-  tags:
-    - "rhocall"
-    - "rhocall/annotate"
-  files:
-    - path: "output/rhocall/test_rhocall.vcf"
-    - path: "output/rhocall/versions.yml"
-
-- name: "rhocall annotate stub"
-  command: nextflow run ./tests/modules/rhocall/annotate -entry test_rhocall_annotate_stub -c ./tests/config/nextflow.config -c ./tests/modules/rhocall/annotate/nextflow.config -stub-run
-  tags:
-    - "rhocall"
-    - "rhocall/annotate"
-  files:
-    - path: "output/rhocall/test_rhocall.vcf"
-    - path: "output/rhocall/versions.yml"
diff --git a/tests/modules/rmarkdownnotebook/main.nf b/tests/modules/rmarkdownnotebook/main.nf
deleted file mode 100644
index fdb7d3b9941..00000000000
--- a/tests/modules/rmarkdownnotebook/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RMARKDOWNNOTEBOOK } from '../../../modules/rmarkdownnotebook/main.nf'
-include { RMARKDOWNNOTEBOOK as RMARKDOWNNOTEBOOK_PARAMETRIZE } from '../../../modules/rmarkdownnotebook/main.nf'
-
-workflow test_rmarkdown {
-
-    input = [ [ id:'test_rmd' ], // meta map
-              file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) ]
-
-    RMARKDOWNNOTEBOOK ( input, [:], [])
-
-}
-
-workflow test_rmarkdown_parametrize {
-
-    input = [ [ id:'test_rmd' ], // meta map
-              file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) ]
-
-    RMARKDOWNNOTEBOOK_PARAMETRIZE(
-        input,
-        [input_filename: "hello.txt", n_iter: 12],
-        file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
-    )
-
-}
-
diff --git a/tests/modules/rmarkdownnotebook/test.yml b/tests/modules/rmarkdownnotebook/test.yml
deleted file mode 100644
index 3645514a6ac..00000000000
--- a/tests/modules/rmarkdownnotebook/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: rmarkdownnotebook test_rmarkdown
-  command: nextflow run ./tests/modules/rmarkdownnotebook -entry test_rmarkdown -c ./tests/config/nextflow.config -c ./tests/modules/rmarkdownnotebook/nextflow.config
-  tags:
-    - rmarkdownnotebook
-  files:
-    - path: output/rmarkdownnotebook/session_info.log
-      contains:
-        - R version 4.1.0
-        - yaml_2.2.1
-    - path: output/rmarkdownnotebook/test_rmd.html
-      contains:
-        - "n_iter = 10"
-
-- name: rmarkdownnotebook test_rmarkdown_parametrize
-  command: nextflow run ./tests/modules/rmarkdownnotebook -entry test_rmarkdown_parametrize -c ./tests/config/nextflow.config -c ./tests/modules/rmarkdownnotebook/nextflow.config
-  tags:
-    - rmarkdownnotebook
-  files:
-    - path: output/rmarkdownnotebook/artifacts/artifact.txt
-      md5sum: b10a8db164e0754105b7a99be72e3fe5
-    - path: output/rmarkdownnotebook/session_info.log
-      contains:
-        - R version 4.1.0
-        - yaml_2.2.1
-    - path: output/rmarkdownnotebook/test_rmd.html
-      contains:
-        - "n_iter = 12"
diff --git a/tests/modules/roary/main.nf b/tests/modules/roary/main.nf
deleted file mode 100644
index 3fae516ce8a..00000000000
--- a/tests/modules/roary/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ROARY } from '../../../modules/roary/main.nf'
-
-workflow test_roary {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
-            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
-        ]
-    ]
-
-    ROARY ( input )
-}
diff --git a/tests/modules/roary/test.yml b/tests/modules/roary/test.yml
deleted file mode 100644
index b6f02593527..00000000000
--- a/tests/modules/roary/test.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-- name: roary test_roary
-  command: nextflow run ./tests/modules/roary -entry test_roary -c ./tests/config/nextflow.config -c ./tests/modules/roary/nextflow.config
-  tags:
-    - roary
-  files:
-    - path: output/roary/results/accessory.header.embl
-      contains: ["ID   Genome standard; DNA; PRO; 1234 BP."]
-    - path: output/roary/results/accessory.tab
-      contains: ["FT"]
-    - path: output/roary/results/accessory_binary_genes.fa
-      md5sum: d4191cf748dd8016ad877857a034bef3
-    - path: output/roary/results/accessory_binary_genes.fa.newick
-      md5sum: d4a2a64e781263ca1b9b3a4bc9d3a6ea
-    - path: output/roary/results/accessory_graph.dot
-      contains: ["/* list of nodes */"]
-    - path: output/roary/results/blast_identity_frequency.Rtab
-      md5sum: 829baa25c3fad94b1af207265452a692
-    - path: output/roary/results/clustered_proteins
-      contains: ["JKHLNHAL_00087"]
-    - path: output/roary/results/core_accessory.header.embl
-      contains: ["ID   Genome standard; DNA; PRO; 1234 BP."]
-    - path: output/roary/results/core_accessory.tab
-      contains: ['FT                   /taxa="test1 test2 test3"']
-    - path: output/roary/results/core_accessory_graph.dot
-      contains: ["/* list of nodes */"]
-    - path: output/roary/results/gene_presence_absence.Rtab
-      contains: ["Gene"]
-    - path: output/roary/results/gene_presence_absence.csv
-      contains: ['"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"']
-    - path: output/roary/results/number_of_conserved_genes.Rtab
-      contains: ["2"]
-    - path: output/roary/results/number_of_genes_in_pan_genome.Rtab
-      contains: ["2"]
-    - path: output/roary/results/number_of_new_genes.Rtab
-      contains: ["2"]
-    - path: output/roary/results/number_of_unique_genes.Rtab
-      contains: ["2"]
-    - path: output/roary/results/summary_statistics.txt
-      md5sum: 3921b5445df6a7ed59408119b8860a58
diff --git a/tests/modules/rsem/calculateexpression/main.nf b/tests/modules/rsem/calculateexpression/main.nf
deleted file mode 100644
index 9d6d3c5cfa1..00000000000
--- a/tests/modules/rsem/calculateexpression/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEM_PREPAREREFERENCE    } from '../../../../modules/rsem/preparereference/main.nf'
-include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/rsem/calculateexpression/main.nf'
-
-workflow test_rsem_calculateexpression {
-
-    input = [
-        [ id:'test', single_end:false, strandedness: 'forward' ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-
-    RSEM_PREPAREREFERENCE ( fasta, gtf )
-    RSEM_CALCULATEEXPRESSION( input, RSEM_PREPAREREFERENCE.out.index )
-}
diff --git a/tests/modules/rsem/calculateexpression/test.yml b/tests/modules/rsem/calculateexpression/test.yml
deleted file mode 100644
index b0251de90a6..00000000000
--- a/tests/modules/rsem/calculateexpression/test.yml
+++ /dev/null
@@ -1,66 +0,0 @@
-- name: rsem calculateexpression test_rsem_calculateexpression
-  command: nextflow run ./tests/modules/rsem/calculateexpression -entry test_rsem_calculateexpression -c ./tests/config/nextflow.config -c ./tests/modules/rsem/calculateexpression/nextflow.config
-  tags:
-    - rsem
-    - rsem/calculateexpression
-  files:
-    - path: output/rsem/rsem/Genome
-      md5sum: a654229fbca6071dcb6b01ce7df704da
-    - path: output/rsem/rsem/Log.out
-    - path: output/rsem/rsem/SA
-      md5sum: 8c3edc46697b72c9e92440d4cf43506c
-    - path: output/rsem/rsem/SAindex
-      md5sum: fd05c149960e72642a8d7c860528ae81
-    - path: output/rsem/rsem/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/rsem/rsem/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/rsem/rsem/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/rsem/rsem/chrStart.txt
-      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
-    - path: output/rsem/rsem/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/rsem/rsem/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/rsem/rsem/geneInfo.tab
-      md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/rsem/rsem/genome.chrlist
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/rsem/rsem/genome.fasta
-      md5sum: f315020d899597c1b57e5fe9f60f4c3e
-    - path: output/rsem/rsem/genome.grp
-      md5sum: c2848a8b6d495956c11ec53efc1de67e
-    - path: output/rsem/rsem/genome.idx.fa
-      md5sum: 050c521a2719c2ae48267c1e65218f29
-    - path: output/rsem/rsem/genome.n2g.idx.fa
-      md5sum: 050c521a2719c2ae48267c1e65218f29
-    - path: output/rsem/rsem/genome.seq
-      md5sum: 94da0c6b88c33e63c9a052a11f4f57c1
-    - path: output/rsem/rsem/genome.ti
-      md5sum: c9e4ae8d4d13a504eec2acf1b8589a66
-    - path: output/rsem/rsem/genome.transcripts.fa
-      md5sum: 050c521a2719c2ae48267c1e65218f29
-    - path: output/rsem/rsem/genomeParameters.txt
-      md5sum: df5a456e3242520cc36e0083a6a7d9dd
-    - path: output/rsem/rsem/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/rsem/rsem/sjdbList.fromGTF.out.tab
-      md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/rsem/rsem/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/rsem/rsem/transcriptInfo.tab
-      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
-    - path: output/rsem/test.genes.results
-      md5sum: c7ec226f76736ea805771e73553ae359
-    - path: output/rsem/test.isoforms.results
-      md5sum: 99f7f80aa505b44ca429fdebbd7dd5d8
-    - path: output/rsem/test.log
-    - path: output/rsem/test.stat/test.cnt
-      md5sum: 76249e6b2f3c104f414aae596ba2c2f4
-    - path: output/rsem/test.stat/test.model
-      md5sum: a7a4bc1734918ef5848604e3362b83e2
-    - path: output/rsem/test.stat/test.theta
-      md5sum: de2e4490c98cc5383a86ae8225fd0a28
-    - path: output/rsem/test.transcript.bam
-      md5sum: ed681d39f5700ffc74d6321525330d93
diff --git a/tests/modules/rsem/preparereference/main.nf b/tests/modules/rsem/preparereference/main.nf
deleted file mode 100644
index 8062737de57..00000000000
--- a/tests/modules/rsem/preparereference/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEM_PREPAREREFERENCE }   from '../../../../modules/rsem/preparereference/main.nf'
-
-workflow test_rsem_preparereference {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-
-    RSEM_PREPAREREFERENCE ( fasta, gtf )
-}
diff --git a/tests/modules/rsem/preparereference/test.yml b/tests/modules/rsem/preparereference/test.yml
deleted file mode 100644
index 1f058bea260..00000000000
--- a/tests/modules/rsem/preparereference/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: rsem preparereference test_rsem_preparereference
-  command: nextflow run ./tests/modules/rsem/preparereference -entry test_rsem_preparereference -c ./tests/config/nextflow.config -c ./tests/modules/rsem/preparereference/nextflow.config
-  tags:
-    - rsem
-    - rsem/preparereference
-  files:
-    - path: output/rsem/rsem/genome.chrlist
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/rsem/rsem/genome.fasta
-      md5sum: f315020d899597c1b57e5fe9f60f4c3e
-    - path: output/rsem/rsem/genome.grp
-      md5sum: c2848a8b6d495956c11ec53efc1de67e
-    - path: output/rsem/rsem/genome.idx.fa
-      md5sum: 050c521a2719c2ae48267c1e65218f29
-    - path: output/rsem/rsem/genome.n2g.idx.fa
-      md5sum: 050c521a2719c2ae48267c1e65218f29
-    - path: output/rsem/rsem/genome.seq
-      md5sum: 94da0c6b88c33e63c9a052a11f4f57c1
-    - path: output/rsem/rsem/genome.ti
-      md5sum: c9e4ae8d4d13a504eec2acf1b8589a66
-    - path: output/rsem/rsem/genome.transcripts.fa
-      md5sum: 050c521a2719c2ae48267c1e65218f29
diff --git a/tests/modules/rseqc/bamstat/main.nf b/tests/modules/rseqc/bamstat/main.nf
deleted file mode 100644
index 4c53a1af0ad..00000000000
--- a/tests/modules/rseqc/bamstat/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEQC_BAMSTAT }   from '../../../../modules/rseqc/bamstat/main.nf'
-
-workflow test_rseqc_bamstat {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    RSEQC_BAMSTAT ( input )
-}
diff --git a/tests/modules/rseqc/bamstat/test.yml b/tests/modules/rseqc/bamstat/test.yml
deleted file mode 100644
index 4cb35d0c185..00000000000
--- a/tests/modules/rseqc/bamstat/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: rseqc bamstat test_rseqc_bamstat
-  command: nextflow run ./tests/modules/rseqc/bamstat -entry test_rseqc_bamstat -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/bamstat/nextflow.config
-  tags:
-    - rseqc
-    - rseqc/bamstat
-  files:
-    - path: output/rseqc/test.bam_stat.txt
-      md5sum: 2675857864c1d1139b2a19d25dc36b09
diff --git a/tests/modules/rseqc/inferexperiment/main.nf b/tests/modules/rseqc/inferexperiment/main.nf
deleted file mode 100644
index 6337063de75..00000000000
--- a/tests/modules/rseqc/inferexperiment/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEQC_INFEREXPERIMENT }   from '../../../../modules/rseqc/inferexperiment/main.nf'
-
-workflow test_rseqc_inferexperiment {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-
-    RSEQC_INFEREXPERIMENT ( input, bed )
-}
diff --git a/tests/modules/rseqc/inferexperiment/test.yml b/tests/modules/rseqc/inferexperiment/test.yml
deleted file mode 100644
index 554f8317a83..00000000000
--- a/tests/modules/rseqc/inferexperiment/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: rseqc inferexperiment test_rseqc_inferexperiment
-  command: nextflow run ./tests/modules/rseqc/inferexperiment -entry test_rseqc_inferexperiment -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/inferexperiment/nextflow.config
-  tags:
-    - rseqc
-    - rseqc/inferexperiment
-  files:
-    - path: output/rseqc/test.infer_experiment.txt
-      md5sum: f9d0bfc239df637cd8aeda40ade3c59a
diff --git a/tests/modules/rseqc/innerdistance/main.nf b/tests/modules/rseqc/innerdistance/main.nf
deleted file mode 100644
index 8cc0ec3eebc..00000000000
--- a/tests/modules/rseqc/innerdistance/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEQC_INNERDISTANCE }   from '../../../../modules/rseqc/innerdistance/main.nf'
-
-workflow test_rseqc_innerdistance {
-    input = [ [ id:'test', single_end: false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    bed = file(params.test_data['sarscov2']['genome']['test_bed12'], checkIfExists: true)
-
-    RSEQC_INNERDISTANCE ( input, bed )
-}
diff --git a/tests/modules/rseqc/innerdistance/test.yml b/tests/modules/rseqc/innerdistance/test.yml
deleted file mode 100644
index c0f480e9b57..00000000000
--- a/tests/modules/rseqc/innerdistance/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: rseqc innerdistance test_rseqc_innerdistance
-  command: nextflow run ./tests/modules/rseqc/innerdistance -entry test_rseqc_innerdistance -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/innerdistance/nextflow.config
-  tags:
-    - rseqc
-    - rseqc/innerdistance
-  files:
-    - path: output/rseqc/test.inner_distance.txt
-      md5sum: a1acc9def0f64a5500d4c4cb47cbe32b
-    - path: output/rseqc/test.inner_distance_freq.txt
-      md5sum: 3fc037501f5899b5da009c8ce02fc25e
-    - path: output/rseqc/test.inner_distance_mean.txt
-      md5sum: 58398b7d5a29a5e564f9e3c50b55996c
-    - path: output/rseqc/test.inner_distance_plot.pdf
-    - path: output/rseqc/test.inner_distance_plot.r
-      md5sum: 5859fbd5b42046d47e8b9aa85077f4ea
diff --git a/tests/modules/rseqc/junctionannotation/main.nf b/tests/modules/rseqc/junctionannotation/main.nf
deleted file mode 100644
index 303dcd854df..00000000000
--- a/tests/modules/rseqc/junctionannotation/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEQC_JUNCTIONANNOTATION }   from '../../../../modules/rseqc/junctionannotation/main.nf'
-
-workflow test_rseqc_junctionannotation {
-    input = [ 
-        [ id:'test', single_end: false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-
-    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-
-    RSEQC_JUNCTIONANNOTATION ( input, bed )
-}
diff --git a/tests/modules/rseqc/junctionannotation/test.yml b/tests/modules/rseqc/junctionannotation/test.yml
deleted file mode 100644
index f2020b10192..00000000000
--- a/tests/modules/rseqc/junctionannotation/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: rseqc junctionannotation test_rseqc_junctionannotation
-  command: nextflow run ./tests/modules/rseqc/junctionannotation -entry test_rseqc_junctionannotation -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/junctionannotation/nextflow.config
-  tags:
-    - rseqc
-    - rseqc/junctionannotation
-  files:
-    - path: output/rseqc/test.junction_annotation.log
-    - path: output/rseqc/test.junction.xls
-    - path: output/rseqc/test.junction_plot.r
diff --git a/tests/modules/rseqc/junctionsaturation/main.nf b/tests/modules/rseqc/junctionsaturation/main.nf
deleted file mode 100644
index eefbb492063..00000000000
--- a/tests/modules/rseqc/junctionsaturation/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEQC_JUNCTIONSATURATION }   from '../../../../modules/rseqc/junctionsaturation/main.nf'
-
-workflow test_rseqc_junctionsaturation {
-    input = [
-        [ id:'test', single_end: false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
-
-    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-
-    RSEQC_JUNCTIONSATURATION ( input, bed )
-}
diff --git a/tests/modules/rseqc/junctionsaturation/test.yml b/tests/modules/rseqc/junctionsaturation/test.yml
deleted file mode 100644
index db9773601df..00000000000
--- a/tests/modules/rseqc/junctionsaturation/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: rseqc junctionsaturation test_rseqc_junctionsaturation
-  command: nextflow run ./tests/modules/rseqc/junctionsaturation -entry test_rseqc_junctionsaturation -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/junctionsaturation/nextflow.config
-  tags:
-    - rseqc/junctionsaturation
-    - rseqc
-  files:
-    - path: output/rseqc/test.junctionSaturation_plot.pdf
-    - path: output/rseqc/test.junctionSaturation_plot.r
-      md5sum: caa6e63dcb477aabb169882b2f30dadd
diff --git a/tests/modules/rseqc/readdistribution/main.nf b/tests/modules/rseqc/readdistribution/main.nf
deleted file mode 100644
index 180367f2600..00000000000
--- a/tests/modules/rseqc/readdistribution/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEQC_READDISTRIBUTION }   from '../../../../modules/rseqc/readdistribution/main.nf'
-
-workflow test_rseqc_readdistribution {
-    input = [ [ id:'test', single_end: false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    bed = file(params.test_data['sarscov2']['genome']['test_bed12'], checkIfExists: true)
-
-    RSEQC_READDISTRIBUTION ( input, bed )
-}
diff --git a/tests/modules/rseqc/readdistribution/test.yml b/tests/modules/rseqc/readdistribution/test.yml
deleted file mode 100644
index e530e92af87..00000000000
--- a/tests/modules/rseqc/readdistribution/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: rseqc readdistribution test_rseqc_readdistribution
-  command: nextflow run ./tests/modules/rseqc/readdistribution -entry test_rseqc_readdistribution -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/readdistribution/nextflow.config
-  tags:
-    - rseqc
-    - rseqc/readdistribution
-  files:
-    - path: output/rseqc/test.read_distribution.txt
-      md5sum: 56893fdc0809d968629a363551a1655f
diff --git a/tests/modules/rseqc/readduplication/main.nf b/tests/modules/rseqc/readduplication/main.nf
deleted file mode 100644
index bcccde5d504..00000000000
--- a/tests/modules/rseqc/readduplication/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEQC_READDUPLICATION }   from '../../../../modules/rseqc/readduplication/main.nf'
-
-workflow test_rseqc_readduplication {
-    input = [ [ id:'test', single_end: false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    RSEQC_READDUPLICATION ( input )
-}
diff --git a/tests/modules/rseqc/readduplication/test.yml b/tests/modules/rseqc/readduplication/test.yml
deleted file mode 100644
index b0c350718f5..00000000000
--- a/tests/modules/rseqc/readduplication/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: rseqc readduplication test_rseqc_readduplication
-  command: nextflow run ./tests/modules/rseqc/readduplication -entry test_rseqc_readduplication -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/readduplication/nextflow.config
-  tags:
-    - rseqc/readduplication
-    - rseqc
-  files:
-    - path: output/rseqc/test.DupRate_plot.pdf
-    - path: output/rseqc/test.DupRate_plot.r
-      md5sum: 3c0325095cee4835b921e57d61c23dca
-    - path: output/rseqc/test.pos.DupRate.xls
-      md5sum: a859bc2031d46bf1cc4336205847caa3
-    - path: output/rseqc/test.seq.DupRate.xls
-      md5sum: ee8783399eec5a18522a6f08bece338b
diff --git a/tests/modules/rseqc/tin/main.nf b/tests/modules/rseqc/tin/main.nf
deleted file mode 100644
index 677e116535d..00000000000
--- a/tests/modules/rseqc/tin/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RSEQC_TIN } from '../../../../modules/rseqc/tin/main.nf'
-
-workflow test_rseqc_tin {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-
-    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-
-    RSEQC_TIN ( input, bed )
-}
diff --git a/tests/modules/rseqc/tin/test.yml b/tests/modules/rseqc/tin/test.yml
deleted file mode 100644
index 9faae20281c..00000000000
--- a/tests/modules/rseqc/tin/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: rseqc tin
-  command: nextflow run ./tests/modules/rseqc/tin -entry test_rseqc_tin -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/tin/nextflow.config
-  tags:
-    - rseqc
-    - rseqc/tin
-  files:
-    - path: output/rseqc/test.paired_end.sorted.summary.txt
-      md5sum: 9d98447e178b89a89f6f5aba7a772fe6
-    - path: output/rseqc/test.paired_end.sorted.tin.xls
-      md5sum: 6b1b1b0dc1dc265342ba8c3f27fa60e6
diff --git a/tests/modules/rtgtools/pedfilter/main.nf b/tests/modules/rtgtools/pedfilter/main.nf
deleted file mode 100644
index a8361e6dee1..00000000000
--- a/tests/modules/rtgtools/pedfilter/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RTGTOOLS_PEDFILTER } from '../../../../modules/rtgtools/pedfilter/main.nf'
-
-workflow test_rtgtools_pedfilter {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
-    ]
-
-    RTGTOOLS_PEDFILTER ( input )
-}
diff --git a/tests/modules/rtgtools/pedfilter/test.yml b/tests/modules/rtgtools/pedfilter/test.yml
deleted file mode 100644
index cb0c29a3f84..00000000000
--- a/tests/modules/rtgtools/pedfilter/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: rtgtools pedfilter test_rtgtools_pedfilter
-  command: nextflow run ./tests/modules/rtgtools/pedfilter -entry test_rtgtools_pedfilter -c ./tests/config/nextflow.config  -c ./tests/modules/rtgtools/pedfilter/nextflow.config
-  tags:
-    - rtgtools/pedfilter
-    - rtgtools
-  files:
-    - path: output/rtgtools/test.vcf.gz
diff --git a/tests/modules/rtgtools/vcfeval/main.nf b/tests/modules/rtgtools/vcfeval/main.nf
deleted file mode 100644
index 9a1c3c71faf..00000000000
--- a/tests/modules/rtgtools/vcfeval/main.nf
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf'
-include { UNTAR } from '../../../modules/untar/main.nf'
-
-workflow test_rtgtools_vcfeval {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true),        
-    ]
-
-    truth = [
-        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    truth_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-
-    evaluation_regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-
-    compressed_sdf = [
-        [],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
-    ]
-
-    sdf = UNTAR( compressed_sdf ).untar
-        .map({
-            meta, folder ->
-                folder
-        })
-    
-
-    RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
-}
-
-workflow test_rtgtools_vcfeval_no_optional_inputs {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
-        [],
-    ]
-
-    truth = [
-        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
-        []
-    ]
-
-    truth_regions = []
-
-    evaluation_regions = []
-
-    compressed_sdf = [
-        [],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
-    ]
-
-    sdf = UNTAR( compressed_sdf ).untar
-        .map({
-            meta, folder ->
-                [folder]
-        })
-
-    RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
-}
diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
deleted file mode 100644
index 33720f66fa5..00000000000
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ /dev/null
@@ -1,75 +0,0 @@
-- name: rtgtools vcfeval test_rtgtools_vcfeval
-  command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c tests/config/nextflow.config
-  tags:
-    - rtgtools
-    - rtgtools/vcfeval
-  files:
-    - path: output/rtgtools/test_results/done
-    - path: output/rtgtools/test_results/fn.vcf.gz
-      md5sum: be9c9106055bfad4c5985bc0d33efd56
-    - path: output/rtgtools/test_results/fn.vcf.gz.tbi
-      md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test_results/fp.vcf.gz
-      md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
-    - path: output/rtgtools/test_results/fp.vcf.gz.tbi
-      md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test_results/non_snp_roc.tsv.gz
-      md5sum: ad5bad32c48f05aef232e2c0e708877a
-    - path: output/rtgtools/test_results/phasing.txt
-      md5sum: 133677dbd8be657439ea2b03fdfb8795
-    - path: output/rtgtools/test_results/progress
-    - path: output/rtgtools/test_results/snp_roc.tsv.gz
-      md5sum: 6785b83d66486e7e6c75c5a5b1574c09
-    - path: output/rtgtools/test_results/summary.txt
-      md5sum: f4c8df93c8bdab603036bbc27b4a28c3
-    - path: output/rtgtools/test_results/tp-baseline.vcf.gz
-      md5sum: be9c9106055bfad4c5985bc0d33efd56
-    - path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
-      md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test_results/tp.vcf.gz
-      md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
-    - path: output/rtgtools/test_results/tp.vcf.gz.tbi
-      md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test_results/vcfeval.log
-    - path: output/rtgtools/test_results/weighted_roc.tsv.gz
-      md5sum: fa7c046ea0084172f1ef91f19de07b2b
-    - path: output/rtgtools/versions.yml
-      md5sum: 270ed7a5a8e347b251eb4aa2198f98e8
-
-- name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs
-  command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config
-  tags:
-    - rtgtools
-    - rtgtools/vcfeval
-  files:
-    - path: output/rtgtools/test_results/done
-    - path: output/rtgtools/test_results/fn.vcf.gz
-      md5sum: c11c889a4f42c8ea325748bd768ea34d
-    - path: output/rtgtools/test_results/fn.vcf.gz.tbi
-      md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test_results/fp.vcf.gz
-      md5sum: 138e85c1cd79f8fea9a33e81ce0c734c
-    - path: output/rtgtools/test_results/fp.vcf.gz.tbi
-      md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test_results/non_snp_roc.tsv.gz
-      md5sum: 34fb78a008dfc0bef02807b8a7012b07
-    - path: output/rtgtools/test_results/phasing.txt
-      md5sum: 133677dbd8be657439ea2b03fdfb8795
-    - path: output/rtgtools/test_results/progress
-    - path: output/rtgtools/test_results/snp_roc.tsv.gz
-      md5sum: a4c5761c2653e2d04fc84c1cea13b1f0
-    - path: output/rtgtools/test_results/summary.txt
-      md5sum: f33feb32f84958fb931063044fba369b
-    - path: output/rtgtools/test_results/tp-baseline.vcf.gz
-      md5sum: d1c2d990899edf127ea5fcca8866fcb0
-    - path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
-      md5sum: 3307008fea47adb75c46d395c5567bc0
-    - path: output/rtgtools/test_results/tp.vcf.gz
-      md5sum: e35b4dab82894eee9b77c81f9bc89cca
-    - path: output/rtgtools/test_results/tp.vcf.gz.tbi
-      md5sum: 45d8f8793140944f129e728299918c88
-    - path: output/rtgtools/test_results/vcfeval.log
-    - path: output/rtgtools/test_results/weighted_roc.tsv.gz
-      md5sum: 5b8efc9e9381f604880412800f58e4e9
-    - path: output/rtgtools/versions.yml
-      md5sum: 55568e4bbe5ab7e634a1f392abb89cc4
diff --git a/tests/modules/salmon/index/main.nf b/tests/modules/salmon/index/main.nf
deleted file mode 100644
index 680b4c6e5a2..00000000000
--- a/tests/modules/salmon/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf'
-
-workflow test_salmon_index {
-    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
-
-    SALMON_INDEX ( genome_fasta, transcript_fasta )
-}
diff --git a/tests/modules/salmon/index/test.yml b/tests/modules/salmon/index/test.yml
deleted file mode 100644
index 07815e37ed4..00000000000
--- a/tests/modules/salmon/index/test.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- name: salmon index
-  command: nextflow run ./tests/modules/salmon/index -entry test_salmon_index -c ./tests/config/nextflow.config -c ./tests/modules/salmon/index/nextflow.config
-  tags:
-    - salmon
-    - salmon/index
-  files:
-    - path: ./output/salmon/salmon/ref_indexing.log
-    - path: ./output/salmon/salmon/refseq.bin
-      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
-    - path: ./output/salmon/salmon/versionInfo.json
-      md5sum: 6c764bd219b7bc17168a99d232c0fe09
-    - path: ./output/salmon/salmon/complete_ref_lens.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/mphf.bin
-      md5sum: 53669a47610e33e031faafd32703b714
-    - path: ./output/salmon/salmon/pre_indexing.log
-    - path: ./output/salmon/salmon/ctable.bin
-    - path: ./output/salmon/salmon/duplicate_clusters.tsv
-      md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: ./output/salmon/salmon/reflengths.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/info.json
-      md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: ./output/salmon/salmon/refAccumLengths.bin
-      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: ./output/salmon/salmon/ctg_offsets.bin
-      md5sum: 27a76542337df436436e66017f66dd25
-    - path: ./output/salmon/salmon/rank.bin
-      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: ./output/salmon/salmon/pos.bin
-    - path: ./output/salmon/salmon/seq.bin
diff --git a/tests/modules/salmon/quant/main.nf b/tests/modules/salmon/quant/main.nf
deleted file mode 100644
index a970f6c5177..00000000000
--- a/tests/modules/salmon/quant/main.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf'
-include { SALMON_QUANT } from '../../../../modules/salmon/quant/main.nf'
-
-workflow test_salmon_quant_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
-    gtf              = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-
-    SALMON_INDEX ( genome_fasta, transcript_fasta )
-    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false, '' )
-
-}
-
-workflow test_salmon_quant_paired_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
-    gtf              = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-
-    SALMON_INDEX ( genome_fasta, transcript_fasta )
-    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false, '' )
-
-}
-
-workflow test_salmon_quant_single_end_lib_type_A {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
-    gtf              = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-
-    SALMON_INDEX ( genome_fasta, transcript_fasta )
-    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false, 'A' )
-
-}
-
diff --git a/tests/modules/salmon/quant/test.yml b/tests/modules/salmon/quant/test.yml
deleted file mode 100644
index 514718fa367..00000000000
--- a/tests/modules/salmon/quant/test.yml
+++ /dev/null
@@ -1,151 +0,0 @@
-- name: salmon quant single-end
-  command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_single_end -c ./tests/config/nextflow.config -c ./tests/modules/salmon/quant/nextflow.config
-  tags:
-    - salmon
-    - salmon/quant
-  files:
-    - path: ./output/salmon/test/cmd_info.json
-    - path: ./output/salmon/test/quant.sf
-      md5sum: 687368b9963874c1797d210310b38516
-    - path: ./output/salmon/test/lib_format_counts.json
-    - path: ./output/salmon/test/quant.genes.sf
-      md5sum: af6d88f109e0d0d6a0826bdf2b3b7e97
-    - path: ./output/salmon/test/logs/salmon_quant.log
-    - path: ./output/salmon/test/aux_info/expected_bias.gz
-      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
-    - path: ./output/salmon/test/aux_info/observed_bias_3p.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: ./output/salmon/test/aux_info/meta_info.json
-    - path: ./output/salmon/test/aux_info/fld.gz
-    - path: ./output/salmon/test/aux_info/ambig_info.tsv
-      md5sum: 2ee3dc3080ad7222e0687481e7a1ee03
-    - path: ./output/salmon/test/aux_info/observed_bias.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: ./output/salmon/test/libParams/flenDist.txt
-      md5sum: 2de170bdc9f6fd237d286429b292bb28
-    - path: ./output/salmon/salmon/ref_indexing.log
-    - path: ./output/salmon/salmon/refseq.bin
-      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
-    - path: ./output/salmon/salmon/versionInfo.json
-      md5sum: 6c764bd219b7bc17168a99d232c0fe09
-    - path: ./output/salmon/salmon/complete_ref_lens.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/mphf.bin
-      md5sum: 53669a47610e33e031faafd32703b714
-    - path: ./output/salmon/salmon/pre_indexing.log
-    - path: ./output/salmon/salmon/ctable.bin
-    - path: ./output/salmon/salmon/duplicate_clusters.tsv
-      md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: ./output/salmon/salmon/reflengths.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/info.json
-      md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: ./output/salmon/salmon/refAccumLengths.bin
-      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: ./output/salmon/salmon/ctg_offsets.bin
-      md5sum: 27a76542337df436436e66017f66dd25
-    - path: ./output/salmon/salmon/rank.bin
-      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: ./output/salmon/salmon/pos.bin
-    - path: ./output/salmon/salmon/seq.bin
-
-- name: salmon quant paired end
-  command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/salmon/quant/nextflow.config
-  tags:
-    - salmon
-    - salmon/quant
-  files:
-    - path: ./output/salmon/test/cmd_info.json
-    - path: ./output/salmon/test/quant.sf
-      md5sum: 4abd35d0a60b5279b394424f0e6ea42d
-    - path: ./output/salmon/test/lib_format_counts.json
-    - path: ./output/salmon/test/quant.genes.sf
-      md5sum: 29c8cd26f609cacd4fb88713df9c71c2
-    - path: ./output/salmon/test/logs/salmon_quant.log
-    - path: ./output/salmon/test/aux_info/expected_bias.gz
-      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
-    - path: ./output/salmon/test/aux_info/observed_bias_3p.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: ./output/salmon/test/aux_info/meta_info.json
-    - path: ./output/salmon/test/aux_info/fld.gz
-    - path: ./output/salmon/test/aux_info/ambig_info.tsv
-      md5sum: 33c0df069da554344869604ea8c18b22
-    - path: ./output/salmon/test/aux_info/observed_bias.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: ./output/salmon/test/libParams/flenDist.txt
-      md5sum: 221f754ed55dd1e34874f9b7b3f9d240
-    - path: ./output/salmon/salmon/ref_indexing.log
-    - path: ./output/salmon/salmon/refseq.bin
-      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
-    - path: ./output/salmon/salmon/versionInfo.json
-      md5sum: 6c764bd219b7bc17168a99d232c0fe09
-    - path: ./output/salmon/salmon/complete_ref_lens.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/mphf.bin
-      md5sum: 53669a47610e33e031faafd32703b714
-    - path: ./output/salmon/salmon/pre_indexing.log
-    - path: ./output/salmon/salmon/ctable.bin
-    - path: ./output/salmon/salmon/duplicate_clusters.tsv
-      md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: ./output/salmon/salmon/reflengths.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/info.json
-      md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: ./output/salmon/salmon/refAccumLengths.bin
-      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: ./output/salmon/salmon/ctg_offsets.bin
-      md5sum: 27a76542337df436436e66017f66dd25
-
-    - path: ./output/salmon/salmon/rank.bin
-      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: ./output/salmon/salmon/pos.bin
-    - path: ./output/salmon/salmon/seq.bin
-
-- name: salmon quant test_salmon_quant_single_end_lib_type_A
-  command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_single_end_lib_type_A -c ./tests/config/nextflow.config -c ./tests/modules/salmon/quant/nextflow.config
-  tags:
-    - salmon/quant
-    - salmon
-  files:
-    - path: ./output/salmon/test/cmd_info.json
-    - path: output/salmon/test/quant.sf
-      md5sum: 687368b9963874c1797d210310b38516
-    - path: ./output/salmon/test/lib_format_counts.json
-    - path: ./output/salmon/test/quant.genes.sf
-      md5sum: af6d88f109e0d0d6a0826bdf2b3b7e97
-    - path: ./output/salmon/test/logs/salmon_quant.log
-    - path: output/salmon/test/aux_info/expected_bias.gz
-      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
-    - path: output/salmon/test/aux_info/observed_bias_3p.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: ./output/salmon/test/aux_info/meta_info.json
-    - path: ./output/salmon/test/aux_info/fld.gz
-    - path: output/salmon/test/aux_info/ambig_info.tsv
-      md5sum: 2ee3dc3080ad7222e0687481e7a1ee03
-    - path: ./output/salmon/test/aux_info/observed_bias.gz
-      md5sum: ef13c06a538e9c34ca9f84212c82f44e
-    - path: output/salmon/test/libParams/flenDist.txt
-      md5sum: 2de170bdc9f6fd237d286429b292bb28
-    - path: ./output/salmon/salmon/ref_indexing.log
-    - path: output/salmon/salmon/refseq.bin
-      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
-    - path: output/salmon/salmon/versionInfo.json
-      md5sum: 6c764bd219b7bc17168a99d232c0fe09
-    - path: output/salmon/salmon/complete_ref_lens.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: output/salmon/salmon/mphf.bin
-      md5sum: 53669a47610e33e031faafd32703b714
-    - path: output/salmon/salmon/duplicate_clusters.tsv
-      md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: output/salmon/salmon/reflengths.bin
-      md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: output/salmon/salmon/info.json
-      md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: output/salmon/salmon/refAccumLengths.bin
-      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: output/salmon/salmon/ctg_offsets.bin
-      md5sum: 27a76542337df436436e66017f66dd25
-    - path: output/salmon/salmon/rank.bin
-      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: ./output/salmon/salmon/pos.bin
-    - path: ./output/salmon/salmon/seq.bin
diff --git a/tests/modules/samblaster/main.nf b/tests/modules/samblaster/main.nf
deleted file mode 100644
index 5831ecfccd6..00000000000
--- a/tests/modules/samblaster/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMBLASTER } from '../../../modules/samblaster/main.nf'
-
-workflow test_samblaster {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_unsorted_bam'], checkIfExists: true) ]
-
-    SAMBLASTER ( input )
-}
diff --git a/tests/modules/samblaster/test.yml b/tests/modules/samblaster/test.yml
deleted file mode 100644
index 8a87bd50f0a..00000000000
--- a/tests/modules/samblaster/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: samblaster test_samblaster
-  command: nextflow run ./tests/modules/samblaster -entry test_samblaster -c ./tests/config/nextflow.config -c ./tests/modules/samblaster/nextflow.config
-  tags:
-    - samblaster
-  files:
-    - path: output/samblaster/test.processed.bam
-      md5sum: 3009528be9f69e7fc8951921583b0016
diff --git a/tests/modules/samtools/ampliconclip/main.nf b/tests/modules/samtools/ampliconclip/main.nf
deleted file mode 100644
index eae70b06fb8..00000000000
--- a/tests/modules/samtools/ampliconclip/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/samtools/ampliconclip/main.nf'
-
-workflow test_samtools_ampliconclip_no_stats_no_rejects {
-
-    input = [ 
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    save_cliprejects = false
-    save_clipstats   = false
-
-    SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
-}
-
-workflow test_samtools_ampliconclip_no_stats_with_rejects {
-
-    input = [ 
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    save_cliprejects = true
-    save_clipstats   = false
-
-    SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
-}
-
-workflow test_samtools_ampliconclip_with_stats_with_rejects {
-
-    input = [ 
-        [ id:'test', single_end:false ],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-    bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    save_cliprejects = true
-    save_clipstats   = true
-
-    SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
-}
diff --git a/tests/modules/samtools/ampliconclip/test.yml b/tests/modules/samtools/ampliconclip/test.yml
deleted file mode 100644
index dd9fdbb74c4..00000000000
--- a/tests/modules/samtools/ampliconclip/test.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-- name: samtools ampliconclip no stats no rejects
-  command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_no_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
-  tags:
-    - samtools
-    - samtools/ampliconclip
-  files:
-    - path: output/samtools/test.bam
-      md5sum: 69e4ba713447864231f6cbbaf036c51d
-
-- name: samtools ampliconclip no stats with rejects
-  command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
-  tags:
-    - samtools
-    - samtools/ampliconclip
-  files:
-    - path: output/samtools/test.bam
-      md5sum: dd2ed9d7cc4ddc070ece2dccc577f94b
-    - path: output/samtools/test.cliprejects.bam
-      md5sum: 7d641f6da838f41d75eaabbd897f60bd
-
-- name: samtools ampliconclip with stats with rejects
-  command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
-  tags:
-    - samtools
-    - samtools/ampliconclip
-  files:
-    - path: output/samtools/test.bam
-      md5sum: 6c19afc0873fba2f4e530eabf61c0735
-    - path: output/samtools/test.cliprejects.bam
-      md5sum: 1dfb61aa80d8e90add324ed61ed17061
-    - path: output/samtools/test.clipstats.txt
-      md5sum: 05ead360a98fab6a678056e326c4f1f3
diff --git a/tests/modules/samtools/bam2fq/main.nf b/tests/modules/samtools/bam2fq/main.nf
deleted file mode 100644
index 928bfe081c4..00000000000
--- a/tests/modules/samtools/bam2fq/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_BAM2FQ } from '../../../../modules/samtools/bam2fq/main.nf'
-
-workflow test_samtools_bam2fq_nosplit {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_converted_bam'], checkIfExists: true) ]
-    split = false
-
-    SAMTOOLS_BAM2FQ ( input, split )
-}
-
-
-workflow test_samtools_bam2fq_withsplit {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_converted_bam'], checkIfExists: true) ]
-    split = true
-
-    SAMTOOLS_BAM2FQ ( input, split )
-}
diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml
deleted file mode 100644
index 4f9472e541f..00000000000
--- a/tests/modules/samtools/bam2fq/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: samtools bam2fq test_samtools_bam2fq_nosplit
-  command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c tests/config/nextflow.config
-  tags:
-    - samtools/bam2fq
-    - samtools
-  files:
-    - path: output/samtools/test_interleaved.fq.gz
-    - path: output/samtools/versions.yml
-      md5sum: 4973eac1b6a8f090d5fcd4456d65a894
-
-- name: samtools bam2fq test_samtools_bam2fq_withsplit
-  command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c tests/config/nextflow.config
-  tags:
-    - samtools/bam2fq
-    - samtools
-  files:
-    - path: output/samtools/test_1.fq.gz
-      md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed
-    - path: output/samtools/test_2.fq.gz
-      md5sum: e679ec035d3208785e704458d6b68c8c
-    - path: output/samtools/test_other.fq.gz
-      md5sum: 709872fc2910431b1e8b7074bfe38c67
-    - path: output/samtools/test_singleton.fq.gz
-      md5sum: 709872fc2910431b1e8b7074bfe38c67
-    - path: output/samtools/versions.yml
-      md5sum: e92d21bbcda2fed7cb438d95c51edff0
diff --git a/tests/modules/samtools/collate/main.nf b/tests/modules/samtools/collate/main.nf
deleted file mode 100644
index 5fec4913ab1..00000000000
--- a/tests/modules/samtools/collate/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_COLLATE } from '../../../../modules/samtools/collate/main.nf'
-
-workflow test_samtools_collate {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    SAMTOOLS_COLLATE ( input, [] )
-}
-
-workflow test_samtools_collate_cram {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    SAMTOOLS_COLLATE ( input, fasta )
-}
diff --git a/tests/modules/samtools/collate/test.yml b/tests/modules/samtools/collate/test.yml
deleted file mode 100644
index 784ede8972b..00000000000
--- a/tests/modules/samtools/collate/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: samtools collate test_samtools_collate
-  command: nextflow run ./tests/modules/samtools/collate -entry test_samtools_collate -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/collate/nextflow.config
-  tags:
-    - samtools/collate
-    - samtools
-  files:
-    - path: output/samtools/test.bam
-      md5sum: dbb8244c28778a970e49577731b158df
-
-- name: samtools collate test_samtools_collate_cram
-  command: nextflow run ./tests/modules/samtools/collate -entry test_samtools_collate_cram -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/collate/nextflow.config
-  tags:
-    - samtools/collate
-    - samtools
-  files:
-    - path: output/samtools/test.bam
-      md5sum: 81aa61ed1f6f3bf6b9c94f70cbf2a177
diff --git a/tests/modules/samtools/collatefastq/main.nf b/tests/modules/samtools/collatefastq/main.nf
deleted file mode 100644
index 928742acc18..00000000000
--- a/tests/modules/samtools/collatefastq/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_COLLATEFASTQ } from '../../../../modules/samtools/collatefastq/main.nf'
-
-workflow test_samtools_collatefastq {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-            ]
-
-    SAMTOOLS_COLLATEFASTQ ( input )
-}
diff --git a/tests/modules/samtools/collatefastq/test.yml b/tests/modules/samtools/collatefastq/test.yml
deleted file mode 100644
index 2b0018853e8..00000000000
--- a/tests/modules/samtools/collatefastq/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: samtools fastq test_samtools_collatefastq
-  command: nextflow run ./tests/modules/samtools/collatefastq -entry test_samtools_collatefastq -c ./tests/config/nextflow.config -c ./tests/modules/samtools/collatefastq/nextflow.config
-  tags:
-    - samtools
-    - samtools/collatefastq
-  files:
-    - path: output/samtools/test_1.fq.gz
-      md5sum: 829732de4e937edca90f27b07e5b501a
-    - path: output/samtools/test_2.fq.gz
-      md5sum: ef27d3809e495620fd93df894280c03a
-    - path: output/samtools/test_other.fq.gz
-      md5sum: 709872fc2910431b1e8b7074bfe38c67
-    - path: output/samtools/test_singleton.fq.gz
-      md5sum: 709872fc2910431b1e8b7074bfe38c67
diff --git a/tests/modules/samtools/convert/main.nf b/tests/modules/samtools/convert/main.nf
deleted file mode 100644
index 01bdfe7f531..00000000000
--- a/tests/modules/samtools/convert/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/convert/main.nf'
-include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/samtools/convert/main.nf'
-
-workflow test_samtools_convert_bamtocram {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
-}
-
-workflow test_samtools_convert_cramtobam {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    SAMTOOLS_CRAMTOBAM ( input, fasta, fai )
-}
diff --git a/tests/modules/samtools/convert/test.yml b/tests/modules/samtools/convert/test.yml
deleted file mode 100644
index 979f36ca7ec..00000000000
--- a/tests/modules/samtools/convert/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: samtools convert test_samtools_convert_bamtocram
-  command: nextflow run tests/modules/samtools/convert -entry test_samtools_convert_bamtocram -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools/convert
-  files:
-    - path: output/samtools/test.cram
-    - path: output/samtools/test.cram.crai
-    - path: output/samtools/versions.yml
-
-- name: samtools convert test_samtools_convert_cramtobam
-  command: nextflow run tests/modules/samtools/convert -entry test_samtools_convert_cramtobam -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools/convert
-  files:
-    - path: output/samtools/test.bam
-      md5sum: c262b6dc15f9b480bdb47d6d018b4b56
-    - path: output/samtools/test.bam.bai
-      md5sum: 6e8f5034f728401bfa841c8e70c62463
-    - path: output/samtools/versions.yml
diff --git a/tests/modules/samtools/depth/main.nf b/tests/modules/samtools/depth/main.nf
deleted file mode 100644
index c6d2dc0e7b9..00000000000
--- a/tests/modules/samtools/depth/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_DEPTH } from '../../../../modules/samtools/depth/main.nf'
-
-workflow test_samtools_depth {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) ]
-
-    SAMTOOLS_DEPTH ( input )
-}
diff --git a/tests/modules/samtools/depth/test.yml b/tests/modules/samtools/depth/test.yml
deleted file mode 100644
index 978134ad047..00000000000
--- a/tests/modules/samtools/depth/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: samtools depth
-  command: nextflow run ./tests/modules/samtools/depth -entry test_samtools_depth -c ./tests/config/nextflow.config -c ./tests/modules/samtools/depth/nextflow.config
-  tags:
-    - samtools/depth
-    - samtools
-  files:
-    - path: output/samtools/test.tsv
-      md5sum: aa27ebf69663ebded553b4d6538219d9
diff --git a/tests/modules/samtools/dict/main.nf b/tests/modules/samtools/dict/main.nf
deleted file mode 100644
index f24a83829aa..00000000000
--- a/tests/modules/samtools/dict/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_DICT } from '../../../../modules/samtools/dict/main.nf'
-
-workflow test_samtools_dict {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    SAMTOOLS_DICT ( input )
-}
diff --git a/tests/modules/samtools/dict/test.yml b/tests/modules/samtools/dict/test.yml
deleted file mode 100644
index 8a71398af6a..00000000000
--- a/tests/modules/samtools/dict/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: samtools dict test_samtools_dict
-  command: nextflow run tests/modules/samtools/dict -entry test_samtools_dict -c tests/config/nextflow.config -c tests/modules/samtools/dict/nextflow.config
-  tags:
-    - samtools
-    - samtools/dict
-  files:
-    - path: output/samtools/genome.fasta.dict
-      contains:
-        - "SN:MT192765.1"
-        - "LN:29829"
-        - "M5:c95f3e5592d0ad9974e41e7f0ea14eb0"
-    - path: output/samtools/versions.yml
-      md5sum: 12cd0c5ce466eefb2dff72625ecbe5c2
diff --git a/tests/modules/samtools/faidx/main.nf b/tests/modules/samtools/faidx/main.nf
deleted file mode 100644
index ea8a2947d15..00000000000
--- a/tests/modules/samtools/faidx/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_FAIDX } from '../../../../modules/samtools/faidx/main.nf'
-
-workflow test_samtools_faidx {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    SAMTOOLS_FAIDX ( input )
-}
-
-workflow test_samtools_faidx_bgzip {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) ]
-
-    SAMTOOLS_FAIDX ( input )
-}
diff --git a/tests/modules/samtools/faidx/test.yml b/tests/modules/samtools/faidx/test.yml
deleted file mode 100644
index 5642d88078b..00000000000
--- a/tests/modules/samtools/faidx/test.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-- name: samtools faidx test_samtools_faidx
-  command: nextflow run tests/modules/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools/faidx
-  files:
-    - path: output/samtools/genome.fasta.fai
-      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
-    - path: output/samtools/versions.yml
-- name: samtools faidx test_samtools_faidx_bgzip
-  command: nextflow run tests/modules/samtools/faidx -entry test_samtools_faidx_bgzip -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools/faidx
-  files:
-    - path: output/samtools/genome.fasta.gz.fai
-      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
-    - path: output/samtools/genome.fasta.gz.gzi
-      md5sum: 7dea362b3fac8e00956a4952a3d4f474
-    - path: output/samtools/versions.yml
diff --git a/tests/modules/samtools/fasta/main.nf b/tests/modules/samtools/fasta/main.nf
deleted file mode 100644
index c0ef91f4fd8..00000000000
--- a/tests/modules/samtools/fasta/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_FASTA } from '../../../../modules/samtools/fasta/main.nf'
-
-workflow test_samtools_fasta {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    SAMTOOLS_FASTA ( input )
-}
diff --git a/tests/modules/samtools/fasta/test.yml b/tests/modules/samtools/fasta/test.yml
deleted file mode 100644
index 6c992cafaf3..00000000000
--- a/tests/modules/samtools/fasta/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: samtools fasta test_samtools_fasta
-  command: nextflow run ./tests/modules/samtools/fasta -entry test_samtools_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/fasta/nextflow.config
-  tags:
-    - samtools
-    - samtools/fasta
-  files:
-    - path: output/samtools/test_1.fasta.gz
-      md5sum: 3abd682290bc7c75f1ce2b80db995237
-    - path: output/samtools/test_2.fasta.gz
-      md5sum: 6ada09ce66f68b8732985e14aac1bf1f
diff --git a/tests/modules/samtools/fastq/main.nf b/tests/modules/samtools/fastq/main.nf
deleted file mode 100644
index 6e7e323ca12..00000000000
--- a/tests/modules/samtools/fastq/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_FASTQ } from '../../../../modules/samtools/fastq/main.nf'
-
-workflow test_samtools_fastq {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-            ]
-
-    SAMTOOLS_FASTQ ( input )
-}
diff --git a/tests/modules/samtools/fastq/test.yml b/tests/modules/samtools/fastq/test.yml
deleted file mode 100644
index ff39d61aa10..00000000000
--- a/tests/modules/samtools/fastq/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: samtools fastq test_samtools_fastq
-  command: nextflow run ./tests/modules/samtools/fastq -entry test_samtools_fastq -c ./tests/config/nextflow.config -c ./tests/modules/samtools/fastq/nextflow.config
-  tags:
-    - samtools
-    - samtools/fastq
-  files:
-    - path: output/samtools/test_2.fastq.gz
-      md5sum: 51e7a469b554de694799bec982fd722e
-    - path: output/samtools/test_1.fastq.gz
-      md5sum: 6c2d5b467eb94e058300271a542e34e6
diff --git a/tests/modules/samtools/fixmate/main.nf b/tests/modules/samtools/fixmate/main.nf
deleted file mode 100644
index cb7c136d25c..00000000000
--- a/tests/modules/samtools/fixmate/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_FIXMATE } from '../../../../modules/samtools/fixmate/main.nf'
-
-workflow test_samtools_fixmate {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
-
-    SAMTOOLS_FIXMATE ( input )
-
-}
diff --git a/tests/modules/samtools/fixmate/test.yml b/tests/modules/samtools/fixmate/test.yml
deleted file mode 100644
index c233f9471eb..00000000000
--- a/tests/modules/samtools/fixmate/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: samtools fixmate test_samtools_fixmate
-  command: nextflow run ./tests/modules/samtools/fixmate -entry test_samtools_fixmate -c ./tests/config/nextflow.config -c ./tests/modules/samtools/fixmate/nextflow.config
-  tags:
-    - samtools
-    - samtools/fixmate
-  files:
-    - path: output/samtools/test.bam
-      md5sum: 13805ea1a9212496a8cb4ce395b25119
diff --git a/tests/modules/samtools/flagstat/main.nf b/tests/modules/samtools/flagstat/main.nf
deleted file mode 100644
index a0e86422276..00000000000
--- a/tests/modules/samtools/flagstat/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_FLAGSTAT } from '../../../../modules/samtools/flagstat/main.nf'
-
-workflow test_samtools_flagstat {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-
-    SAMTOOLS_FLAGSTAT ( input )
-}
diff --git a/tests/modules/samtools/flagstat/test.yml b/tests/modules/samtools/flagstat/test.yml
deleted file mode 100644
index 4351a2b7359..00000000000
--- a/tests/modules/samtools/flagstat/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: samtools flagstat test_samtools_flagstat
-  command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/flagstat/nextflow.config
-  tags:
-    - samtools/flagstat
-    - samtools
-  files:
-    - path: output/samtools/test.flagstat
-      md5sum: 4f7ffd1e6a5e85524d443209ac97d783
diff --git a/tests/modules/samtools/getrg/main.nf b/tests/modules/samtools/getrg/main.nf
deleted file mode 100644
index 3e92149e270..00000000000
--- a/tests/modules/samtools/getrg/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_GETRG } from '../../../../modules/samtools/getrg/main.nf'
-
-workflow test_samtools_getrg {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    SAMTOOLS_GETRG ( input )
-}
diff --git a/tests/modules/samtools/getrg/test.yml b/tests/modules/samtools/getrg/test.yml
deleted file mode 100644
index 8c7dc17f51a..00000000000
--- a/tests/modules/samtools/getrg/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: samtools getrg test_samtools_getrg
-  command: nextflow run ./tests/modules/samtools/getrg -entry test_samtools_getrg -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/getrg/nextflow.config
-  tags:
-    - samtools/getrg
-    - samtools
-  files:
-    - path: output/samtools/readgroups.txt
-      md5sum: 7b1d2d10a82a0c4fa6b22673559e41f6
diff --git a/tests/modules/samtools/idxstats/main.nf b/tests/modules/samtools/idxstats/main.nf
deleted file mode 100644
index f3de76a0d82..00000000000
--- a/tests/modules/samtools/idxstats/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_IDXSTATS } from '../../../../modules/samtools/idxstats/main.nf'
-
-workflow test_samtools_idxstats {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-            ]
-
-    SAMTOOLS_IDXSTATS ( input )
-}
diff --git a/tests/modules/samtools/idxstats/test.yml b/tests/modules/samtools/idxstats/test.yml
deleted file mode 100644
index 84a65dbdbe5..00000000000
--- a/tests/modules/samtools/idxstats/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: samtools idxstats test_samtools_idxstats
-  command: nextflow run ./tests/modules/samtools/idxstats -entry test_samtools_idxstats -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/idxstats/nextflow.config
-  tags:
-    - samtools/idxstats
-    - samtools
-  files:
-    - path: output/samtools/test.idxstats
-      md5sum: df60a8c8d6621100d05178c93fb053a2
diff --git a/tests/modules/samtools/index/main.nf b/tests/modules/samtools/index/main.nf
deleted file mode 100644
index 3592a99a5ec..00000000000
--- a/tests/modules/samtools/index/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI  } from '../../../../modules/samtools/index/main.nf'
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../modules/samtools/index/main.nf'
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI  } from '../../../../modules/samtools/index/main.nf'
-
-workflow test_samtools_index_bai {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    SAMTOOLS_INDEX_BAI ( input )
-}
-
-workflow test_samtools_index_crai {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
-            ]
-
-    SAMTOOLS_INDEX_CRAI ( input )
-}
-
-workflow test_samtools_index_csi {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-
-    SAMTOOLS_INDEX_CSI ( input )
-}
diff --git a/tests/modules/samtools/index/test.yml b/tests/modules/samtools/index/test.yml
deleted file mode 100644
index 096841668c5..00000000000
--- a/tests/modules/samtools/index/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: samtools index test_samtools_index_bai
-  command: nextflow run ./tests/modules/samtools/index -entry test_samtools_index_bai -c ./tests/config/nextflow.config -c ./tests/modules/samtools/index/nextflow.config
-  tags:
-    - samtools
-    - samtools/index
-  files:
-    - path: output/samtools/test.paired_end.sorted.bam.bai
-      md5sum: 704c10dd1326482448ca3073fdebc2f4
-
-- name: samtools index test_samtools_index_crai
-  command: nextflow run ./tests/modules/samtools/index -entry test_samtools_index_crai -c ./tests/config/nextflow.config -c ./tests/modules/samtools/index/nextflow.config
-  tags:
-    - samtools
-    - samtools/index
-  files:
-    - path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai
-      md5sum: 14bc3bd5c89cacc8f4541f9062429029
-
-- name: samtools index test_samtools_index_csi
-  command: nextflow run ./tests/modules/samtools/index -entry test_samtools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/samtools/index/nextflow.config
-  tags:
-    - samtools
-    - samtools/index
-  files:
-    - path: output/samtools/test.paired_end.sorted.bam.csi
-      md5sum: 8d63373007553e74d823fc2b9cbcf84d
diff --git a/tests/modules/samtools/markdup/main.nf b/tests/modules/samtools/markdup/main.nf
deleted file mode 100644
index 0628e3d75fe..00000000000
--- a/tests/modules/samtools/markdup/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_COLLATE } from '../../../../modules/samtools/collate/main.nf'
-include { SAMTOOLS_FIXMATE } from '../../../../modules/samtools/fixmate/main.nf'
-include { SAMTOOLS_SORT    } from '../../../../modules/samtools/sort/main.nf'
-include { SAMTOOLS_MARKDUP } from '../../../../modules/samtools/markdup/main.nf'
-
-workflow test_samtools_markdup {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    SAMTOOLS_COLLATE ( input, [] )
-    SAMTOOLS_FIXMATE ( SAMTOOLS_COLLATE.out.bam )
-    SAMTOOLS_SORT ( SAMTOOLS_FIXMATE.out.bam )
-    SAMTOOLS_MARKDUP ( SAMTOOLS_SORT.out.bam, [] )
-
-}
diff --git a/tests/modules/samtools/markdup/test.yml b/tests/modules/samtools/markdup/test.yml
deleted file mode 100644
index 98da5b11d4e..00000000000
--- a/tests/modules/samtools/markdup/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: samtools markdup test_samtools_markdup
-  command: nextflow run ./tests/modules/samtools/markdup -entry test_samtools_markdup -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/markdup/nextflow.config
-  tags:
-    - samtools/markdup
-    - samtools
-  files:
-    - path: output/samtools/test.markdup.bam
-      md5sum: 75f35284e20970d279a0baac5bbf8ee0
diff --git a/tests/modules/samtools/merge/main.nf b/tests/modules/samtools/merge/main.nf
deleted file mode 100644
index 0d01eb7203c..00000000000
--- a/tests/modules/samtools/merge/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf'
-
-workflow test_samtools_merge {
-    input = [ [ id: 'test' ], // meta map
-              [ 
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
-              ]
-            ]
-
-    SAMTOOLS_MERGE ( input, [], [] )
-}
-
-workflow test_samtools_merge_cram {
-    input = [ [ id: 'test' ], // meta map
-              [ 
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-              ]
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    SAMTOOLS_MERGE ( input, fasta, fai )
-}
-
-workflow test_samtools_merge_single_file {
-    input = [ [ id: 'test' ], // meta map
-              [
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-              ]
-            ]
-
-    SAMTOOLS_MERGE ( input, [], [] )
-}
diff --git a/tests/modules/samtools/merge/test.yml b/tests/modules/samtools/merge/test.yml
deleted file mode 100644
index 20594a28bd8..00000000000
--- a/tests/modules/samtools/merge/test.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-- name: samtools merge test_samtools_merge
-  command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge -c ./tests/config/nextflow.config -c ./tests/modules/samtools/merge/nextflow.config
-  tags:
-    - samtools
-    - samtools/merge
-  files:
-    - path: output/samtools/test.bam
-
-- name: samtools merge test_samtools_merge_cram
-  command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/merge/nextflow.config
-  tags:
-    - samtools
-    - samtools/merge
-  files:
-    - path: output/samtools/test.cram
-
-- name: samtools merge test_samtools_merge_single_file
-  command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge_single_file -c ./tests/config/nextflow.config -c ./tests/modules/samtools/merge/nextflow.config
-  tags:
-    - samtools
-    - samtools/merge
-  files:
-    - path: output/samtools/test.bam
-      md5sum: 6e38ae132fadae4cb4915814d6f872b2
diff --git a/tests/modules/samtools/mpileup/main.nf b/tests/modules/samtools/mpileup/main.nf
deleted file mode 100644
index f7fd4b43e06..00000000000
--- a/tests/modules/samtools/mpileup/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_MPILEUP } from '../../../../modules/samtools/mpileup/main.nf'
-
-workflow test_samtools_mpileup {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                []
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    SAMTOOLS_MPILEUP ( input, fasta )
-}
-
-workflow test_samtools_mpileup_intervals {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    SAMTOOLS_MPILEUP ( input, fasta )
-}
diff --git a/tests/modules/samtools/mpileup/test.yml b/tests/modules/samtools/mpileup/test.yml
deleted file mode 100644
index a7240136ee0..00000000000
--- a/tests/modules/samtools/mpileup/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: samtools mpileup test_samtools_mpileup
-  command: nextflow run tests/modules/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools/mpileup
-  files:
-    - path: output/samtools/test.mpileup.gz
-      md5sum: 29455c36377196e8bc9cf831cf17b5dc
-    - path: output/samtools/versions.yml
-
-- name: samtools mpileup test_samtools_mpileup_intervals
-  command: nextflow run tests/modules/samtools/mpileup -entry test_samtools_mpileup_intervals -c tests/config/nextflow.config
-  tags:
-    - samtools
-    - samtools/mpileup
-  files:
-    - path: output/samtools/test.mpileup.gz
-      md5sum: d0538ec23b294245748ced92484b9a8d
-    - path: output/samtools/versions.yml
diff --git a/tests/modules/samtools/sort/main.nf b/tests/modules/samtools/sort/main.nf
deleted file mode 100644
index 9853b3556ea..00000000000
--- a/tests/modules/samtools/sort/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_SORT } from '../../../../modules/samtools/sort/main.nf'
-
-workflow test_samtools_sort  {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-            ]
-
-    SAMTOOLS_SORT ( input )
-}
diff --git a/tests/modules/samtools/sort/test.yml b/tests/modules/samtools/sort/test.yml
deleted file mode 100644
index e7bfd59849d..00000000000
--- a/tests/modules/samtools/sort/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: samtools sort
-  command: nextflow run ./tests/modules/samtools/sort -entry test_samtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/samtools/sort/nextflow.config
-  tags:
-    - samtools
-    - samtools/sort
-  files:
-    - path: output/samtools/test.sorted.bam
-      md5sum: f00f5d392fd5c531e1fd528d9f57b32b
diff --git a/tests/modules/samtools/stats/main.nf b/tests/modules/samtools/stats/main.nf
deleted file mode 100644
index d83cbf4a6f2..00000000000
--- a/tests/modules/samtools/stats/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_STATS } from '../../../../modules/samtools/stats/main.nf'
-
-workflow test_samtools_stats {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-            ]
-
-    SAMTOOLS_STATS ( input, [])
-}
-
-workflow test_samtools_stats_cram {
-   input = [ [ id: 'test', single_end:true ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
-            ]
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    SAMTOOLS_STATS ( input, fasta )
-}
diff --git a/tests/modules/samtools/stats/test.yml b/tests/modules/samtools/stats/test.yml
deleted file mode 100644
index ae0c1dbcfcc..00000000000
--- a/tests/modules/samtools/stats/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: samtools stats test_samtools_stats
-  command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/stats/nextflow.config
-  tags:
-    - samtools/stats
-    - samtools
-  files:
-    - path: output/samtools/test.stats
-      md5sum: 5e6fa3805f6d6b330262456746709239
-
-- name: samtools stats test_samtools_stats_cram
-  command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/stats/nextflow.config
-  tags:
-    - samtools/stats
-    - samtools
-  files:
-    - path: output/samtools/test.stats
-      md5sum: 916a8e5bfd97a53f806e5a14565631bb
diff --git a/tests/modules/samtools/view/main.nf b/tests/modules/samtools/view/main.nf
deleted file mode 100644
index e9db03ed09c..00000000000
--- a/tests/modules/samtools/view/main.nf
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf'
-
-workflow test_samtools_view {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-                []
-            ]
-
-    SAMTOOLS_VIEW ( input, [], [] )
-}
-
-workflow test_samtools_view_cram {
-   input = [ [ id: 'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
-            ]
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    SAMTOOLS_VIEW ( input, fasta, [] )
-}
-
-workflow test_samtools_view_convert {
-    input = [ [ id: 'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                []
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    SAMTOOLS_VIEW ( input, fasta, [] )
-}
-
-workflow test_samtools_view_index {
-    input = [ [ id: 'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                []
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    SAMTOOLS_VIEW ( input, fasta, [] )
-}
-
-workflow test_samtools_view_filter {
-    input = [ [ id: 'test' ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                []
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    qname = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true)
-
-    SAMTOOLS_VIEW ( input, fasta, qname )
-}
-
-workflow test_samtools_view_stubs {
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
-                []
-            ]
-
-    SAMTOOLS_VIEW ( input, [], [] )
-}
diff --git a/tests/modules/samtools/view/test.yml b/tests/modules/samtools/view/test.yml
deleted file mode 100644
index 34c947249ee..00000000000
--- a/tests/modules/samtools/view/test.yml
+++ /dev/null
@@ -1,56 +0,0 @@
-- name: samtools view test_samtools_view
-  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
-  tags:
-    - samtools/view
-    - samtools
-  files:
-    - path: output/samtools/test.bam
-      md5sum: e6a9285be7b1c616dc4e17679fce5f1e
-
-- name: samtools view test_samtools_view_cram
-  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_cram -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
-  tags:
-    - samtools/view
-    - samtools
-  files:
-    - path: output/samtools/test.cram
-
-- name: samtools view test_samtools_view_convert
-  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_convert -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
-  tags:
-    - samtools/view
-    - samtools
-  files:
-    - path: output/samtools/test.bam
-      md5sum: 4f4a97da17db79c78b1912da3cdc1d8f
-
-- name: samtools view test_samtools_view_index
-  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_index -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
-  tags:
-    - samtools/view
-    - samtools
-  files:
-    - path: output/samtools/test.bam
-      md5sum: b2d2482cea94adfc9628473792b0d215
-    - path: output/samtools/test.bam.csi
-      md5sum: 343a2085b436cab2123147dafd255607
-
-- name: samtools view test_samtools_view_filter
-  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_filter -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
-  tags:
-    - samtools/view
-    - samtools
-  files:
-    - path: output/samtools/test.bam
-      md5sum: d8e20876423cb1123a559e4347115249
-    - path: output/samtools/test.bam.csi
-      md5sum: b1d688576e59529271333aa50b3ad3ae
-
-- name: samtools view test_samtools_view_stubs
-  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/view/nextflow.config
-  tags:
-    - samtools/view
-    - samtools
-  files:
-    - path: output/samtools/test.bam
-      md5sum: e6a9285be7b1c616dc4e17679fce5f1e
diff --git a/tests/modules/scoary/main.nf b/tests/modules/scoary/main.nf
deleted file mode 100644
index 5f080b7d62d..00000000000
--- a/tests/modules/scoary/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SCOARY } from '../../../modules/scoary/main.nf'
-
-workflow test_scoary {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("https://github.com/AdmiralenOla/Scoary/raw/master/scoary/exampledata/Gene_presence_absence.csv", checkIfExists: true),
-              file("https://github.com/AdmiralenOla/Scoary/raw/master/scoary/exampledata/Tetracycline_resistance.csv", checkIfExists: true) ]
-
-    tree = []
-    SCOARY ( input, tree)
-}
diff --git a/tests/modules/scoary/test.yml b/tests/modules/scoary/test.yml
deleted file mode 100644
index 7134409345e..00000000000
--- a/tests/modules/scoary/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: scoary test_scoary
-  command: nextflow run ./tests/modules/scoary -entry test_scoary -c ./tests/config/nextflow.config -c ./tests/modules/scoary/nextflow.config
-  tags:
-    - scoary
-  files:
-    - path: output/scoary/Bogus_trait.results.csv
-      md5sum: 9550c692bbe6ff0ac844357bfabb809b
-    - path: output/scoary/Tetracycline_resistance.results.csv
-      md5sum: a87740818ab4de69a758fc75d7b879dd
diff --git a/tests/modules/scramble/clusteranalysis/main.nf b/tests/modules/scramble/clusteranalysis/main.nf
deleted file mode 100644
index d31bac7201c..00000000000
--- a/tests/modules/scramble/clusteranalysis/main.nf
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SCRAMBLE_CLUSTERANALYSIS   } from '../../../../modules/scramble/clusteranalysis/main.nf'
-include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../modules/scramble/clusteridentifier/main.nf'
-
-workflow test_scramble_clusteranalysis {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['scramble']['bam'], checkIfExists: true),   
-        file(params.test_data['homo_sapiens']['scramble']['bam_bai'], checkIfExists: true),   
-        []
-    ]
-
-    fasta = []
-    mei_ref = []
-
-    SCRAMBLE_CLUSTERIDENTIFIER(
-        input,
-        fasta
-    )
-
-    SCRAMBLE_CLUSTERANALYSIS (
-        SCRAMBLE_CLUSTERIDENTIFIER.out.clusters,
-        fasta,
-        mei_ref
-    )
-}
-
-workflow test_scramble_clusteranalysis_fasta {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['scramble']['cram'], checkIfExists: true),   
-        file(params.test_data['homo_sapiens']['scramble']['cram_crai'], checkIfExists: true),   
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['scramble']['fasta'], checkIfExists: true)
-    mei_ref = []
-
-    SCRAMBLE_CLUSTERIDENTIFIER(
-        input,
-        fasta
-    )
-
-    SCRAMBLE_CLUSTERANALYSIS (
-        SCRAMBLE_CLUSTERIDENTIFIER.out.clusters,
-        fasta,
-        mei_ref
-    )
-}
\ No newline at end of file
diff --git a/tests/modules/scramble/clusteranalysis/test.yml b/tests/modules/scramble/clusteranalysis/test.yml
deleted file mode 100644
index a0599ea37c8..00000000000
--- a/tests/modules/scramble/clusteranalysis/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: scramble clusteranalysis test_scramble_clusteranalysis
-  command: nextflow run ./tests/modules/scramble/clusteranalysis -entry test_scramble_clusteranalysis -c ./tests/config/nextflow.config  -c ./tests/modules/scramble/clusteranalysis/nextflow.config
-  tags:
-    - scramble/clusteranalysis
-    - scramble
-  files:
-    - path: output/scramble/test.clusters.txt
-      md5sum: 9b2777a44bfbcff8fac1bf67c3985f1f
-    - path: output/scramble/test_MEIs.txt
-      md5sum: a14c40c7e5f3630defde68ae1de51bca
-
-- name: scramble clusteranalysis test_scramble_clusteranalysis_fasta
-  command: nextflow run ./tests/modules/scramble/clusteranalysis -entry test_scramble_clusteranalysis_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/scramble/clusteranalysis/nextflow.config
-  tags:
-    - scramble/clusteranalysis
-    - scramble
-  files:
-    - path: output/scramble/test.clusters.txt
-      md5sum: 9b2777a44bfbcff8fac1bf67c3985f1f
-    - path: output/scramble/test.vcf
-      contains: [fileformat=VCFv4.2]
-    - path: output/scramble/test_MEIs.txt
-      md5sum: a14c40c7e5f3630defde68ae1de51bca
-    - path: output/scramble/test_PredictedDeletions.txt
-      md5sum: 1fa0d3d0a58fdf81bd259b3c71774ba8
diff --git a/tests/modules/scramble/clusteridentifier/main.nf b/tests/modules/scramble/clusteridentifier/main.nf
deleted file mode 100644
index 6aea7f535ab..00000000000
--- a/tests/modules/scramble/clusteridentifier/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../modules/scramble/clusteridentifier/main.nf'
-
-workflow test_scramble_clusteridentifier_bam {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['scramble']['bam'], checkIfExists: true),   
-        file(params.test_data['homo_sapiens']['scramble']['bam_bai'], checkIfExists: true),   
-        []
-    ]
-
-    fasta = []
-
-    SCRAMBLE_CLUSTERIDENTIFIER ( input, fasta )
-}
-
-workflow test_scramble_clusteridentifier_cram {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['scramble']['cram'], checkIfExists: true),   
-        file(params.test_data['homo_sapiens']['scramble']['cram_crai'], checkIfExists: true),   
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['scramble']['fasta'], checkIfExists: true)
-
-    SCRAMBLE_CLUSTERIDENTIFIER ( input, fasta )
-}
diff --git a/tests/modules/scramble/clusteridentifier/test.yml b/tests/modules/scramble/clusteridentifier/test.yml
deleted file mode 100644
index c10a802e396..00000000000
--- a/tests/modules/scramble/clusteridentifier/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: scramble clusteridentifier test_scramble_clusteridentifier_bam
-  command: nextflow run ./tests/modules/scramble/clusteridentifier -entry test_scramble_clusteridentifier_bam -c ./tests/config/nextflow.config -c ./tests/modules/scramble/clusteridentifier/nextflow.config
-  tags:
-    - scramble/clusteridentifier
-    - scramble
-  files:
-    - path: output/scramble/test.clusters.txt
-      md5sum: 9b2777a44bfbcff8fac1bf67c3985f1f
-
-- name: scramble clusteridentifier test_scramble_clusteridentifier_cram
-  command: nextflow run ./tests/modules/scramble/clusteridentifier -entry test_scramble_clusteridentifier_cram -c ./tests/config/nextflow.config -c ./tests/modules/scramble/clusteridentifier/nextflow.config
-  tags:
-    - scramble/clusteridentifier
-    - scramble
-  files:
-    - path: output/scramble/test.clusters.txt
-      md5sum: 9b2777a44bfbcff8fac1bf67c3985f1f
diff --git a/tests/modules/seacr/callpeak/main.nf b/tests/modules/seacr/callpeak/main.nf
deleted file mode 100644
index 230d3a4c15a..00000000000
--- a/tests/modules/seacr/callpeak/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEACR_CALLPEAK } from '../../../../modules/seacr/callpeak/main.nf'
-
-workflow test_seacr_callpeak {
-    input = [ [ id:'test_1'],
-              file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_1'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_2'], checkIfExists: true) 
-            ]
-
-    SEACR_CALLPEAK ( input, 0.05 )
-}
-
-workflow test_seacr_callpeak_threshold {
-    input = [ [ id:'test_1'],
-              file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_1'], checkIfExists: true),
-              []
-            ]
-
-    SEACR_CALLPEAK ( input, 0.05 )
-}
\ No newline at end of file
diff --git a/tests/modules/seacr/callpeak/test.yml b/tests/modules/seacr/callpeak/test.yml
deleted file mode 100644
index 83c1c59a8d0..00000000000
--- a/tests/modules/seacr/callpeak/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: seacr callpeak
-  command: nextflow run ./tests/modules/seacr/callpeak -entry test_seacr_callpeak -c ./tests/config/nextflow.config -c ./tests/modules/seacr/callpeak/nextflow.config
-  tags:
-    - seacr
-    - seacr/callpeak
-  files:
-    - path: output/seacr/test_1.stringent.bed
-      md5sum: a3cb0c7c4ffa895788da3f0d6371b7df
-
-- name: seacr callpeak threshold
-  command: nextflow run ./tests/modules/seacr/callpeak -entry test_seacr_callpeak_threshold -c ./tests/config/nextflow.config -c ./tests/modules/seacr/callpeak/nextflow.config
-  tags:
-    - seacr
-    - seacr/callpeak
-  files:
-    - path: output/seacr/test_1.stringent.bed
-      md5sum: 1d23015c7087f7b48cc3139d53fd3463
diff --git a/tests/modules/seqkit/pair/main.nf b/tests/modules/seqkit/pair/main.nf
deleted file mode 100644
index 42bc9587780..00000000000
--- a/tests/modules/seqkit/pair/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQKIT_PAIR } from '../../../../modules/seqkit/pair/main.nf'
-
-workflow test_seqkit_pair {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    SEQKIT_PAIR ( input )
-}
diff --git a/tests/modules/seqkit/pair/test.yml b/tests/modules/seqkit/pair/test.yml
deleted file mode 100644
index 30373d69efa..00000000000
--- a/tests/modules/seqkit/pair/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: seqkit pair test_seqkit_pair
-  command: nextflow run tests/modules/seqkit/pair -entry test_seqkit_pair -c tests/config/nextflow.config
-  tags:
-    - seqkit/pair
-    - seqkit
-  files:
-    - path: output/seqkit/test_1.paired.fastq.gz
-      md5sum: fbfe7e8bdbc29abaaf58b6f1a32448e5
-    - path: output/seqkit/test_2.paired.fastq.gz
-      md5sum: 7d3c0912e5adc2674e8ecc1e647381b3
-    - path: output/seqkit/versions.yml
-      md5sum: 3086293bc986fc2ece38b1951d090819
diff --git a/tests/modules/seqkit/replace/main.nf b/tests/modules/seqkit/replace/main.nf
deleted file mode 100644
index 5c4058e7a95..00000000000
--- a/tests/modules/seqkit/replace/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQKIT_REPLACE } from '../../../../modules/seqkit/replace/main.nf'
-include { SEQKIT_REPLACE as SEQKIT_REPLACEUNCOMP } from '../../../../modules/seqkit/replace/main.nf'
-
-workflow test_seqkit_replace {
-
-    input = [ [ id:'test' ],   // meta map
-              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-            ]
-
-    SEQKIT_REPLACE ( input )
-}
-
-workflow test_seqkit_replace_uncomp {
-
-    input = [ [ id:'test' ],   // meta map
-              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-            ]
-
-    SEQKIT_REPLACEUNCOMP ( input )
-}
diff --git a/tests/modules/seqkit/replace/test.yml b/tests/modules/seqkit/replace/test.yml
deleted file mode 100644
index 94c3a5efff2..00000000000
--- a/tests/modules/seqkit/replace/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: seqkit replace test_seqkit_replace
-  command: nextflow run tests/modules/seqkit/replace -entry test_seqkit_replace -c tests/config/nextflow.config
-  tags:
-    - seqkit
-    - seqkit/replace
-  files:
-    - path: output/seqkit/test.fasta.gz
-      md5sum: 053847219695c0a923d02352442d7abf
-    - path: output/seqkit/versions.yml
-      md5sum: dc9d18b7836c9db00a3032fd191bd831
-
-- name: seqkit replace test_seqkit_replace_uncomp
-  command: nextflow run tests/modules/seqkit/replace -entry test_seqkit_replace_uncomp -c tests/config/nextflow.config
-  tags:
-    - seqkit
-    - seqkit/replace
-  files:
-    - path: output/seqkit/test..fasta
-      md5sum: 05d3294a62c72f5489f067c1da3c2f6c
-    - path: output/seqkit/versions.yml
-      md5sum: 3b88128487ec949f0bdeecebc375c407
diff --git a/tests/modules/seqkit/split2/main.nf b/tests/modules/seqkit/split2/main.nf
deleted file mode 100644
index acb9d41bbb1..00000000000
--- a/tests/modules/seqkit/split2/main.nf
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../modules/seqkit/split2/main.nf'
-include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE   } from '../../../../modules/seqkit/split2/main.nf'
-include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART   } from '../../../../modules/seqkit/split2/main.nf'
-
-workflow test_seqkit_split2_single_end_length {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SEQKIT_SPLIT2_LENGTH ( input )
-}
-
-workflow test_seqkit_split2_single_end_size {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SEQKIT_SPLIT2_SIZE ( input )
-}
-
-workflow test_seqkit_split2_single_end_part {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SEQKIT_SPLIT2_PART ( input )
-}
-
-workflow test_seqkit_split2_paired_end_length {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SEQKIT_SPLIT2_LENGTH ( input )
-}
-
-workflow test_seqkit_split2_paired_end_size {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SEQKIT_SPLIT2_SIZE ( input )
-}
-
-workflow test_seqkit_split2_paired_end_part {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SEQKIT_SPLIT2_PART ( input )
-}
diff --git a/tests/modules/seqkit/split2/test.yml b/tests/modules/seqkit/split2/test.yml
deleted file mode 100644
index 00368e22d81..00000000000
--- a/tests/modules/seqkit/split2/test.yml
+++ /dev/null
@@ -1,95 +0,0 @@
-- name: seqkit split2 test_seqkit_split2_single_end_length
-  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config
-  tags:
-    - seqkit
-    - seqkit/split2
-  files:
-    - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
-    - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: 45cccacb4676bca33beb17064322a781
-    - path: output/seqkit/versions.yml
-      md5sum: 2d5a709d129be364687cc0b561efa532
-
-- name: seqkit split2 test_seqkit_split2_single_end_size
-  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
-  tags:
-    - seqkit
-    - seqkit/split2
-  files:
-    - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: b09324606fb3636b51448d6a007d2c71
-    - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: f7873475d463e3b4d21dccbf8e859270
-    - path: output/seqkit/versions.yml
-      md5sum: 490d00accd1092a8eca4e83ed809bad3
-
-- name: seqkit split2 test_seqkit_split2_single_end_part
-  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
-  tags:
-    - seqkit
-    - seqkit/split2
-  files:
-    - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: a9d29d08e27246b6d36e21e5def405e3
-    - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: 6d547a959adcd027dd1a8734e195dd7d
-    - path: output/seqkit/test/test_1.part_003.fastq.gz
-      md5sum: 6d63cc8400dd2a96d808514fb18278ee
-    - path: output/seqkit/versions.yml
-      md5sum: 90431cd3d28954f656988230d4481115
-
-- name: seqkit split2 test_seqkit_split2_paired_end_length
-  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
-  tags:
-    - seqkit
-    - seqkit/split2
-  files:
-    - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: 7f489b2374c5fcc155a60ce2365a7bb7
-    - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: 45cccacb4676bca33beb17064322a781
-    - path: output/seqkit/test/test_2.part_001.fastq.gz
-      md5sum: 160b5fd363ff7cad8af9d914269d6426
-    - path: output/seqkit/test/test_2.part_002.fastq.gz
-      md5sum: 18bc5434cf55706394cccb44e6108561
-    - path: output/seqkit/versions.yml
-      md5sum: 9272afc1a126ae997a712edeef317f22
-
-- name: seqkit split2 test_seqkit_split2_paired_end_size
-  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
-  tags:
-    - seqkit
-    - seqkit/split2
-  files:
-    - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: b09324606fb3636b51448d6a007d2c71
-    - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: f7873475d463e3b4d21dccbf8e859270
-    - path: output/seqkit/test/test_2.part_001.fastq.gz
-      md5sum: c0602b62aae860dd284c0eb0062c24dd
-    - path: output/seqkit/test/test_2.part_002.fastq.gz
-      md5sum: 5bc7a98b618100b29910eb41c4c9ac0d
-    - path: output/seqkit/versions.yml
-      md5sum: af66912ae8abc493f77f70e3bf473144
-
-- name: seqkit split2 test_seqkit_split2_paired_end_part
-  command: nextflow run tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
-  tags:
-    - seqkit
-    - seqkit/split2
-  files:
-    - path: output/seqkit/test/test_1.part_001.fastq.gz
-      md5sum: a9d29d08e27246b6d36e21e5def405e3
-    - path: output/seqkit/test/test_1.part_002.fastq.gz
-      md5sum: 6d547a959adcd027dd1a8734e195dd7d
-    - path: output/seqkit/test/test_1.part_003.fastq.gz
-      md5sum: 6d63cc8400dd2a96d808514fb18278ee
-    - path: output/seqkit/test/test_2.part_001.fastq.gz
-      md5sum: b51a1bed106e4ec0c9be7d9e224d0616
-    - path: output/seqkit/test/test_2.part_002.fastq.gz
-      md5sum: 079078a7f86114ae29cda8c00d5a7fc9
-    - path: output/seqkit/test/test_2.part_003.fastq.gz
-      md5sum: 6987941bf8c4a37565e333029ba41ca0
-    - path: output/seqkit/versions.yml
-      md5sum: 193bc5f0c429076f816ab0a529c4c1fc
diff --git a/tests/modules/seqkit/stats/main.nf b/tests/modules/seqkit/stats/main.nf
deleted file mode 100644
index 774421154d9..00000000000
--- a/tests/modules/seqkit/stats/main.nf
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQKIT_STATS } from '../../../../modules/seqkit/stats/main.nf'
-
-workflow test_seqkit_stats_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    SEQKIT_STATS ( input )
-}
-
-workflow test_seqkit_stats_paired_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    SEQKIT_STATS ( input )
-}
-
-workflow test_seqkit_stats_nanopore {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
-    ]
-
-    SEQKIT_STATS ( input )
-}
-
-workflow test_seqkit_stats_genome_fasta {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-    ]
-
-    SEQKIT_STATS ( input )
-}
-
-workflow test_seqkit_stats_transcriptome_fasta {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true),
-    ]
-
-    SEQKIT_STATS ( input )
-}
diff --git a/tests/modules/seqkit/stats/test.yml b/tests/modules/seqkit/stats/test.yml
deleted file mode 100644
index fdf4533f56f..00000000000
--- a/tests/modules/seqkit/stats/test.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-- name: seqkit stats test_seqkit_stats_single_end
-  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_single_end -c tests/config/nextflow.config
-  tags:
-    - seqkit/stats
-    - seqkit
-  files:
-    - path: output/seqkit/test.tsv
-      md5sum: e23227d089a7e04b0ec0cb547c4aadff
-    - path: output/seqkit/versions.yml
-      md5sum: d67f0c16feb9df77b11f6c91bbdf9926
-
-- name: seqkit stats test_seqkit_stats_paired_end
-  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_paired_end -c tests/config/nextflow.config
-  tags:
-    - seqkit/stats
-    - seqkit
-  files:
-    - path: output/seqkit/test.tsv
-      md5sum: 9de20dc39fb01285e3f0c382fda9db52
-    - path: output/seqkit/versions.yml
-      md5sum: bd8881933b953d07f2600e2e6a88ebf3
-
-- name: seqkit stats test_seqkit_stats_nanopore
-  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_nanopore -c tests/config/nextflow.config
-  tags:
-    - seqkit/stats
-    - seqkit
-  files:
-    - path: output/seqkit/test.tsv
-      md5sum: 5da1709eb5ae64fa3b2d624bffe2e7aa
-    - path: output/seqkit/versions.yml
-      md5sum: 565632701fbe048f7ba99f1865bd48ca
-
-- name: seqkit stats test_seqkit_stats_genome_fasta
-  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_genome_fasta -c tests/config/nextflow.config
-  tags:
-    - seqkit/stats
-    - seqkit
-  files:
-    - path: output/seqkit/test.tsv
-      md5sum: f64489767a4e769539ef3faf83260184
-    - path: output/seqkit/versions.yml
-      md5sum: 782fcdeaa922c8bb532ffa5808849d87
-
-- name: seqkit stats test_seqkit_stats_transcriptome_fasta
-  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_transcriptome_fasta -c tests/config/nextflow.config
-  tags:
-    - seqkit/stats
-    - seqkit
-  files:
-    - path: output/seqkit/test.tsv
-      md5sum: fbb975b665a08c8862fcd1268613a945
-    - path: output/seqkit/versions.yml
-      md5sum: db99b016d986d26102ec398264a58410
diff --git a/tests/modules/seqsero2/main.nf b/tests/modules/seqsero2/main.nf
deleted file mode 100644
index 9587bf9ffa5..00000000000
--- a/tests/modules/seqsero2/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQSERO2 } from '../../../modules/seqsero2/main.nf'
-
-workflow test_seqsero2 {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    SEQSERO2 ( input )
-}
diff --git a/tests/modules/seqsero2/test.yml b/tests/modules/seqsero2/test.yml
deleted file mode 100644
index 0ebb7324f1c..00000000000
--- a/tests/modules/seqsero2/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: seqsero2 test_seqsero2
-  command: nextflow run ./tests/modules/seqsero2 -entry test_seqsero2 -c ./tests/config/nextflow.config -c ./tests/modules/seqsero2/nextflow.config
-  tags:
-    - seqsero2
-  files:
-    - path: output/seqsero2/results/SeqSero_log.txt
-      md5sum: d00242dfa734b5abb3622a6048f0b4fb
-    - path: output/seqsero2/results/SeqSero_result.tsv
-      contains: ["Sample", "Predicted", "Note"]
-    - path: output/seqsero2/results/SeqSero_result.txt
-      contains: ["Sample", "Predicted", "Note"]
diff --git a/tests/modules/seqtk/mergepe/main.nf b/tests/modules/seqtk/mergepe/main.nf
deleted file mode 100644
index b8e12213ef7..00000000000
--- a/tests/modules/seqtk/mergepe/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQTK_MERGEPE } from '../../../../modules/seqtk/mergepe/main.nf'
-
-//
-// Test with single-end data
-//
-
-workflow test_seqtk_mergepe_single_end {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-
-    SEQTK_MERGEPE ( input )
-}
-
-//
-// Test with paired-end data
-//
-
-workflow test_seqtk_mergepe_paired_end {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SEQTK_MERGEPE ( input )
-}
diff --git a/tests/modules/seqtk/mergepe/test.yml b/tests/modules/seqtk/mergepe/test.yml
deleted file mode 100644
index 9d355f7c82d..00000000000
--- a/tests/modules/seqtk/mergepe/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: seqtk mergepe test_seqtk_mergepe_single_end
-  command: nextflow run ./tests/modules/seqtk/mergepe -entry test_seqtk_mergepe_single_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/mergepe/nextflow.config
-  tags:
-    - seqtk/mergepe
-    - seqtk
-  files:
-    - path: output/seqtk/test.processed.fastq.gz
-      contains:
-        - "@"
-        - "+"
-
-- name: seqtk mergepe test_seqtk_mergepe_paired_end
-  command: nextflow run ./tests/modules/seqtk/mergepe -entry test_seqtk_mergepe_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/mergepe/nextflow.config
-  tags:
-    - seqtk/mergepe
-    - seqtk
-  files:
-    - path: output/seqtk/test.processed.fastq.gz
-      contains:
-        - "@"
-        - "+"
diff --git a/tests/modules/seqtk/rename/main.nf b/tests/modules/seqtk/rename/main.nf
deleted file mode 100644
index 1f81352d24b..00000000000
--- a/tests/modules/seqtk/rename/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQTK_RENAME } from '../../../../modules/seqtk/rename/main.nf'
-
-workflow test_seqtk_rename {
-    input = [ [ id:'test' ],   // meta map
-              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-            ]
-    SEQTK_RENAME ( input )
-}
-
-workflow test_seqtk_rename_fq {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    SEQTK_RENAME ( input )
-}
diff --git a/tests/modules/seqtk/rename/test.yml b/tests/modules/seqtk/rename/test.yml
deleted file mode 100644
index ffbc8849147..00000000000
--- a/tests/modules/seqtk/rename/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: seqtk rename test_seqtk_rename
-  command: nextflow run tests/modules/seqtk/rename -entry test_seqtk_rename -c tests/config/nextflow.config
-  tags:
-    - seqtk
-    - seqtk/rename
-  files:
-    - path: output/seqtk/test.renamed.fasta.gz
-      contains:
-        - ">test1"
-
-- name: seqtk rename test_seqtk_rename_fq
-  command: nextflow run tests/modules/seqtk/rename -entry test_seqtk_rename_fq -c tests/config/nextflow.config
-  tags:
-    - seqtk
-    - seqtk/rename
-  files:
-    - path: output/seqtk/test.renamed.fastq.gz
-      contains:
-        - "@test1"
-        - "@test2"
-        - "@test3"
diff --git a/tests/modules/seqtk/sample/main.nf b/tests/modules/seqtk/sample/main.nf
deleted file mode 100644
index 6899ef62fcc..00000000000
--- a/tests/modules/seqtk/sample/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQTK_SAMPLE } from '../../../../modules/seqtk/sample/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_seqtk_sample_single_end {
-
-    input = [ [ id:'test', single_end:true ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-
-    SEQTK_SAMPLE ( input, 50 )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_seqtk_sample_paired_end {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SEQTK_SAMPLE ( input, 50 )
-}
diff --git a/tests/modules/seqtk/sample/test.yml b/tests/modules/seqtk/sample/test.yml
deleted file mode 100644
index 2a677e0ad6a..00000000000
--- a/tests/modules/seqtk/sample/test.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-- name: seqtk sample test_seqtk_sample_single_end
-  command: nextflow run ./tests/modules/seqtk/sample -entry test_seqtk_sample_single_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/sample/nextflow.config
-  tags:
-    - seqtk
-    - seqtk/sample
-  files:
-    - path: output/seqtk/test.sampled.fastq.gz
-      contains:
-        - "@ERR5069949"
-
-- name: seqtk sample test_seqtk_sample_paired_end
-  command: nextflow run ./tests/modules/seqtk/sample -entry test_seqtk_sample_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/sample/nextflow.config
-  tags:
-    - seqtk
-    - seqtk/sample
-  files:
-    - path: output/seqtk/test.sampled_1.fastq.gz
-      contains:
-        - "@ERR5069949"
-    - path: output/seqtk/test.sampled_2.fastq.gz
-      contains:
-        - "@ERR5069949"
diff --git a/tests/modules/seqtk/seq/main.nf b/tests/modules/seqtk/seq/main.nf
deleted file mode 100644
index 4351b8a961a..00000000000
--- a/tests/modules/seqtk/seq/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQTK_SEQ } from '../../../../modules/seqtk/seq/main.nf'
-
-workflow test_seqtk_seq {
-    input = [ [ id:'test' ],   // meta map
-              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-            ]
-    SEQTK_SEQ ( input )
-}
-
-workflow test_seqtk_seq_fq {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    SEQTK_SEQ ( input )
-}
\ No newline at end of file
diff --git a/tests/modules/seqtk/seq/test.yml b/tests/modules/seqtk/seq/test.yml
deleted file mode 100644
index 0d709c57d31..00000000000
--- a/tests/modules/seqtk/seq/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: seqtk seq test_seqtk_seq
-  command: nextflow run tests/modules/seqtk/seq -entry test_seqtk_seq -c tests/config/nextflow.config
-  tags:
-    - seqtk/seq
-    - seqtk
-  files:
-    - path: output/seqtk/test.seqtk-seq.fasta.gz
-      md5sum: 50d73992c8c7e56dc095ef47ec52a754
-
-- name: seqtk seq test_seqtk_seq_fq
-  command: nextflow run tests/modules/seqtk/seq -entry test_seqtk_seq_fq -c tests/config/nextflow.config
-  tags:
-    - seqtk/seq
-    - seqtk
-  files:
-    - path: output/seqtk/test.seqtk-seq.fasta.gz
-      contains:
-        - ">ERR5069949"
diff --git a/tests/modules/seqtk/subseq/main.nf b/tests/modules/seqtk/subseq/main.nf
deleted file mode 100644
index 608b7c2f069..00000000000
--- a/tests/modules/seqtk/subseq/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQTK_SUBSEQ } from '../../../../modules/seqtk/subseq/main.nf'
-
-workflow test_seqtk_subseq {
-    
-    sequences = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    filter_list = file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true)
-
-    SEQTK_SUBSEQ ( sequences, filter_list )
-}
diff --git a/tests/modules/seqtk/subseq/test.yml b/tests/modules/seqtk/subseq/test.yml
deleted file mode 100644
index 4003e3ab89c..00000000000
--- a/tests/modules/seqtk/subseq/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: seqtk subseq test_seqtk_subseq
-  command: nextflow run ./tests/modules/seqtk/subseq -entry test_seqtk_subseq -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/subseq/nextflow.config
-  tags:
-    - seqtk
-    - seqtk/subseq
-  files:
-    - path: output/seqtk/genome.fasta.filtered.fa.gz
-      md5sum: 488001c0fbedabf24d3e10fe7f96c78a
diff --git a/tests/modules/sequenzautils/bam2seqz/main.nf b/tests/modules/sequenzautils/bam2seqz/main.nf
deleted file mode 100755
index fcd4c7c721c..00000000000
--- a/tests/modules/sequenzautils/bam2seqz/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../modules/sequenzautils/bam2seqz/main.nf'
-
-workflow test_sequenzautils_bam2seqz {
-
-    tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
-
-    input = [ [ id:'test' ], // meta map
-              tumourbam,
-              normalbam
-            ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    wig   = file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true)
-
-    SEQUENZAUTILS_BAM2SEQZ ( input, fasta, wig )
-}
diff --git a/tests/modules/sequenzautils/bam2seqz/test.yml b/tests/modules/sequenzautils/bam2seqz/test.yml
deleted file mode 100644
index f3ea6cf0ba2..00000000000
--- a/tests/modules/sequenzautils/bam2seqz/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: sequenzautils bam2seqz
-  command: nextflow run ./tests/modules/sequenzautils/bam2seqz -entry test_sequenzautils_bam2seqz -c ./tests/config/nextflow.config -c ./tests/modules/sequenzautils/bam2seqz/nextflow.config
-  tags:
-    - sequenzautils
-    - sequenzautils/bam2seqz
-  files:
-    - path: output/sequenzautils/test.gz
-      md5sum: 12b41979a498ac10c0aff162b12e6a6e
diff --git a/tests/modules/sequenzautils/gcwiggle/main.nf b/tests/modules/sequenzautils/gcwiggle/main.nf
deleted file mode 100644
index b25e037eb82..00000000000
--- a/tests/modules/sequenzautils/gcwiggle/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQUENZAUTILS_GCWIGGLE } from '../../../../modules/sequenzautils/gcwiggle/main.nf'
-
-workflow test_sequenzautils_gcwiggle {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-            ]
-
-    SEQUENZAUTILS_GCWIGGLE ( input )
-}
diff --git a/tests/modules/sequenzautils/gcwiggle/test.yml b/tests/modules/sequenzautils/gcwiggle/test.yml
deleted file mode 100644
index 21ddc4ab0ef..00000000000
--- a/tests/modules/sequenzautils/gcwiggle/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: sequenzautils gcwiggle
-  command: nextflow run ./tests/modules/sequenzautils/gcwiggle -entry test_sequenzautils_gcwiggle -c ./tests/config/nextflow.config -c ./tests/modules/sequenzautils/gcwiggle/nextflow.config
-  tags:
-    - sequenzautils
-    - sequenzautils/gcwiggle
-  files:
-    - path: output/sequenzautils/test.wig.gz
diff --git a/tests/modules/seqwish/induce/main.nf b/tests/modules/seqwish/induce/main.nf
deleted file mode 100644
index b83a904f2ff..00000000000
--- a/tests/modules/seqwish/induce/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQWISH_INDUCE } from '../../../../modules/seqwish/induce/main.nf'
-
-workflow test_seqwish_induce_transcriptome {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['transcriptome_paf'], checkIfExists: true)],
-              [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-            ]
-
-    SEQWISH_INDUCE ( input )
-}
-
-workflow test_seqwish_induce_pangenome {
-    input = [ [ id:'test' ], // meta map
-            [ file(params.test_data['homo_sapiens']['pangenome']['pangenome_paf'], checkIfExists: true)],
-            [ file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa'], checkIfExists: true) ]
-        ]
-
-    SEQWISH_INDUCE ( input )
-}
diff --git a/tests/modules/seqwish/induce/test.yml b/tests/modules/seqwish/induce/test.yml
deleted file mode 100644
index 8a700f3e8af..00000000000
--- a/tests/modules/seqwish/induce/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: seqwish induce transcriptome
-  command: nextflow run ./tests/modules/seqwish/induce -entry test_seqwish_induce_transcriptome -c ./tests/config/nextflow.config -c ./tests/modules/seqwish/induce/nextflow.config
-  tags:
-    - seqwish
-    - seqwish/induce
-  files:
-    - path: output/seqwish/test.gfa
-      md5sum: 216a02d3aca322a457c31a62c628548e
-
-- name: seqwish induce pangenome
-  command: nextflow run ./tests/modules/seqwish/induce -entry test_seqwish_induce_pangenome -c ./tests/config/nextflow.config -c ./tests/modules/seqwish/induce/nextflow.config
-  tags:
-    - seqwish
-    - seqwish/induce
-  files:
-    - path: output/seqwish/test.gfa
-      md5sum: a73e998dc13a75d86d4685b12625d784
diff --git a/tests/modules/seroba/run/main.nf b/tests/modules/seroba/run/main.nf
deleted file mode 100644
index 62df1d3ff75..00000000000
--- a/tests/modules/seroba/run/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEROBA_RUN } from '../../../../modules/seroba/run/main.nf'
-
-workflow test_seroba_run {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true),
-                file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ]
-            ]
-
-    SEROBA_RUN ( input )
-}
diff --git a/tests/modules/seroba/run/test.yml b/tests/modules/seroba/run/test.yml
deleted file mode 100644
index 2aa6f81488e..00000000000
--- a/tests/modules/seroba/run/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: seroba run test_seroba_run
-  command: nextflow run ./tests/modules/seroba/run -entry test_seroba_run -c ./tests/config/nextflow.config  -c ./tests/modules/seroba/run/nextflow.config
-  tags:
-    - seroba
-    - seroba/run
-  files:
-    - path: output/seroba/test/test.tsv
-      md5sum: 28b2ce33df270172e6a39db4429e684b
diff --git a/tests/modules/sexdeterrmine/main.nf b/tests/modules/sexdeterrmine/main.nf
deleted file mode 100644
index fc777905fec..00000000000
--- a/tests/modules/sexdeterrmine/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_DEPTH } from '../../../modules/samtools/depth/main.nf'
-include { SEXDETERRMINE } from '../../../modules/sexdeterrmine/main.nf'
-
-workflow test_sexdeterrmine {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test3_single_end_markduplicates_sorted_bam'], checkIfExists: true) ]
-
-    SAMTOOLS_DEPTH ( input )
-    SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )
-}
diff --git a/tests/modules/sexdeterrmine/test.yml b/tests/modules/sexdeterrmine/test.yml
deleted file mode 100644
index bb3f701ed3f..00000000000
--- a/tests/modules/sexdeterrmine/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: sexdeterrmine test_sexdeterrmine
-  command: nextflow run tests/modules/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config
-  tags:
-    - sexdeterrmine
-  files:
-    - path: output/samtools/test.tsv
-      md5sum: fa2992ca1ea93a6e1b3e838476191935
-    - path: output/samtools/versions.yml
-      md5sum: dbd04b700335c8ad236bd667254c8dd8
-    - path: output/sexdeterrmine/sexdeterrmine.json
-      md5sum: bafb2419bb8630eda29a251c20e97166
-    - path: output/sexdeterrmine/test_sexdet.tsv
-      md5sum: 1cf8a2b97b38353eb97a96ab872dcca9
-    - path: output/sexdeterrmine/versions.yml
-      md5sum: 077361101e8e7997aec3da8a01e59eee
diff --git a/tests/modules/shasta/main.nf b/tests/modules/shasta/main.nf
deleted file mode 100644
index 3838d1d4648..00000000000
--- a/tests/modules/shasta/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SHASTA } from '../../../modules/shasta/main.nf'
-
-workflow test_shasta {
-    
-    input = [ 
-        [ id:'test', model:'Nanopore-Dec2019' ], // meta map
-        [ file(params.test_data['candidatus_portiera_aleyrodidarum']['nanopore']['test_fastq_gz']) ],
-    ]
-
-    SHASTA ( input )
-}
diff --git a/tests/modules/shasta/test.yml b/tests/modules/shasta/test.yml
deleted file mode 100644
index 9b9b054caf6..00000000000
--- a/tests/modules/shasta/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: shasta test_shasta
-  command: nextflow run ./tests/modules/shasta -entry test_shasta -c ./tests/config/nextflow.config  -c ./tests/modules/shasta/nextflow.config
-  tags:
-    - shasta
-  files:
-    - path: output/shasta/ShastaRun/Assembly-BothStrands-NoSequence.gfa
-    - path: output/shasta/ShastaRun/Assembly-BothStrands.gfa
-    - path: output/shasta/ShastaRun/Assembly.fasta
-    - path: output/shasta/ShastaRun/Assembly.gfa
-    - path: output/shasta/ShastaRun/AssemblySummary.csv
-    - path: output/shasta/ShastaRun/AssemblySummary.html
-    - path: output/shasta/ShastaRun/AssemblySummary.json
-    - path: output/shasta/ShastaRun/Binned-ReadLengthHistogram.csv
-      md5sum: f7997650e6ff2b060c583c6fa796628e
-    - path: output/shasta/ShastaRun/DisjointSetsHistogram.csv
-      md5sum: eecb9fae34b719dad64952257e2398a6
-    - path: output/shasta/ShastaRun/LowHashBucketHistogram.csv
-      md5sum: e5eb4a0d28ade913de6584928f32b7aa
-    - path: output/shasta/ShastaRun/MarkerGraphEdgeCoverageHistogram.csv
-      md5sum: 37ecac444067fbf4e0d96dc2705a9ada
-    - path: output/shasta/ShastaRun/MarkerGraphVertexCoverageHistogram.csv
-      md5sum: ccb236ab97ab1b9964b4856aa47d3c94
-    - path: output/shasta/ShastaRun/ReadGraphComponents.csv
-    - path: output/shasta/ShastaRun/ReadLengthHistogram.csv
-      md5sum: ccb25c4850ba2682fd1d452d6596d7bc
-    - path: output/shasta/ShastaRun/ReadLowHashStatistics.csv
-      md5sum: 2431d47341b239cb6edf8e3a7a76021f
-    - path: output/shasta/ShastaRun/ReadSummary.csv
-      md5sum: 8e0bffccf7afae54a937266949d118af
-    - path: output/shasta/ShastaRun/index.html
-      md5sum: 2d067ccc873b94a73e7300fe597db135
-    - path: output/shasta/ShastaRun/shasta.conf
-      md5sum: cba4aebac8a74eb5868f4a20f04bc618
-    - path: output/shasta/test_Assembly.fasta.gz
-    - path: output/shasta/test_Assembly.gfa.gz
diff --git a/tests/modules/shasum/main.nf b/tests/modules/shasum/main.nf
deleted file mode 100644
index 817ea6f08da..00000000000
--- a/tests/modules/shasum/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SHASUM } from '../../../modules/shasum/main.nf'
-
-workflow test_shasum {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    SHASUM ( input )
-}
diff --git a/tests/modules/shasum/test.yml b/tests/modules/shasum/test.yml
deleted file mode 100644
index 6778d156049..00000000000
--- a/tests/modules/shasum/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: shasum test_shasum
-  command: nextflow run tests/modules/shasum -entry test_shasum -c tests/config/nextflow.config
-  tags:
-    - shasum
-  files:
-    - path: output/shasum/test.paired_end.bam.sha256
-      md5sum: 138a19e100f09fc975ea1b717da9b6dd
-    - path: output/shasum/versions.yml
diff --git a/tests/modules/shigatyper/main.nf b/tests/modules/shigatyper/main.nf
deleted file mode 100644
index eb4df084543..00000000000
--- a/tests/modules/shigatyper/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SHIGATYPER } from '../../../modules/shigatyper/main.nf'
-
-workflow test_shigatyper_pe {
-    
-    input = [ 
-        [ id:'test', single_end:false, is_ont:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    SHIGATYPER ( input )
-}
-
-workflow test_shigatyper_se {
-    
-    input = [ 
-        [ id:'test', single_end:true, is_ont:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    SHIGATYPER ( input )
-}
-
-workflow test_shigatyper_ont {
-    
-    input = [ 
-        [ id:'test', single_end:true, is_ont:true ], // meta map
-        [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
-    ]
-
-    SHIGATYPER ( input )
-}
diff --git a/tests/modules/shigatyper/test.yml b/tests/modules/shigatyper/test.yml
deleted file mode 100644
index 9dda573be42..00000000000
--- a/tests/modules/shigatyper/test.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-- name: shigatyper test_shigatyper_pe
-  command: nextflow run tests/modules/shigatyper -entry test_shigatyper_pe -c tests/config/nextflow.config -c tests/modules/shigatyper/nextflow.config
-  tags:
-    - shigatyper
-  files:
-    - path: output/shigatyper/test.tsv
-      md5sum: 4f7d38c956993800546b9acb9881d717
-    - path: output/shigatyper/versions.yml
-      md5sum: d8ca45ed88dfba9bc570c01e4b49773b
-
-- name: shigatyper test_shigatyper_se
-  command: nextflow run tests/modules/shigatyper -entry test_shigatyper_se -c tests/config/nextflow.config -c tests/modules/shigatyper/nextflow.config
-  tags:
-    - shigatyper
-  files:
-    - path: output/shigatyper/test.tsv
-      md5sum: 4f7d38c956993800546b9acb9881d717
-    - path: output/shigatyper/versions.yml
-      md5sum: 8bbf165da5a5df3b7771a33aad197eec
-
-- name: shigatyper test_shigatyper_ont
-  command: nextflow run tests/modules/shigatyper -entry test_shigatyper_ont -c tests/config/nextflow.config -c tests/modules/shigatyper/nextflow.config
-  tags:
-    - shigatyper
-  files:
-    - path: output/shigatyper/test.tsv
-      md5sum: 4f7d38c956993800546b9acb9881d717
-    - path: output/shigatyper/versions.yml
-      md5sum: 0da333e1178e9e7e84a9116ad5a5ff71
diff --git a/tests/modules/shovill/main.nf b/tests/modules/shovill/main.nf
deleted file mode 100644
index 2416022f31a..00000000000
--- a/tests/modules/shovill/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SHOVILL                    } from '../../../modules/shovill/main.nf'
-include { SHOVILL as SHOVILL_SKESA   } from '../../../modules/shovill/main.nf'
-include { SHOVILL as SHOVILL_MEGAHIT } from '../../../modules/shovill/main.nf'
-include { SHOVILL as SHOVILL_VELVET  } from '../../../modules/shovill/main.nf'
-
-workflow test_shovill {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true),
-                file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ]
-            ]
-
-    SHOVILL ( input )
-}
-
-workflow test_shovill_megahit {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SHOVILL_MEGAHIT ( input )
-}
-
-workflow test_shovill_skesa {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SHOVILL_SKESA ( input )
-}
-
-workflow test_shovill_velvet {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SHOVILL_VELVET ( input )
-}
diff --git a/tests/modules/shovill/test.yml b/tests/modules/shovill/test.yml
deleted file mode 100644
index 6fdd2f3f3ad..00000000000
--- a/tests/modules/shovill/test.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-- name: shovill with spades
-  command: nextflow run ./tests/modules/shovill -entry test_shovill -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config
-  tags:
-    - shovill
-  files:
-    - path: output/shovill/contigs.gfa
-      md5sum: 277af5d8ae8a0d2432db59a316226828
-    - path: output/shovill/spades.fasta
-      md5sum: 2506fc2af3a24397a3c5d3fbda0861fb
-    # MD5sum not reproducible (timestamp)
-    - path: output/shovill/contigs.fa
-    - path: output/shovill/shovill.corrections
-    - path: output/shovill/shovill.log
-
-- name: shovill with megahit
-  command: nextflow run ./tests/modules/shovill -entry test_shovill_megahit -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config
-  tags:
-    - shovill
-  files:
-    - path: output/shovill/shovill.corrections
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    # MD5sum not reproducible (timestamp, contig order)
-    - path: output/shovill/contigs.fa
-    - path: output/shovill/contigs.fastg
-    - path: output/shovill/megahit.fasta
-    - path: output/shovill/shovill.log
-
-- name: shovill with skesa
-  command: nextflow run ./tests/modules/shovill -entry test_shovill_skesa -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config
-  tags:
-    - shovill
-  files:
-    - path: output/shovill/shovill.corrections
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/shovill/skesa.fasta
-      md5sum: 8157837dbe8315922f588dafa7af5ef8
-    # MD5sum not reproducible (timestamp)
-    - path: output/shovill/contigs.fa
-    - path: output/shovill/shovill.log
-
-- name: shovill with velvet
-  command: nextflow run ./tests/modules/shovill -entry test_shovill_velvet -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config
-  tags:
-    - shovill
-  files:
-    # MD5sum not reproducible (timestamp, contig order)
-    - path: output/shovill/contigs.fa
-    - path: output/shovill/contigs.LastGraph
-    - path: output/shovill/shovill.corrections
-    - path: output/shovill/shovill.log
-    - path: output/shovill/velvet.fasta
diff --git a/tests/modules/sistr/main.nf b/tests/modules/sistr/main.nf
deleted file mode 100644
index 4bd8484470f..00000000000
--- a/tests/modules/sistr/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SISTR } from '../../../modules/sistr/main.nf'
-
-workflow test_sistr {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
-    ]
-
-    SISTR ( input )
-}
diff --git a/tests/modules/sistr/test.yml b/tests/modules/sistr/test.yml
deleted file mode 100644
index 88182f28c98..00000000000
--- a/tests/modules/sistr/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: sistr test_sistr
-  command: nextflow run tests/modules/sistr -entry test_sistr -c tests/config/nextflow.config
-  tags:
-    - sistr
-  files:
-    - path: output/sistr/test-allele.fasta
-      md5sum: 144a74999eb9dd01520be5c61e8bd210
-    - path: output/sistr/test-allele.json
-      md5sum: 3eb993c9489904621f539a93ff9a90ec
-    - path: output/sistr/test-cgmlst.csv
-      md5sum: c50a2144955fe1b98a6d5792bf295088
-    - path: output/sistr/test.tab
-      contains: ["cgmlst_ST", "serovar", "matched"]
-    - path: output/sistr/versions.yml
-      md5sum: 8b852f002c3ce67e3f6498da15b28296
diff --git a/tests/modules/slimfastq/main.nf b/tests/modules/slimfastq/main.nf
deleted file mode 100644
index 40d44285f42..00000000000
--- a/tests/modules/slimfastq/main.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SLIMFASTQ } from '../../../modules/slimfastq/main.nf'
-
-workflow test_slimfastq_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-
-    SLIMFASTQ ( input )
-}
-
-workflow test_slimfastq_paired_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-         file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
-    ]
-
-    SLIMFASTQ ( input )
-}
-
-workflow test_slimfastq_nanopore {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
-    ]
-
-    SLIMFASTQ ( input )
-}
-
-workflow test_slimfastq_pacbio {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true)
-    ]
-
-    SLIMFASTQ ( input )
-}
diff --git a/tests/modules/slimfastq/test.yml b/tests/modules/slimfastq/test.yml
deleted file mode 100644
index f0d8b446a65..00000000000
--- a/tests/modules/slimfastq/test.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-- name: slimfastq test_slimfastq_single_end
-  command: nextflow run tests/modules/slimfastq -entry test_slimfastq_single_end -c tests/config/nextflow.config
-  tags:
-    - slimfastq
-  files:
-    - path: output/slimfastq/test.sfq
-      md5sum: 6a942eeca6c99ee9a9a0cedab5d246f1
-    - path: output/slimfastq/versions.yml
-      md5sum: f52351f5c9e6259af02745c8eae5c780
-
-- name: slimfastq test_slimfastq_paired_end
-  command: nextflow run tests/modules/slimfastq -entry test_slimfastq_paired_end -c tests/config/nextflow.config
-  tags:
-    - slimfastq
-  files:
-    - path: output/slimfastq/test_1.sfq
-      md5sum: 6a942eeca6c99ee9a9a0cedab5d246f1
-    - path: output/slimfastq/test_2.sfq
-      md5sum: 0d2c60b52a39f7c2cb7843e848d90afd
-    - path: output/slimfastq/versions.yml
-      md5sum: 6239853705877651a4851c4cb6d62da4
-
-- name: slimfastq test_slimfastq_nanopore
-  command: nextflow run tests/modules/slimfastq -entry test_slimfastq_nanopore -c tests/config/nextflow.config
-  tags:
-    - slimfastq
-  files:
-    - path: output/slimfastq/test.sfq
-      md5sum: e17f14d64d3a75356b03ff2f9e8881f7
-    - path: output/slimfastq/versions.yml
-      md5sum: 33153f1103482a2bd35cb2f4c337c5e8
-
-- name: slimfastq test_slimfastq_pacbio
-  command: nextflow run tests/modules/slimfastq -entry test_slimfastq_pacbio -c tests/config/nextflow.config
-  tags:
-    - slimfastq
-  files:
-    - path: output/slimfastq/test.sfq
-      md5sum: 9e8389e47e6ddf8c25e92412dd628339
-    - path: output/slimfastq/versions.yml
-      md5sum: 1982789c3d5c7de37c0a9351e4ae63f7
diff --git a/tests/modules/snapaligner/align/main.nf b/tests/modules/snapaligner/align/main.nf
deleted file mode 100644
index 1a1c6d06968..00000000000
--- a/tests/modules/snapaligner/align/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
-include { SNAPALIGNER_ALIGN } from '../../../../modules/snapaligner/align/main.nf'
-
-workflow test_snapaligner_single {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-    ]
-
-    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
-    SNAPALIGNER_ALIGN ( input, SNAPALIGNER_INDEX.out.index )
-}
-
-workflow test_snapaligner_paired {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
-    ]
-
-    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
-    SNAPALIGNER_ALIGN ( input, SNAPALIGNER_INDEX.out.index )
-}
diff --git a/tests/modules/snapaligner/align/test.yml b/tests/modules/snapaligner/align/test.yml
deleted file mode 100644
index b7e63f10251..00000000000
--- a/tests/modules/snapaligner/align/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: snapaligner align test_snapaligner_single
-  command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_single -c ./tests/config/nextflow.config  -c ./tests/modules/snapaligner/align/nextflow.config
-  tags:
-    - snapaligner/align
-    - snapaligner
-  files:
-    - path: output/snapaligner/test.bam
-      md5sum: 9958e511fe759012cd11b7ef1f097639
-    - path: output/snapaligner/test.bam.bai
-      md5sum: f180c68a77445b317a22e3f1d6e6e114
-
-- name: snapaligner align test_snapaligner_paired
-  command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_paired -c ./tests/config/nextflow.config  -c ./tests/modules/snapaligner/align/nextflow.config
-  tags:
-    - snapaligner/align
-    - snapaligner
-  files:
-    - path: output/snapaligner/test.bam
-      md5sum: cf656d5f18afa6a97825a685e1b2b141
-    - path: output/snapaligner/test.bam.bai
-      md5sum: fa2226d7f5b0b4b15d014332f94a8b84
diff --git a/tests/modules/snapaligner/index/main.nf b/tests/modules/snapaligner/index/main.nf
deleted file mode 100644
index 4cebb876226..00000000000
--- a/tests/modules/snapaligner/index/main.nf
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
-
-workflow test_snapaligner_index {
-    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
-}
diff --git a/tests/modules/snapaligner/index/test.yml b/tests/modules/snapaligner/index/test.yml
deleted file mode 100644
index 2c4b49351c9..00000000000
--- a/tests/modules/snapaligner/index/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: snapaligner index test_snapaligner_index
-  command: nextflow run tests/modules/snapaligner/index -entry test_snapaligner_index -c tests/config/nextflow.config
-  tags:
-    - snapaligner/index
-    - snapaligner
-  files:
-    - path: output/snapaligner/snap/Genome
-      md5sum: 7e189c954142ba37460332b467e34ed4
-    - path: output/snapaligner/snap/GenomeIndex
-      md5sum: 298da8bcb1134f7b24379a792a7a46f8
-    - path: output/snapaligner/snap/GenomeIndexHash
-    - path: output/snapaligner/snap/OverflowTable
-    - path: output/snapaligner/versions.yml
diff --git a/tests/modules/snippy/core/main.nf b/tests/modules/snippy/core/main.nf
deleted file mode 100644
index be78d8bdf44..00000000000
--- a/tests/modules/snippy/core/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNIPPY_RUN } from '../../../../modules/snippy/run/main.nf'
-include { SNIPPY_CORE } from '../../../../modules/snippy/core/main.nf'
-
-workflow test_snippy_core {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['candidatus_portiera_aleyrodidarum']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['candidatus_portiera_aleyrodidarum']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    reference = file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
-
-    SNIPPY_RUN ( input, reference )
-    SNIPPY_RUN.out.vcf.collect{meta, vcf -> vcf}.map{ vcf -> [[id:'snippy-core'], vcf]}.set{ ch_merge_vcf }
-    SNIPPY_RUN.out.aligned_fa.collect{meta, aligned_fa -> aligned_fa}.map{ aligned_fa -> [[id:'snippy-core'], aligned_fa]}.set{ ch_merge_aligned_fa }
-    ch_merge_vcf.join( ch_merge_aligned_fa ).set{ ch_snippy_core }
-    SNIPPY_CORE( ch_snippy_core, reference )
-
-}
diff --git a/tests/modules/snippy/core/test.yml b/tests/modules/snippy/core/test.yml
deleted file mode 100644
index 792dc3dc3da..00000000000
--- a/tests/modules/snippy/core/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: snippy core test_snippy_core
-  command: nextflow run ./tests/modules/snippy/core -entry test_snippy_core -c ./tests/config/nextflow.config  -c ./tests/modules/snippy/core/nextflow.config
-  tags:
-    - snippy
-    - snippy/core
-  files:
-    - path: output/snippy/snippy-core.aln
-      md5sum: 23cf80454a83849977aeb7193a5eab8e
-    - path: output/snippy/snippy-core.full.aln
-      md5sum: fcadf17c2c8109fe4491ab7e7df6e261
-    - path: output/snippy/snippy-core.tab
-      md5sum: 1eb437b4d82d8dbc93649b0edf94abc8
-    - path: output/snippy/snippy-core.txt
-      md5sum: 243961814f44b9a6cac48b69f02b4349
-    - path: output/snippy/snippy-core.vcf
-      md5sum: 8b4ff1f2e7f1cef9d168dad5d70e642a
diff --git a/tests/modules/snippy/run/main.nf b/tests/modules/snippy/run/main.nf
deleted file mode 100644
index bfc4082e158..00000000000
--- a/tests/modules/snippy/run/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNIPPY_RUN } from '../../../../modules/snippy/run/main.nf'
-
-workflow test_snippy_run {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    SNIPPY_RUN ( input, reference )
-}
diff --git a/tests/modules/snippy/run/test.yml b/tests/modules/snippy/run/test.yml
deleted file mode 100644
index 10e24f558d5..00000000000
--- a/tests/modules/snippy/run/test.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-- name: snippy run test_snippy_run
-  command: |
-    nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config
-  tags:
-    - snippy/run
-    - snippy
-  files:
-    - path: output/snippy/test/test.aligned.fa
-      md5sum: 47e3390d4167edf1955d162d37aca5e3
-    - path: output/snippy/test/test.bam
-    - path: output/snippy/test/test.bam.bai
-    - path: output/snippy/test/test.bed
-    - path: output/snippy/test/test.consensus.fa
-      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
-    - path: output/snippy/test/test.consensus.subs.fa
-      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
-    - path: output/snippy/test/test.csv
-      md5sum: 322f942115e5945c2041a88246166703
-    - path: output/snippy/test/test.filt.vcf
-      contains: ["fileformat", "freebayes", "CHROM"]
-    - path: output/snippy/test/test.gff
-      md5sum: df19e1b84ba6f691d20c72b397c88abf
-    - path: output/snippy/test/test.html
-      md5sum: 1ccbf0ffcadae1a6b2e11681d24c9938
-    - path: output/snippy/test/test.log
-      contains: ["snippy", "consensus", "subs"]
-    - path: output/snippy/test/test.raw.vcf
-      contains: ["fileformat", "freebayes", "CHROM"]
-    - path: output/snippy/test/test.tab
-      md5sum: beb9bde3bce985e53e8feba9ec5b136e
-    - path: output/snippy/test/test.txt
-      contains: ["DateTime", "ReadFiles", "VariantTotal"]
-    - path: output/snippy/test/test.vcf
-      contains: ["fileformat", "freebayes", "CHROM"]
-    - path: output/snippy/test/test.vcf.gz
-    - path: output/snippy/test/test.vcf.gz.csi
-      md5sum: bed9fa291c220a1ba04eb2d448932ffc
-    - path: output/snippy/versions.yml
-      md5sum: 518aad56c4dbefb6cbcde5ab38cf7b5d
diff --git a/tests/modules/snpdists/main.nf b/tests/modules/snpdists/main.nf
deleted file mode 100644
index be6d745c451..00000000000
--- a/tests/modules/snpdists/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNPDISTS } from '../../../modules/snpdists/main.nf'
-
-workflow test_snpdists {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
-
-    SNPDISTS ( input )
-}
diff --git a/tests/modules/snpdists/test.yml b/tests/modules/snpdists/test.yml
deleted file mode 100644
index c23945ce170..00000000000
--- a/tests/modules/snpdists/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: snpdists
-  command: nextflow run ./tests/modules/snpdists -entry test_snpdists -c ./tests/config/nextflow.config -c ./tests/modules/snpdists/nextflow.config
-  tags:
-    - snpdists
-  files:
-    - path: output/snpdists/test.tsv
-      md5sum: 0018e5ec43990eb16abe2411fff4e47e
diff --git a/tests/modules/snpeff/main.nf b/tests/modules/snpeff/main.nf
deleted file mode 100644
index 81c44c105b2..00000000000
--- a/tests/modules/snpeff/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNPEFF } from '../../../modules/snpeff/main.nf'
-
-workflow test_snpeff {
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-    ]
-
-    SNPEFF ( input, "WBcel235.105", [] )
-}
diff --git a/tests/modules/snpeff/test.yml b/tests/modules/snpeff/test.yml
deleted file mode 100644
index b7d3c7a42d2..00000000000
--- a/tests/modules/snpeff/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: snpeff test_snpeff
-  command: nextflow run ./tests/modules/snpeff -entry test_snpeff -c ./tests/config/nextflow.config -c ./tests/modules/snpeff/nextflow.config
-  tags:
-    - snpeff
-  files:
-    - path: output/snpeff/test.ann.vcf
-      md5sum: e933384e572fc5ed0cce0faf1c0b2cc9
-    - path: output/snpeff/test.csv
-    - path: output/snpeff/test.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a
-    - path: output/snpeff/snpEff_summary.html
diff --git a/tests/modules/snpsift/split/main.nf b/tests/modules/snpsift/split/main.nf
deleted file mode 100644
index 4579fee32f8..00000000000
--- a/tests/modules/snpsift/split/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNPSIFT_SPLIT } from '../../../../modules/snpsift/split/main.nf'
-
-workflow test_snpsift_split_base {
-
-    input = [ [ id:'test', split:true], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true) ]
-
-    SNPSIFT_SPLIT ( input )
-}
-
-workflow test_snpsift_split_gz {
-
-    input = [ [ id:'test', split:true ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
-
-    SNPSIFT_SPLIT ( input )
-}
-
-workflow test_snpsift_join {
-
-    input = [   [ id:'test', split:false ], // meta map
-                [   file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
-            ]
-
-    SNPSIFT_SPLIT ( input )
-
-}
diff --git a/tests/modules/snpsift/split/test.yml b/tests/modules/snpsift/split/test.yml
deleted file mode 100644
index 529fbca59a5..00000000000
--- a/tests/modules/snpsift/split/test.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-- name: snpsift split test_snpsift_split_base
-  command: nextflow run tests/modules/snpsift/split -entry test_snpsift_split_base -c tests/config/nextflow.config
-  tags:
-    - snpsift/split
-    - snpsift
-  files:
-    - path: output/snpsift/test.rnaseq.chr22.vcf
-      md5sum: 1bb8724dcbe6fa3101a814c0be51d1ea
-    - path: output/snpsift/versions.yml
-      md5sum: 2b9f6b788db6c4fcbf258db763d8fab7
-
-- name: snpsift split test_snpsift_split_gz
-  command: nextflow run tests/modules/snpsift/split -entry test_snpsift_split_gz -c tests/config/nextflow.config
-  tags:
-    - snpsift/split
-    - snpsift
-  files:
-    - path: output/snpsift/test.MT192765.1.vcf
-      md5sum: 9d491cfa84067450342ba8e66c75e5b8
-    - path: output/snpsift/versions.yml
-      md5sum: 6bd63376670d6c1445caea2f31a3f579
-
-- name: snpsift split test_snpsift_join
-  command: nextflow run tests/modules/snpsift/split -entry test_snpsift_join -c tests/config/nextflow.config
-  tags:
-    - snpsift/split
-    - snpsift
-  files:
-    - path: output/snpsift/test.joined.vcf
-      md5sum: c400c7458524d889e0967b06ed72534f
-    - path: output/snpsift/versions.yml
-      md5sum: be54682a73d3b91a17eacc0e533448f5
diff --git a/tests/modules/snpsites/main.nf b/tests/modules/snpsites/main.nf
deleted file mode 100644
index f780167393f..00000000000
--- a/tests/modules/snpsites/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNPSITES } from '../../../modules/snpsites/main.nf'
-
-workflow test_snpsites {
-    
-    input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
-
-    SNPSITES ( input )
-}
diff --git a/tests/modules/snpsites/test.yml b/tests/modules/snpsites/test.yml
deleted file mode 100644
index 9d80dd514bf..00000000000
--- a/tests/modules/snpsites/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: snpsites
-  command: nextflow run ./tests/modules/snpsites -entry test_snpsites -c ./tests/config/nextflow.config -c ./tests/modules/snpsites/nextflow.config
-  tags:
-    - snpsites
-  files:
-    - path: output/snpsites/filtered_alignment.fas
-      md5sum: f96c7513003e878e16fa9eac9fcda0f4
-    - path: output/snpsites/constant.sites.txt
-      md5sum: 8b9b226e3787f7baaefce07405af22c9
diff --git a/tests/modules/somalier/extract/main.nf b/tests/modules/somalier/extract/main.nf
deleted file mode 100644
index 3b56e0653f4..00000000000
--- a/tests/modules/somalier/extract/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SOMALIER_EXTRACT } from '../../../../modules/somalier/extract/main.nf'
-
-fasta       = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-
-fasta_fai   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-sites       = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/sites_chr21.hg38.vcf.gz", checkIfExists: true)
-
-
-workflow test_somalier_extract {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true)
-    ]
-
-    SOMALIER_EXTRACT ( input, [fasta, fasta_fai], sites )
-}
diff --git a/tests/modules/somalier/extract/test.yml b/tests/modules/somalier/extract/test.yml
deleted file mode 100644
index 356b2c7fc45..00000000000
--- a/tests/modules/somalier/extract/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: somalier extract test_somalier_extract
-  command: nextflow run ./tests/modules/somalier/extract/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/extract/nextflow.config -entry test_somalier_extract
-  tags:
-    - somalier/extract
-    - somalier
-  files:
-    - path: output/somalier/normal.somalier
-      md5sum: 21f0b980edd42ddaa8ab964959c1de02
diff --git a/tests/modules/somalier/relate/main.nf b/tests/modules/somalier/relate/main.nf
deleted file mode 100644
index 030e5b2a175..00000000000
--- a/tests/modules/somalier/relate/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SOMALIER_RELATE } from '../../../../modules/somalier/relate/main.nf'
-
-
-workflow test_somalier_relate {
-
-    input = [ [ id:'cohort', single_end:false ], // meta map
-        [ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/normal.somalier", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/tumour.somalier", checkIfExists: true) ]
-    ]
-
-    SOMALIER_RELATE (input,[],[])
-}
-
-
-workflow test_somalier_relate_ped_groups {
-
-input = [ [ id:'cohort', single_end:false ], // meta map
-    [ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/normal.somalier", checkIfExists: true),
-    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/tumour.somalier", checkIfExists: true) ]
-]
-
-    groups = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/groups.txt", checkIfExists: true)
-    ped = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/family.ped", checkIfExists: true)
-
-    SOMALIER_RELATE (input,groups,ped)
-}
diff --git a/tests/modules/somalier/relate/test.yml b/tests/modules/somalier/relate/test.yml
deleted file mode 100644
index b2e886ef649..00000000000
--- a/tests/modules/somalier/relate/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: somalier relate test_somalier_relate
-  command: nextflow run ./tests/modules/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/relate/nextflow.config -entry test_somalier_relate
-  tags:
-    - somalier/relate
-    - somalier
-  files:
-    - path: output/somalier/cohort.html
-      md5sum: 03cac9b2c67a8a06f63e07f83ee11e18
-    - path: output/somalier/cohort.pairs.tsv
-      md5sum: 54d1e9fca1bf9d747d4254c6fa98edcf
-    - path: output/somalier/cohort.samples.tsv
-      md5sum: 97257d88886db1325c4d7d10cefa7169
-
-- name: somalier relate test_somalier_relate_ped_groups
-  command: nextflow run ./tests/modules/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/relate/nextflow.config -entry test_somalier_relate_ped_groups
-  tags:
-    - somalier/relate
-    - somalier
-  files:
-    - path: output/somalier/cohort.html
-      md5sum: 0d573016c9279ccdfdcfd4eb01d73b89
-    - path: output/somalier/cohort.pairs.tsv
-      md5sum: 8655714f1e5359329188e9f501168131
-    - path: output/somalier/cohort.samples.tsv
-      md5sum: 38ef93340e55fbeef47640abda9e48b0
diff --git a/tests/modules/sourmash/sketch/main.nf b/tests/modules/sourmash/sketch/main.nf
deleted file mode 100644
index c9288c593e4..00000000000
--- a/tests/modules/sourmash/sketch/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SOURMASH_SKETCH } from '../../../../modules/sourmash/sketch/main.nf'
-
-workflow test_sourmash_sketch {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    SOURMASH_SKETCH ( input )
-}
diff --git a/tests/modules/sourmash/sketch/test.yml b/tests/modules/sourmash/sketch/test.yml
deleted file mode 100644
index 5bd18967f5b..00000000000
--- a/tests/modules/sourmash/sketch/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: sourmash sketch test_sourmash_sketch
-  command: nextflow run tests/modules/sourmash/sketch -entry test_sourmash_sketch -c tests/config/nextflow.config
-  tags:
-    - sourmash
-    - sourmash/sketch
-  files:
-    - path: output/sourmash/test.sig
-      md5sum: 4b0dee307e35fc670cd0d416321e4961
-    - path: output/sourmash/versions.yml
-      md5sum: ec70dabc3e4b3bf11d39c17a99ca4bc6
diff --git a/tests/modules/spades/main.nf b/tests/modules/spades/main.nf
deleted file mode 100644
index 3710eeb716c..00000000000
--- a/tests/modules/spades/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SPADES } from '../../../modules/spades/main.nf'
-
-workflow test_spades_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
-              [],
-              []
-            ]
-    SPADES ( input, [] )
-}
-
-workflow test_spades_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
-              [],
-              []
-            ]
-
-    SPADES ( input, [] )
-}
-
-workflow test_spades_illumina_nanopore {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
-              [],
-              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    SPADES ( input, [] )
-}
-
-// that isnt perfect, because CCS reads should rather be used with -s instead of --pacbio
-workflow test_spades_illumina_pacbio {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
-              [ file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true) ],
-              []
-            ]
-
-    SPADES ( input, [] )
-}
diff --git a/tests/modules/spades/test.yml b/tests/modules/spades/test.yml
deleted file mode 100644
index d016c1a0181..00000000000
--- a/tests/modules/spades/test.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-- name: spades test_spades_single_end
-  command: nextflow run ./tests/modules/spades -entry test_spades_single_end -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config
-  tags:
-    - spades
-  files:
-    - path: output/spades/test.assembly.gfa.gz
-      md5sum: e5eab229363a906954a07df00e2495a6
-    - path: output/spades/test.contigs.fa.gz
-      md5sum: 64f6b339872b934138c6efd6baa445f4
-    - path: output/spades/test.scaffolds.fa.gz
-      md5sum: 64f6b339872b934138c6efd6baa445f4
-    - path: output/spades/test.spades.log
-
-- name: spades test_spades_paired_end
-  command: nextflow run ./tests/modules/spades -entry test_spades_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config
-  tags:
-    - spades
-  files:
-    - path: output/spades/test.assembly.gfa.gz
-      md5sum: c8614fb69907ae832a1359a054af240f
-    - path: output/spades/test.contigs.fa.gz
-      md5sum: eab5165b3cda96c235aaa1388010cb27
-    - path: output/spades/test.spades.log
-    - path: output/spades/warnings.log
-
-- name: spades test_spades_illumina_nanopore
-  command: nextflow run ./tests/modules/spades -entry test_spades_illumina_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config
-  tags:
-    - spades
-  files:
-    - path: output/spades/test.assembly.gfa.gz
-      md5sum: e438534f14e107f005efdd659adeba6a
-    - path: output/spades/test.contigs.fa.gz
-      md5sum: 027b0e54bfd8f4bc359e751e094133ef
-    - path: output/spades/test.scaffolds.fa.gz
-      md5sum: 027b0e54bfd8f4bc359e751e094133ef
-    - path: output/spades/test.spades.log
-    - path: output/spades/warnings.log
-
-- name: spades test_spades_illumina_pacbio
-  command: nextflow run ./tests/modules/spades -entry test_spades_illumina_pacbio -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config
-  tags:
-    - spades
-  files:
-    - path: output/spades/test.assembly.gfa.gz
-      md5sum: 22f92cbade8f25be3ac170eaf09f4c7b
-    - path: output/spades/test.contigs.fa.gz
-      md5sum: bb2d294a5752a6f3a208834b8799ec98
-    - path: output/spades/test.scaffolds.fa.gz
-      md5sum: 65aa6e3364925ec617fffda3e84b4cbc
-    - path: output/spades/test.spades.log
-    - path: output/spades/warnings.log
diff --git a/tests/modules/spatyper/main.nf b/tests/modules/spatyper/main.nf
deleted file mode 100644
index 655845c72f0..00000000000
--- a/tests/modules/spatyper/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SPATYPER } from '../../../modules/spatyper/main.nf'
-include { SPATYPER as SPATYPER_ENRICH } from '../../../modules/spatyper/main.nf'
-
-workflow test_spatyper {
-    input = [ [ id:'test' ],
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    repeats = []
-    repeat_order = []
-
-    SPATYPER ( input, repeats, repeat_order )
-}
-
-workflow test_spatyper_enrich {
-    input = [ [ id:'test' ],
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    repeats = []
-    repeat_order = []
-
-    SPATYPER_ENRICH ( input, repeats, repeat_order )
-}
diff --git a/tests/modules/spatyper/test.yml b/tests/modules/spatyper/test.yml
deleted file mode 100644
index 6e1f814456a..00000000000
--- a/tests/modules/spatyper/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: spatyper test_spatyper
-  command: nextflow run ./tests/modules/spatyper -entry test_spatyper -c ./tests/config/nextflow.config -c ./tests/modules/spatyper/nextflow.config
-  tags:
-    - spatyper
-  files:
-    - path: output/spatyper/test.tsv
-      md5sum: a698352823875171696e5e7ed7015c13
-
-- name: spatyper test_spatyper_enrich
-  command: nextflow run ./tests/modules/spatyper -entry test_spatyper_enrich -c ./tests/config/nextflow.config -c ./tests/modules/spatyper/nextflow.config
-  tags:
-    - spatyper
-  files:
-    - path: output/spatyper/test.tsv
-      md5sum: a698352823875171696e5e7ed7015c13
diff --git a/tests/modules/sratools/fasterqdump/main.nf b/tests/modules/sratools/fasterqdump/main.nf
deleted file mode 100644
index daa7a5aee13..00000000000
--- a/tests/modules/sratools/fasterqdump/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR } from '../../../../modules/untar/main.nf'
-include { SRATOOLS_FASTERQDUMP } from '../../../../modules/sratools/fasterqdump/main.nf'
-
-workflow test_sratools_fasterqdump_single_end {
-
-    archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]
-    UNTAR ( archive )
-
-    def input = Channel.of([ id:'test_single_end', single_end:true ])
-        .combine(UNTAR.out.untar.map{ it[1] })
-
-    SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
-}
-
-workflow test_sratools_fasterqdump_paired_end {
-
-    archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]
-    UNTAR ( archive )
-
-    def input = Channel.of([ id:'test_paired_end', single_end:false ])
-        .combine(UNTAR.out.untar.map{ it[1] })
-
-    SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
-}
diff --git a/tests/modules/sratools/fasterqdump/test.yml b/tests/modules/sratools/fasterqdump/test.yml
deleted file mode 100644
index 6fbf608cc49..00000000000
--- a/tests/modules/sratools/fasterqdump/test.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-- name: sratools fasterqdump test_sratools_fasterqdump_single_end
-  command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config
-  tags:
-    - sratools
-    - sratools/fasterqdump
-  files:
-    - path: output/sratools/SRR13255544.fastq.gz
-      md5sum: 1054c7b71884acdb5eed8a378f18be82
-    - path: output/untar/SRR13255544/SRR13255544.sra
-      md5sum: 466d05dafb2eec672150754168010b4d
-    - path: output/sratools/versions.yml
-      contains:
-        - "sratools: 2.11.0"
-
-- name: sratools fasterqdump test_sratools_fasterqdump_paired_end
-  command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config
-  tags:
-    - sratools
-    - sratools/fasterqdump
-  files:
-    - path: output/sratools/SRR11140744_1.fastq.gz
-      md5sum: 193809c784a4ea132ab2a253fa4f55b6
-    - path: output/sratools/SRR11140744_2.fastq.gz
-      md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
-    - path: output/untar/SRR11140744/SRR11140744.sra
-      md5sum: 065666caf5b2d5dfb0cb25d5f3abe659
-    - path: output/sratools/versions.yml
-      contains:
-        - "sratools: 2.11.0"
diff --git a/tests/modules/sratools/prefetch/main.nf b/tests/modules/sratools/prefetch/main.nf
deleted file mode 100644
index cf9794abea5..00000000000
--- a/tests/modules/sratools/prefetch/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SRATOOLS_PREFETCH } from '../../../../modules/sratools/prefetch/main.nf'
-
-workflow test_sratools_prefetch {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        'DRR000774'
-    ]
-
-    SRATOOLS_PREFETCH(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
-}
diff --git a/tests/modules/sratools/prefetch/test.yml b/tests/modules/sratools/prefetch/test.yml
deleted file mode 100644
index a6c213f8a59..00000000000
--- a/tests/modules/sratools/prefetch/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: sratools prefetch test_sratools_prefetch
-  command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow.config
-  tags:
-    - sratools/prefetch
-    - sratools
-  files:
-    - path: output/sratools/DRR000774/DRR000774.sra
-      md5sum: 7647dba20c89c0e3d7ad13842f060eb0
-    - path: output/sratools/versions.yml
-      contains:
-        - "sratools: 2.11.0"
diff --git a/tests/modules/srst2/srst2/main.nf b/tests/modules/srst2/srst2/main.nf
deleted file mode 100644
index 7d51937b848..00000000000
--- a/tests/modules/srst2/srst2/main.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SRST2_SRST2 } from '../../../../modules/srst2/srst2/main.nf'
-
-workflow test_srst2_srst2_exit {
-
-    input = [
-        [ id:'test', single_end:false, db:"test"], // meta map
-        [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
-//        [("")]
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')
-    ]
-
-    SRST2_SRST2(input)
-}
-
-workflow test_srst2_srst2_mlst {
-
-    input = [
-        [ id:'test', single_end:false, db:"mlst"], // meta map
-        [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_1.fastq.gz", checkIfExists: true),
-          file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_2.fastq.gz", checkIfExists: true) ],
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/MLST_DB.fas')
-    ]
-
-    SRST2_SRST2(input)
-}
-
-workflow test_srst2_srst2_paired_end {
-
-    input = [
-        [ id:'test', single_end:false, db:"gene"], // meta map
-        [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')  // Change to params.test_data syntax after the data is included in tests/config/test_data.config
-    ]
-
-    SRST2_SRST2(input)
-}
-
-workflow test_srst2_srst2_single_end {
-
-    input = [
-        [ id:'test', single_end:true, db:"gene" ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')  // Change to params.test_data syntax after the data is included in tests/config/test_data.config
-    ]
-
-    SRST2_SRST2(input)
-}
diff --git a/tests/modules/srst2/srst2/test.yml b/tests/modules/srst2/srst2/test.yml
deleted file mode 100644
index f7621f4f812..00000000000
--- a/tests/modules/srst2/srst2/test.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-- name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db
-  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_exit -c tests/config/nextflow.config
-  tags:
-    - srst2/srst2
-    - srst2
-  exit_code: 1
-
-- name: srst2 srst2 test_srst2_srst2_mlst
-  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config
-  tags:
-    - srst2/srst2
-    - srst2
-  files:
-    - path: output/srst2/test__SRR9067271.MLST_DB.pileup
-      contains:
-        - "dnaJ-1	2	C	17	.........,.......	FFFFFFFFFFFFFFFFF"
-    - path: output/srst2/test__SRR9067271.MLST_DB.sorted.bam
-    - path: output/srst2/test__mlst__MLST_DB__results.txt
-      md5sum: ec1b1f69933401d67c57f64cad11a098
-    - path: output/srst2/versions.yml
-      md5sum: a0c256a2fd3636069710b8ef22ee5ea7
-
-- name: srst2 srst2 test_srst2_srst2_paired_end
-  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config
-  tags:
-    - srst2/srst2
-    - srst2
-  files:
-    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
-      md5sum: 099aa6cacec5524b311f606debdfb3a9
-    - path: output/srst2/test__test1.resFinder_20180221_srst2.pileup
-      md5sum: 64b512ff495b828c456405ec7b676ad1
-    - path: output/srst2/test__test1.resFinder_20180221_srst2.sorted.bam
-    - path: output/srst2/versions.yml
-      md5sum: b446a70f1a2b4f60757829bcd744a214
-
-- name: srst2 srst2 test_srst2_srst2_single_end
-  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config
-  tags:
-    - srst2/srst2
-    - srst2
-  files:
-    - path: output/srst2/test__fullgenes__resFinder_20180221_srst2__results.txt
-      md5sum: d0762ef8c38afd0e0a34cce52ed1a3db
-    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
-      md5sum: b8850c6644406d8b131e471ecc3f9013
-    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.pileup
-      md5sum: 5f6279dc8124aa762a9dfe3d7a871277
-    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.sorted.bam
-    - path: output/srst2/versions.yml
-      md5sum: 790fe00493c6634d17801a930073218b
diff --git a/tests/modules/ssuissero/main.nf b/tests/modules/ssuissero/main.nf
deleted file mode 100644
index aa285133c83..00000000000
--- a/tests/modules/ssuissero/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SSUISSERO } from '../../../modules/ssuissero/main.nf'
-
-workflow test_ssuissero {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
-    ]
-
-    SSUISSERO ( input )
-}
diff --git a/tests/modules/ssuissero/test.yml b/tests/modules/ssuissero/test.yml
deleted file mode 100644
index ff61b2679ae..00000000000
--- a/tests/modules/ssuissero/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: ssuissero test_ssuissero
-  command: nextflow run tests/modules/ssuissero -entry test_ssuissero -c tests/config/nextflow.config
-  tags:
-    - ssuissero
-  files:
-    - path: output/ssuissero/test_serotyping_res.tsv
-      md5sum: 559dd2ca386eeb58f3975e3204ce9d43
-    - path: output/ssuissero/versions.yml
-      md5sum: be29b478690b2047e0413ffe01c85e1e
diff --git a/tests/modules/stadeniolib/scramble/main.nf b/tests/modules/stadeniolib/scramble/main.nf
deleted file mode 100644
index d29c6dd8292..00000000000
--- a/tests/modules/stadeniolib/scramble/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STADENIOLIB_SCRAMBLE } from '../../../../modules/stadeniolib/scramble/main.nf'
-
-workflow test_stadeniolib {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-
-    STADENIOLIB_SCRAMBLE ( input, file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true), [])
-}
diff --git a/tests/modules/stadeniolib/scramble/test.yml b/tests/modules/stadeniolib/scramble/test.yml
deleted file mode 100644
index cea6fb702e4..00000000000
--- a/tests/modules/stadeniolib/scramble/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: stadeniolib test_stadeniolib
-  command: nextflow run tests/modules/stadeniolib -entry test_stadeniolib -c tests/config/nextflow.config
-  tags:
-    - stadeniolib
-  files:
-    - path: output/stadeniolib/test.cram
-    - path: output/stadeniolib/versions.yml
diff --git a/tests/modules/staphopiasccmec/main.nf b/tests/modules/staphopiasccmec/main.nf
deleted file mode 100644
index 8ea310ce38f..00000000000
--- a/tests/modules/staphopiasccmec/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STAPHOPIASCCMEC } from '../../../modules/staphopiasccmec/main.nf'
-include { STAPHOPIASCCMEC as STAPHOPIASCCMEC_HAMMING } from '../../../modules/staphopiasccmec/main.nf'
-
-workflow test_staphopiasccmec {
-    
-    input = [ [ id:'test' ],
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    STAPHOPIASCCMEC ( input )
-}
-
-workflow test_staphopiasccmec_hamming {
-    
-    input = [ [ id:'test' ],
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    STAPHOPIASCCMEC_HAMMING ( input )
-}
diff --git a/tests/modules/staphopiasccmec/test.yml b/tests/modules/staphopiasccmec/test.yml
deleted file mode 100644
index ac3f66da300..00000000000
--- a/tests/modules/staphopiasccmec/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: staphopiasccmec test_staphopiasccmec
-  command: nextflow run ./tests/modules/staphopiasccmec -entry test_staphopiasccmec -c ./tests/config/nextflow.config -c ./tests/modules/staphopiasccmec/nextflow.config
-  tags:
-    - staphopiasccmec
-  files:
-    - path: output/staphopiasccmec/test.tsv
-      md5sum: e6460d4164f3af5b290c5ccdb11343bf
-
-- name: staphopiasccmec test_staphopiasccmec_hamming
-  command: nextflow run ./tests/modules/staphopiasccmec -entry test_staphopiasccmec_hamming -c ./tests/config/nextflow.config -c ./tests/modules/staphopiasccmec/nextflow.config
-  tags:
-    - staphopiasccmec
-  files:
-    - path: output/staphopiasccmec/test.tsv
-      md5sum: 164cda1b05b3b6814c1f0786d93ca070
diff --git a/tests/modules/star/align/main.nf b/tests/modules/star/align/main.nf
deleted file mode 100644
index bf305d5412e..00000000000
--- a/tests/modules/star/align/main.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STAR_GENOMEGENERATE               } from '../../../../modules/star/genomegenerate/main.nf'
-include { STAR_ALIGN                        } from '../../../../modules/star/align/main.nf'
-include { STAR_ALIGN as STAR_FOR_ARRIBA     } from '../../../../modules/star/align/main.nf'
-include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../modules/star/align/main.nf'
-
-workflow test_star_alignment_single_end {
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
-    ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    star_ignore_sjdbgtf = false
-    seq_platform = 'illumina'
-    seq_center = false
-
-    STAR_GENOMEGENERATE ( fasta, gtf )
-    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-}
-
-workflow test_star_alignment_paired_end {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    star_ignore_sjdbgtf = false
-    seq_platform = 'illumina'
-    seq_center = false
-
-    STAR_GENOMEGENERATE ( fasta, gtf )
-    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-}
-
-
-workflow test_star_alignment_paired_end_for_fusion {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    star_ignore_sjdbgtf = false
-    seq_platform = 'illumina'
-    seq_center = false
-
-    STAR_GENOMEGENERATE ( fasta, gtf )
-    STAR_FOR_ARRIBA ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-}
-
-workflow test_star_alignment_paired_end_for_starfusion {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    star_ignore_sjdbgtf = false
-    seq_platform = false
-    seq_center = false
-
-    STAR_GENOMEGENERATE ( fasta, gtf )
-    STAR_FOR_STARFUSION ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-}
diff --git a/tests/modules/star/align/test.yml b/tests/modules/star/align/test.yml
deleted file mode 100644
index b75802954e8..00000000000
--- a/tests/modules/star/align/test.yml
+++ /dev/null
@@ -1,193 +0,0 @@
-- name: star align test_star_alignment_single_end
-  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
-  tags:
-    - star/align
-    - star
-  files:
-    - path: output/star/star/Genome
-      md5sum: a654229fbca6071dcb6b01ce7df704da
-    - path: output/star/star/Log.out
-    - path: output/star/star/SA
-      md5sum: 8c3edc46697b72c9e92440d4cf43506c
-    - path: output/star/star/SAindex
-      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
-    - path: output/star/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/star/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/star/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/star/star/chrStart.txt
-      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
-    - path: output/star/star/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/star/star/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/star/star/geneInfo.tab
-      md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/star/star/genomeParameters.txt
-      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
-    - path: output/star/star/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/star/star/sjdbList.fromGTF.out.tab
-      md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/star/star/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/star/star/transcriptInfo.tab
-      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
-    - path: output/star/test.Aligned.out.bam
-      md5sum: 63de6af2210e138b49d7b4d570c6e67f
-    - path: output/star/test.Log.final.out
-    - path: output/star/test.Log.out
-    - path: output/star/test.Log.progress.out
-    - path: output/star/test.SJ.out.tab
-
-- name: star align test_star_alignment_paired_end
-  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
-  tags:
-    - star/align
-    - star
-  files:
-    - path: output/star/star/Genome
-      md5sum: a654229fbca6071dcb6b01ce7df704da
-    - path: output/star/star/Log.out
-    - path: output/star/star/SA
-      md5sum: 8c3edc46697b72c9e92440d4cf43506c
-    - path: output/star/star/SAindex
-      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
-    - path: output/star/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/star/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/star/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/star/star/chrStart.txt
-      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
-    - path: output/star/star/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/star/star/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/star/star/geneInfo.tab
-      md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/star/star/genomeParameters.txt
-      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
-    - path: output/star/star/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/star/star/sjdbList.fromGTF.out.tab
-      md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/star/star/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/star/star/transcriptInfo.tab
-      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
-    - path: output/star/test.Aligned.out.bam
-      md5sum: 7cdef439bc8092bfefb4d091bf8ee6ab
-    - path: output/star/test.Log.final.out
-    - path: output/star/test.Log.out
-    - path: output/star/test.Log.progress.out
-    - path: output/star/test.SJ.out.tab
-
-- name: star align test_star_alignment_paired_end_for_fusion
-  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end_for_fusion -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
-  tags:
-    - star/align
-    - star
-  files:
-    - path: output/star/star/Genome
-      md5sum: a654229fbca6071dcb6b01ce7df704da
-    - path: output/star/star/Log.out
-    - path: output/star/star/SA
-      md5sum: 8c3edc46697b72c9e92440d4cf43506c
-    - path: output/star/star/SAindex
-      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
-    - path: output/star/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/star/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/star/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/star/star/chrStart.txt
-      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
-    - path: output/star/star/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/star/star/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/star/star/geneInfo.tab
-      md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/star/star/genomeParameters.txt
-      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
-    - path: output/star/star/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/star/star/sjdbList.fromGTF.out.tab
-      md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/star/star/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/star/star/transcriptInfo.tab
-      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
-    - path: output/star/test.Aligned.out.bam
-      md5sum: 5dbc36fce7b72628c809bbc7d3d67973
-    - path: output/star/test.Log.final.out
-    - path: output/star/test.Log.out
-    - path: output/star/test.Log.progress.out
-    - path: output/star/test.SJ.out.tab
-
-- name: star align test_star_alignment_paired_end_for_starfusion
-  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end_for_starfusion -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
-  tags:
-    - star/align
-    - star
-  files:
-    - path: output/star/star/Genome
-      md5sum: a654229fbca6071dcb6b01ce7df704da
-    - path: output/star/star/Log.out
-    - path: output/star/star/SA
-      md5sum: 8c3edc46697b72c9e92440d4cf43506c
-    - path: output/star/star/SAindex
-      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
-    - path: output/star/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/star/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/star/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/star/star/chrStart.txt
-      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
-    - path: output/star/star/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/star/star/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/star/star/geneInfo.tab
-      md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/star/star/genomeParameters.txt
-      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
-    - path: output/star/star/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/star/star/sjdbList.fromGTF.out.tab
-      md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/star/star/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/star/star/transcriptInfo.tab
-      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
-    - path: output/star/test.Aligned.out.bam
-      md5sum: d85858bf55a523121dde762046a34c5c
-    - path: output/star/test.Chimeric.out.junction
-      md5sum: ae87d1a24180f5a35cf6b47fdfdd0539
-    - path: output/star/test.Log.final.out
-    - path: output/star/test.Log.out
-    - path: output/star/test.Log.progress.out
-    - path: output/star/test.SJ.out.tab
-
-- name: star align test_star_alignment_single_end stub
-  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config -stub-run
-  tags:
-    - star/align
-    - star
-  files:
-    - path: output/star/test.Aligned.unsort.out.bam
-    - path: output/star/test.Log.final.out
-    - path: output/star/test.Log.out
-    - path: output/star/test.Log.progress.out
-    - path: output/star/test.Chimeric.out.junction
-    - path: output/star/test.unmapped_1.fastq.gz
-    - path: output/star/test.unmapped_2.fastq.gz
-    - path: output/star/test.tab
-    - path: output/star/test.out.sam
diff --git a/tests/modules/star/genomegenerate/main.nf b/tests/modules/star/genomegenerate/main.nf
deleted file mode 100644
index 316014784d5..00000000000
--- a/tests/modules/star/genomegenerate/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf'
-
-workflow test_star_genomegenerate {
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf   = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-
-    STAR_GENOMEGENERATE ( fasta, gtf )
-}
diff --git a/tests/modules/star/genomegenerate/test.yml b/tests/modules/star/genomegenerate/test.yml
deleted file mode 100644
index d980764ca2a..00000000000
--- a/tests/modules/star/genomegenerate/test.yml
+++ /dev/null
@@ -1,60 +0,0 @@
-- name: star genomegenerate test_star_genomegenerate
-  command: nextflow run ./tests/modules/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/star/genomegenerate/nextflow.config
-  tags:
-    - star
-    - star/genomegenerate
-  files:
-    - path: output/star/star/Genome
-      md5sum: a654229fbca6071dcb6b01ce7df704da
-    - path: output/star/star/Log.out
-    - path: output/star/star/SA
-      md5sum: 8c3edc46697b72c9e92440d4cf43506c
-    - path: output/star/star/SAindex
-      md5sum: d0fbf2789ee1e9f60c352ba3655d9de4
-    - path: output/star/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/star/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/star/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/star/star/chrStart.txt
-      md5sum: 8d3291e6bcdbe9902fbd7c887494173f
-    - path: output/star/star/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/star/star/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/star/star/geneInfo.tab
-      md5sum: 8b608537307443ffaee4927d2b428805
-    - path: output/star/star/genomeParameters.txt
-      md5sum: 5a1ec027e575c3d7c1851e6b80fb8c5d
-    - path: output/star/star/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/star/star/sjdbList.fromGTF.out.tab
-      md5sum: 8760c33e966dad0b39f440301ebbdee4
-    - path: output/star/star/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/star/star/transcriptInfo.tab
-      md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
-
-- name: star genomegenerate test_star_genomegenerate stub
-  command: nextflow run ./tests/modules/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/star/genomegenerate/nextflow.config -stub-run
-  tags:
-    - star
-    - star/genomegenerate
-  files:
-    - path: output/star/star/Genome
-    - path: output/star/star/Log.out
-    - path: output/star/star/SA
-    - path: output/star/star/SAindex
-    - path: output/star/star/chrLength.txt
-    - path: output/star/star/chrName.txt
-    - path: output/star/star/chrNameLength.txt
-    - path: output/star/star/chrStart.txt
-    - path: output/star/star/exonGeTrInfo.tab
-    - path: output/star/star/exonInfo.tab
-    - path: output/star/star/geneInfo.tab
-    - path: output/star/star/genomeParameters.txt
-    - path: output/star/star/sjdbInfo.txt
-    - path: output/star/star/sjdbList.fromGTF.out.tab
-    - path: output/star/star/sjdbList.out.tab
-    - path: output/star/star/transcriptInfo.tab
diff --git a/tests/modules/stranger/main.nf b/tests/modules/stranger/main.nf
deleted file mode 100644
index 4a930c19ce6..00000000000
--- a/tests/modules/stranger/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
-include { STRANGER } from '../../../modules/stranger/main.nf'
-
-
-input = [ [ id:'test', gender:'male' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        ]
-fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
-
-
-workflow test_stranger {
-    EXPANSIONHUNTER ( input, fasta, variant_catalog )
-    STRANGER ( EXPANSIONHUNTER.out.vcf, variant_catalog )
-}
-
-workflow test_stranger_without_optional_variant_catalog {
-    EXPANSIONHUNTER ( input, fasta, variant_catalog )
-    STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
-}
-
-workflow test_stranger_without_optional_variant_catalog_stubs {
-    EXPANSIONHUNTER ( input, fasta, variant_catalog )
-    STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
-}
diff --git a/tests/modules/stranger/test.yml b/tests/modules/stranger/test.yml
deleted file mode 100644
index bf922c86a40..00000000000
--- a/tests/modules/stranger/test.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-- name: stranger test_stranger
-  command: nextflow run tests/modules/stranger -entry test_stranger -c tests/config/nextflow.config
-  tags:
-    - stranger
-  files:
-    - path: output/expansionhunter/test.vcf
-      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
-    - path: output/expansionhunter/versions.yml
-      md5sum: f3962a6eecfddf9682414c0f605a885a
-    - path: output/stranger/test.vcf.gz
-      md5sum: 68b0ca1319851134ffa8793a4704dc11
-    - path: output/stranger/versions.yml
-      md5sum: 5ec35fd835fb1be50bc3e7c004310fc0
-
-- name: stranger test_stranger_without_optional_variant_catalog
-  command: nextflow run tests/modules/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config
-  tags:
-    - stranger
-  files:
-    - path: output/expansionhunter/test.vcf
-      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
-    - path: output/expansionhunter/versions.yml
-      md5sum: c95af9e6d8cd9bd2ce1090ca4e7a6020
-    - path: output/stranger/test.vcf.gz
-      md5sum: bbe15159195681d5c18596d3ad85c78f
-    - path: output/stranger/versions.yml
-      md5sum: 8558542a007e90ea5dcdceed3f12585d
-
-- name: stranger test_stranger_without_optional_variant_catalog_stubs
-  command: nextflow run tests/modules/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config -stub-run
-  tags:
-    - stranger
-  files:
-    - path: output/expansionhunter/test.vcf
-    - path: output/expansionhunter/versions.yml
-    - path: output/stranger/test.vcf.gz
-    - path: output/stranger/versions.yml
diff --git a/tests/modules/strelka/germline/main.nf b/tests/modules/strelka/germline/main.nf
deleted file mode 100644
index 312a4f720a2..00000000000
--- a/tests/modules/strelka/germline/main.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STRELKA_GERMLINE } from '../../../../modules/strelka/germline/main.nf'
-
-workflow test_strelka_germline {
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        [],
-        []
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    STRELKA_GERMLINE ( input, fasta, fai)
-}
-
-workflow test_strelka_germline_target_bed {
-
-    input = [
-        [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    STRELKA_GERMLINE ( input, fasta, fai)
-}
-
diff --git a/tests/modules/strelka/germline/test.yml b/tests/modules/strelka/germline/test.yml
deleted file mode 100644
index 8db81aa06ea..00000000000
--- a/tests/modules/strelka/germline/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: strelka germline test_strelka_germline
-  command: nextflow run ./tests/modules/strelka/germline -entry test_strelka_germline -c ./tests/config/nextflow.config -c ./tests/modules/strelka/germline/nextflow.config
-  tags:
-    - strelka
-    - strelka/germline
-  files:
-    - path: output/strelka/test.genome.vcf.gz
-    - path: output/strelka/test.genome.vcf.gz.tbi
-    - path: output/strelka/test.variants.vcf.gz
-    - path: output/strelka/test.variants.vcf.gz.tbi
-
-- name: strelka germline test_strelka_germline_target_bed
-  command: nextflow run ./tests/modules/strelka/germline -entry test_strelka_germline_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/strelka/germline/nextflow.config
-  tags:
-    - strelka
-    - strelka/germline
-  files:
-    - path: output/strelka/test.genome.vcf.gz
-    - path: output/strelka/test.genome.vcf.gz.tbi
-    - path: output/strelka/test.variants.vcf.gz
-    - path: output/strelka/test.variants.vcf.gz.tbi
diff --git a/tests/modules/strelka/somatic/main.nf b/tests/modules/strelka/somatic/main.nf
deleted file mode 100644
index ab75f0e2012..00000000000
--- a/tests/modules/strelka/somatic/main.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STRELKA_SOMATIC } from '../../../../modules/strelka/somatic/main.nf'
-
-workflow test_strelka_somatic {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        [],[],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    STRELKA_SOMATIC (input, fasta, fai )
-}
-
-workflow test_strelka_best_practices_somatic {
-
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz_tbi'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-
-    STRELKA_SOMATIC ( input, fasta, fai )
-}
diff --git a/tests/modules/strelka/somatic/test.yml b/tests/modules/strelka/somatic/test.yml
deleted file mode 100644
index 787f3b19dcc..00000000000
--- a/tests/modules/strelka/somatic/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: strelka somatic test_strelka_somatic
-  command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config
-  tags:
-    - strelka
-    - strelka/somatic
-  files:
-    - path: output/strelka/test.somatic_indels.vcf.gz
-    - path: output/strelka/test.somatic_indels.vcf.gz.tbi
-    - path: output/strelka/test.somatic_snvs.vcf.gz
-    - path: output/strelka/test.somatic_snvs.vcf.gz.tbi
-
-- name: strelka somatic test_strelka_best_practices_somatic
-  command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka_best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config
-  tags:
-    - strelka
-    - strelka/somatic
-  files:
-    - path: output/strelka/test.somatic_indels.vcf.gz
-    - path: output/strelka/test.somatic_indels.vcf.gz.tbi
-    - path: output/strelka/test.somatic_snvs.vcf.gz
-    - path: output/strelka/test.somatic_snvs.vcf.gz.tbi
diff --git a/tests/modules/stringtie/merge/main.nf b/tests/modules/stringtie/merge/main.nf
deleted file mode 100644
index 3fe32902595..00000000000
--- a/tests/modules/stringtie/merge/main.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
-include { STRINGTIE_MERGE     } from '../../../../modules/stringtie/merge/main.nf'
-
-/*
- * Test with forward strandedness
- */
-workflow test_stringtie_forward_merge {
-    input = [
-        [ id:'test', strandedness:'forward' ], // meta map
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    ]
-    annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-
-    STRINGTIE_STRINGTIE ( input, annotation_gtf )
-    STRINGTIE_STRINGTIE
-        .out
-        .transcript_gtf
-        .map { it -> it[1] }
-        .set { stringtie_gtf }
-
-    STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
-}
-
-/*
- * Test with reverse strandedness
- */
-workflow test_stringtie_reverse_merge {
-    input = [
-        [ id:'test', strandedness:'reverse' ], // meta map
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    ]
-    annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-
-    STRINGTIE_STRINGTIE ( input, annotation_gtf )
-    STRINGTIE_STRINGTIE
-        .out
-        .transcript_gtf
-        .map { it -> it[1] }
-        .set { stringtie_gtf }
-
-    STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
-}
diff --git a/tests/modules/stringtie/merge/test.yml b/tests/modules/stringtie/merge/test.yml
deleted file mode 100644
index fb25bf63fa9..00000000000
--- a/tests/modules/stringtie/merge/test.yml
+++ /dev/null
@@ -1,69 +0,0 @@
-- name: stringtie merge forward-strand
-  command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
-  tags:
-    - stringtie
-    - stringtie/merge
-  files:
-    - path: output/stringtie/stringtie.merged.gtf
-      md5sum: d959eb2fab0db48ded7275e0a2e83c05
-    - path: output/stringtie/test.ballgown/e2t.ctab
-      md5sum: 9ae42e056c955a88a883e5e917840d77
-    - path: output/stringtie/test.ballgown/e_data.ctab
-      md5sum: adbedee7b2f84c70362ad6dfa57442b7
-    - path: output/stringtie/test.ballgown/i2t.ctab
-      md5sum: 658131af118cfb416939044fdb5411de
-    - path: output/stringtie/test.ballgown/i_data.ctab
-      md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
-    - path: output/stringtie/test.ballgown/t_data.ctab
-      md5sum: 92a98902784e7406ffe054d2adbabc7c
-    - path: output/stringtie/test.coverage.gtf
-    - path: output/stringtie/test.gene.abundance.txt
-      md5sum: 8bcd8e2730ed3337e2730186dbc184f3
-    - path: output/stringtie/test.transcripts.gtf
-      md5sum: a914bd55b68a4b5f607738b17861e362
-
-- name: stringtie merge test_stringtie_reverse_merge
-  command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
-  tags:
-    - stringtie
-    - stringtie/merge
-  files:
-    - path: output/stringtie/stringtie.merged.gtf
-      md5sum: 6da479298d73d5b3216d4e1576a2bdf4
-    - path: output/stringtie/test.ballgown/e2t.ctab
-      md5sum: 9ae42e056c955a88a883e5e917840d77
-    - path: output/stringtie/test.ballgown/e_data.ctab
-      md5sum: fd8496d3957ade3b2c0853155f9a67da
-    - path: output/stringtie/test.ballgown/i2t.ctab
-      md5sum: 658131af118cfb416939044fdb5411de
-    - path: output/stringtie/test.ballgown/i_data.ctab
-      md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
-    - path: output/stringtie/test.ballgown/t_data.ctab
-      md5sum: 92a98902784e7406ffe054d2adbabc7c
-    - path: output/stringtie/test.coverage.gtf
-    - path: output/stringtie/test.gene.abundance.txt
-      md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
-    - path: output/stringtie/test.transcripts.gtf
-      md5sum: 9dcdc9577c0fdbb25089eda210267546
-
-- name: stringtie merge forward-strand stub
-  command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config -stub-run
-  tags:
-    - stringtie
-    - stringtie/merge
-  files:
-    - path: output/stringtie/stringtie.merged.gtf
-    - path: output/stringtie/test.coverage.gtf
-    - path: output/stringtie/test.gene.abundance.txt
-    - path: output/stringtie/test.transcripts.gtf
-
-- name: stringtie merge test_stringtie_reverse_merge stub
-  command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config -stub-run
-  tags:
-    - stringtie
-    - stringtie/merge
-  files:
-    - path: output/stringtie/stringtie.merged.gtf
-    - path: output/stringtie/test.coverage.gtf
-    - path: output/stringtie/test.gene.abundance.txt
-    - path: output/stringtie/test.transcripts.gtf
diff --git a/tests/modules/stringtie/stringtie/main.nf b/tests/modules/stringtie/stringtie/main.nf
deleted file mode 100644
index 463e4b98183..00000000000
--- a/tests/modules/stringtie/stringtie/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
-//
-// Test with forward strandedness
-//
-workflow test_stringtie_forward {
-    input = [
-        [ id:'test', strandedness:'forward' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    ]
-    annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-
-    STRINGTIE_STRINGTIE ( input, annotation_gtf )
-}
-
-//
-// Test with reverse strandedness
-//
-workflow test_stringtie_reverse {
-    input = [
-        [ id:'test', strandedness:'reverse' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    ]
-    annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
-
-    STRINGTIE_STRINGTIE ( input, annotation_gtf )
-}
diff --git a/tests/modules/stringtie/stringtie/test.yml b/tests/modules/stringtie/stringtie/test.yml
deleted file mode 100644
index 034b88d3808..00000000000
--- a/tests/modules/stringtie/stringtie/test.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-- name: stringtie stringtie forward
-  command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config
-  tags:
-    - stringtie
-    - stringtie/stringtie
-  files:
-    - path: ./output/stringtie/test.transcripts.gtf
-    - path: ./output/stringtie/test.gene.abundance.txt
-      md5sum: 7d8bce7f2a922e367cedccae7267c22e
-    - path: ./output/stringtie/test.coverage.gtf
-    - path: ./output/stringtie/test.ballgown/e_data.ctab
-      md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
-    - path: ./output/stringtie/test.ballgown/i_data.ctab
-      md5sum: be3abe09740603213f83d50dcf81427f
-    - path: ./output/stringtie/test.ballgown/t_data.ctab
-      md5sum: 3b66c065da73ae0dd41cc332eff6a818
-    - path: ./output/stringtie/test.ballgown/i2t.ctab
-      md5sum: 8a117c8aa4334b4c2d4711932b006fb4
-    - path: ./output/stringtie/test.ballgown/e2t.ctab
-      md5sum: e981c0038295ae54b63cedb1083f1540
-
-- name: stringtie stringtie reverse
-  command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config
-  tags:
-    - stringtie
-    - stringtie/stringtie
-  files:
-    - path: ./output/stringtie/test.transcripts.gtf
-    - path: ./output/stringtie/test.gene.abundance.txt
-      md5sum: 7385b870b955dae2c2ab78a70cf05cce
-    - path: ./output/stringtie/test.coverage.gtf
-    - path: ./output/stringtie/test.ballgown/e_data.ctab
-      md5sum: 879b6696029d19c4737b562e9d149218
-    - path: ./output/stringtie/test.ballgown/i_data.ctab
-      md5sum: be3abe09740603213f83d50dcf81427f
-    - path: ./output/stringtie/test.ballgown/t_data.ctab
-      md5sum: 3b66c065da73ae0dd41cc332eff6a818
-    - path: ./output/stringtie/test.ballgown/i2t.ctab
-      md5sum: 8a117c8aa4334b4c2d4711932b006fb4
-    - path: ./output/stringtie/test.ballgown/e2t.ctab
-      md5sum: e981c0038295ae54b63cedb1083f1540
-
-- name: stringtie stringtie forward stub
-  command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config -stub-run
-  tags:
-    - stringtie
-    - stringtie/stringtie
-  files:
-    - path: ./output/stringtie/test.transcripts.gtf
-    - path: ./output/stringtie/test.gene.abundance.txt
-    - path: ./output/stringtie/test.coverage.gtf
-    - path: ./output/stringtie/test.ballgown
-
-- name: stringtie stringtie reverse stub
-  command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config -stub-run
-  tags:
-    - stringtie
-    - stringtie/stringtie
-  files:
-    - path: ./output/stringtie/test.transcripts.gtf
-    - path: ./output/stringtie/test.gene.abundance.txt
-    - path: ./output/stringtie/test.coverage.gtf
-    - path: ./output/stringtie/test.ballgown
diff --git a/tests/modules/subread/featurecounts/main.nf b/tests/modules/subread/featurecounts/main.nf
deleted file mode 100644
index a8fa5c755ed..00000000000
--- a/tests/modules/subread/featurecounts/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SUBREAD_FEATURECOUNTS } from '../../../../modules/subread/featurecounts/main.nf'
-
-workflow test_subread_featurecounts_forward {
-    
-    def input = []
-    input = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
-
-    SUBREAD_FEATURECOUNTS ( input )
-}
-
-workflow test_subread_featurecounts_reverse {
-    
-    def input = []
-    input = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
-
-    SUBREAD_FEATURECOUNTS ( input )
-}
-
-workflow test_subread_featurecounts_unstranded {
-    
-    def input = []
-    input = [ [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
-
-    SUBREAD_FEATURECOUNTS ( input )
-}
\ No newline at end of file
diff --git a/tests/modules/subread/featurecounts/test.yml b/tests/modules/subread/featurecounts/test.yml
deleted file mode 100644
index 7cc24457b96..00000000000
--- a/tests/modules/subread/featurecounts/test.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-- name: subread featurecounts test_subread_featurecounts_forward
-  command: nextflow run ./tests/modules/subread/featurecounts -entry test_subread_featurecounts_forward -c ./tests/config/nextflow.config -c ./tests/modules/subread/featurecounts/nextflow.config
-  tags:
-    - subread
-    - subread/featurecounts
-  files:
-    - path: output/subread/test.featureCounts.txt
-      md5sum: 0012df4c0a0e47eec1440017ab34f75f
-    - path: output/subread/test.featureCounts.txt.summary
-      md5sum: 8f602ff9a8ef467af43294e80b367cdf
-
-- name: subread featurecounts test_subread_featurecounts_reverse
-  command: nextflow run ./tests/modules/subread/featurecounts -entry test_subread_featurecounts_reverse -c ./tests/config/nextflow.config -c ./tests/modules/subread/featurecounts/nextflow.config
-  tags:
-    - subread
-    - subread/featurecounts
-  files:
-    - path: output/subread/test.featureCounts.txt
-      md5sum: 8175816b8260ed444d59232bd7e7120b
-    - path: output/subread/test.featureCounts.txt.summary
-      md5sum: 7cfa30ad678b9bc1bc63afbb0281547b
-
-- name: subread featurecounts test_subread_featurecounts_unstranded
-  command: nextflow run ./tests/modules/subread/featurecounts -entry test_subread_featurecounts_unstranded -c ./tests/config/nextflow.config -c ./tests/modules/subread/featurecounts/nextflow.config
-  tags:
-    - subread
-    - subread/featurecounts
-  files:
-    - path: output/subread/test.featureCounts.txt
-      md5sum: 3307d31b44a5d6bb3389786bb8f4e91f
-    - path: output/subread/test.featureCounts.txt.summary
-      md5sum: 23164b79f9f23f11c82820db61a35560
diff --git a/tests/modules/svdb/merge/main.nf b/tests/modules/svdb/merge/main.nf
deleted file mode 100644
index 3cbb4b44544..00000000000
--- a/tests/modules/svdb/merge/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SVDB_MERGE } from '../../../../modules/svdb/merge/main.nf'
-
-workflow test_svdb_merge {
-
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
-            ]
-    priority = [ 'tiddit', 'cnvnator']
-
-    SVDB_MERGE ( input, priority )
-}
-
-workflow test_svdb_merge_noprio {
-
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
-            ]
-
-    SVDB_MERGE ( input, [] )
-}
diff --git a/tests/modules/svdb/merge/test.yml b/tests/modules/svdb/merge/test.yml
deleted file mode 100644
index 5af282aeeaa..00000000000
--- a/tests/modules/svdb/merge/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: svdb merge test_svdb_merge
-  command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config
-  tags:
-    - svdb
-    - svdb/merge
-  files:
-    - path: output/svdb/test_sv_merge.vcf.gz
-- name: svdb merge test_svdb_merge_noprio
-  command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config
-  tags:
-    - svdb
-    - svdb/merge
-  files:
-    - path: output/svdb/test_sv_merge.vcf.gz
-- name: svdb merge test_svdb_merge_noprio stub
-  command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config -stub
-  tags:
-    - svdb
-    - svdb/merge
-  files:
-    - path: output/svdb/test_sv_merge.vcf.gz
diff --git a/tests/modules/svdb/query/main.nf b/tests/modules/svdb/query/main.nf
deleted file mode 100644
index c014320f09f..00000000000
--- a/tests/modules/svdb/query/main.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SVDB_QUERY } from '../../../../modules/svdb/query/main.nf'
-
-workflow test_svdb_query {
-
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_sv_vcf'], checkIfExists: true) ]
-            ]
-
-    vcf_db = [
-                file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_sv_vcf_gz'], checkIfExists: true)
-            ]
-
-    in_occs = ['AC']
-    in_frqs = ['AF']
-    out_occs = ['gnomad_svAC']
-    out_frqs = ['gnomad_svAF']
-
-    SVDB_QUERY ( input, in_occs, in_frqs, out_occs, out_frqs, vcf_db )
-}
-
-workflow test_svdb_query_multiple {
-
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test_sv_vcf'], checkIfExists: true) ]
-            ]
-
-    vcf_db = [
-                file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_sv_vcf_gz'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['genome']['gnomad2_r2_1_1_sv_vcf_gz'], checkIfExists: true)
-            ]
-
-    in_occs = ['AC','AC']
-    in_frqs = ['AF','AF']
-    out_occs = ['gnomad_svAC','gnomad_svAC']
-    out_frqs = ['gnomad_svAF','gnomad_svAF']
-
-    SVDB_QUERY ( input, in_occs, in_frqs, out_occs, out_frqs, vcf_db )
-}
diff --git a/tests/modules/svdb/query/test.yml b/tests/modules/svdb/query/test.yml
deleted file mode 100644
index a7cbe3a681c..00000000000
--- a/tests/modules/svdb/query/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: svdb query
-  command: nextflow run ./tests/modules/svdb/query -entry test_svdb_query -c ./tests/config/nextflow.config -c ./tests/modules/svdb/query/nextflow.config
-  tags:
-    - svdb
-    - svdb/query
-  files:
-    - path: output/svdb/test_query.vcf
-
-- name: svdb query multiple
-  command: nextflow run ./tests/modules/svdb/query -entry test_svdb_query_multiple -c ./tests/config/nextflow.config -c ./tests/modules/svdb/query/nextflow.config
-  tags:
-    - svdb
-    - svdb/query
-  files:
-    - path: output/svdb/test_query.vcf
diff --git a/tests/modules/svtk/standardize/main.nf b/tests/modules/svtk/standardize/main.nf
deleted file mode 100644
index 6601edbd456..00000000000
--- a/tests/modules/svtk/standardize/main.nf
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SVTK_STANDARDIZE } from '../../../../modules/svtk/standardize/main.nf'
-include { MANTA_GERMLINE   } from '../../../../modules/manta/germline/main.nf'
-
-workflow test_svtk_standardize {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    MANTA_GERMLINE(
-        input,
-        fasta,
-        fasta_fai
-    )
-
-    SVTK_STANDARDIZE ( 
-        MANTA_GERMLINE.out.diploid_sv_vcf,
-        fasta_fai
-    )
-}
-
-workflow test_svtk_standardize_no_contigs {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    MANTA_GERMLINE(
-        input,
-        fasta,
-        fasta_fai
-    )
-
-    SVTK_STANDARDIZE ( 
-        MANTA_GERMLINE.out.diploid_sv_vcf,
-        []
-    )
-}
diff --git a/tests/modules/svtk/standardize/test.yml b/tests/modules/svtk/standardize/test.yml
deleted file mode 100644
index 764cfe2fc67..00000000000
--- a/tests/modules/svtk/standardize/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: svtk standardize test_svtk_standardize
-  command: nextflow run ./tests/modules/svtk/standardize -entry test_svtk_standardize -c ./tests/config/nextflow.config -c ./tests/modules/svtk/standardize/nextflow.config
-  tags:
-    - svtk
-    - svtk/standardize
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.diploid_sv.vcf.gz
-    - path: output/manta/test.diploid_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/svtk/test.std.vcf.gz
-      md5sum: f7530f3bc7e6020e758cc996adc8ae35
-
-- name: svtk standardize test_svtk_standardize_no_contigs
-  command: nextflow run ./tests/modules/svtk/standardize -entry test_svtk_standardize_no_contigs -c ./tests/config/nextflow.config -c ./tests/modules/svtk/standardize/nextflow.config
-  tags:
-    - svtk
-    - svtk/standardize
-  files:
-    - path: output/manta/test.candidate_small_indels.vcf.gz
-    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.candidate_sv.vcf.gz
-    - path: output/manta/test.candidate_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/manta/test.diploid_sv.vcf.gz
-    - path: output/manta/test.diploid_sv.vcf.gz.tbi
-      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
-    - path: output/svtk/test.std.vcf.gz
-      md5sum: ea67be7438a0fb72db8096e1bc1bb957
diff --git a/tests/modules/tabix/bgzip/main.nf b/tests/modules/tabix/bgzip/main.nf
deleted file mode 100644
index 1be82fa5d16..00000000000
--- a/tests/modules/tabix/bgzip/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TABIX_BGZIP } from '../../../../modules/tabix/bgzip/main.nf'
-include { TABIX_BGZIP as TABIX_BGZIP_WITH_GZI } from '../../../../modules/tabix/bgzip/main.nf'
-
-workflow test_tabix_bgzip_compress {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
-            ]
-
-    TABIX_BGZIP ( input )
-}
-
-workflow test_tabix_bgzip_compress_gzi {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
-            ]
-
-    TABIX_BGZIP_WITH_GZI ( input )
-}
-
-workflow test_tabix_bgzip_decompress {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ]
-            ]
-
-    TABIX_BGZIP ( input )
-}
diff --git a/tests/modules/tabix/bgzip/test.yml b/tests/modules/tabix/bgzip/test.yml
deleted file mode 100644
index 53e00ccbf6e..00000000000
--- a/tests/modules/tabix/bgzip/test.yml
+++ /dev/null
@@ -1,28 +0,0 @@
-- name: tabix bgzip compress
-  command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_compress -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
-  tags:
-    - tabix
-    - tabix/bgzip
-  files:
-    - path: ./output/tabix/test.vcf.gz
-      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
-    - path: ./output/tabix/test.vcf.gz.gzi
-      should_exist: false
-- name: tabix bgzip compress gzi
-  command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_compress_gzi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
-  tags:
-    - tabix
-    - tabix/bgzip
-  files:
-    - path: ./output/tabix/test.vcf.gz
-      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
-    - path: ./output/tabix/test.vcf.gz.gzi
-      md5sum: 7dea362b3fac8e00956a4952a3d4f474
-- name: tabix bgzip decompress
-  command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_decompress -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
-  tags:
-    - tabix
-    - tabix/bgzip
-  files:
-    - path: ./output/tabix/test.bed
-      md5sum: fe4053cf4de3aebbdfc3be2efb125a74
diff --git a/tests/modules/tabix/bgziptabix/main.nf b/tests/modules/tabix/bgziptabix/main.nf
deleted file mode 100644
index b2ff70d0175..00000000000
--- a/tests/modules/tabix/bgziptabix/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TABIX_BGZIPTABIX } from '../../../../modules/tabix/bgziptabix/main.nf'
-
-workflow test_tabix_bgziptabix {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
-            ]
-
-    TABIX_BGZIPTABIX ( input )
-}
diff --git a/tests/modules/tabix/bgziptabix/test.yml b/tests/modules/tabix/bgziptabix/test.yml
deleted file mode 100644
index ed614d7efa4..00000000000
--- a/tests/modules/tabix/bgziptabix/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: tabix bgziptabix test_tabix_bgziptabix
-  command: nextflow run ./tests/modules/tabix/bgziptabix -entry test_tabix_bgziptabix -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgziptabix/nextflow.config
-  tags:
-    - tabix/bgziptabix
-    - tabix
-  files:
-    - path: output/tabix/test.vcf.gz
-      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
-    - path: output/tabix/test.vcf.gz.tbi
-      md5sum: 36e11bf96ed0af4a92caa91a68612d64
diff --git a/tests/modules/tabix/tabix/main.nf b/tests/modules/tabix/tabix/main.nf
deleted file mode 100644
index da26f4d7ef5..00000000000
--- a/tests/modules/tabix/tabix/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TABIX_TABIX as TABIX_BED     } from '../../../../modules/tabix/tabix/main.nf'
-include { TABIX_TABIX as TABIX_GFF     } from '../../../../modules/tabix/tabix/main.nf'
-include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../modules/tabix/tabix/main.nf'
-include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../modules/tabix/tabix/main.nf'
-
-workflow test_tabix_tabix_bed {
-    input = [ [ id:'B.bed' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ] 
-            ]
-
-    TABIX_BED ( input )
-}
-
-workflow test_tabix_tabix_gff {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ] 
-            ]
-
-    TABIX_GFF ( input )
-}
-
-workflow test_tabix_tabix_vcf_tbi {
-    input = [ [ id:'test.vcf' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] 
-            ]
-
-    TABIX_VCF_TBI ( input )
-}
-
-workflow test_tabix_tabix_vcf_csi {
-    input = [ [ id:'test.vcf' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
-            ]
-
-    TABIX_VCF_CSI ( input )
-}
diff --git a/tests/modules/tabix/tabix/test.yml b/tests/modules/tabix/tabix/test.yml
deleted file mode 100644
index 6d168ef5d9c..00000000000
--- a/tests/modules/tabix/tabix/test.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-- name: tabix tabix bed
-  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_bed -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
-  tags:
-    - tabix
-    - tabix/tabix
-  files:
-    - path: ./output/tabix/test.bed.gz.tbi
-      md5sum: 5b40851ab6b8ccf7946313c86481c0df
-- name: tabix tabix gff
-  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_gff -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
-  tags:
-    - tabix
-    - tabix/tabix
-  files:
-    - path: ./output/tabix/genome.gff3.gz.tbi
-      md5sum: f79a67d95a98076e04fbe0455d825926
-- name: tabix tabix vcf
-  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
-  tags:
-    - tabix
-    - tabix/tabix
-  files:
-    - path: output/tabix/test.vcf.gz.tbi
-      md5sum: 36e11bf96ed0af4a92caa91a68612d64
-- name: tabix tabix vcf csi
-  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
-  tags:
-    - tabix
-    - tabix/tabix
-  files:
-    - path: output/tabix/test.vcf.gz.csi
-      md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd
diff --git a/tests/modules/tailfindr/main.nf b/tests/modules/tailfindr/main.nf
deleted file mode 100644
index a5c3b7d94b0..00000000000
--- a/tests/modules/tailfindr/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TAILFINDR } from '../../../modules/tailfindr/main.nf'
-
-workflow test_tailfindr {
-    
-    input = [
-        [ id: 'test' ], // meta map
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/tailfindr/test.fast5', checkIfExists: true)
-    ]
-
-    TAILFINDR ( input )
-}
diff --git a/tests/modules/tailfindr/test.yml b/tests/modules/tailfindr/test.yml
deleted file mode 100644
index 16f08c4e1a9..00000000000
--- a/tests/modules/tailfindr/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: "tailfindr"
-  command: nextflow run ./tests/modules/tailfindr -entry test_tailfindr -c ./tests/config/nextflow.config -c ./tests/modules/tailfindr/nextflow.config
-  tags:
-    - "tailfindr"
-  files:
-    - path: "output/tailfindr/test.csv.gz"
-      md5sum: 329e856d529dfd1ab31b0dedffc71f3c
-    - path: output/tailfindr/versions.yml
-      md5sum: 3a4e99bd95d9489da261b12a0ad740bb
diff --git a/tests/modules/tbprofiler/profile/main.nf b/tests/modules/tbprofiler/profile/main.nf
deleted file mode 100644
index 0141a77fad2..00000000000
--- a/tests/modules/tbprofiler/profile/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TBPROFILER_PROFILE } from '../../../../modules/tbprofiler/profile/main.nf'
-
-workflow test_tbprofiler_profile_illumina {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    TBPROFILER_PROFILE ( input )
-}
-
-workflow test_tbprofiler_profile_nanopore {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
-    ]
-
-    TBPROFILER_PROFILE ( input )
-}
diff --git a/tests/modules/tbprofiler/profile/test.yml b/tests/modules/tbprofiler/profile/test.yml
deleted file mode 100644
index 6e30b784499..00000000000
--- a/tests/modules/tbprofiler/profile/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: tbprofiler profile illumina
-  command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_illumina -c ./tests/config/nextflow.config -c ./tests/modules/tbprofiler/profile/nextflow.config
-  tags:
-    - tbprofiler
-    - tbprofiler/profile
-  files:
-    - path: output/tbprofiler/bam/test.bam
-    - path: output/tbprofiler/results/test.results.json
-      contains: ["genome_positions", "locus_tag", "tbprofiler_version"]
-    - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz
-
-- name: tbprofiler profile nanopore
-  command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/tbprofiler/profile/nextflow.config
-  tags:
-    - tbprofiler
-    - tbprofiler/profile
-  files:
-    - path: output/tbprofiler/bam/test.bam
-    - path: output/tbprofiler/results/test.results.json
-      contains: ["genome_positions", "locus_tag", "tbprofiler_version"]
-    - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz
diff --git a/tests/modules/tiddit/cov/main.nf b/tests/modules/tiddit/cov/main.nf
deleted file mode 100644
index 0032c759921..00000000000
--- a/tests/modules/tiddit/cov/main.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TIDDIT_COV as TIDDIT_COV_BED } from '../../../../modules/tiddit/cov/main.nf'
-include { TIDDIT_COV as TIDDIT_COV_WIG } from '../../../../modules/tiddit/cov/main.nf'
-
-workflow test_tiddit_cov_cram_bed {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    TIDDIT_COV_BED ( input, fasta )
-}
-
-workflow test_tiddit_cov_bam_bed {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-
-    TIDDIT_COV_BED ( input, [] )
-}
-
-workflow test_tiddit_cov_cram_wig {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    TIDDIT_COV_WIG ( input, fasta )
-}
-
-workflow test_tiddit_cov_bam_wig {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-
-    TIDDIT_COV_WIG ( input, [] )
-}
diff --git a/tests/modules/tiddit/cov/test.yml b/tests/modules/tiddit/cov/test.yml
deleted file mode 100644
index 916cc9e38b7..00000000000
--- a/tests/modules/tiddit/cov/test.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- name: tiddit cov test_tiddit_cov_cram_bed
-  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
-  tags:
-    - tiddit
-    - tiddit/cov
-  files:
-    - path: output/tiddit/test.bed
-      md5sum: 3b1a28c62a5f25bbba77c1042e9abdf7
-
-- name: tiddit cov test_tiddit_cov_bam_bed
-  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
-  tags:
-    - tiddit
-    - tiddit/cov
-  files:
-    - path: output/tiddit/test.bed
-      md5sum: 9d1474f1c7c6516205254077087bb026
-
-- name: tiddit cov test_tiddit_cov_cram_wig
-  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
-  tags:
-    - tiddit
-    - tiddit/cov
-  files:
-    - path: output/tiddit/test.wig
-      md5sum: ca3645fd0c3491c86c075c91d16d57c4
-
-- name: tiddit cov test_tiddit_cov_bam_wig
-  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
-  tags:
-    - tiddit
-    - tiddit/cov
-  files:
-    - path: output/tiddit/test.wig
-      md5sum: 44bea2ac6a56774738e65773065da670
diff --git a/tests/modules/tiddit/sv/main.nf b/tests/modules/tiddit/sv/main.nf
deleted file mode 100644
index 2f944129dbf..00000000000
--- a/tests/modules/tiddit/sv/main.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BWA_INDEX                    } from '../../../../modules/bwa/index/main.nf'
-include { TIDDIT_SV                    } from '../../../../modules/tiddit/sv/main.nf'
-include { TIDDIT_SV as TIDDIT_SV_NOBWA } from '../../../../modules/tiddit/sv/main.nf'
-
-workflow test_tiddit_sv_bam {
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX( fasta )
-
-    TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
-}
-
-workflow test_tiddit_sv_cram {
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    BWA_INDEX( fasta )
-
-    TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
-}
-
-workflow test_tiddit_sv_nobwa_bam {
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    TIDDIT_SV_NOBWA ( input, fasta, [])
-}
-
-workflow test_tiddit_sv_nobwa_cram {
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
-        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    TIDDIT_SV_NOBWA ( input, fasta, [])
-}
diff --git a/tests/modules/tiddit/sv/test.yml b/tests/modules/tiddit/sv/test.yml
deleted file mode 100644
index 5bbfe4aea93..00000000000
--- a/tests/modules/tiddit/sv/test.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-- name: tiddit sv test_tiddit_sv_bam
-  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_bam -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
-  tags:
-    - tiddit
-    - tiddit/sv
-  files:
-    - path: output/tiddit/test.ploidies.tab
-      md5sum: 6319d3611f7b6b94425a184d274b3dfc
-    - path: output/tiddit/test.vcf
-      md5sum: 157907671297c34bacfd3e73eff9bbdf
-
-- name: tiddit sv test_tiddit_sv_cram
-  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_cram -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
-  tags:
-    - tiddit
-    - tiddit/sv
-  files:
-    - path: output/tiddit/test.ploidies.tab
-      md5sum: f1162a940ddc8b963f6e0e506bb5c136
-    - path: output/tiddit/test.vcf
-      md5sum: 56687eeffa452f78f18d54a69dd17c78
-
-- name: tiddit sv test_tiddit_sv_nobwa_bam
-  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_nobwa_bam -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
-  tags:
-    - tiddit
-    - tiddit/sv
-  files:
-    - path: output/tiddit/test.ploidies.tab
-      md5sum: 6319d3611f7b6b94425a184d274b3dfc
-    - path: output/tiddit/test.vcf
-      md5sum: ddac94f9cd4f991b6ce2052d7f78a525
-
-- name: tiddit sv test_tiddit_sv_nobwa_cram
-  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_nobwa_cram -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
-  tags:
-    - tiddit
-    - tiddit/sv
-  files:
-    - path: output/tiddit/test.ploidies.tab
-      md5sum: f1162a940ddc8b963f6e0e506bb5c136
-    - path: output/tiddit/test.vcf
-      md5sum: 680e60574cc28d38c9673a916ecd675c
diff --git a/tests/modules/transdecoder/longorf/main.nf b/tests/modules/transdecoder/longorf/main.nf
deleted file mode 100644
index 90f75d193a9..00000000000
--- a/tests/modules/transdecoder/longorf/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TRANSDECODER_LONGORF } from '../../../../modules/transdecoder/longorf/main.nf'
-
-workflow test_transdecoder_longorf {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
-    ]
-
-    TRANSDECODER_LONGORF ( input )
-}
diff --git a/tests/modules/transdecoder/longorf/test.yml b/tests/modules/transdecoder/longorf/test.yml
deleted file mode 100644
index 4e88f0e824e..00000000000
--- a/tests/modules/transdecoder/longorf/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: transdecoder longorf test_transdecoder_longorf
-  command: nextflow run tests/modules/transdecoder/longorf -entry test_transdecoder_longorf -c tests/config/nextflow.config
-  tags:
-    - transdecoder
-    - transdecoder/longorf
-  files:
-    - path: output/transdecoder/versions.yml
-      md5sum: 15cffd5b1119e63d52dc754caf0f2d3c
-    - path: output/transdecoder/test/base_freqs.dat
-      md5sum: 5226ef383532e9b16c16b03e35ce181e
-    - path: output/transdecoder/test/longest_orfs.cds
-      md5sum: 041ac609e4c4ffb38676b1f88365be0f
-    - path: output/transdecoder/test/longest_orfs.gff3
-      md5sum: 96062ef88364f6bf1368d65cd1aad350
-    - path: output/transdecoder/test/longest_orfs.pep
-      md5sum: 0b903d36040676efeb2c50ab5ba46bbd
diff --git a/tests/modules/transdecoder/predict/main.nf b/tests/modules/transdecoder/predict/main.nf
deleted file mode 100644
index 02026a37984..00000000000
--- a/tests/modules/transdecoder/predict/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TRANSDECODER_PREDICT } from '../../../../modules/transdecoder/predict/main.nf'
-include { TRANSDECODER_LONGORF } from '../../../../modules/transdecoder/longorf/main.nf'
-
-workflow test_transdecoder_predict {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
-    
-    TRANSDECODER_LONGORF ( input )
-    TRANSDECODER_PREDICT ( input, TRANSDECODER_LONGORF.out.folder )
-
-}
-
diff --git a/tests/modules/transdecoder/predict/test.yml b/tests/modules/transdecoder/predict/test.yml
deleted file mode 100644
index cf2c0d0770b..00000000000
--- a/tests/modules/transdecoder/predict/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: transdecoder predict test_transdecoder_predict
-  command: nextflow run tests/modules/transdecoder/predict -entry test_transdecoder_predict -c tests/config/nextflow.config
-  tags:
-    - transdecoder
-    - transdecoder/predict
-  files:
-    - path: output/transdecoder/genome.fasta.transdecoder.bed
-    - path: output/transdecoder/genome.fasta.transdecoder.cds
-    - path: output/transdecoder/genome.fasta.transdecoder.gff3
-    - path: output/transdecoder/genome.fasta.transdecoder.pep
-    - path: output/transdecoder/versions.yml
-      md5sum: 2847cc159dc93e9014b57d76987623ea
diff --git a/tests/modules/trimgalore/main.nf b/tests/modules/trimgalore/main.nf
deleted file mode 100644
index adeda539eb8..00000000000
--- a/tests/modules/trimgalore/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { TRIMGALORE } from '../../../modules/trimgalore/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_trimgalore_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    TRIMGALORE ( input )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_trimgalore_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    TRIMGALORE ( input )
-}
diff --git a/tests/modules/trimgalore/test.yml b/tests/modules/trimgalore/test.yml
deleted file mode 100644
index ecbd2b5af38..00000000000
--- a/tests/modules/trimgalore/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: trimgalore single-end
-  command: nextflow run ./tests/modules/trimgalore/ -entry test_trimgalore_single_end -c ./tests/config/nextflow.config -c ./tests/modules/trimgalore/nextflow.config
-  tags:
-    - trimgalore
-  files:
-    # These can't be md5'd reliably
-    # TODO Test for includes
-    - path: ./output/trimgalore/test.fastq.gz_trimming_report.txt
-    - path: ./output/trimgalore/test_trimmed.fq.gz
-
-- name: trimgalore paired-end
-  command: nextflow run ./tests/modules/trimgalore/ -entry test_trimgalore_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/trimgalore/nextflow.config
-  tags:
-    - trimgalore
-  files:
-    # These can't be md5'd reliably
-    # TODO Test for includes
-    - path: ./output/trimgalore/test_2_val_2.fq.gz
-    - path: ./output/trimgalore/test_1_val_1.fq.gz
-    - path: ./output/trimgalore/test_1.fastq.gz_trimming_report.txt
-    - path: ./output/trimgalore/test_2.fastq.gz_trimming_report.txt
diff --git a/tests/modules/trimmomatic/main.nf b/tests/modules/trimmomatic/main.nf
deleted file mode 100644
index bd87f1b6120..00000000000
--- a/tests/modules/trimmomatic/main.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-nextflow.enable.dsl = 2
-
-include {
-    TRIMMOMATIC as TRIMMOMATIC_SE
-    TRIMMOMATIC as TRIMMOMATIC_PE
-    TRIMMOMATIC
-} from '../../../modules/trimmomatic/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_trimmomatic_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    TRIMMOMATIC_SE ( input )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_trimmomatic_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    TRIMMOMATIC_PE ( input )
-}
-
-//
-// Failing test with no adaptor
-//
-workflow test_trimmomatic_no_adaptor {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    TRIMMOMATIC ( input )
-}
diff --git a/tests/modules/trimmomatic/test.yml b/tests/modules/trimmomatic/test.yml
deleted file mode 100644
index 12fe44fa385..00000000000
--- a/tests/modules/trimmomatic/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: trimmomatic single-end
-  command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_single_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
-  tags:
-    - "trimmomatic"
-  files:
-    - path: "output/trimmomatic/test.SE.paired.trim.fastq.gz"
-    - path: "output/trimmomatic/test.log"
-      md5sum: e4c3f619e9b0e26847f8f3e3d9af319b
-
-- name: trimmomatic paired-end
-  command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
-  tags:
-    - "trimmomatic"
-  files:
-    - path: "output/trimmomatic/test.log"
-      md5sum: 9629761761a34576b3484bf4174f681f
-    - path: "output/trimmomatic/test.paired.trim_1.fastq.gz"
-    - path: "output/trimmomatic/test.unpaired.trim_1.fastq.gz"
-    - path: "output/trimmomatic/test.paired.trim_2.fastq.gz"
-    - path: "output/trimmomatic/test.unpaired.trim_2.fastq.gz"
-
-- name: trimmomatic no adapter specified
-  command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_no_adaptor -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
-  tags:
-    - "trimmomatic"
-  exit_code: 1
diff --git a/tests/modules/ucsc/bedclip/main.nf b/tests/modules/ucsc/bedclip/main.nf
deleted file mode 100755
index 8ccfd3b0b5f..00000000000
--- a/tests/modules/ucsc/bedclip/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UCSC_BEDCLIP } from '../../../../modules/ucsc/bedclip/main.nf'
-
-workflow test_ucsc_bedclip {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_bedgraph'], checkIfExists: true)
-            ]
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-
-    UCSC_BEDCLIP ( input, sizes )
-}
diff --git a/tests/modules/ucsc/bedclip/test.yml b/tests/modules/ucsc/bedclip/test.yml
deleted file mode 100755
index bcf22c71d0c..00000000000
--- a/tests/modules/ucsc/bedclip/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: ucsc bedclip
-  command: nextflow run ./tests/modules/ucsc/bedclip -entry test_ucsc_bedclip -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedclip/nextflow.config
-  tags:
-    - ucsc
-    - ucsc/bedclip
-  files:
-    - path: output/ucsc/test.clip.bedGraph
-      md5sum: e02395e1f7c593b3f79563067159ebc2
diff --git a/tests/modules/ucsc/bedgraphtobigwig/main.nf b/tests/modules/ucsc/bedgraphtobigwig/main.nf
deleted file mode 100644
index c6db7225b74..00000000000
--- a/tests/modules/ucsc/bedgraphtobigwig/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UCSC_BEDGRAPHTOBIGWIG  } from '../../../../modules/ucsc/bedgraphtobigwig/main.nf'
-
-workflow test_ucsc_bedgraphtobigwig {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_bedgraph'], checkIfExists: true) ]
-            ]
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-
-    UCSC_BEDGRAPHTOBIGWIG ( input, sizes )
-}
diff --git a/tests/modules/ucsc/bedgraphtobigwig/test.yml b/tests/modules/ucsc/bedgraphtobigwig/test.yml
deleted file mode 100644
index 2a532a62ab0..00000000000
--- a/tests/modules/ucsc/bedgraphtobigwig/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: ucsc bedgraphtobigwig
-  command: nextflow run ./tests/modules/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedgraphtobigwig/nextflow.config
-  tags:
-    - ucsc
-    - ucsc/bedgraphtobigwig
-  files:
-    - path: output/ucsc/test.bigWig
-      md5sum: 910ecc7f57e3bbd5fac5a8edba4f615d
diff --git a/tests/modules/ucsc/bedtobigbed/main.nf b/tests/modules/ucsc/bedtobigbed/main.nf
deleted file mode 100644
index 36a9b423e2d..00000000000
--- a/tests/modules/ucsc/bedtobigbed/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UCSC_BEDTOBIGBED } from '../../../../modules/ucsc/bedtobigbed/main.nf'
-include { UCSC_BEDTOBIGBED as UCSC_BEDTOBIGBED_AS } from '../../../../modules/ucsc/bedtobigbed/main.nf'
-
-workflow test_ucsc_bedtobigbed {
-    input = [ [ id: 'test' ], // meta map 
-              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
-            ]
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-
-    UCSC_BEDTOBIGBED ( input, sizes, [] )
-}
-
-workflow test_ucsc_bedtobigbed_autosql {
-    input = [ [ id: 'test' ], // meta map
-              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
-            ]
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-    autosql = file(params.test_data['sarscov2']['genome']['bed_autosql'], checkIfExists: true)
-
-    UCSC_BEDTOBIGBED_AS ( input, sizes, autosql )
-}
diff --git a/tests/modules/ucsc/bedtobigbed/test.yml b/tests/modules/ucsc/bedtobigbed/test.yml
deleted file mode 100644
index 718b1864bab..00000000000
--- a/tests/modules/ucsc/bedtobigbed/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: ucsc bedtobigbed
-  command: nextflow run ./tests/modules/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedtobigbed/nextflow.config
-  tags:
-    - ucsc
-    - ucsc/bedtobigbed
-  files:
-    - path: output/ucsc/test.bigBed
-      md5sum: 3c2400aab8f7a3ac333905c7484d9a24
-- name: ucsc bedtobigbed autosql
-  command: nextflow run ./tests/modules/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed_autosql -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedtobigbed/nextflow.config
-  tags:
-    - ucsc
-    - ucsc/bedtobigbed
-  files:
-    - path: output/ucsc/test.bigBed
-      md5sum: 6dc69a14b95bcceee98e9e6b3c3def09
diff --git a/tests/modules/ucsc/bigwigaverageoverbed/main.nf b/tests/modules/ucsc/bigwigaverageoverbed/main.nf
deleted file mode 100644
index 3b20dc32ef3..00000000000
--- a/tests/modules/ucsc/bigwigaverageoverbed/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../modules/ucsc/bigwigaverageoverbed/main.nf'
-
-workflow test_ucsc_bigwigaverageoverbed {
-    input = [
-        [ id: 'test' ], // meta map
-        [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
-    ]
-    bigwig = file(params.test_data['sarscov2']['illumina']['test_bigwig'], checkIfExists: true)
-
-    UCSC_BIGWIGAVERAGEOVERBED ( input, bigwig )
-}
diff --git a/tests/modules/ucsc/bigwigaverageoverbed/test.yml b/tests/modules/ucsc/bigwigaverageoverbed/test.yml
deleted file mode 100644
index 7344c9440cc..00000000000
--- a/tests/modules/ucsc/bigwigaverageoverbed/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: ucsc bigwigaverageoverbed test_ucsc_bigwigaverageoverbed
-  command: nextflow run ./tests/modules/ucsc/bigwigaverageoverbed -entry test_ucsc_bigwigaverageoverbed -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bigwigaverageoverbed/nextflow.config
-  tags:
-    - ucsc
-    - ucsc/bigwigaverageoverbed
-  files:
-    - path: output/ucsc/test.tab
-      md5sum: d92334d90353577571eaf777933dce9b
diff --git a/tests/modules/ucsc/liftover/main.nf b/tests/modules/ucsc/liftover/main.nf
deleted file mode 100644
index 168193f4e31..00000000000
--- a/tests/modules/ucsc/liftover/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UCSC_LIFTOVER } from '../../../../modules/ucsc/liftover/main.nf'
-
-workflow test_ucsc_liftover {
-    
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]
-    chain =  file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
-
-    UCSC_LIFTOVER ( input, chain )
-}
diff --git a/tests/modules/ucsc/liftover/test.yml b/tests/modules/ucsc/liftover/test.yml
deleted file mode 100644
index c301618986a..00000000000
--- a/tests/modules/ucsc/liftover/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: ucsc liftover test_ucsc_liftover
-  command: nextflow run ./tests/modules/ucsc/liftover -entry test_ucsc_liftover -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/liftover/nextflow.config
-  tags:
-    - ucsc
-    - ucsc/liftover
-  files:
-    - path: output/ucsc/test.lifted.bed
-      md5sum: fd5878470257a8a0edeaa8b9374bd520
-    - path: output/ucsc/test.unlifted.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/modules/ucsc/wigtobigwig/main.nf b/tests/modules/ucsc/wigtobigwig/main.nf
deleted file mode 100644
index 2abbe5b2609..00000000000
--- a/tests/modules/ucsc/wigtobigwig/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UCSC_WIGTOBIGWIG } from '../../../../modules/ucsc/wigtobigwig/main.nf'
-
-workflow test_ucsc_wigtobigwig {
-
-    input = [ [ id:'test', single_end:false ], // meta map,
-                file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true) ]
-
-    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-
-    UCSC_WIGTOBIGWIG ( input, sizes )
-}
diff --git a/tests/modules/ucsc/wigtobigwig/test.yml b/tests/modules/ucsc/wigtobigwig/test.yml
deleted file mode 100644
index aa478bc319c..00000000000
--- a/tests/modules/ucsc/wigtobigwig/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: ucsc wigtobigwig test_ucsc_wigtobigwig
-  command: nextflow run ./tests/modules/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/wigtobigwig/nextflow.config
-  tags:
-    - ucsc
-    - ucsc/wigtobigwig
-  files:
-    - path: output/ucsc/test.bw
-      md5sum: b64af7003665dc51fae958216b06ed95
-    - path: output/ucsc/versions.yml
-      md5sum: 7e14421c65faf5165389f34806acdb12
-
-- name: ucsc wigtobigwig test_ucsc_wigtobigwig stub
-  command: nextflow run ./tests/modules/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/wigtobigwig/nextflow.config -stub
-  tags:
-    - ucsc
-    - ucsc/wigtobigwig
-  files:
-    - path: output/ucsc/test.bw
-    - path: output/ucsc/versions.yml
diff --git a/tests/modules/ultra/align/main.nf b/tests/modules/ultra/align/main.nf
deleted file mode 100644
index 14795077564..00000000000
--- a/tests/modules/ultra/align/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP        } from '../../../../modules/gunzip/main.nf'
-include { GFFREAD       } from '../../../../modules/gffread/main.nf'
-include { ULTRA_INDEX   } from '../../../../modules/ultra/index/main.nf'
-include { ULTRA_ALIGN   } from '../../../../modules/ultra/align/main.nf'
-
-workflow test_ultra_align {
-
-    input = [
-        [ id:'test', single_end:false ],
-        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
-    ]
-
-    genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf    = file(params.test_data['homo_sapiens']['genome']['genome_gtf']  , checkIfExists: true)
-
-    GUNZIP ( input )
-    GFFREAD ( gtf )
-    ULTRA_INDEX ( genome, GFFREAD.out.gtf )
-    ULTRA_ALIGN ( GUNZIP.out.gunzip, genome, ULTRA_INDEX.out.index )
-}
diff --git a/tests/modules/ultra/align/test.yml b/tests/modules/ultra/align/test.yml
deleted file mode 100644
index 7e26f9a5fb5..00000000000
--- a/tests/modules/ultra/align/test.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-- name: ultra align test_ultra_align
-  command: nextflow run ./tests/modules/ultra/align -entry test_ultra_align -c ./tests/config/nextflow.config  -c ./tests/modules/ultra/align/nextflow.config
-  tags:
-    - ultra/align
-    - ultra
-  files:
-    - path: output/gffread/genome_sorted.gtf
-      md5sum: c0b034860c679a354cd093109ed90437
-    - path: output/gunzip/test_hifi.fastq
-      md5sum: 20e41c569d5828c1e87337e13a5185d3
-    - path: output/ultra/all_splice_pairs_annotations.pickle
-    - path: output/ultra/all_splice_sites_annotations.pickle
-    - path: output/ultra/chr_to_id.pickle
-    - path: output/ultra/database.db
-    - path: output/ultra/exon_choordinates_to_id.pickle
-    - path: output/ultra/flank_choordinates.pickle
-    - path: output/ultra/gene_to_small_segments.pickle
-    - path: output/ultra/id_to_chr.pickle
-    - path: output/ultra/max_intron_chr.pickle
-    - path: output/ultra/parts_to_segments.pickle
-    - path: output/ultra/ref_exon_sequences.pickle
-    - path: output/ultra/ref_flank_sequences.pickle
-    - path: output/ultra/ref_part_sequences.pickle
-    - path: output/ultra/ref_segment_sequences.pickle
-    - path: output/ultra/refs_id_lengths.pickle
-    - path: output/ultra/refs_lengths.pickle
-    - path: output/ultra/segment_id_to_choordinates.pickle
-    - path: output/ultra/segment_to_gene.pickle
-    - path: output/ultra/segment_to_ref.pickle
-    - path: output/ultra/splices_to_transcripts.pickle
-    - path: output/ultra/test.bam
-      md5sum: b34c3631a899ba800602ff07b8183f87
-    - path: output/ultra/transcripts_to_splices.pickle
diff --git a/tests/modules/ultra/index/main.nf b/tests/modules/ultra/index/main.nf
deleted file mode 100644
index 82056b4762d..00000000000
--- a/tests/modules/ultra/index/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ULTRA_INDEX } from '../../../../modules/ultra/index/main.nf'
-include { GFFREAD     } from '../../../../modules/gffread/main.nf'
-
-workflow test_ultra_index {
-
-    genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    gtf    = file(params.test_data['homo_sapiens']['genome']['genome_gtf']  , checkIfExists: true)
-    GFFREAD ( gtf )
-
-    ULTRA_INDEX ( genome, GFFREAD.out.gtf )
-}
diff --git a/tests/modules/ultra/index/test.yml b/tests/modules/ultra/index/test.yml
deleted file mode 100644
index 36dcf093b92..00000000000
--- a/tests/modules/ultra/index/test.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-- name: ultra index test_ultra_index
-  command: nextflow run ./tests/modules/ultra/index -entry test_ultra_index -c ./tests/config/nextflow.config  -c ./tests/modules/ultra/index/nextflow.config
-  tags:
-    - ultra
-    - ultra/index
-  files:
-    - path: output/gffread/genome_sorted.gtf
-      md5sum: c0b034860c679a354cd093109ed90437
-    - path: output/ultra/all_splice_pairs_annotations.pickle
-    - path: output/ultra/all_splice_sites_annotations.pickle
-    - path: output/ultra/chr_to_id.pickle
-    - path: output/ultra/database.db
-    - path: output/ultra/exon_choordinates_to_id.pickle
-    - path: output/ultra/flank_choordinates.pickle
-    - path: output/ultra/gene_to_small_segments.pickle
-    - path: output/ultra/id_to_chr.pickle
-    - path: output/ultra/max_intron_chr.pickle
-    - path: output/ultra/parts_to_segments.pickle
-    - path: output/ultra/ref_exon_sequences.pickle
-    - path: output/ultra/ref_flank_sequences.pickle
-    - path: output/ultra/ref_part_sequences.pickle
-    - path: output/ultra/ref_segment_sequences.pickle
-    - path: output/ultra/refs_id_lengths.pickle
-    - path: output/ultra/refs_lengths.pickle
-    - path: output/ultra/segment_id_to_choordinates.pickle
-    - path: output/ultra/segment_to_gene.pickle
-    - path: output/ultra/segment_to_ref.pickle
-    - path: output/ultra/splices_to_transcripts.pickle
-    - path: output/ultra/transcripts_to_splices.pickle
diff --git a/tests/modules/ultra/pipeline/main.nf b/tests/modules/ultra/pipeline/main.nf
deleted file mode 100644
index 483d48fcdab..00000000000
--- a/tests/modules/ultra/pipeline/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ULTRA_PIPELINE } from '../../../../modules/ultra/pipeline/main.nf'
-include { GUNZIP         } from '../../../../modules/gunzip/main.nf'
-include { GFFREAD        } from '../../../../modules/gffread/main.nf'
-
-workflow test_ultra_pipeline {
-
-    input = [
-        [ id:'test', single_end:false ],
-        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
-    ]
-    GUNZIP ( input )
-
-    gtf    = file(params.test_data['homo_sapiens']['genome']['genome_gtf']  , checkIfExists: true)
-    genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    GFFREAD ( gtf )
-
-    ULTRA_PIPELINE ( GUNZIP.out.gunzip, genome, GFFREAD.out.gtf )
-}
diff --git a/tests/modules/ultra/pipeline/test.yml b/tests/modules/ultra/pipeline/test.yml
deleted file mode 100644
index d424ba73613..00000000000
--- a/tests/modules/ultra/pipeline/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: ultra pipeline test_ultra_pipeline
-  command: nextflow run ./tests/modules/ultra/pipeline -entry test_ultra_pipeline -c ./tests/config/nextflow.config -c ./tests/modules/ultra/pipeline/nextflow.config
-  tags:
-    - ultra
-    - ultra/pipeline
-  files:
-    - path: output/gffread/genome_sorted.gtf
-      md5sum: c0b034860c679a354cd093109ed90437
-    - path: output/gunzip/test_hifi.fastq
-      md5sum: 20e41c569d5828c1e87337e13a5185d3
-    - path: output/ultra/test.sam
-      md5sum: a37a1f9594a3099522dc1f6a903b2b12
diff --git a/tests/modules/umitools/dedup/main.nf b/tests/modules/umitools/dedup/main.nf
deleted file mode 100644
index 1edcb287605..00000000000
--- a/tests/modules/umitools/dedup/main.nf
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UMITOOLS_EXTRACT } from '../../../../modules/umitools/extract/main.nf'
-include { BWA_INDEX        } from '../../../../modules/bwa/index/main.nf'
-include { BWA_MEM          } from '../../../../modules/bwa/mem/main.nf'
-include { SAMTOOLS_INDEX   } from '../../../../modules/samtools/index/main.nf'
-include { UMITOOLS_DEDUP   } from '../../../../modules/umitools/dedup/main.nf'
-
-//
-// Test with no UMI
-//
-workflow test_umitools_dedup_no_umi {
-    input = [ 
-        [ id:'test'], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-    get_output_stats = false
-
-    UMITOOLS_DEDUP ( input, get_output_stats )
-}
-
-//
-// Test with single-end data without --output-stats
-//
-workflow test_umitools_dedup_single_end_no_stats {
-    input = [ 
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    get_output_stats = false
-
-    UMITOOLS_EXTRACT ( input )
-    BWA_INDEX ( fasta )
-    BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
-    SAMTOOLS_INDEX ( BWA_MEM.out.bam )
-    UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
-}
-
-//
-// Test with paired-end data without --output-stats
-//
-workflow test_umitools_dedup_paired_end_no_stats {
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        [ 
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    get_output_stats = false
-
-    UMITOOLS_EXTRACT ( input )
-    BWA_INDEX ( fasta )
-    BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
-    SAMTOOLS_INDEX ( BWA_MEM.out.bam )
-    UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
-}
-
-//
-// Test with paired-end data with --output-stats
-//
-workflow test_umitools_dedup_paired_end_stats {
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        [ 
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    get_output_stats = true
-
-    UMITOOLS_EXTRACT ( input )
-    BWA_INDEX ( fasta )
-    BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
-    SAMTOOLS_INDEX ( BWA_MEM.out.bam )
-    UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
-}
diff --git a/tests/modules/umitools/dedup/test.yml b/tests/modules/umitools/dedup/test.yml
deleted file mode 100644
index 5a92a35a29d..00000000000
--- a/tests/modules/umitools/dedup/test.yml
+++ /dev/null
@@ -1,87 +0,0 @@
-- name: umitools dedup test_umitools_dedup_no_umi
-  command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_no_umi -c ./tests/config/nextflow.config  -c ./tests/modules/umitools/dedup/nextflow.config
-  tags:
-    - umitools/dedup
-    - umitools
-  files:
-    - path: output/umitools/test.dedup.bam
-
-- name: umitools dedup test_umitools_dedup_single_end_no_stats
-  command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_single_end_no_stats -c ./tests/config/nextflow.config  -c ./tests/modules/umitools/dedup/nextflow.config
-  tags:
-    - umitools/dedup
-    - umitools
-  files:
-    - path: output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-    - path: output/bwa/test.bam
-      md5sum: 3ecbe569cadb9b6c881917ce60779f75
-    - path: output/samtools/test.bam.bai
-      md5sum: 095af0ad3921212597ffd7c342ecd5a0
-    - path: output/umitools/test.dedup.bam
-    - path: output/umitools/test.umi_extract.fastq.gz
-    - path: output/umitools/test.umi_extract.log
-
-- name: umitools dedup test_umitools_dedup_paired_end_no_stats
-  command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config  -c ./tests/modules/umitools/dedup/nextflow.config
-  tags:
-    - umitools/dedup
-    - umitools
-  files:
-    - path: output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-    - path: output/bwa/test.bam
-      md5sum: e7dcbac1825bf210409b762dbb4fec8f
-    - path: output/samtools/test.bam.bai
-      md5sum: f75780d1de7860329b7fb4afeadc4bed
-    - path: output/umitools/test.dedup.bam
-    - path: output/umitools/test.umi_extract.log
-    - path: output/umitools/test.umi_extract_1.fastq.gz
-    - path: output/umitools/test.umi_extract_2.fastq.gz
-
-- name: umitools dedup test_umitools_dedup_paired_end_stats
-  command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config  -c ./tests/modules/umitools/dedup/nextflow.config
-  tags:
-    - umitools/dedup
-    - umitools
-  files:
-    - path: output/bwa/bwa/genome.amb
-      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: output/bwa/bwa/genome.ann
-      md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-    - path: output/bwa/test.bam
-      md5sum: e7dcbac1825bf210409b762dbb4fec8f
-    - path: output/samtools/test.bam.bai
-      md5sum: f75780d1de7860329b7fb4afeadc4bed
-    - path: output/umitools/test.dedup.bam
-    - path: output/umitools/test.dedup_edit_distance.tsv
-      md5sum: c247a49b58768e6e2e86a6c08483e612
-    - path: output/umitools/test.dedup_per_umi.tsv
-      md5sum: 10e35ca37f2bfb521ac6dd7314951a68
-    - path: output/umitools/test.dedup_per_umi_per_position.tsv
-      md5sum: 2e1a12e6f720510880068deddeefe063
-    - path: output/umitools/test.umi_extract.log
-    - path: output/umitools/test.umi_extract_1.fastq.gz
-    - path: output/umitools/test.umi_extract_2.fastq.gz
diff --git a/tests/modules/umitools/extract/main.nf b/tests/modules/umitools/extract/main.nf
deleted file mode 100644
index 3baac16a8c6..00000000000
--- a/tests/modules/umitools/extract/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UMITOOLS_EXTRACT } from '../../../../modules/umitools/extract/main.nf'
-
-//
-// Test with single-end data
-//
-workflow test_umitools_extract_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    UMITOOLS_EXTRACT ( input )
-}
-
-//
-// Test with paired-end data
-//
-workflow test_umitools_extract_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    UMITOOLS_EXTRACT ( input )
-}
-
diff --git a/tests/modules/umitools/extract/test.yml b/tests/modules/umitools/extract/test.yml
deleted file mode 100644
index 336cd1229f8..00000000000
--- a/tests/modules/umitools/extract/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: umitools extract test_umitools_extract_single_end
-  command: nextflow run tests/modules/umitools/extract -entry test_umitools_extract_single_end -c tests/config/nextflow.config
-  tags:
-    - umitools/extract
-    - umitools
-  files:
-    - path: output/umitools/test.umi_extract.fastq.gz
-      should_exist: true
-    - path: output/umitools/test.umi_extract.log
-      contains: ["job finished in"]
-    - path: output/umitools/versions.yml
-      md5sum: 397e6972343f9d7b8eae387fc18c12c7
-
-- name: umitools extract test_umitools_extract_paired_end
-  command: nextflow run tests/modules/umitools/extract -entry test_umitools_extract_paired_end -c tests/config/nextflow.config
-  tags:
-    - umitools/extract
-    - umitools
-  files:
-    - path: output/umitools/test.umi_extract.log
-      contains: ["job finished in"]
-    - path: output/umitools/test.umi_extract_1.fastq.gz
-      should_exist: true
-    - path: output/umitools/test.umi_extract_2.fastq.gz
-      should_exist: true
-    - path: output/umitools/versions.yml
-      md5sum: 0aec6f919d62b7b79f6d0c5d79411464
diff --git a/tests/modules/unicycler/main.nf b/tests/modules/unicycler/main.nf
deleted file mode 100644
index 861b139bff5..00000000000
--- a/tests/modules/unicycler/main.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNICYCLER } from '../../../modules/unicycler/main.nf'
-
-workflow test_unicycler_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true) ],
-              []
-            ]
-
-    UNICYCLER ( input )
-}
-
-workflow test_unicycler_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
-              []
-            ]
-
-    UNICYCLER ( input )
-}
-
-workflow test_unicycler_shortreads_longreads {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
-              [ file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
-            ]
-
-    UNICYCLER ( input )
-}
diff --git a/tests/modules/unicycler/test.yml b/tests/modules/unicycler/test.yml
deleted file mode 100644
index e25845aab50..00000000000
--- a/tests/modules/unicycler/test.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-- name: unicycler test_unicycler_single_end
-  command: nextflow run ./tests/modules/unicycler -entry test_unicycler_single_end -c ./tests/config/nextflow.config -c ./tests/modules/unicycler/nextflow.config
-  tags:
-    - unicycler
-  files:
-    - path: output/unicycler/test.assembly.gfa.gz
-    - path: output/unicycler/test.scaffolds.fa.gz
-    - path: output/unicycler/test.unicycler.log
-      contains:
-        - "Assembly complete"
-
-- name: unicycler test_unicycler_paired_end
-  command: nextflow run ./tests/modules/unicycler -entry test_unicycler_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/unicycler/nextflow.config
-  tags:
-    - unicycler
-  files:
-    - path: output/unicycler/test.assembly.gfa.gz
-    - path: output/unicycler/test.scaffolds.fa.gz
-    - path: output/unicycler/test.unicycler.log
-      contains:
-        - "Assembly complete"
-
-- name: unicycler test_unicycler_shortreads_longreads
-  command: nextflow run ./tests/modules/unicycler -entry test_unicycler_shortreads_longreads -c ./tests/config/nextflow.config -c ./tests/modules/unicycler/nextflow.config
-  tags:
-    - unicycler
-  files:
-    - path: output/unicycler/test.assembly.gfa.gz
-    - path: output/unicycler/test.scaffolds.fa.gz
-    - path: output/unicycler/test.unicycler.log
-      contains:
-        - "Assembly complete"
diff --git a/tests/modules/untar/main.nf b/tests/modules/untar/main.nf
deleted file mode 100644
index 079f3aebbb4..00000000000
--- a/tests/modules/untar/main.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR } from '../../../modules/untar/main.nf'
-
-workflow test_untar {
-    input = [
-        [],
-        file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
-    ]
-
-    UNTAR ( input )
-}
-
-
-workflow test_untar_different_output_path {
-    input = [
-        [],
-        file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
-    ]
-
-    UNTAR ( input )
-}
-
-
-workflow test_untar_onlyfiles {
-    input = [
-        [],
-        file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true)
-    ]
-
-    UNTAR ( input )
-}
diff --git a/tests/modules/untar/test.yml b/tests/modules/untar/test.yml
deleted file mode 100644
index 8ebb2d12768..00000000000
--- a/tests/modules/untar/test.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: untar test_untar
-  command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config  -c ./tests/modules/untar/nextflow.config
-  tags:
-    - untar
-  files:
-    - path: output/untar/kraken2/hash.k2d
-      md5sum: 8b8598468f54a7087c203ad0190555d9
-    - path: output/untar/kraken2/opts.k2d
-      md5sum: a033d00cf6759407010b21700938f543
-    - path: output/untar/kraken2/taxo.k2d
-      md5sum: 094d5891cdccf2f1468088855c214b2c
-
-- name: untar test_untar_different_output_path
-  command: nextflow run ./tests/modules/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config  -c ./tests/modules/untar/nextflow.config
-  tags:
-    - untar
-  files:
-    - path: output/untar/flowcell/RunInfo.xml
-      md5sum: 03038959f4dd181c86bc97ae71fe270a
-
-- name: untar test_untar_onlyfiles
-  command: nextflow run ./tests/modules/untar -entry test_untar_onlyfiles -c ./tests/config/nextflow.config  -c ./tests/modules/untar/nextflow.config
-  tags:
-    - untar
-  files:
-    - path: output/untar/hello/hello.txt
-      md5sum: e59ff97941044f85df5297e1c302d260
diff --git a/tests/modules/unzip/main.nf b/tests/modules/unzip/main.nf
deleted file mode 100644
index 6f7cc030648..00000000000
--- a/tests/modules/unzip/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNZIP } from '../../../modules/unzip/main.nf'
-
-workflow test_unzip {
-
-    archive = [
-        [],
-        file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
-    ]
-
-    UNZIP ( archive )
-}
diff --git a/tests/modules/unzip/test.yml b/tests/modules/unzip/test.yml
deleted file mode 100644
index 8016b4fa5ba..00000000000
--- a/tests/modules/unzip/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: unzip
-  command: nextflow run ./tests/modules/unzip -entry test_unzip -c ./tests/config/nextflow.config -c ./tests/modules/unzip/nextflow.config
-  tags:
-    - unzip
-  files:
-    - path: output/unzip/ncbi_taxmap/
-    - path: output/unzip/ncbi_taxmap/ncbi.map
-      md5sum: de30dbba85f9070612b632e2a5a95952
-    - path: output/unzip/ncbi_taxmap/ncbi.tre
-      md5sum: 4029dd2091c685b9a86ddd9d0d870db0
diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf
deleted file mode 100644
index 557c5bbe8ae..00000000000
--- a/tests/modules/vardictjava/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
-
-workflow test_vardictjava_bam {
-    
-    bam_input_ch = Channel.value([
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-    ])
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)   
-    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    VARDICTJAVA ( bam_input_ch, fasta, fasta_fai )
-}
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
deleted file mode 100644
index d7ff54c0dd2..00000000000
--- a/tests/modules/vardictjava/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: vardictjava test_vardictjava_bam
-  command: nextflow run ./tests/modules/vardictjava -entry test_vardictjava_bam -c ./tests/config/nextflow.config -c ./tests/modules/vardictjava/nextflow.config
-  tags:
-    - vardictjava
-  files:
-    - path: output/vardictjava/test.vcf.gz
-      md5sum: 3f1f227afc532bddeb58f16fd3013fc8
diff --git a/tests/modules/variantbam/main.nf b/tests/modules/variantbam/main.nf
deleted file mode 100644
index 016a9104ba1..00000000000
--- a/tests/modules/variantbam/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VARIANTBAM } from '../../../modules/variantbam/main.nf'
-
-workflow test_variantbam {
-
-    input = [ [ id:'test', single_end:false ],
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-
-    VARIANTBAM ( input )
-}
diff --git a/tests/modules/variantbam/test.yml b/tests/modules/variantbam/test.yml
deleted file mode 100644
index 1c9550ed8d3..00000000000
--- a/tests/modules/variantbam/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: variantbam test_variantbam
-  command: nextflow run ./tests/modules/variantbam -entry test_variantbam -c ./tests/config/nextflow.config -c ./tests/modules/variantbam/nextflow.config
-  tags:
-    - variantbam
-  files:
-    - path: output/variantbam/test.bam
-      md5sum: fc08f065475d60b3b06ee32920564d4b
diff --git a/tests/modules/vcf2db/main.nf b/tests/modules/vcf2db/main.nf
deleted file mode 100644
index 0d4be5d23e1..00000000000
--- a/tests/modules/vcf2db/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VCF2DB } from '../../../modules/vcf2db/main.nf'
-
-workflow test_vcf2db {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
-    ]
-
-    VCF2DB ( input )
-}
diff --git a/tests/modules/vcf2db/test.yml b/tests/modules/vcf2db/test.yml
deleted file mode 100644
index df276b1c72d..00000000000
--- a/tests/modules/vcf2db/test.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-- name: vcf2db test_vcf2db
-  command: nextflow run ./tests/modules/vcf2db -entry test_vcf2db -c ./tests/config/nextflow.config -c ./tests/modules/vcf2db/nextflow.config
-  tags:
-    - vcf2db
-  files:
-    - path: output/vcf2db/test.db
diff --git a/tests/modules/vcf2maf/main.nf b/tests/modules/vcf2maf/main.nf
deleted file mode 100644
index 57f3a6cb4c2..00000000000
--- a/tests/modules/vcf2maf/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VCF2MAF } from '../../../modules/vcf2maf/main.nf'
-include { UNTAR   } from '../../../modules/untar/main.nf'
-
-workflow test_vcf2maf_no_vep {
-
-    input_vcf = [
-        [ id:'test' ],
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
-    ]
-    fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    VCF2MAF ( input_vcf, fasta, [] )
-}
-
-workflow test_vcf2maf_vep {
-
-    input_vcf = [
-        [ id:'test' ],
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
-    ]
-    fasta     = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
-    vep_cache = [ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['vep_cache'], checkIfExists: true) ]
-
-    vep_cache_unpacked = UNTAR(vep_cache).untar.map { it[1] }
-    VCF2MAF ( input_vcf, fasta, vep_cache_unpacked)
-}
diff --git a/tests/modules/vcf2maf/test.yml b/tests/modules/vcf2maf/test.yml
deleted file mode 100644
index c0a7b4eb0d1..00000000000
--- a/tests/modules/vcf2maf/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: vcf2maf test_vcf2maf_no_vep
-  command: nextflow run ./tests/modules/vcf2maf -entry test_vcf2maf_no_vep -c ./tests/config/nextflow.config  -c ./tests/modules/vcf2maf/nextflow.config
-  tags:
-    - vcf2maf
-  files:
-    - path: output/vcf2maf/test.maf
-      md5sum: c7f357efa774fd5c4003d84f05212ed0
-
-- name: vcf2maf test_vcf2maf_vep
-  command: nextflow run ./tests/modules/vcf2maf -entry test_vcf2maf_vep -c ./tests/config/nextflow.config  -c ./tests/modules/vcf2maf/nextflow.config
-  tags:
-    - vcf2maf
-  files:
-    - path: output/vcf2maf/test.maf
-      md5sum: bf114692a2f421225926c9b651eff161
diff --git a/tests/modules/vcfanno/main.nf b/tests/modules/vcfanno/main.nf
deleted file mode 100644
index a1fe7c1aba3..00000000000
--- a/tests/modules/vcfanno/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR } from '../../../modules/untar/main.nf'
-include { VCFANNO } from '../../../modules/vcfanno/main.nf'
-
-workflow test_vcfanno {
-
-    input = [
-        [ id:'test_compressed', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
-    resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( resource_dir )
-    VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
-}
-
-workflow test_vcfanno_uncompressed {
-
-    input = [ 
-        [ id:'test_uncompressed', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
-        [] 
-    ]
-
-    toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
-    resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( resource_dir )
-    VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
-}
diff --git a/tests/modules/vcfanno/test.yml b/tests/modules/vcfanno/test.yml
deleted file mode 100644
index cb9a8b044b4..00000000000
--- a/tests/modules/vcfanno/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: vcfanno test_vcfanno
-  command: nextflow run ./tests/modules/vcfanno -entry test_vcfanno -c ./tests/config/nextflow.config  -c ./tests/modules/vcfanno/nextflow.config
-  tags:
-    - vcfanno
-  files:
-    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz
-      md5sum: eba4b55d81148d9c316cda68a5c0ad6d
-    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz.tbi
-      md5sum: ec47aa09f0248f4f32ae12fb7ba03f34
-    - path: output/vcfanno/test_compressed_annotated.vcf
-      md5sum: 90ceb2fd2e06e781846d69c3981db665
-
-- name: vcfanno test_vcfanno_uncompressed
-  command: nextflow run ./tests/modules/vcfanno -entry test_vcfanno_uncompressed -c ./tests/config/nextflow.config  -c ./tests/modules/vcfanno/nextflow.config
-  tags:
-    - vcfanno
-  files:
-    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz
-      md5sum: eba4b55d81148d9c316cda68a5c0ad6d
-    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz.tbi
-      md5sum: ec47aa09f0248f4f32ae12fb7ba03f34
-    - path: output/vcfanno/test_uncompressed_annotated.vcf
-      md5sum: 90ceb2fd2e06e781846d69c3981db665
diff --git a/tests/modules/vcflib/vcfbreakmulti/main.nf b/tests/modules/vcflib/vcfbreakmulti/main.nf
deleted file mode 100644
index 7e973300dac..00000000000
--- a/tests/modules/vcflib/vcfbreakmulti/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VCFLIB_VCFBREAKMULTI } from '../../../../modules/vcflib/vcfbreakmulti/main.nf'
-
-workflow test_vcflib_vcfbreakmulti {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    VCFLIB_VCFBREAKMULTI ( input )
-}
diff --git a/tests/modules/vcflib/vcfbreakmulti/test.yml b/tests/modules/vcflib/vcfbreakmulti/test.yml
deleted file mode 100644
index d8ed82db392..00000000000
--- a/tests/modules/vcflib/vcfbreakmulti/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: vcflib vcfbreakmulti
-  command: nextflow run ./tests/modules/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config
-  tags:
-    - vcflib/vcfbreakmulti
-    - vcflib
-  files:
-    - path: output/vcflib/test.breakmulti.vcf.gz
-      md5sum: 666d2d970399cf219dc1dc1eadff9170
-
-- name: vcflib vcfbreakmulti stub
-  command: nextflow run ./tests/modules/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config -stub
-  tags:
-    - vcflib/vcfbreakmulti
-    - vcflib
-  files:
-    - path: output/vcflib/test.breakmulti.vcf.gz
diff --git a/tests/modules/vcflib/vcfuniq/main.nf b/tests/modules/vcflib/vcfuniq/main.nf
deleted file mode 100644
index f2c8e6f89f2..00000000000
--- a/tests/modules/vcflib/vcfuniq/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VCFLIB_VCFUNIQ } from '../../../../modules/vcflib/vcfuniq/main.nf'
-
-workflow test_vcflib_vcfuniq {
-    
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    VCFLIB_VCFUNIQ ( input )
-}
diff --git a/tests/modules/vcflib/vcfuniq/test.yml b/tests/modules/vcflib/vcfuniq/test.yml
deleted file mode 100644
index aadcd77facc..00000000000
--- a/tests/modules/vcflib/vcfuniq/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: vcflib vcfuniq
-  command: nextflow run ./tests/modules/vcflib/vcfuniq -entry test_vcflib_vcfuniq -c ./tests/config/nextflow.config -c ./tests/modules/vcflib/vcfuniq/nextflow.config
-  tags:
-    - vcflib
-    - vcflib/vcfuniq
-  files:
-    - path: output/vcflib/test.uniq.vcf.gz
-      md5sum: c5f2a6a912964c45e8231140420561f9
diff --git a/tests/modules/vcftools/main.nf b/tests/modules/vcftools/main.nf
deleted file mode 100644
index 21f9aa88481..00000000000
--- a/tests/modules/vcftools/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VCFTOOLS as VCFTOOLS_BASE     } from '../../../modules/vcftools/main.nf'
-include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../modules/vcftools/main.nf'
-
-workflow test_vcftools_vcf_base {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-            ]
-
-    VCFTOOLS_BASE ( input, [], [] )
-}
-
-workflow test_vcftools_vcfgz_base {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-            ]
-
-    VCFTOOLS_BASE ( input, [], [] )
-}
-
-workflow test_vcftools_vcf_optional {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
-            ]
-    bed   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-
-    VCFTOOLS_OPTIONAL ( input, bed, [] )
-}
-
-workflow test_vcftools_vcfgz_optional {
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
-            ]
-    bed   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-
-    VCFTOOLS_OPTIONAL ( input, bed, [] )
-}
diff --git a/tests/modules/vcftools/test.yml b/tests/modules/vcftools/test.yml
deleted file mode 100644
index 5314ea75804..00000000000
--- a/tests/modules/vcftools/test.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- name: vcftools test_vcftools_vcf_base
-  command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcf_base -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config
-  tags:
-    - vcftools
-  files:
-    - path: output/vcftools/test.frq
-      md5sum: 7f126655f17268fd1a338734f62868e9
-
-- name: vcftools test_vcftools_vcfgz_base
-  command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcfgz_base -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config
-  tags:
-    - vcftools
-  files:
-    - path: output/vcftools/test.frq
-      md5sum: 7f126655f17268fd1a338734f62868e9
-
-- name: vcftools test_vcftools_vcf_optional
-  command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcf_optional -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config
-  tags:
-    - vcftools
-  files:
-    - path: output/vcftools/test.frq
-      md5sum: 7f126655f17268fd1a338734f62868e9
-
-- name: vcftools test_vcftools_vcfgz_optional
-  command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcfgz_optional -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config
-  tags:
-    - vcftools
-  files:
-    - path: output/vcftools/test.frq
-      md5sum: 7f126655f17268fd1a338734f62868e9
diff --git a/tests/modules/vsearch/sintax/main.nf b/tests/modules/vsearch/sintax/main.nf
deleted file mode 100644
index 14112f0bf9c..00000000000
--- a/tests/modules/vsearch/sintax/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VSEARCH_SINTAX } from '../../../../modules/vsearch/sintax/main.nf'
-
-workflow test_vsearch_sintax {
-    
-    query = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    db = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
-
-    VSEARCH_SINTAX ( [[id:'test'], query], db )
-}
diff --git a/tests/modules/vsearch/sintax/test.yml b/tests/modules/vsearch/sintax/test.yml
deleted file mode 100644
index 5c5abd0a6c6..00000000000
--- a/tests/modules/vsearch/sintax/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: vsearch sintax test_vsearch_sintax
-  command: nextflow run ./tests/modules/vsearch/sintax -entry test_vsearch_sintax -c ./tests/config/nextflow.config  -c ./tests/modules/vsearch/sintax/nextflow.config
-  tags:
-    - vsearch
-    - vsearch/sintax
-  files:
-    - path: output/vsearch/test.tsv
-      md5sum: 93bc75fb89343e23fbae971df157b14a
diff --git a/tests/modules/vsearch/usearchglobal/main.nf b/tests/modules/vsearch/usearchglobal/main.nf
deleted file mode 100644
index 90dc31917f6..00000000000
--- a/tests/modules/vsearch/usearchglobal/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VSEARCH_USEARCHGLOBAL } from '../../../../modules/vsearch/usearchglobal/main.nf'
-
-workflow test_vsearch_usearchglobal {
-    
-    query = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
-    db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    idcutoff = 0.985
-    outoption = "xcfert"  // Nonsense text to check default case.
-    columns = "" 
-    VSEARCH_USEARCHGLOBAL ( [[id:'test'], query], db, idcutoff, outoption, columns )
-}
-
-workflow test_vsearch_usearchglobal_userout {
-    
-    query = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
-    db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    idcutoff = 0.985
-    outoption = "userout"
-    columns = "query+target+id" 
-    VSEARCH_USEARCHGLOBAL ( [[id:'test'], query], db, idcutoff, outoption, columns )
-}
diff --git a/tests/modules/vsearch/usearchglobal/test.yml b/tests/modules/vsearch/usearchglobal/test.yml
deleted file mode 100644
index 227d728f047..00000000000
--- a/tests/modules/vsearch/usearchglobal/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: vsearch usearchglobal test_vsearch_usearchglobal
-  command: nextflow run ./tests/modules/vsearch/usearchglobal -entry test_vsearch_usearchglobal -c ./tests/config/nextflow.config  -c ./tests/modules/vsearch/usearchglobal/nextflow.config
-  tags:
-    - vsearch/usearchglobal
-    - vsearch
-  files:
-    - path: output/vsearch/test.aln
-      contains:
-        - "vsearch --usearch_global transcriptome.fasta --db genome.fasta --id 0.985 --threads 2 --alnout test.aln"
-        - "Query >lcl|MT192765.1_cds_QIK50427.1_2"
-        - "%Id   TLen  Target"
-        - "100%  29829  MT192765.1"
-        - "Query  3822nt >lcl|MT192765.1_cds_QIK50427.1_2"
-        - "Target 29829nt >MT192765.1"
-        - "Qry 21249 + CAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAA 21291"
-        - "Tgt 21506 + CAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAA 21548"
-        - "21291 cols, 21290 ids (100.0%), 1 gaps (0.0%)"
-
-- name: vsearch usearchglobal test_vsearch_usearchglobal_userout
-  command: nextflow run ./tests/modules/vsearch/usearchglobal -entry test_vsearch_usearchglobal_userout -c ./tests/config/nextflow.config  -c ./tests/modules/vsearch/usearchglobal/nextflow.config
-  tags:
-    - vsearch/usearchglobal
-    - vsearch
-  files:
-    - path: output/vsearch/test.tsv
-      md5sum: b6cc50f7c8d18cb82e74dab70ed4baab
diff --git a/tests/modules/whamg/main.nf b/tests/modules/whamg/main.nf
deleted file mode 100644
index 82561f58e79..00000000000
--- a/tests/modules/whamg/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { WHAMG } from '../../../modules/whamg/main.nf'
-
-workflow test_whamg_bam {
-    
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    WHAMG ( input, fasta )
-}
diff --git a/tests/modules/whamg/test.yml b/tests/modules/whamg/test.yml
deleted file mode 100644
index 33f1a9507c7..00000000000
--- a/tests/modules/whamg/test.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-- name: whamg test_whamg_bam
-  command: nextflow run ./tests/modules/whamg -entry test_whamg_bam -c ./tests/config/nextflow.config  -c ./tests/modules/whamg/nextflow.config
-  tags:
-    - whamg
-  files:
-    - path: output/whamg/test.vcf.gz
diff --git a/tests/modules/yara/index/main.nf b/tests/modules/yara/index/main.nf
deleted file mode 100644
index 89eb0f7de25..00000000000
--- a/tests/modules/yara/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { YARA_INDEX } from '../../../../modules/yara/index/main.nf'
-
-workflow test_yara_index {
-
-    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    YARA_INDEX ( input )
-}
diff --git a/tests/modules/yara/index/test.yml b/tests/modules/yara/index/test.yml
deleted file mode 100644
index a8d178661f9..00000000000
--- a/tests/modules/yara/index/test.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-- name: yara index test_yara_index
-  command: nextflow run ./tests/modules/yara/index -entry test_yara_index -c ./tests/config/nextflow.config -c ./tests/modules/yara/index/nextflow.config
-  tags:
-    - yara/index
-    - yara
-  files:
-    - path: output/yara/yara/yara.rid.limits
-      md5sum: 8b814661f30a0c9e350bfbcb454930ce
-    - path: output/yara/yara/yara.sa.len
-      md5sum: 45677f66c28c79c02250ceb8b58645e8
-    - path: output/yara/yara/yara.sa.ind
-      md5sum: 464314583efb5f07260b0efecc29a1ce
-    - path: output/yara/yara/yara.lf.drp
-      md5sum: 3ef99a87a4e44513f46d42f4261f7842
-    - path: output/yara/yara/yara.txt.size
-      md5sum: 063987b3c3f747be7d2b8043c9d91000
-    - path: output/yara/yara/yara.rid.concat
-      md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
-    - path: output/yara/yara/yara.txt.concat
-      md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
-    - path: output/yara/yara/yara.lf.drs
-      md5sum: 55a54008ad1ba589aa210d2629c1df41
-    - path: output/yara/yara/yara.txt.limits
-      md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
-    - path: output/yara/yara/yara.sa.val
-      md5sum: ce57cc82e2d3ae7b9824210f54168ce9
-    - path: output/yara/yara/yara.lf.pst
-      md5sum: e8daba34298e99e42942435286f9b3f0
-    - path: output/yara/yara/yara.lf.drv
-      md5sum: cf6408307fe9fd7f99c33f521bf95550
diff --git a/tests/modules/yara/mapper/main.nf b/tests/modules/yara/mapper/main.nf
deleted file mode 100644
index 18800eb3194..00000000000
--- a/tests/modules/yara/mapper/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-
-include { YARA_INDEX  } from '../../../../modules/yara/index/main.nf'
-include { YARA_MAPPER } from '../../../../modules/yara/mapper/main.nf'
-
-workflow test_yara_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    YARA_INDEX ( fasta )
-    YARA_MAPPER ( input, YARA_INDEX.out.index )
-}
-
-workflow test_yara_paired_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    YARA_INDEX ( fasta )
-    YARA_MAPPER ( input, YARA_INDEX.out.index )
-}
diff --git a/tests/modules/yara/mapper/test.yml b/tests/modules/yara/mapper/test.yml
deleted file mode 100644
index 3bfddc5b5c3..00000000000
--- a/tests/modules/yara/mapper/test.yml
+++ /dev/null
@@ -1,71 +0,0 @@
-- name: yara mapper test_yara_single_end
-  command: nextflow run ./tests/modules/yara/mapper -entry test_yara_single_end -c ./tests/config/nextflow.config -c ./tests/modules/yara/mapper/nextflow.config
-  tags:
-    - yara/mapper
-    - yara
-  files:
-    - path: output/yara/test.mapped.bam
-    - path: output/yara/test.mapped.bam.bai
-    - path: output/yara/yara/yara.txt.size
-      md5sum: 063987b3c3f747be7d2b8043c9d91000
-    - path: output/yara/yara/yara.lf.drs
-      md5sum: 55a54008ad1ba589aa210d2629c1df41
-    - path: output/yara/yara/yara.lf.pst
-      md5sum: e8daba34298e99e42942435286f9b3f0
-    - path: output/yara/yara/yara.sa.len
-      md5sum: 45677f66c28c79c02250ceb8b58645e8
-    - path: output/yara/yara/yara.rid.concat
-      md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
-    - path: output/yara/yara/yara.txt.concat
-      md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
-    - path: output/yara/yara/yara.sa.val
-      md5sum: ce57cc82e2d3ae7b9824210f54168ce9
-    - path: output/yara/yara/yara.sa.ind
-      md5sum: 464314583efb5f07260b0efecc29a1ce
-    - path: output/yara/yara/yara.rid.limits
-      md5sum: 8b814661f30a0c9e350bfbcb454930ce
-    - path: output/yara/yara/yara.lf.drp
-      md5sum: 3ef99a87a4e44513f46d42f4261f7842
-    - path: output/yara/yara/yara.txt.limits
-      md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
-    - path: output/yara/yara/yara.lf.drv
-      md5sum: cf6408307fe9fd7f99c33f521bf95550
-    - path: output/yara/yara/yara.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-
-- name: yara mapper test_yara_paired_end
-  command: nextflow run ./tests/modules/yara/mapper -entry test_yara_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/yara/mapper/nextflow.config
-  tags:
-    - yara/mapper
-    - yara
-  files:
-    - path: output/yara/test_2.mapped.bam
-    - path: output/yara/test_2.mapped.bam.bai
-    - path: output/yara/test_1.mapped.bam
-    - path: output/yara/test_1.mapped.bam.bai
-    - path: output/yara/yara/yara.txt.size
-      md5sum: 063987b3c3f747be7d2b8043c9d91000
-    - path: output/yara/yara/yara.lf.drs
-      md5sum: 55a54008ad1ba589aa210d2629c1df41
-    - path: output/yara/yara/yara.lf.pst
-      md5sum: e8daba34298e99e42942435286f9b3f0
-    - path: output/yara/yara/yara.sa.len
-      md5sum: 45677f66c28c79c02250ceb8b58645e8
-    - path: output/yara/yara/yara.rid.concat
-      md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
-    - path: output/yara/yara/yara.txt.concat
-      md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
-    - path: output/yara/yara/yara.sa.val
-      md5sum: ce57cc82e2d3ae7b9824210f54168ce9
-    - path: output/yara/yara/yara.sa.ind
-      md5sum: 464314583efb5f07260b0efecc29a1ce
-    - path: output/yara/yara/yara.rid.limits
-      md5sum: 8b814661f30a0c9e350bfbcb454930ce
-    - path: output/yara/yara/yara.lf.drp
-      md5sum: 3ef99a87a4e44513f46d42f4261f7842
-    - path: output/yara/yara/yara.txt.limits
-      md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
-    - path: output/yara/yara/yara.lf.drv
-      md5sum: cf6408307fe9fd7f99c33f521bf95550
-    - path: output/yara/yara/yara.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
diff --git a/tests/subworkflows/nf-core/align_bowtie2/main.nf b/tests/subworkflows/nf-core/align_bowtie2/main.nf
index 9870242d4af..160c1bf3c95 100644
--- a/tests/subworkflows/nf-core/align_bowtie2/main.nf
+++ b/tests/subworkflows/nf-core/align_bowtie2/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' addParams( options: [:] )
+include { BOWTIE2_BUILD } from '../../../../modules/nf-core/bowtie2/build/main.nf' addParams( options: [:] )
 include { ALIGN_BOWTIE2 } from '../../../../subworkflows/nf-core/align_bowtie2/main.nf' addParams( 'samtools_sort_options': ['suffix': '.sorted'] )
 
 workflow test_align_bowtie2_single_end {