Refactor of line lenght >127 cols for in- and outputs

UMCUGenetics · Jan 29, 2024 · 42b7f7e · 42b7f7e
1 parent de29560
commit 42b7f7e
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Showing 26 changed files with 56 additions and 28 deletions.
diff --git a/ControlFREEC/11.5/Freec.nf b/ControlFREEC/11.5/Freec.nf
@@ -10,7 +10,8 @@ process Freec {
 
     output:
         tuple(val(sample_id), path("${bam_file.name}_ratio.txt"), path("${bam_file.name}_CNVs"), emit: cnv)
-        tuple(val(sample_id), path("${bam_file.name}_sample.cpn"), path("${bam_file.name}_ratio.BedGraph"), path("${bam_file.name}_info.txt"), emit: other)
+        tuple(val(sample_id), path("${bam_file.name}_sample.cpn"), path("${bam_file.name}_ratio.BedGraph"),
+            path("${bam_file.name}_info.txt"), emit: other)
 
     script:
         def config = "${sample_id}.config"

diff --git a/GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf b/GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf
@@ -9,7 +9,8 @@ process BaseRecalibrator {
         tuple(val(sample_id), path(bam_file), path(bai_file), val(chr))
 
     output:
-        tuple(val(sample_id), path("${bam_file.baseName}.bqsr.${chr}.bam"), path("${bam_file.baseName}.bqsr.${chr}.bai"), emit: bam_file)
+        tuple(val(sample_id), path("${bam_file.baseName}.bqsr.${chr}.bam"), path("${bam_file.baseName}.bqsr.${chr}.bai"),
+            emit: bam_file)
 
     script:
         """

diff --git a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf
@@ -9,7 +9,8 @@ process GenotypeGVCFs {
         tuple(val(analysis_id), path(gvcf_files), path(gvcf_idx_files), path(interval_file))
 
     output:
-        tuple(val(analysis_id), path("${analysis_id}_${interval_file.baseName}.vcf"), path("${analysis_id}_${interval_file.baseName}.vcf.idx"), emit:vcf_file)
+        tuple(val(analysis_id), path("${analysis_id}_${interval_file.baseName}.vcf"),
+            path("${analysis_id}_${interval_file.baseName}.vcf.idx"), emit: vcf_file)
 
     script:
         def input_files = gvcf_files.collect{"$it"}.join(" -V ")

diff --git a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf
@@ -9,7 +9,8 @@ process HaplotypeCaller {
         tuple(val(analysis_id), path(bam_files), path(bai_files), path(interval_file))
 
     output:
-        tuple(val(analysis_id), path("${analysis_id}.${interval_file.baseName}.vcf"), path("${analysis_id}.${interval_file.baseName}.vcf.idx"), emit: vcf_file)
+        tuple(val(analysis_id), path("${analysis_id}.${interval_file.baseName}.vcf"),
+            path("${analysis_id}.${interval_file.baseName}.vcf.idx"), emit: vcf_file)
 
     script:
         def input_files = bam_files.collect{"$it"}.join(" --input_file ")
@@ -34,7 +35,8 @@ process HaplotypeCallerGVCF {
         tuple(val(sample_id), path(bam_file), path(bai_file), path(interval_file))
 
     output:
-        tuple(val(sample_id), path("${sample_id}_${interval_file.baseName}.g.vcf"), path("${sample_id}_${interval_file.baseName}.g.vcf.idx"), path(interval_file), emit: vcf_file)
+        tuple(val(sample_id), path("${sample_id}_${interval_file.baseName}.g.vcf"),
+            path("${sample_id}_${interval_file.baseName}.g.vcf.idx"), path(interval_file), emit: vcf_file)
 
     script:
         """

diff --git a/GATK/3.8-1-0-gf15c1c3ef/IndelRealigner.nf b/GATK/3.8-1-0-gf15c1c3ef/IndelRealigner.nf
@@ -9,7 +9,8 @@ process IndelRealigner {
         tuple(val(sample_id), path(bam_file), path(bai_file), val(chr), path(target_intervals))
 
     output:
-        tuple(val(sample_id), path("${bam_file.baseName}.realigned.${chr}.bam"), path("${bam_file.baseName}.realigned.${chr}.bai"), emit: bam_file)
+        tuple(val(sample_id), path("${bam_file.baseName}.realigned.${chr}.bam"),
+            path("${bam_file.baseName}.realigned.${chr}.bai"), emit: bam_file)
 
     script:
         """

diff --git a/GATK/3.8-1-0-gf15c1c3ef/SelectVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/SelectVariants.nf
@@ -9,7 +9,8 @@ process SelectVariantsSample {
         tuple(val(analysis_id), path(vcf_file), path(vcf_idx_file), val(sample_id))
 
     output:
-        tuple(val(sample_id), path("${sample_id}_${vcf_file.baseName}.vcf"), path("${sample_id}_${vcf_file.baseName}.vcf.idx"), emit: vcf_file)
+        tuple(val(sample_id), path("${sample_id}_${vcf_file.baseName}.vcf"),
+            path("${sample_id}_${vcf_file.baseName}.vcf.idx"), emit: vcf_file)
 
     script:
         """

diff --git a/GATK/3.8-1-0-gf15c1c3ef/VariantFiltration.nf b/GATK/3.8-1-0-gf15c1c3ef/VariantFiltration.nf
@@ -9,7 +9,8 @@ process VariantFiltrationSnpIndel {
         tuple(val(analysis_id), path(vcf_file), path(vcf_idx_file))
 
     output:
-        tuple(val(analysis_id), path("${vcf_file.baseName}.filter.vcf"), path("${vcf_file.baseName}.filter.vcf.idx"), emit: vcf_file)
+        tuple(val(analysis_id), path("${vcf_file.baseName}.filter.vcf"), path("${vcf_file.baseName}.filter.vcf.idx"),
+            emit: vcf_file)
 
     script:
         """

diff --git a/GATK/4.1.3.0/CombineGVCFs.nf b/GATK/4.1.3.0/CombineGVCFs.nf
@@ -8,7 +8,8 @@ process CombineGVCFs {
     input:
       tuple(val(run_id), val(interval), path(gvcf_chunks), path(gvcf_chunk_idxs), path(interval_file))
     output:
-      tuple(val(run_id), val(interval), path("${run_id}.${interval}.g.vcf"), path("${run_id}.${interval}.g.vcf.idx"), path(interval_file), emit: combined_gvcfs)
+      tuple(val(run_id), val(interval), path("${run_id}.${interval}.g.vcf"), path("${run_id}.${interval}.g.vcf.idx"),
+        path(interval_file), emit: combined_gvcfs)
 
     script:
         vcfs = gvcf_chunks.join(' -V ')

diff --git a/GATK/4.1.3.0/GenotypeGVCFs.nf b/GATK/4.1.3.0/GenotypeGVCFs.nf
@@ -9,7 +9,8 @@ process GenotypeGVCFs {
         tuple(val(run_id), val(interval), path(gvcf), path(gvcfidx), path(interval_file))
 
     output:
-        tuple(val(run_id), val(interval), path("${run_id}.${interval}.vcf"),path("${run_id}.${interval}.vcf.idx"),path(interval_file), emit : genotyped_vcfs)
+        tuple(val(run_id), val(interval), path("${run_id}.${interval}.vcf"),path("${run_id}.${interval}.vcf.idx"),
+            path(interval_file), emit: genotyped_vcfs)
 
     script:
         """

diff --git a/GATK/4.1.3.0/HaplotypeCaller.nf b/GATK/4.1.3.0/HaplotypeCaller.nf
@@ -9,7 +9,8 @@ process HaplotypeCaller {
         tuple(val(sample_id), path(bam), path(bai), path(interval_file))
 
     output:
-        tuple(val(sample_id), val(int_tag) ,path("${sample_id}.${int_tag}${ext}"), path("${sample_id}.${int_tag}${ext}.idx"), path(interval_file), emit: htcaller_vcfs)
+        tuple(val(sample_id), val(int_tag) ,path("${sample_id}.${int_tag}${ext}"), path("${sample_id}.${int_tag}${ext}.idx"),
+            path(interval_file), emit: htcaller_vcfs)
 
     script:
         int_tag = interval_file.toRealPath().toString().split("/")[-2]

diff --git a/GATK/4.1.3.0/SelectVariants.nf b/GATK/4.1.3.0/SelectVariants.nf
@@ -9,7 +9,8 @@ process SelectVariants {
         tuple(val(run_id), val(interval), path(vcf), path(vcfidx), val(type))
 
     output:
-        tuple(val(run_id), val(interval), val(type), path("${run_id}.${interval}.${type}.tmp.vcf"), path("${run_id}.${interval}.${type}.tmp.vcf.idx"), emit: selected_vcfs)
+        tuple(val(run_id), val(interval), val(type), path("${run_id}.${interval}.${type}.tmp.vcf"),
+            path("${run_id}.${interval}.${type}.tmp.vcf.idx"), emit: selected_vcfs)
 
     script:
         select_type = type == 'SNP' ? '--select-type SNP --select-type NO_VARIATION' : '--select-type INDEL --select-type MIXED'

diff --git a/GATK/4.1.3.0/VariantAnnotator.nf b/GATK/4.1.3.0/VariantAnnotator.nf
@@ -9,7 +9,8 @@ process VariantAnnotator {
         tuple(val(run_id), path(vcf), path(vcfidx))
 
     output:
-        tuple(val(run_id), path("${vcf.baseName}_${db_name}.vcf"), path("${vcf.baseName}_${db_name}.vcf.idx"), emit: annotated_vcfs)
+        tuple(val(run_id), path("${vcf.baseName}_${db_name}.vcf"), path("${vcf.baseName}_${db_name}.vcf.idx"),
+            emit: annotated_vcfs)
 
     script:
         db_file = file(params.genome_variant_annotator_db).getBaseName()

diff --git a/GATK/4.1.3.0/VariantFiltration.nf b/GATK/4.1.3.0/VariantFiltration.nf
@@ -9,7 +9,8 @@ process VariantFiltration {
         tuple(val(run_id), val(interval), val(type), path(vcf), path(vcfidx))
 
     output:
-        tuple(val(run_id), val(interval), val(type), path("${run_id}.${interval}.${type}.filtered_variants.vcf"), path("${run_id}.${interval}.${type}.filtered_variants.vcf.idx"), emit: filtered_vcfs)
+        tuple(val(run_id), val(interval), val(type), path("${run_id}.${interval}.${type}.filtered_variants.vcf"),
+            path("${run_id}.${interval}.${type}.filtered_variants.vcf.idx"), emit: filtered_vcfs)
 
     script:
         if (type == 'SNP'){

diff --git a/GATK/4.2.1.0/MergeVcfs.nf b/GATK/4.2.1.0/MergeVcfs.nf
@@ -9,7 +9,8 @@ process MergeVcfs {
         tuple(val(output_name), path(vcf_files), path(vcf_idx_files))
 
     output:
-        tuple(val(output_name), path("${output_name}${ext_vcf}"), path("${output_name}${ext_vcf}${ext_vcf_index}"), emit:vcf_file)
+        tuple(val(output_name), path("${output_name}${ext_vcf}"), path("${output_name}${ext_vcf}${ext_vcf_index}"),
+            emit: vcf_file)
 
     script:
         def input_files = vcf_files.collect{"$it"}.join(" --INPUT ")
@@ -35,7 +36,8 @@ process MergeGvcfs {
         tuple(val(output_name), path(vcf_files), path(vcf_idx_files))
 
     output:
-        tuple(val(output_name), path("${output_name}${ext_gvcf}"), path("${output_name}${ext_gvcf}${ext_gvcf_index}"), emit:vcf_file)
+        tuple(val(output_name), path("${output_name}${ext_gvcf}"), path("${output_name}${ext_gvcf}${ext_gvcf_index}"),
+            emit: vcf_file)
 
     script:
         def input_files = vcf_files.collect{"$it"}.join(" --INPUT ")

diff --git a/GATK/4.2.1.0/VariantFiltration.nf b/GATK/4.2.1.0/VariantFiltration.nf
@@ -9,7 +9,8 @@ process VariantFiltrationSnpIndel {
         tuple(val(analysis_id), path(vcf_file), path(vcf_idx_file))
 
     output:
-        tuple(val(analysis_id), path("${vcf_file.simpleName}.filter${ext_vcf}"), path("${vcf_file.simpleName}.filter${ext_vcf}${ext_vcf_index}"), emit: vcf_file)
+        tuple(val(analysis_id), path("${vcf_file.simpleName}.filter${ext_vcf}"),
+            path("${vcf_file.simpleName}.filter${ext_vcf}${ext_vcf_index}"), emit: vcf_file)
 
     script:
         ext_vcf = params.compress || vcf_file.getExtension() == ".gz" ? ".vcf.gz" : ".vcf"

diff --git a/Sambamba/0.7.0/Markdup.nf b/Sambamba/0.7.0/Markdup.nf
@@ -8,7 +8,8 @@ process Markdup {
     input:
         tuple(val(sample_id), val(rg_id), path(bam_file), path(bai_file))
     output:
-        tuple(val(sample_id), val(rg_id), path("${bam_file.baseName}.markdup.bam"), path("${bam_file.baseName}.markdup.bam.bai"), emit: bam_file)
+        tuple(val(sample_id), val(rg_id), path("${bam_file.baseName}.markdup.bam"),
+            path("${bam_file.baseName}.markdup.bam.bai"), emit: bam_file)
 
     script:
         """

diff --git a/Sambamba/0.7.0/ViewSort.nf b/Sambamba/0.7.0/ViewSort.nf
@@ -9,7 +9,8 @@ process ViewSort {
         tuple(val(sample_id), val(rg_id), path(sam_file))
 
     output:
-        tuple(val(sample_id), val(rg_id), path("${sam_file.baseName}.sort.bam"), path("${sam_file.baseName}.sort.bam.bai"), emit: bam_file)
+        tuple(val(sample_id), val(rg_id), path("${sam_file.baseName}.sort.bam"), path("${sam_file.baseName}.sort.bam.bai"),
+            emit: bam_file)
 
     script:
         """

diff --git a/Sambamba/0.7.0/ViewSubsample.nf b/Sambamba/0.7.0/ViewSubsample.nf
@@ -9,7 +9,8 @@ process Subsample {
         tuple(val(sample_id), val(fraction), path(bam_file), path(bai_file))
 
     output:
-        tuple(val(sample_id), path("${bam_file.baseName}.subsample.bam"), path("${bam_file.baseName}.subsample.bam.bai"), emit: bam_file)
+        tuple(val(sample_id), path("${bam_file.baseName}.subsample.bam"), path("${bam_file.baseName}.subsample.bam.bai"),
+            emit: bam_file)
 
     script:
         """

diff --git a/Sambamba/0.7.0/ViewUnmapped.nf b/Sambamba/0.7.0/ViewUnmapped.nf
@@ -9,7 +9,8 @@ process ViewUnmapped {
         tuple(val(sample_id), path(bam_file), path(bai_file))
 
     output:
-        tuple(val(sample_id), path("${bam_file.baseName}.unmapped.bam"), path("${bam_file.baseName}.unmapped.bam.bai"), emit: bam_file)
+        tuple(val(sample_id), path("${bam_file.baseName}.unmapped.bam"), path("${bam_file.baseName}.unmapped.bam.bai"),
+            emit: bam_file)
 
     script:
         """

diff --git a/bash/MergeFastQs.nf b/bash/MergeFastQs.nf
@@ -10,7 +10,8 @@ process MergeFastqs {
         tuple(val(sample_id), val(flowcell), path(fastq))
 
     output:
-        tuple(val(sample_id), val(flowcell), val(read_nr) ,path("${sample_id}_${flowcell}_${read_nr}.fastq.gz"), emit : merged_fastqs)
+        tuple(val(sample_id), val(flowcell), val(read_nr) ,path("${sample_id}_${flowcell}_${read_nr}.fastq.gz"),
+            emit: merged_fastqs)
 
 
     script:

diff --git a/fgbio/1.1.0/CallMolecularConsensusReads.nf b/fgbio/1.1.0/CallMolecularConsensusReads.nf
@@ -9,7 +9,8 @@ process CallMolecularConsensusReads {
         tuple(val(sample_id), val(flowcell), val(machine), val(run_nr), path(bam))
 
     output:
-        tuple(val(sample_id), val(flowcell), val(machine), val(run_nr), path("${sample_id}.u.consensus.bam"), emit : consensus_bams)
+        tuple(val(sample_id), val(flowcell), val(machine), val(run_nr), path("${sample_id}.u.consensus.bam"),
+            emit: consensus_bams)
 
     script:
         """

diff --git a/fgbio/1.1.0/FilterConsensusReads.nf b/fgbio/1.1.0/FilterConsensusReads.nf
@@ -9,7 +9,8 @@ process FilterConsensusReads {
         tuple(val(sample_id), val(flowcell), val(machine), val(run_nr), path(bam))
 
     output:
-        tuple(val(sample_id), val(flowcell), val(machine), val(run_nr), path("${sample_id}.u.consensus.filtered.bam"), emit: filtered_bams)
+        tuple(val(sample_id), val(flowcell), val(machine), val(run_nr), path("${sample_id}.u.consensus.filtered.bam"),
+            emit: filtered_bams)
 
     script:
         """

diff --git a/fgbio/1.1.0/SortBam.nf b/fgbio/1.1.0/SortBam.nf
@@ -9,7 +9,8 @@ process SortBam {
         tuple(val(sample_id), val(flowcell), val(machine), val(run_nr), path(bam))
 
     output:
-        tuple(val(sample_id), val(flowcell), val(machine), val(run_nr), path("${sample_id}.u.grouped.sorted.bam"), emit: sorted_bams)
+        tuple(val(sample_id), val(flowcell), val(machine), val(run_nr), path("${sample_id}.u.grouped.sorted.bam"),
+            emit: sorted_bams)
 
     script:
         """

diff --git a/snpEff/4.3t/SnpSiftAnnotate.nf b/snpEff/4.3t/SnpSiftAnnotate.nf
@@ -10,7 +10,8 @@ process SNPSiftAnnotate {
         tuple(val(run_id), path(vcf), path(vcfidx))
 
     output:
-        tuple(val(run_id), path("${vcf.baseName}_${db_name}.vcf"), path("${vcf.baseName}_${db_name}.vcf.idx"), emit: snpsift_annoted_vcfs)
+        tuple(val(run_id), path("${vcf.baseName}_${db_name}.vcf"), path("${vcf.baseName}_${db_name}.vcf.idx"),
+            emit: snpsift_annoted_vcfs)
 
     script:
         db_file = file(params.genome_snpsift_annotate_db).getBaseName()

diff --git a/snpEff/4.3t/SnpSiftDbnsfp.nf b/snpEff/4.3t/SnpSiftDbnsfp.nf
@@ -10,7 +10,8 @@ process SNPSiftDbnsfp {
         tuple(val(run_id), path(vcf), path(vcfidx))
 
     output:
-        tuple(val(run_id), path("${vcf.baseName}_dbnsfp.vcf"), path("${vcf.baseName}_dbnsfp.vcf.idx"), emit : snpsift_dbnsfp_vcfs)
+        tuple(val(run_id), path("${vcf.baseName}_dbnsfp.vcf"), path("${vcf.baseName}_dbnsfp.vcf.idx"),
+            emit: snpsift_dbnsfp_vcfs)
 
     script:
         """

diff --git a/snpEff/4.3t/snpEffFilter.nf b/snpEff/4.3t/snpEffFilter.nf
@@ -10,7 +10,8 @@ process SNPEffFilter {
         tuple(val(run_id), path(vcf), path(vcfidx))
 
     output:
-        tuple(val(run_id), path("${vcf.baseName}.filtered_variants.vcf"), path("${vcf.baseName}.filtered_variants.vcf.idx"), emit: snpeff_filtered_vcfs)
+        tuple(val(run_id), path("${vcf.baseName}.filtered_variants.vcf"), path("${vcf.baseName}.filtered_variants.vcf.idx"),
+            emit: snpeff_filtered_vcfs)
 
     script:
         """