Merge pull request #80 from UMCUGenetics/release/v0.7.3

Release/v0.7.3
UMCUGenetics · Mar 29, 2024 · 5a84a32 · 5a84a32
2 parents 4cd4aa4 + 354666b
commit 5a84a32
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Showing 84 changed files with 224 additions and 197 deletions.
diff --git a/BCFtools/1.10.2/View.nf b/BCFtools/1.10.2/View.nf
@@ -7,10 +7,10 @@ process View_bcf_vcf {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-    tuple sample_id, file(bcf_file)
+    tuple(val(sample_id), file(bcf_file))
 
     output:
-    tuple sample_id, file("${bcf_file.baseName}.vcf")
+    tuple(val(sample_id), file("${bcf_file.baseName}.vcf"))
 
     script:
     """

diff --git a/BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf b/BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf
@@ -4,12 +4,12 @@ process BWAMapping {
     label 'BWA_0_7_17_Mem'
     container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:bwa-0.7.17_samtools-1.9'
     shell = ['/bin/bash', '-euo', 'pipefail']
-    
+
     input:
-        tuple (sample_id, rg_id, path(fastq))
+        tuple(val(sample_id), val(rg_id), path(fastq))
 
     output:
-        tuple (sample_id, rg_id, path("${rg_id}_sorted.bam"), path("${rg_id}_sorted.bai"), emit: mapped_bams)
+        tuple(val(sample_id), val(rg_id), path("${rg_id}_sorted.bam"), path("${rg_id}_sorted.bai"), emit: mapped_bams)
 
     script:
         def barcode = rg_id.split('_')[1]

diff --git a/BWA/0.7.17/BWASW.nf b/BWA/0.7.17/BWASW.nf
@@ -6,10 +6,10 @@ process BWASW {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, rg_id, path(fastq))
+        tuple(val(sample_id), val(rg_id), path(fastq))
 
     output:
-        tuple(sample_id, rg_id, path("${fastq[0].simpleName}.sam"), emit: sam_file)
+        tuple(val(sample_id), val(rg_id), path("${fastq[0].simpleName}.sam"), emit: sam_file)
 
     script:
         """

diff --git a/BWA/0.7.17/MEM.nf b/BWA/0.7.17/MEM.nf
@@ -6,10 +6,10 @@ process MEM {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, rg_id, path(fastq))
+        tuple(val(sample_id), val(rg_id), path(fastq))
 
     output:
-        tuple(sample_id, rg_id, path("${fastq[0].simpleName}.sam"), emit: sam_file)
+        tuple(val(sample_id), val(rg_id), path("${fastq[0].simpleName}.sam"), emit: sam_file)
 
     script:
         def barcode = rg_id.split('_')[1]

diff --git a/BamUtil/1.0.14/ClipOverlap.nf b/BamUtil/1.0.14/ClipOverlap.nf
@@ -6,10 +6,10 @@ process ClipOverlap {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-    tuple sample_id, rg_id, file(bam_file), file(bai_file)
+    tuple(val(sample_id), val(rg_id), file(bam_file), file(bai_file))
 
     output:
-    tuple sample_id, rg_id, file("${bam_file.baseName}.clipped.bam")
+    tuple(val(sample_id), val(rg_id), file("${bam_file.baseName}.clipped.bam"))
 
     script:
     """

diff --git a/ControlFREEC/11.5/AssessSignificance.nf b/ControlFREEC/11.5/AssessSignificance.nf
@@ -6,10 +6,10 @@ process AssessSignificance {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(ratio_file), path(cnv_file))
+        tuple(val(sample_id), path(ratio_file), path(cnv_file))
 
     output:
-        tuple(sample_id, path("${cnv_file.name}.p.value.txt"), emit: cnv_pvalue)
+        tuple(val(sample_id), path("${cnv_file.name}.p.value.txt"), emit: cnv_pvalue)
 
     script:
         """

diff --git a/ControlFREEC/11.5/Freec.nf b/ControlFREEC/11.5/Freec.nf
@@ -6,11 +6,12 @@ process Freec {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(bam_file), path(bai_file))
+        tuple(val(sample_id), path(bam_file), path(bai_file))
 
     output:
-        tuple(sample_id, path("${bam_file.name}_ratio.txt"), path("${bam_file.name}_CNVs"), emit: cnv)
-        tuple(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}_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)
 
     script:
         def config = "${sample_id}.config"

diff --git a/ControlFREEC/11.5/MakeGraph.nf b/ControlFREEC/11.5/MakeGraph.nf
@@ -6,10 +6,10 @@ process MakeGraph {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(ratio_file), path(cnv_file))
+        tuple(val(sample_id), path(ratio_file), path(cnv_file))
 
     output:
-        tuple(sample_id, path("${ratio_file.name}.png"), path("${ratio_file.name}.log2.png"), emit: ratio_png)
+        tuple(val(sample_id), path("${ratio_file.name}.png"), path("${ratio_file.name}.log2.png"), emit: ratio_png)
 
     script:
         """

diff --git a/ControlFREEC/11.5/MakeKaryotype.nf b/ControlFREEC/11.5/MakeKaryotype.nf
@@ -6,10 +6,10 @@ process MakeKaryotype {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(ratio_file), path(cnv_file))
+        tuple(val(sample_id), path(ratio_file), path(cnv_file))
 
     output:
-        tuple(sample_id, path("*_karyotype.pdf"), emit: karyotype_pdf)
+        tuple(val(sample_id), path("*_karyotype.pdf"), emit: karyotype_pdf)
 
     script:
         """

diff --git a/FastQC/0.11.5/FastQC.nf b/FastQC/0.11.5/FastQC.nf
@@ -6,7 +6,7 @@ process FastQC {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple (sample_id, rg_id, path(fastq) )
+        tuple(val(sample_id), val(rg_id), path(fastq))
 
     output:
         path("*_fastqc.{zip,html}", emit: fastqc_reports)

diff --git a/FastQC/0.11.8/FastQC.nf b/FastQC/0.11.8/FastQC.nf
@@ -5,7 +5,7 @@ process FastQC {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, rg_id, path(fastq))
+        tuple(val(sample_id), val(rg_id), path(fastq))
 
     output:
         path("*_fastqc.{zip,html}", emit: report)

diff --git a/Fastp/0.14.1/Fastp.nf b/Fastp/0.14.1/Fastp.nf
@@ -5,10 +5,10 @@ process Fastp {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, rg_id, path(fastq_files))
+        tuple(val(sample_id), val(rg_id), path(fastq_files))
 
     output:
-        tuple(sample_id, rg_id, path("*.fastq.gz"), emit: fastqs_cleaned)
+        tuple(val(sample_id), val(rg_id), path("*.fastq.gz"), emit: fastqs_cleaned)
         path("${sample_id}_fastp.json", emit: qc_report)
 
     script:

diff --git a/Fastp/0.20.1/Fastp.nf b/Fastp/0.20.1/Fastp.nf
@@ -5,10 +5,10 @@ process Fastp {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, rg_id, path(fastq_files))
+        tuple(val(sample_id), val(rg_id), path(fastq_files))
 
     output:
-        tuple(sample_id, rg_id, path("*.fastq.gz"), emit: fastqs_cleaned)
+        tuple(val(sample_id), val(rg_id), path("*.fastq.gz"), emit: fastqs_cleaned)
         path("${sample_id}_fastp.json", emit: qc_report)
 
     script:

diff --git a/GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf b/GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf
@@ -6,10 +6,11 @@ process BaseRecalibrator {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(bam_file), path(bai_file), chr)
+        tuple(val(sample_id), path(bam_file), path(bai_file), val(chr))
 
     output:
-        tuple(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/CatVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf
@@ -6,10 +6,10 @@ process CatVariantsGVCF {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(gvcf_files), path(gvcf_idx_files))
+        tuple(val(sample_id), path(gvcf_files), path(gvcf_idx_files))
 
     output:
-        tuple(sample_id, path("${sample_id}.g.vcf.gz"), path("${sample_id}.g.vcf.gz.tbi"), emit:vcf_file)
+        tuple(val(sample_id), path("${sample_id}.g.vcf.gz"), path("${sample_id}.g.vcf.gz.tbi"), emit:vcf_file)
 
     script:
         def input_files = gvcf_files.collect{"$it"}.join(" -V ")

diff --git a/GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf
@@ -6,10 +6,10 @@ process CombineVariants {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(analysis_id, path(vcf_files), path(vcf_idx_files))
+        tuple(val(analysis_id), path(vcf_files), path(vcf_idx_files))
 
     output:
-        tuple(analysis_id, path("${analysis_id}.vcf"), path("${analysis_id}.vcf.idx"), emit:vcf_file)
+        tuple(val(analysis_id), path("${analysis_id}.vcf"), path("${analysis_id}.vcf.idx"), emit:vcf_file)
 
     script:
         def input_files = vcf_files.collect{"$it"}.join(" -V ")
@@ -30,10 +30,10 @@ process CombineVariantsGVCF {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(vcf_files), path(vcf_idx_files))
+        tuple(val(sample_id), path(vcf_files), path(vcf_idx_files))
 
     output:
-        tuple(sample_id, path("${sample_id}.g.vcf"), path("${sample_id}.g.vcf.idx"), emit:vcf_file)
+        tuple(val(sample_id), path("${sample_id}.g.vcf"), path("${sample_id}.g.vcf.idx"), emit:vcf_file)
 
     script:
         def input_files = vcf_files.collect{"$it"}.join(" -V ")

diff --git a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf
@@ -6,10 +6,11 @@ process GenotypeGVCFs {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(analysis_id, path(gvcf_files), path(gvcf_idx_files), path(interval_file))
+        tuple(val(analysis_id), path(gvcf_files), path(gvcf_idx_files), path(interval_file))
 
     output:
-        tuple(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
@@ -6,10 +6,11 @@ process HaplotypeCaller {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(analysis_id, path(bam_files), path(bai_files), path(interval_file))
+        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 ")
@@ -31,10 +32,11 @@ process HaplotypeCallerGVCF {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(bam_file), path(bai_file), path(interval_file))
+        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
@@ -6,10 +6,11 @@ process IndelRealigner {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(bam_file), path(bai_file), chr, path(target_intervals))
+        tuple(val(sample_id), path(bam_file), path(bai_file), val(chr), path(target_intervals))
 
     output:
-        tuple(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/RealignerTargetCreator.nf b/GATK/3.8-1-0-gf15c1c3ef/RealignerTargetCreator.nf
@@ -6,10 +6,10 @@ process RealignerTargetCreator {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(bam_file), path(bai_file), chr)
+        tuple(val(sample_id), path(bam_file), path(bai_file), val(chr))
 
     output:
-        tuple(sample_id, chr, path("${bam_file.baseName}.target_intervals.${chr}.list"), emit: interval_list)
+        tuple(val(sample_id), val(chr), path("${bam_file.baseName}.target_intervals.${chr}.list"), emit: interval_list)
 
     script:
         """

diff --git a/GATK/3.8-1-0-gf15c1c3ef/SelectVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/SelectVariants.nf
@@ -6,10 +6,11 @@ process SelectVariantsSample {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(analysis_id, path(vcf_file), path(vcf_idx_file), sample_id)
+        tuple(val(analysis_id), path(vcf_file), path(vcf_idx_file), val(sample_id))
 
     output:
-        tuple(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/UnifiedGenotyper.nf b/GATK/3.8-1-0-gf15c1c3ef/UnifiedGenotyper.nf
@@ -6,10 +6,10 @@ process UnifiedGenotyper {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, path(bam_file), path(bai_file))
+        tuple(val(sample_id), path(bam_file), path(bai_file))
 
     output:
-        tuple(sample_id, path("${sample_id}.vcf"), emit: vcf_file)
+        tuple(val(sample_id), path("${sample_id}.vcf"), emit: vcf_file)
 
     script:
 

diff --git a/GATK/3.8-1-0-gf15c1c3ef/VariantFiltration.nf b/GATK/3.8-1-0-gf15c1c3ef/VariantFiltration.nf
@@ -6,10 +6,11 @@ process VariantFiltrationSnpIndel {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(analysis_id, path(vcf_file), path(vcf_idx_file))
+        tuple(val(analysis_id), path(vcf_file), path(vcf_idx_file))
 
     output:
-        tuple(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/BaseRecalibration.nf b/GATK/4.1.3.0/BaseRecalibration.nf
@@ -6,10 +6,10 @@ process BaseRecalibration {
     container = 'library://sawibo/default/bioinf-tools:gatk4.1.3.0'
     shell = ['/bin/bash', '-euo', 'pipefail']
     input:
-        tuple (sample_id, file(bam), path(bai),path(recal_table), path(interval_file))
+        tuple(val(sample_id), file(bam), path(bai),path(recal_table), path(interval_file))
 
     output:
-        tuple (sample_id, int_tag, path("${sample_id}.${int_tag}_recalibrated.bam"), path("${sample_id}.${int_tag}_recalibrated.bai"), path(interval_file), emit: recalibrated_bams)
+        tuple(val(sample_id), val(int_tag), path("${sample_id}.${int_tag}_recalibrated.bam"), path("${sample_id}.${int_tag}_recalibrated.bai"), path(interval_file), emit: recalibrated_bams)
 
     script:
         int_tag = interval_file.toRealPath().toString().split("/")[-2]

diff --git a/GATK/4.1.3.0/BaseRecalibrationTable.nf b/GATK/4.1.3.0/BaseRecalibrationTable.nf
@@ -6,10 +6,10 @@ process BaseRecalibrationTable {
     container = 'library://sawibo/default/bioinf-tools:gatk4.1.3.0'
     shell = ['/bin/bash', '-euo', 'pipefail']
     input:
-        tuple (sample_id, path(bam), path(bai), path(interval_file))
+        tuple(val(sample_id), path(bam), path(bai), path(interval_file))
 
     output:
-        tuple (sample_id, path("${sample_id}.${int_tag}.recal.table"), emit: recalibration_tables)
+        tuple(val(sample_id), path("${sample_id}.${int_tag}.recal.table"), emit: recalibration_tables)
 
     script:
         known = params.genome_known_sites ? '--known-sites ' + params.genome_known_sites.join(' --known-sites ') : ''

diff --git a/GATK/4.1.3.0/CollectMultipleMetrics.nf b/GATK/4.1.3.0/CollectMultipleMetrics.nf
@@ -6,7 +6,7 @@ process CollectMultipleMetrics {
   container = 'library://sawibo/default/bioinf-tools:gatk4.1.3.0'
   shell = ['/bin/bash', '-euo', 'pipefail']
   input:
-    tuple (sample_id, path(bam))
+    tuple(val(sample_id), path(bam))
 
   output:
     path ("${sample_id}.multiple_metrics*", emit : multiple_metrics)

diff --git a/GATK/4.1.3.0/CollectWGSMetrics.nf b/GATK/4.1.3.0/CollectWGSMetrics.nf
@@ -6,7 +6,7 @@ process CollectWGSMetrics {
   container = 'library://sawibo/default/bioinf-tools:gatk4.1.3.0'
   shell = ['/bin/bash', '-euo', 'pipefail']
   input:
-    tuple (sample_id, path(bam))
+    tuple(val(sample_id), path(bam))
 
   output:
     path ("${sample_id}.wgs_metrics.txt" , emit: wgs_metrics)

diff --git a/GATK/4.1.3.0/CombineGVCFs.nf b/GATK/4.1.3.0/CombineGVCFs.nf
@@ -6,9 +6,10 @@ process CombineGVCFs {
     container = 'library://sawibo/default/bioinf-tools:gatk4.1.3.0'
     shell = ['/bin/bash', '-euo', 'pipefail']
     input:
-      tuple (run_id, interval, path(gvcf_chunks), path(gvcf_chunk_idxs), path(interval_file))
+      tuple(val(run_id), val(interval), path(gvcf_chunks), path(gvcf_chunk_idxs), path(interval_file))
     output:
-      tuple (run_id, 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/GatherBaseRecalibrationTables.nf b/GATK/4.1.3.0/GatherBaseRecalibrationTables.nf
@@ -6,10 +6,10 @@ process GatherBaseRecalibrationTables {
     container = 'library://sawibo/default/bioinf-tools:gatk4.1.3.0'
     shell = ['/bin/bash', '-euo', 'pipefail']
     input:
-        tuple (sample_id, path(bqsr_tables))
+        tuple(val(sample_id), path(bqsr_tables))
 
     output:
-        tuple (sample_id, path("${sample_id}.recal.table"), emit : gathered_recalibration_tables)
+        tuple(val(sample_id), path("${sample_id}.recal.table"), emit : gathered_recalibration_tables)
 
     script:
         tables = bqsr_tables.join(' -I ')