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

Release/v0.7.3

Author: melferink

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:
     """

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]

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:
         """

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]

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:
     """

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:
         """

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"

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:
         """

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:
         """

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)