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Feature/upgrade nextflow #74

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merged 7 commits into from
Aug 8, 2023
Merged

Feature/upgrade nextflow #74

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46cc332
Add val() to value inputs and outputs
rernst Jul 28, 2023
f233e75
Add val() to value inputs and outputs
rernst Jul 28, 2023
6120111
Add val() to value inputs and outputs
rernst Jul 28, 2023
b51f699
Merge branch 'feature/upgrade_nextflow' of github.com:UMCUGenetics/Ne…
rernst Jul 28, 2023
c34fea5
Add val() to value inputs and outputs
rernst Jul 28, 2023
b9cc20a
Add missing brackets and fix review comments
rernst Aug 8, 2023
841c1db
Merge branch 'develop' into feature/upgrade_nextflow
rernst Aug 8, 2023
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4 changes: 2 additions & 2 deletions BCFtools/1.10.2/View.nf
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Expand Up @@ -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:
"""
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6 changes: 3 additions & 3 deletions BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf
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Expand Up @@ -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]
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4 changes: 2 additions & 2 deletions BWA/0.7.17/BWASW.nf
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Expand Up @@ -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:
"""
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4 changes: 2 additions & 2 deletions BWA/0.7.17/MEM.nf
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Expand Up @@ -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]
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4 changes: 2 additions & 2 deletions BamUtil/1.0.14/ClipOverlap.nf
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Expand Up @@ -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:
"""
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4 changes: 2 additions & 2 deletions ControlFREEC/11.5/AssessSignificance.nf
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Expand Up @@ -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:
"""
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6 changes: 3 additions & 3 deletions ControlFREEC/11.5/Freec.nf
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Expand Up @@ -6,11 +6,11 @@ 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"
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4 changes: 2 additions & 2 deletions ControlFREEC/11.5/MakeGraph.nf
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Expand Up @@ -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:
"""
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4 changes: 2 additions & 2 deletions ControlFREEC/11.5/MakeKaryotype.nf
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Expand Up @@ -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:
"""
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2 changes: 1 addition & 1 deletion FastQC/0.11.5/FastQC.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion FastQC/0.11.8/FastQC.nf
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Expand Up @@ -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)
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4 changes: 2 additions & 2 deletions Fastp/0.14.1/Fastp.nf
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Expand Up @@ -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:
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4 changes: 2 additions & 2 deletions Fastp/0.20.1/Fastp.nf
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Expand Up @@ -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:
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4 changes: 2 additions & 2 deletions GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf
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Expand Up @@ -6,10 +6,10 @@ 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:
"""
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4 changes: 2 additions & 2 deletions GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf
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Expand Up @@ -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 ")
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8 changes: 4 additions & 4 deletions GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf
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Expand Up @@ -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 ")
Expand All @@ -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 ")
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4 changes: 2 additions & 2 deletions GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf
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Expand Up @@ -6,10 +6,10 @@ 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 ")
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4 changes: 2 additions & 2 deletions GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf
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Expand Up @@ -6,7 +6,7 @@ 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)
Expand All @@ -31,7 +31,7 @@ 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)
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4 changes: 2 additions & 2 deletions GATK/3.8-1-0-gf15c1c3ef/IndelRealigner.nf
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Expand Up @@ -6,10 +6,10 @@ 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:
"""
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4 changes: 2 additions & 2 deletions GATK/3.8-1-0-gf15c1c3ef/RealignerTargetCreator.nf
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Expand Up @@ -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:
"""
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4 changes: 2 additions & 2 deletions GATK/3.8-1-0-gf15c1c3ef/SelectVariants.nf
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Expand Up @@ -6,10 +6,10 @@ 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:
"""
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4 changes: 2 additions & 2 deletions GATK/3.8-1-0-gf15c1c3ef/UnifiedGenotyper.nf
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Expand Up @@ -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:

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4 changes: 2 additions & 2 deletions GATK/3.8-1-0-gf15c1c3ef/VariantFiltration.nf
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Expand Up @@ -6,10 +6,10 @@ 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:
"""
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4 changes: 2 additions & 2 deletions GATK/4.1.3.0/BaseRecalibration.nf
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Expand Up @@ -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]
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4 changes: 2 additions & 2 deletions GATK/4.1.3.0/BaseRecalibrationTable.nf
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Expand Up @@ -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 ') : ''
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2 changes: 1 addition & 1 deletion GATK/4.1.3.0/CollectMultipleMetrics.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion GATK/4.1.3.0/CollectWGSMetrics.nf
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Expand Up @@ -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 ("${sample_id}.wgs_metrics.txt" , emit: wgs_metrics)
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4 changes: 2 additions & 2 deletions GATK/4.1.3.0/CombineGVCFs.nf
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Expand Up @@ -6,9 +6,9 @@ process CombineGVCFs {
container = 'library://sawibo/default/bioinf-tools:gatk4.1.3.0'
shell = ['/bin/bash', '-euo', 'pipefail']
input:
tuple (run_id, interval, path(gvcf_chunks), path(gvcf_chunk_idxs), path(interval_file))
tuple(val(run_id), val(interval), path(gvcf_chunks), path(gvcf_chunk_idxs), path(interval_file))
output:
tuple (run_id, interval, path("${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 ')
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4 changes: 2 additions & 2 deletions GATK/4.1.3.0/GatherBaseRecalibrationTables.nf
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Expand Up @@ -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 ')
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4 changes: 2 additions & 2 deletions GATK/4.1.3.0/GenotypeGVCFs.nf
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Expand Up @@ -6,10 +6,10 @@ process GenotypeGVCFs {
container = 'library://sawibo/default/bioinf-tools:gatk4.1.3.0'
shell = ['/bin/bash', '-euo', 'pipefail']
input:
tuple (run_id, interval, path(gvcf), path(gvcfidx), path(interval_file))
tuple(val(run_id), val(interval), path(gvcf), path(gvcfidx), path(interval_file))

output:
tuple (run_id, 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:
"""
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