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Feature/nextflow upgrade 23 10 0 #77

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merged 25 commits into from
Mar 27, 2024
Merged

Feature/nextflow upgrade 23 10 0 #77

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a16bed5
Merge pull request #69 from UMCUGenetics/develop
melferink May 17, 2023
64ea49a
Merge pull request #70 from UMCUGenetics/release/v0.7.0
melferink May 25, 2023
fcd72d7
Merge branch 'develop' into release/v0.7.1
rernst Jun 8, 2023
7bf677e
Merge pull request #72 from UMCUGenetics/release/v0.7.1
rernst Jun 9, 2023
5f303eb
Merge remote-tracking branch 'origin/develop' into release/v0.7.2
ellendejong Aug 1, 2023
4cd4aa4
Merge pull request #75 from UMCUGenetics/release/v0.7.2
rernst Aug 7, 2023
edffeff
Refactor of separate input names to val() wrapped input names
BasMonkey Jan 3, 2024
3236fc0
Refactor of separate input names to val() wrapped input names
BasMonkey Jan 3, 2024
928949b
Refactor of separate input names to val() wrapped input names for ana…
BasMonkey Jan 3, 2024
b21cfea
Refactor of separate input names to val() wrapped input names for ana…
BasMonkey Jan 3, 2024
87cfc32
Refactor even more separate input names to val() wrapped input names
BasMonkey Jan 3, 2024
ececda8
Refactor even more separate input names to val() wrapped input names
BasMonkey Jan 3, 2024
01b3291
Refactor of separate output names to val() wrapped output names
BasMonkey Jan 3, 2024
e921481
Refactor of more separate output names to val() wrapped output names
BasMonkey Jan 3, 2024
bcd9178
Refactor of a forgotten separate output name to val() wrapped output …
BasMonkey Jan 3, 2024
8537935
Refactor of another separate output name to val() wrapped output name
BasMonkey Jan 3, 2024
36f8a12
Refactor of separate output names to val() wrapped output names
BasMonkey Jan 3, 2024
11136c5
Refactor of separate output names to val() wrapped output names
BasMonkey Jan 4, 2024
771ec51
Refactor of tuple (...) to tuple(...)
BasMonkey Jan 12, 2024
6d19b9c
Removed whitespaces at the end of a tuple
BasMonkey Jan 12, 2024
1d4f005
Refactor max line length to <127 cols
BasMonkey Jan 15, 2024
de29560
Revert "Refactor max line length to <127 cols"
BasMonkey Jan 29, 2024
42b7f7e
Refactor of line lenght >127 cols for in- and outputs
BasMonkey Jan 29, 2024
65f7693
Merge branch develop into feature/nextflow_upgrade_23_10_0
BasMonkey Feb 9, 2024
263d65d
Refactor of all baseDir to projectDir
BasMonkey Mar 8, 2024
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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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4 changes: 2 additions & 2 deletions BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf
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Expand Up @@ -6,10 +6,10 @@ process BWAMapping {
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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Original file line number Diff line number Diff line change
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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Original file line number Diff line number Diff line change
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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