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Merge pull request #529 from maxulysse/dev_dont_publish_versions_yml
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fix saveAs parameter for publishDir directive
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@maxulysse
maxulysse authored Apr 29, 2022
2 parents adef6e2 + 5067bbb commit 787741d
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Showing 2 changed files with 57 additions and 38 deletions.
1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#454](https://github.com/nf-core/sarek/pull/454) - Input is optional (can actually be found automatically by `Sarek` if previously run)
- [#463](https://github.com/nf-core/sarek/pull/463), [#468](https://github.com/nf-core/sarek/pull/468) - Fix `nf-core lint`
- [#513](https://github.com/nf-core/sarek/pull/513), [#527](https://github.com/nf-core/sarek/pull/527) - CNV is back
- [#529](https://github.com/nf-core/sarek/pull/529) - Do not save `versions.yml` files

### Deprecated

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94 changes: 56 additions & 38 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -199,17 +199,17 @@ process {
[
path: { "${params.outdir}/reports/trimgalore/${meta.id}/fastqc" },
mode: params.publish_dir_mode,
pattern: "*.{html,zip}"
pattern: "*{html,zip}"
],
[
path: { "${params.outdir}/trimgalore/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "*.fq.gz"
pattern: "*fq.gz"
],
[
path: { "${params.outdir}/reports/trimgalore/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "*.txt"
pattern: "*txt"
]
]
}
Expand Down Expand Up @@ -244,8 +244,9 @@ process {
ext.when = { params.split_fastq > 1 }
publishDir = [
enabled: params.save_split_fastqs,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/${meta.sample}/seqkit" },
mode: params.publish_dir_mode
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand Down Expand Up @@ -273,7 +274,7 @@ process {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/${meta.id}/mapped" },
pattern: "*.bam",
pattern: "*bam",
saveAs: { (params.save_bam_mapped || (params.skip_tools && params.skip_tools.contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? it : null }
]
}
Expand All @@ -293,24 +294,21 @@ process {

// MARKDUPLICATES

withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' {
withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY|GATK4_MARKDUPLICATES' {
ext.prefix = { "${meta.id}.md" }
ext.when = { !(params.skip_tools && params.skip_tools.contains('markduplicates_report')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
pattern: "*metrics"
path: { "${params.outdir}/reports/${meta.id}/markduplicates" },
pattern: "metrics"
]
}

withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' {
ext.when = { !(params.skip_tools && params.skip_tools.contains('markduplicates_report')) }
}

withName: 'GATK4_MARKDUPLICATES' {
ext.args = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
ext.prefix = { "${meta.id}.md" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/${meta.id}/markduplicates" },
pattern: "*metrics"
]
}

withName: 'GATK4_MARKDUPLICATES_SPARK' {
Expand Down Expand Up @@ -351,7 +349,7 @@ process {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/${meta.id}/recal_table" },
pattern: "*.table"
pattern: "*table"
]
}

Expand Down Expand Up @@ -398,7 +396,7 @@ process {
[
path: { "${params.outdir}/reports/fastqc/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "*.{html,zip}"
pattern: "*{html,zip}"
]
]
}
Expand All @@ -409,23 +407,26 @@ process {
ext.when = { !(params.skip_tools && params.skip_tools.contains('bamqc')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/qualimap/${meta.id}" }
path: { "${params.outdir}/reports/qualimap/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'SAMTOOLS_STATS' {
ext.when = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/samtools_stats/${meta.id}" }
path: { "${params.outdir}/reports/samtools_stats/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'DEEPTOOLS_BAMCOVERAGE' {
ext.when = { !(params.skip_tools && params.skip_tools.contains('deeptools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/deeptools/${meta.id}" }
path: { "${params.outdir}/reports/deeptools/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -435,15 +436,17 @@ process {
ext.when = { !(params.skip_tools && params.skip_tools.contains('bamqc')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/qualimap/${meta.id}" }
path: { "${params.outdir}/reports/qualimap/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'NFCORE_SAREK:SAREK:CRAM_QC:SAMTOOLS_STATS' {
ext.when = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/samtools_stats/${meta.id}" }
path: { "${params.outdir}/reports/samtools_stats/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand Down Expand Up @@ -502,7 +505,8 @@ process{
publishDir = [
enabled: !params.no_intervals,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" }
path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'FREEBAYES' {
Expand All @@ -511,13 +515,15 @@ process{
publishDir = [
enabled: params.no_intervals,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" }
path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName : 'TABIX_VC_FREEBAYES' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" }
path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -527,7 +533,8 @@ process{
publishDir = [
enabled: !params.no_intervals,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" }
path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'HAPLOTYPECALLER' {
Expand Down Expand Up @@ -630,7 +637,7 @@ process{
enabled: !params.no_intervals,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
pattern: "*{mpileup}"
pattern: "*mpileup"
]
}

Expand Down Expand Up @@ -680,7 +687,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
pattern: "*{.bed}"
pattern: "*bed"
]
}

Expand All @@ -689,7 +696,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
pattern: "*{.circos.txt}"
pattern: "*circos.txt"
]
}

Expand All @@ -698,7 +705,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
pattern: "*{png}"
pattern: "*png"
]
}

Expand All @@ -708,7 +715,7 @@ process{
enabled: params.no_intervals,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
pattern: "*{mpileup}"
pattern: "*mpileup"
]
}

Expand All @@ -721,7 +728,8 @@ process{
withName: 'GATK4_CALCULATECONTAMINATION' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -738,7 +746,8 @@ process{
ext.prefix = {"${meta.id}.filtered"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -748,23 +757,26 @@ process{
publishDir = [
enabled: !params.no_intervals,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'GETPILEUPSUMMARIES.*' {
publishDir = [
enabled: params.no_intervals,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'MERGEMUTECTSTATS' {
ext.prefix = { "${meta.id}.vcf.gz" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand Down Expand Up @@ -865,6 +877,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -874,8 +887,9 @@ process{
enabled: !params.no_intervals,
mode: params.publish_dir_mode,
//use ${meta.tumor_id}_vs_${meta_normal_id} to publish in the same directory as the remainders of the
//somatic output whilst keeping the filename prefix identifieable for status type
path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" }
//somatic output whilst keeping the filename prefix identifiable for status type
path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -884,6 +898,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -892,6 +907,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/msisensorpro" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -910,6 +926,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/bcftools" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -919,6 +936,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/vcftools" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand Down

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