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Try to simplify params.tools usage #1667

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Try to simplify params.tools usage #1667

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8 changes: 4 additions & 4 deletions conf/modules/aligner.config
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Original file line number Diff line number Diff line change
Expand Up @@ -46,8 +46,8 @@ process {
if (params.save_output_as_bam &&
(
params.save_mapped ||
(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) &&
!(params.tools && params.tools.split(',').contains('sentieon_dedup'))
(params.skip_tools && params.skip_tools.contains('markduplicates')) &&
!(params.tools && params.tools.contains('sentieon_dedup'))
) && (meta.size * meta.num_lanes == 1)
) { "mapped/${meta.id}/${it}" }
else { null }
Expand All @@ -60,7 +60,7 @@ process {
// However if it's skipped, reads need to be coordinate-sorted
// Only name sort if Spark for Markduplicates + duplicate marking is not skipped
// Currently SENTIEON_BWAMEM only supports coordinate sorting the reads.
ext.args2 = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('markduplicates'))) ? '-n' : '' }
ext.args2 = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.contains('markduplicates'))) ? '-n' : '' }
}

withName: 'BWAMEM.*_MEM|SENTIEON_BWAMEM' {
Expand All @@ -75,7 +75,7 @@ process {
path: { "${params.outdir}/preprocessing/" },
pattern: "*{bam,bai}",
// Only save if (save_output_as_bam AND (no_markduplicates OR save_mapped ))
saveAs: { (params.save_output_as_bam && (params.save_mapped || params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) ? "mapped/${meta.id}/${it}" : null }
saveAs: { (params.save_output_as_bam && (params.save_mapped || params.skip_tools && params.skip_tools.contains('markduplicates'))) ? "mapped/${meta.id}/${it}" : null }
]
}

Expand Down
16 changes: 8 additions & 8 deletions conf/modules/annotate.config
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
process {

// SNPEFF
if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) {
if (params.tools && (params.tools.contains('snpeff') || params.tools.contains('merge'))) {
withName: 'SNPEFF_SNPEFF' {
ext.args = { '-nodownload -canon -v' }
ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' }
Expand All @@ -25,14 +25,14 @@ process {
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" },
pattern: "*{csv,html,genes.txt}",
saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
saveAs: { params.tools.contains('snpeff') ? it : null }
]
]
}
}

// VEP
if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
if (params.tools && (params.tools.contains('vep') || params.tools.contains('merge'))) {
withName: 'ENSEMBLVEP_VEP' {
ext.args = { [
"--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html",
Expand Down Expand Up @@ -62,7 +62,7 @@ process {
}

// BCFTOOLS ANNOTATE
if (params.tools && params.tools.split(',').contains('bcfann')) {
if (params.tools && params.tools.contains('bcfann')) {
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' {
ext.args = { '--output-type z' }
ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' }
Expand All @@ -75,7 +75,7 @@ process {
}

// SNPEFF THEN VEP
if (params.tools && params.tools.split(',').contains('merge')) {
if (params.tools && params.tools.contains('merge')) {
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP' {
ext.args = { [
"--stats_file ${vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html",
Expand All @@ -93,7 +93,7 @@ process {
}

// ALL ANNOTATION TOOLS
if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge') || params.tools.split(',').contains('bcfann'))) {
if (params.tools && (params.tools.contains('snpeff') || params.tools.contains('vep') || params.tools.contains('merge') || params.tools.contains('bcfann'))) {
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' {
ext.prefix = { input.name - '.vcf' }
publishDir = [
Expand All @@ -104,13 +104,13 @@ process {
}
}

if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) {
if (params.tools && (params.tools.contains('snpeff') || params.tools.contains('merge'))) {
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
pattern: "*{gz,gz.tbi}",
saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
saveAs: { params.tools.contains('snpeff') ? it : null }
]
}
}
Expand Down
2 changes: 1 addition & 1 deletion conf/modules/ascat.config
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ process {
"min_map_qual": params.ascat_min_map_qual
]
}
ext.when = { params.tools && params.tools.split(',').contains('ascat') }
ext.when = { params.tools && params.tools.contains('ascat') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/ascat/${meta.id}/" },
Expand Down
8 changes: 4 additions & 4 deletions conf/modules/cnvkit.config
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Expand Up @@ -17,7 +17,7 @@ process {

withName: 'CNVKIT_BATCH' {
ext.args = { params.wes ? "--method hybrid --diagram --scatter" : "--method wgs --diagram --scatter" }
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
ext.when = { params.tools && params.tools.contains('cnvkit') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
Expand All @@ -26,7 +26,7 @@ process {
}

withName: '.*:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL' {
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
ext.when = { params.tools && params.tools.contains('cnvkit') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
Expand All @@ -47,7 +47,7 @@ process {
withName: 'CNVKIT_EXPORT' {
ext.args = "vcf"
ext.prefix = { "${meta.id}.cnvcall" }
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
ext.when = { params.tools && params.tools.contains('cnvkit') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
Expand All @@ -57,7 +57,7 @@ process {

withName: 'CNVKIT_GENEMETRICS' {
ext.prefix = { "${cnr.baseName}.genemetrics" }
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
ext.when = { params.tools && params.tools.contains('cnvkit') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
Expand Down
2 changes: 1 addition & 1 deletion conf/modules/controlfreec.config
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ process {
}

withName: 'FREEC_.*' {
ext.when = { params.tools && params.tools.split(',').contains('controlfreec') }
ext.when = { params.tools && params.tools.contains('controlfreec') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
Expand Down
2 changes: 1 addition & 1 deletion conf/modules/deepvariant.config
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Expand Up @@ -18,7 +18,7 @@ process {
withName: 'DEEPVARIANT' {
ext.args = { params.wes ? "--model_type WES" : "--model_type WGS" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.baseName}" }
ext.when = { params.tools && params.tools.split(',').contains('deepvariant') }
ext.when = { params.tools && params.tools.contains('deepvariant') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
Expand Down
4 changes: 2 additions & 2 deletions conf/modules/download_cache.config
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ process {

// SNPEFF
withName: 'SNPEFF_DOWNLOAD' {
ext.when = { params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge')) }
ext.when = { params.tools && (params.tools.contains('snpeff') || params.tools.contains('merge')) }
publishDir = [
mode: params.publish_dir_mode,
path: { params.outdir_cache ? "${params.outdir_cache}/": "${params.outdir}/cache/" }
Expand All @@ -26,7 +26,7 @@ process {

// VEP
withName: 'ENSEMBLVEP_DOWNLOAD' {
ext.when = { params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge')) }
ext.when = { params.tools && (params.tools.contains('vep') || params.tools.contains('merge')) }
ext.args = { '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' }
publishDir = [
mode: params.publish_dir_mode,
Expand Down
4 changes: 2 additions & 2 deletions conf/modules/freebayes.config
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Expand Up @@ -28,7 +28,7 @@ process {
ext.args = { '--min-alternate-fraction 0.1 --min-mapping-quality 1' }
//To make sure no naming conflicts ensure with module BCFTOOLS_SORT & the naming being correct in the output folder
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.baseName}" }
ext.when = { params.tools && params.tools.split(',').contains('freebayes') }
ext.when = { params.tools && params.tools.contains('freebayes') }
publishDir = [
enabled: false
]
Expand All @@ -53,7 +53,7 @@ process {
}

// PAIR_VARIANT_CALLING
if (params.tools && params.tools.split(',').contains('freebayes')) {
if (params.tools && params.tools.contains('freebayes')) {
withName: '.*:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES' {
ext.args = { "--pooled-continuous \
--pooled-discrete \
Expand Down
4 changes: 2 additions & 2 deletions conf/modules/haplotypecaller.config
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Expand Up @@ -18,7 +18,7 @@ process {
withName: 'GATK4_HAPLOTYPECALLER' {
ext.args = { params.joint_germline ? "-ERC GVCF" : "" }
ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.baseName}.g" :"${meta.id}.haplotypecaller.${intervals.baseName}" ) }
ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') }
ext.when = { params.tools && params.tools.contains('haplotypecaller') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/"},
Expand Down Expand Up @@ -53,7 +53,7 @@ process {
]
}

if (params.tools && params.tools.split(',').contains('haplotypecaller')) {
if (params.tools && params.tools.contains('haplotypecaller')) {
withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)' {
ext.prefix = { "${meta.id}.realigned" }
publishDir = [
Expand Down
4 changes: 2 additions & 2 deletions conf/modules/lofreq.config
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Expand Up @@ -14,12 +14,12 @@
//LOFREQ

process {
if (params.tools && params.tools.split(',').contains('lofreq')) {
if (params.tools && params.tools.contains('lofreq')) {

withName: "LOFREQ_CALLPARALLEL" {
ext.args = { "--call-indels" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.lofreq" : "${meta.id}.lofreq.${intervals.baseName}" }
ext.when = { params.tools && params.tools.split(',').contains('lofreq') }
ext.when = { params.tools && params.tools.contains('lofreq') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
Expand Down
2 changes: 1 addition & 1 deletion conf/modules/manta.config
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Expand Up @@ -14,7 +14,7 @@
// MANTA

process {
if (params.tools && params.tools.split(',').contains('manta')) {
if (params.tools && params.tools.contains('manta')) {
withName: 'MANTA_GERMLINE|MANTA_TUMORONLY|MANTA_SOMATIC' {
ext.args = { params.wes ? "--exome" : '' }
ext.prefix = { "${meta.id}.manta" }
Expand Down
14 changes: 7 additions & 7 deletions conf/modules/markduplicates.config
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ process {

withName: 'NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS' {
ext.prefix = { "${meta.id}.md.cram" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
ext.when = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/samtools/${meta.id}" },
Expand All @@ -48,8 +48,8 @@ process {
// Run only when mapping should be saved as CRAM or when no MD is done
ext.when = (params.save_mapped && !params.save_output_as_bam) ||
(
(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) &&
!(params.tools && params.tools.split(',').contains('sentieon_dedup'))
(params.skip_tools && params.skip_tools.contains('markduplicates')) &&
!(params.tools && params.tools.contains('sentieon_dedup'))
)
publishDir = [
// Never publish if BAM only should be published
Expand All @@ -62,7 +62,7 @@ process {

withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' {
ext.prefix = { "${meta.id}.md.cram" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) }
ext.when = { !(params.skip_tools && params.skip_tools.contains('markduplicates_report')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/markduplicates/${meta.id}" },
Expand All @@ -73,7 +73,7 @@ process {
withName: 'GATK4_MARKDUPLICATES' {
ext.args = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT'
ext.prefix = { "${meta.id}.md.cram" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) }
ext.when = { !(params.skip_tools && params.skip_tools.contains('markduplicates')) }
publishDir = [
[
mode: params.publish_dir_mode,
Expand All @@ -85,7 +85,7 @@ process {
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/" },
pattern: "*metrics",
saveAs: { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) ? "markduplicates/${meta.id}/${it}" : null}
saveAs: { !(params.skip_tools && params.skip_tools.contains('markduplicates_report')) ? "markduplicates/${meta.id}/${it}" : null}
]
]
}
Expand Down Expand Up @@ -113,7 +113,7 @@ process {

withName: 'NFCORE_SAREK:SAREK:CRAM_TO_BAM' {
ext.when = { params.save_output_as_bam }
if (params.tools && params.tools.split(',').contains('sentieon_dedup')) {
if (params.tools && params.tools.contains('sentieon_dedup')) {
ext.prefix = { "${meta.id}.dedup" }
publishDir = [
mode: params.publish_dir_mode,
Expand Down
18 changes: 9 additions & 9 deletions conf/modules/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ process {
// QC
withName: 'FASTQC' {
ext.args = { '--quiet' }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('fastqc')) }
ext.when = { !(params.skip_tools && params.skip_tools.contains('fastqc')) }
publishDir = [
[
path: { "${params.outdir}/reports/fastqc/${meta.id}" },
Expand All @@ -42,7 +42,7 @@ process {

withName: 'NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS' {
ext.prefix = { "${meta.id}.sorted.cram" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
ext.when = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/samtools/${meta.id}" },
Expand All @@ -60,30 +60,30 @@ process {
withName: 'MOSDEPTH' {
ext.args = { !params.wes ? "-n --fast-mode --by 500" : ""}
ext.prefix = {
if (params.tools && params.tools.split(',').contains('sentieon_dedup')) {
if (params.tools && params.tools.contains('sentieon_dedup')) {
"${meta.id}.dedup"
} else if (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) {
} else if (params.skip_tools && params.skip_tools.contains('markduplicates')) {
"${meta.id}.sorted"
} else {
"${meta.id}.md"
}
}
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('mosdepth')) }
ext.when = { !(params.skip_tools && params.skip_tools.contains('mosdepth')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/mosdepth/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'))) {
if (!(params.skip_tools && params.skip_tools.contains('baserecalibrator'))) {
withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH' {
ext.prefix = { "${meta.id}.recal" }
}

withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS' {
ext.prefix = { "${meta.id}.recal.cram" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
ext.when = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/samtools/${meta.id}" },
Expand All @@ -95,7 +95,7 @@ process {
// VCF
withName: 'BCFTOOLS_STATS' {
ext.prefix = { vcf.baseName - ".vcf" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('bcftools')) }
ext.when = { !(params.skip_tools && params.skip_tools.contains('bcftools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/bcftools/${meta.variantcaller}/${meta.id}/" },
Expand All @@ -105,7 +105,7 @@ process {

withName: 'VCFTOOLS_.*' {
ext.prefix = { variant_file.baseName - ".vcf" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('vcftools')) }
ext.when = { !(params.skip_tools && params.skip_tools.contains('vcftools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/vcftools/${meta.variantcaller}/${meta.id}/" },
Expand Down
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