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update outputs varcallers + ci tests
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@SusiJo
SusiJo committed Jul 13, 2022
1 parent 71901f2 commit 4e30625
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Showing 4 changed files with 216 additions and 189 deletions.
76 changes: 44 additions & 32 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -514,17 +514,18 @@ process{

// DEEPVARIANT
withName: 'MERGE_DEEPVARIANT_.*' {
ext.prefix = {"${meta.id}.deepvariant"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" },
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'MERGE_DEEPVARIANT_GVCF' {
ext.prefix = {"${meta.id}.g"}
ext.prefix = {"${meta.id}.deepvariant.g"}
}
withName: 'DEEPVARIANT' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}_${intervals.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.simpleName}" }
ext.args = { params.wes ? "--model_type WES" : "--model_type WGS" }
ext.when = { params.tools && params.tools.contains('deepvariant') }
publishDir = [
Expand All @@ -535,6 +536,7 @@ process{
]
}
withName : 'TABIX_VC_DEEPVARIANT_.*' {
ext.prefix = {"${meta.id}.deepvariant"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" },
Expand All @@ -544,15 +546,16 @@ process{

// FREEBAYES
withName: 'MERGE_FREEBAYES' {
ext.prefix = { "${meta.id}.freebayes" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'FREEBAYES' {
//To make sure no naming conflicts ensue with module BCFTOOLS_SORT & the naming being correct in the output folder
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${meta.id}_${target_bed.simpleName}.freebayes" }
//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.simpleName}" }
ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1'
ext.when = { params.tools && params.tools.contains('freebayes') }
publishDir = [
Expand All @@ -561,7 +564,7 @@ process{
}

withName: 'BCFTOOLS_SORT' {
ext.prefix = { "${vcf.baseName.minus(".freebayes.vcf")}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/" },
Expand All @@ -580,7 +583,7 @@ process{

// HAPLOTYPECALLER
withName: 'MERGE_HAPLOTYPECALLER.*' {
ext.prefix = { params.joint_germline ? "${meta.id}.g" : "${meta.id}" }
ext.prefix = { params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" },
Expand All @@ -590,7 +593,7 @@ process{

withName: 'HAPLOTYPECALLER' {
ext.args = { params.joint_germline ? "-ERC GVCF" : "" }
ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.g" : "${meta.id}" ) : ( params.joint_germline ? "${meta.id}_${intervals.simpleName}.g" :"${meta.id}_${intervals.simpleName}" ) }
ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) }
ext.when = { params.tools && params.tools.contains('haplotypecaller') }
publishDir = [
mode: params.publish_dir_mode,
Expand All @@ -605,6 +608,7 @@ process{
]
}
withName: 'FILTERVARIANTTRANCHES' {
ext.prefix = {"${meta.id}.haplotypecaller"}
ext.args = { "--info-key CNN_1D" }
publishDir = [
mode: params.publish_dir_mode,
Expand All @@ -614,6 +618,7 @@ process{
}

withName: 'GENOTYPEGVCFS' {
ext.prefix = {"${meta.id}.haplotypecaller"}
ext.when = { params.tools && params.tools.contains('haplotypecaller') && params.joint_germline}
publishDir = [
mode: params.publish_dir_mode,
Expand All @@ -631,16 +636,16 @@ process{
]
}
withName: 'MERGE_MANTA_DIPLOID' {
ext.prefix = {"${meta.id}.diploid_sv"}
ext.prefix = {"${meta.id}.manta.diploid_sv"}
}
withName: 'MERGE_MANTA_SMALL_INDELS' {
ext.prefix = {"${meta.id}.candidate_small_indels"}
ext.prefix = {"${meta.id}.manta.candidate_small_indels"}
}
withName: 'MERGE_MANTA_SV' {
ext.prefix = {"${meta.id}.candidate_sv"}
ext.prefix = {"${meta.id}.manta.candidate_sv"}
}
withName: 'MANTA.*' {
ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${target_bed.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.manta" : "${meta.id}.manta.${target_bed.simpleName}" }
ext.args = { params.wes ? "--exome" : "" }
ext.when = { params.tools && params.tools.contains('manta') }
publishDir = [
Expand All @@ -660,13 +665,13 @@ process{
]
}
withName: 'MERGE_STRELKA' {
ext.prefix = {"${meta.id}.variants"}
ext.prefix = {"${meta.id}.strelka.variants"}
}
withName: 'MERGE_STRELKA_GENOME' {
ext.prefix = {"${meta.id}.genome"}
ext.prefix = {"${meta.id}.strelka.genome"}
}
withName: 'STRELKA_.*' {
ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${target_bed.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.simpleName}" }
ext.args = { params.wes ? "--exome" : "" }
ext.when = { params.tools && params.tools.contains('strelka') }
publishDir = [
Expand All @@ -681,14 +686,15 @@ process{
withName: 'TIDDIT_SV' {
ext.when = { params.tools && params.tools.contains('tiddit') }
ext.args = { bwa_index ? "" : "--skip_assembly" }
ext.prefix = { "${meta.id}.tiddit" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
pattern: "*tab",
]
}
withName : 'TABIX_BGZIP_TIDDIT_SV' {
ext.prefix = { "${meta.id}.vcf" }
ext.prefix = { "${meta.id}.tiddit.vcf" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
Expand Down Expand Up @@ -825,20 +831,22 @@ process{

//MANTA
withName: 'MERGE_MANTA_TUMOR' {
ext.prefix = {"${meta.id}.tumor_sv"}
ext.prefix = {"${meta.id}.manta.tumor_sv"}
}

//MUTECT2
withName: 'CALCULATECONTAMINATION' {
ext.args = { "-tumor-segmentation ${meta.id}.segmentation.table" }
publishDir = [
ext.prefix = { "${meta.id}.mutect2" }
ext.args = { "-tumor-segmentation ${meta.id}.mutect2.segmentation.table" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/mutect2/${filename}" }
]
}

withName: 'MERGE_MUTECT2.*' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
Expand All @@ -847,7 +855,7 @@ process{
}

withName: 'FILTERMUTECTCALLS.*'{
ext.prefix = {"${meta.id}.filtered"}
ext.prefix = {"${meta.id}.mutect2.filtered"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
Expand All @@ -856,6 +864,7 @@ process{
}

withName: 'GATHERPILEUPSUMMARIES' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
Expand All @@ -864,6 +873,7 @@ process{
}

withName: 'GATHERPILEUPSUMMARIES_.*' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
Expand All @@ -872,7 +882,7 @@ process{
}

withName: 'GETPILEUPSUMMARIES.*' {
ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${intervals.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
Expand All @@ -882,6 +892,7 @@ process{
}

withName: 'GETPILEUPSUMMARIES_.*' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
Expand All @@ -891,7 +902,7 @@ process{
}

withName: 'LEARNREADORIENTATIONMODEL'{
ext.prefix = { "${meta.id}.artifactprior" }
ext.prefix = { "${meta.id}.mutect2.artifactprior" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
Expand All @@ -900,7 +911,7 @@ process{
}

withName: 'MERGEMUTECTSTATS' {
ext.prefix = { "${meta.id}" }
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
Expand All @@ -909,7 +920,7 @@ process{
}

withName: 'MUTECT2'{
ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${intervals.simpleName}" }
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
ext.when = { params.tools && params.tools.contains('mutect2') }
ext.args = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" : "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" }
publishDir = [
Expand Down Expand Up @@ -1042,7 +1053,7 @@ process{

//MANTA
withName: 'MERGE_MANTA_SOMATIC' {
ext.prefix = {"${meta.id}.somatic_sv"}
ext.prefix = {"${meta.id}.manta.somatic_sv"}
}

//MUTECT2
Expand All @@ -1065,23 +1076,24 @@ process{

//STRELKA
withName: 'MERGE_STRELKA_INDELS' {
ext.prefix = {"${meta.id}.somatic_indels"}
ext.prefix = {"${meta.id}.strelka.somatic_indels"}
}
withName: 'MERGE_STRELKA_SNVS' {
ext.prefix = {"${meta.id}.somatic_snvs"}
ext.prefix = {"${meta.id}.strelka.somatic_snvs"}
}

//TIDDIT
withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
ext.prefix = {"${meta.id}.normal.vcf"}
ext.prefix = {"${meta.id}.tiddit.normal.vcf"}
}

withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' {
ext.prefix = {"${meta.id}.tumor.vcf"}
ext.prefix = {"${meta.id}.tiddit.tumor.vcf"}
}

//SVDB
withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:SVDB_MERGE' {
ext.prefix = { "${meta.id}.tiddit" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
Expand All @@ -1092,20 +1104,20 @@ process{
// VCF QC
withName: 'BCFTOOLS_STATS'{
ext.when = { !(params.skip_tools && params.skip_tools.contains('bcftools')) }
ext.prefix = { "${meta.variantcaller}.${vcf.baseName.minus(".vcf")}" }
ext.prefix = { "${vcf.baseName.minus(".vcf")}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/bcftools" },
path: { "${params.outdir}/reports/bcftools/${meta.id}/${meta.variantcaller}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'VCFTOOLS_.*'{
ext.when = { !(params.skip_tools && params.skip_tools.contains('vcftools')) }
ext.prefix = { "${meta.variantcaller}.${variant_file.baseName.minus(".vcf")}" }
ext.prefix = { "${variant_file.baseName.minus(".vcf")}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/vcftools" },
path: { "${params.outdir}/reports/vcftools/${meta.id}/${meta.variantcaller}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
Expand Down
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