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modules.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Config file for defining DSL2 per module options and publishing paths
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Available keys to override module options:
ext.args = Additional arguments appended to command in module.
ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
ext.prefix = File name prefix for output files.
ext.when = When to run the module.
----------------------------------------------------------------------------------------
*/
process {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
withName: CUSTOM_DUMPSOFTWAREVERSIONS {
cache = false
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/pipeline_info" },
pattern: '*_versions.yml'
]
}
// PREPARE_GENOME
withName: 'BWAMEM1_INDEX' {
ext.when = { !params.bwa && params.step == "mapping" && params.aligner == "bwa-mem" }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference" },
pattern: "bwa"
]
}
withName: 'BWAMEM2_INDEX' {
ext.when = { !params.bwa && params.step == "mapping" && params.aligner == "bwa-mem2" }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference" },
pattern: "bwamem2"
]
}
withName: 'DRAGMAP_HASHTABLE' {
ext.when = { !params.bwa && params.step == "mapping" && params.aligner == "dragmap" }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference" },
pattern: "dragmap"
]
}
withName: 'GATK4_CREATESEQUENCEDICTIONARY' {
ext.when = { !params.dict && params.step != "annotate" && params.step != "controlfreec" }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/dict" },
pattern: "*dict"
]
}
withName: 'MSISENSORPRO_SCAN' {
ext.when = { params.tools && params.tools.split(',').contains('msisensorpro') }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/msi" },
pattern: "*list"
]
}
withName: 'SAMTOOLS_FAIDX' {
ext.when = { !params.fasta_fai && params.step != "annotate" }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/fai" },
pattern: "*fai"
]
}
withName: 'TABIX_DBSNP' {
ext.when = { !params.dbsnp_tbi && params.dbsnp && (params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('mutect2')) }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/dbsnp" },
pattern: "*vcf.gz.tbi"
]
}
withName: 'TABIX_GERMLINE_RESOURCE' {
ext.when = { !params.germline_resource_tbi && params.germline_resource && params.tools && params.tools.split(',').contains('mutect2') }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/germline_resource" },
pattern: "*vcf.gz.tbi"
]
}
withName: 'TABIX_KNOWN_INDELS' {
ext.when = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && params.tools.split(',').contains('haplotypecaller')) ) }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/known_indels" },
pattern: "*vcf.gz.tbi"
]
}
withName: 'TABIX_PON' {
ext.when = { !params.pon_tbi && params.pon && params.tools && params.tools.split(',').contains('mutect2') }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/pon" },
pattern: "*vcf.gz.tbi"
]
}
withName: 'UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT'{
ext.when = { params.tools && params.tools.split(',').contains('ascat')}
}
withName: 'UNTAR_CHR_DIR'{
ext.when = { params.tools && params.tools.split(',').contains('controlfreec')}
}
withName: 'CNVKIT_ANTITARGET' {
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/cnvkit" },
pattern: "*{bed}"
]
}
withName: 'CNVKIT_REFERENCE' {
ext.prefix = "cnvkit"
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/cnvkit" },
pattern: "*{cnn}"
]
}
// PREPARE INTERVALS
withName: 'CREATE_INTERVALS_BED' {
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/intervals" },
pattern: "*bed"
]
}
withName: 'GATK4_INTERVALLISTTOBED' {
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/intervals" },
pattern: "*bed"
]
}
withName: 'TABIX_BGZIPTABIX_INTERVAL_SPLIT' {
ext.prefix = {"${meta.id}"}
publishDir = [
enabled: params.save_reference,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/intervals" },
pattern: "*bed.gz"
]
}
// BAM TO FASTQ
withName: 'COLLATE_FASTQ_MAP'{
ext.args2 = '-N'
ext.prefix = {"${meta.id}.mapped"}
}
withName: 'COLLATE_FASTQ_UNMAP'{
ext.args2 = '-N'
ext.prefix = {"${meta.id}.unmapped"}
}
withName: 'SAMTOOLS_VIEW_MAP_MAP' {
ext.args = '-b -f1 -F12'
ext.prefix = {"${meta.id}.map_map"}
}
withName: 'SAMTOOLS_VIEW_MAP_UNMAP' {
ext.args = '-b -f8 -F260'
ext.prefix = {"${meta.id}.map_unmap"}
}
withName: 'SAMTOOLS_VIEW_UNMAP_MAP' {
ext.args = '-b -f4 -F264'
ext.prefix = {"${meta.id}.unmap_map"}
}
withName: 'SAMTOOLS_VIEW_UNMAP_UNMAP' {
ext.args = '-b -f12 -F256'
ext.prefix = {"${meta.id}.unmap_unmap"}
}
// TRIMMING
withName: FASTP {
ext.args = [ "",
params.trim_fastq ?: "--disable_adapter_trimming",
params.clip_r1 > 0 ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1.
params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
params.clip_r2 > 0 ? "--trim_front2 ${params.clip_r2}" : "", //Remove bp from the 5' end of read 2.
params.three_prime_clip_r2 > 0 ? "--trim_tail2 ${params.three_prime_clip_r2}" : "", // Remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.
params.trim_nextseq ? "--trim_poly_g" : "", // Apply the --nextseq=X option, to trim based on quality after removing poly-G tails.
params.split_fastq > 0 ? "--split_by_lines ${params.split_fastq * 4}" : "",
].join(" ").trim()
publishDir = [
[
path: { "${params.outdir}/reports/fastp/${meta.sample}" },
mode: params.publish_dir_mode,
pattern: "*.{html,json,log}"
],
[
enabled: params.save_trimmed || params.save_split_fastqs,
path: { "${params.outdir}/preprocessing/fastp/${meta.sample}/" },
mode: params.publish_dir_mode,
pattern: "*.fastp.fastq.gz"
]
]
}
// UMI Subworkflow
withName: 'BAM2FASTQ' {
ext.args = '-T RX'
ext.when = { params.umi_read_structure }
}
withName: 'CALLUMICONSENSUS' {
ext.args = '-M 1 -S Coordinate'
ext.prefix = {"${meta.id}_umi-consensus"}
}
if (params.umi_read_structure) {
withName: "NFCORE_SAREK:SAREK:CREATE_UMI_CONSENSUS:MAPPING_UMI:BWAMEM.*_MEM" {
ext.args = { "-K 100000000 -p -C -Y -R ${meta.read_group}" }
ext.args2 = '-bS'
ext.prefix = {"${meta.id}.umi_unsorted"}
}
withName: ".*DRAGMAP_ALIGN" {
ext.args2 = '-bS'
ext.prefix = {"${meta.id}.umi_unsorted"}
}
}
withName: 'SAMBLASTER' {
ext.args = '-M --addMateTags'
ext.prefix = {"${meta.id}_unsorted_tagged"}
}
// MAPPING
if (params.step == 'mapping') {
withName: ".*BWAMEM1_MEM" {
ext.when = { params.aligner == "bwa-mem" }
}
withName: ".*BWAMEM2_MEM" {
ext.when = { params.aligner == "bwa-mem2" }
}
withName: ".*DRAGMAP_ALIGN" {
ext.when = { params.aligner == "dragmap" }
ext.args = { "--RGSM ${meta.read_group}" }
}
withName: "NFCORE_SAREK:SAREK:GATK4_MAPPING:(BWAMEM.*_MEM|DRAGMAP_ALIGN)" {
// Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof
// However if it's skipped, reads need to be coordinate-sorted
// Only name sort if Spark for Markduplicates + duplicate marking is not skipped
ext.args2 = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('markduplicates'))) ? '-n' : '' }
ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/" },
pattern: "*bam",
saveAs: { (params.save_bam_mapped || (params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? "mapped/${meta.id}/${it}" : null }
]
}
withName: "NFCORE_SAREK:SAREK:GATK4_MAPPING:BWAMEM.*_MEM" {
// Using -B 3 for tumor samples
ext.args = { meta.status == 1 ? "-K 100000000 -Y -B 3 -R ${meta.read_group}" : "-K 100000000 -Y -R ${meta.read_group}" }
}
}
withName: 'MERGE_BAM|INDEX_MERGE_BAM' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/mapped/${meta.id}/" },
pattern: "*{bam,bai}"
]
}
// MARKDUPLICATES
withName: 'SAMTOOLS_CRAMTOBAM.*'{
ext.args = "-b"
}
withName: 'SAMTOOLS_STATS_CRAM'{
ext.prefix = { (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) ? "${meta.id}.sorted.cram" : "${meta.id}.md.cram" }
}
withName: 'SAMTOOLS_BAMTOCRAM.*' {
// BAM provided for step Markduplicates either run through MD or Convert -> then saved as md.cram
// BAM files provided for step prepare_recal are converted and run through BQSR -> then saved as md.cram
// BAM files provided for step recal are converted and run through BQSR II -> then saved as md.cram
ext.args = "-C"
ext.prefix = { (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) ? "${meta.id}.sorted" : "${meta.id}.md" }
publishDir = [
enabled: !params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) ? "${params.outdir}/preprocessing/mapped/${meta.id}/" : "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
pattern: "*{cram,crai}"
]
}
withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' {
ext.prefix = { "${meta.id}.md" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/markduplicates/${meta.id}" },
pattern: "*metrics"
]
}
withName: 'GATK4_MARKDUPLICATES' {
ext.args = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
ext.prefix = { "${meta.id}.md" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) }
publishDir = [
[
enabled: params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
pattern: "*{bam,bai}"
],
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/" },
pattern: "*metrics",
saveAs: { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) ? "markduplicates/${meta.id}/${it}" : null}
]
]
}
withName: 'GATK4_MARKDUPLICATES_SPARK' {
ext.args = '--remove-sequencing-duplicates false -VS LENIENT'
ext.prefix = { "${meta.id}.md.cram" }
publishDir = [
enabled: !params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
pattern: "*{cram,crai}"
]
}
withName: 'INDEX_MARKDUPLICATES' {
publishDir = [
enabled: !params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
pattern: "*{cram,crai}"
]
}
if (params.use_gatk_spark && params.use_gatk_spark.split(',').contains('markduplicates')) {
withName: 'NFCORE_SAREK:SAREK:MARKDUPLICATES_SPARK:SAMTOOLS_CRAMTOBAM'{
ext.prefix = { "${meta.id}.md" }
ext.when = { params.save_output_as_bam}
publishDir = [
enabled: params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
pattern: "*{md.bam,md.bam.bai}"
]
}
}
// PREPARE_RECALIBRATION
withName: 'BASERECALIBRATOR|BASERECALIBRATOR_SPARK' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/" },
pattern: "*table",
saveAs: { meta.num_intervals > 1 ? null : "recal_table/${meta.id}/${it}" }
]
}
withName: 'GATHERBQSRREPORTS' {
ext.prefix = {"${meta.id}.recal"}
ext.when = { meta.num_intervals > 1 }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/recal_table/${meta.id}/" },
pattern: "*table",
]
}
// RECALIBRATE
withName: 'APPLYBQSR|APPLYBQSR_SPARK' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }
publishDir = [
enabled: !params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/" },
pattern: "*cram",
saveAs: { meta.num_intervals > 1 ? null : "recalibrated/${meta.id}/${it}" }
]
}
if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) {
withName: 'NFCORE_SAREK:SAREK:(RECALIBRATE|RECALIBRATE_SPARK):MERGE_INDEX_CRAM:MERGE_CRAM' {
ext.prefix = { "${meta.id}.recal" }
ext.when = { meta.num_intervals > 1 }
publishDir = [
enabled: !params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" },
pattern: "*cram"
]
}
withName: 'NFCORE_SAREK:SAREK:(RECALIBRATE|RECALIBRATE_SPARK):MERGE_INDEX_CRAM:INDEX_CRAM' {
publishDir = [
enabled: !params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" },
pattern: "*{recal.cram,recal.cram.crai}"
]
}
}
withName: 'SAMTOOLS_CRAMTOBAM_RECAL'{
ext.prefix = { "${meta.id}.recal" }
ext.when = { params.save_output_as_bam}
publishDir = [
enabled: params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" },
pattern: "*{recal.bam,recal.bam.bai}"
]
}
withName: 'SAMTOOLS_BAMTOCRAM_VARIANTCALLING' {
ext.prefix = { "${meta.id}.recal" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" },
pattern: "*{cram,crai}"
]
}
// QC
withName: 'FASTQC' {
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
ext.args = '--quiet'
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('fastqc')) }
publishDir = [
[
path: { "${params.outdir}/reports/fastqc/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "*{html,zip}"
]
]
}
if (params.step == 'mapping' || params.step == 'markduplicates') {
withName: 'NFCORE_SAREK:SAREK:CRAM_QC:SAMTOOLS_STATS' {
ext.prefix = { "${meta.id}.cram" }
}
}
withName: 'SAMTOOLS_STATS' {
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/samtools/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'MOSDEPTH' {
ext.args = { !params.wes ? "-n --fast-mode --by 500" : ""}
ext.prefix = { params.skip_tools && params.skip_tools.split(',').contains('markduplicates') ? "${meta.id}.sorted" : "${meta.id}.md" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('mosdepth')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/mosdepth/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
}
if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) {
withName: 'NFCORE_SAREK:SAREK:CRAM_QC:MOSDEPTH' {
ext.prefix = { "${meta.id}.recal" }
}
withName: 'NFCORE_SAREK:SAREK:CRAM_QC:SAMTOOLS_STATS' {
ext.prefix = { "${meta.id}.recal.cram" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/samtools/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}
// VARIANT CALLING
process{
// CNVKIT
withName: 'CNVKIT_BATCH' {
ext.args = { params.wes ? "--method hybrid --diagram --scatter" : "--method wgs --diagram --scatter" }
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
pattern: "*{bed,cnn,cnr,cns,pdf,png}"
]
}
// DEEPVARIANT
withName: 'MERGE_DEEPVARIANT_.*' {
ext.prefix = {"${meta.id}.deepvariant"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/deepvariant/${meta.id}/" },
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'MERGE_DEEPVARIANT_GVCF' {
ext.prefix = {"${meta.id}.deepvariant.g"}
}
withName: 'DEEPVARIANT' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.simpleName}" }
ext.args = { params.wes ? "--model_type WES" : "--model_type WGS" }
ext.when = { params.tools && params.tools.split(',').contains('deepvariant') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
pattern: "*vcf.gz",
saveAs: { meta.num_intervals > 1 ? null : "deepvariant/${meta.id}/${it}" }
]
}
withName : 'TABIX_VC_DEEPVARIANT_.*' {
ext.prefix = {"${meta.id}.deepvariant"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/deepvariant/${meta.id}/" },
pattern: "*tbi"
]
}
// FREEBAYES
withName: 'MERGE_FREEBAYES' {
ext.prefix = { "${meta.id}.freebayes" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/freebayes/${meta.id}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'FREEBAYES' {
//To make sure no naming conflicts ensure with module BCFTOOLS_SORT & the naming being correct in the output folder
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" }
ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1'
ext.when = { params.tools && params.tools.split(',').contains('freebayes') }
}
withName: 'BCFTOOLS_SORT' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
pattern: "*vcf.gz",
saveAs: { meta.num_intervals > 1 ? null : "freebayes/${meta.id}/${it}" }
]
}
withName : 'TABIX_VC_FREEBAYES' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/freebayes/${meta.id}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
// HAPLOTYPECALLER
withName: 'MERGE_HAPLOTYPECALLER.*' {
ext.prefix = { params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'HAPLOTYPECALLER' {
ext.args = { params.joint_germline ? "-ERC GVCF" : "" }
ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) }
ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') }
publishDir = [
enabled: !params.joint_germline,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/"},
pattern: "*{vcf.gz,vcf.gz.tbi}",
saveAs: { meta.num_intervals > 1 ? null : "haplotypecaller/${meta.id}/${it}" }
]
}
withName: 'FILTERVARIANTTRANCHES' {
ext.prefix = {"${meta.id}.haplotypecaller"}
ext.args = { "--info-key CNN_1D" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/"},
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'GATK4_GENOMICSDBIMPORT' {
ext.prefix = { meta.num_intervals > 1 ? meta.intervals_name : "joint_interval" }
ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') && params.joint_germline && !params.no_intervals}
}
withName: 'GATK4_GENOTYPEGVCFS' {
ext.prefix = { meta.num_intervals > 1 ? meta.intervals_name : "joint_germline" }
}
withName: 'MERGE_GENOTYPEGVCFS' {
ext.prefix = "joint_germline"
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/haplotypecaller/joint_variant_calling/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'VARIANTRECALIBRATOR_INDEL' {
ext.prefix = { "${meta.id}_INDEL" }
ext.args = "-an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode INDEL"
publishDir = [
enabled: false
]
}
withName: 'VARIANTRECALIBRATOR_SNP' {
ext.prefix = { "${meta.id}_SNP" }
ext.args = "-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP"
publishDir = [
enabled: false
]
}
withName: 'GATK4_APPLYVQSR_SNP'{
ext.prefix = { "${meta.id}_SNP" }
ext.args = '--truth-sensitivity-filter-level 99.9 -mode SNP'
}
withName: 'GATK4_APPLYVQSR_INDEL'{
ext.prefix = { "${meta.id}_INDEL" }
ext.args = '--truth-sensitivity-filter-level 99.9 -mode INDEL'
}
withName: 'MERGE_VQSR' {
ext.prefix = "joint_germline_recalibrated"
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/haplotypecaller/joint_variant_calling/"},
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
}
// MANTA
withName: 'MERGE_MANTA.*' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/manta/${meta.id}/" },
pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'MERGE_MANTA_DIPLOID' {
ext.prefix = {"${meta.id}.manta.diploid_sv"}
}
withName: 'MERGE_MANTA_SMALL_INDELS' {
ext.prefix = {"${meta.id}.manta.candidate_small_indels"}
}
withName: 'MERGE_MANTA_SV' {
ext.prefix = {"${meta.id}.manta.candidate_sv"}
}
withName: 'MANTA.*' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.manta" : "${meta.id}.manta.${target_bed.simpleName}" }
ext.args = { params.wes ? "--exome" : "" }
ext.when = { params.tools && params.tools.split(',').contains('manta') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}",
saveAs: { meta.num_intervals > 1 ? null : "manta/${meta.id}/${it}" }
]
}
// STRELKA
withName: 'MERGE_STRELKA.*' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/strelka/${meta.id}/" },
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'MERGE_STRELKA' {
ext.prefix = {"${meta.id}.strelka.variants"}
}
withName: 'MERGE_STRELKA_GENOME' {
ext.prefix = {"${meta.id}.strelka.genome"}
}
withName: 'STRELKA_.*' {
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.simpleName}" }
ext.args = { params.wes ? "--exome" : "" }
ext.when = { params.tools && params.tools.split(',').contains('strelka') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
pattern: "*{vcf.gz,vcf.gz.tbi}",
saveAs: { meta.num_intervals > 1 ? null : "strelka/${meta.id}/${it}" }
]
}
//TIDDIT
withName: 'TIDDIT_SV' {
ext.when = { params.tools && params.tools.split(',').contains('tiddit') }
ext.args = { bwa_index ? "" : "--skip_assembly" }
ext.prefix = { "${meta.id}.tiddit" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },
pattern: "*tab",
]
}
withName : 'TABIX_BGZIP_TIDDIT_SV' {
ext.prefix = { "${meta.id}.tiddit" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
}
// TUMOR_VARIANT_CALLING
//CONTROLFREEC
withName: 'ASSESS_SIGNIFICANCE' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
pattern: "*{.p.value.txt}"
]
}
withName: 'CAT_MPILEUP' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/mpileup/${meta.id}/" },
pattern: "*{mpileup.gz}",
]
}
withName: 'FREEC_.*' {
ext.when = { params.tools && params.tools.split(',').contains('controlfreec') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
pattern: "*{BedGraph,cpn,txt,_CNVs}"
]
}
withName: 'FREEC_TUMORONLY'{
ext.args = {[
"sample":[
inputformat: 'pileup',
mateorientation: 'FR'
],
"general" :[
bedgraphoutput: "TRUE",
breakpointthreshold: params.wes ? "1.2" : "0.8", //Values taken from Freec example configs
breakpointtype: params.wes ? "4" : "2", // Values taken from Freec example configs
coefficientofvariation: params.cf_coeff,
contamination: params.cf_contamination ?: "",
contaminationadjustment: params.cf_contamination_adjustment ? "TRUE" : "",
forcegccontentnormalization: params.wes ? "1" : "0",
minimalsubclonepresence: params.wes ? "30" : "20",
noisydata: params.wes ? "TRUE" : "FALSE",
ploidy: params.cf_ploidy,
printNA: params.wes ? "FALSE" : "TRUE",
readcountthreshold: params.wes ? "50" : "10",
sex: meta.sex,
//uniquematch: not set
window: params.cf_window ?: ""
],
"BAF":[
minimalcoverageperposition: params.cf_mincov ?: "",
minimalqualityperposition: params.cf_minqual ?: "",
//"shiftinquality": (optional)not set
]
]
}
}
withName: 'FREEC2BED' {
ext.args = { "${params.cf_ploidy}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
pattern: "*bed"
]
}
withName: 'FREEC2CIRCOS' {
ext.args = { "${params.cf_ploidy}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
pattern: "*circos.txt"
]
}
withName: 'MAKEGRAPH' {
ext.args = { "${params.cf_ploidy}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
pattern: "*png"
]
}
withName: 'SAMTOOLS_MPILEUP' {
ext.when = { params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('mpileup')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/mpileup/${meta.id}/" },
pattern: "*mpileup.gz",
saveAs: { meta.num_intervals > 1 ? null : it }
]
}
//MANTA
withName: 'MERGE_MANTA_TUMOR' {
ext.prefix = {"${meta.id}.manta.tumor_sv"}
}
//MUTECT2
withName: 'CALCULATECONTAMINATION' {
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 : "mutect2/${meta.id}/${filename}" }
]
}
withName: 'MERGE_MUTECT2.*' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/mutect2/${meta.id}" },
pattern: "*{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'FILTERMUTECTCALLS.*'{
ext.prefix = {"${meta.id}.mutect2.filtered"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : "mutect2/${meta.id}/${filename}" }
]
}
withName: 'GATHERPILEUPSUMMARIES' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'GATHERPILEUPSUMMARIES_.*' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/mutect2/${meta.tumor_id}_vs_${meta.normal_id}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
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/" },
pattern: "*.table",
saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.id}/${it}" }
]
}
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/" },
pattern: "*.table",
saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.tumor_id}_vs_${meta.normal_id}/${it}" }
]
}
withName: 'LEARNREADORIENTATIONMODEL'{
ext.prefix = { "${meta.id}.mutect2.artifactprior" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'MERGEMUTECTSTATS' {
ext.prefix = { "${meta.id}.mutect2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'MUTECT2'{
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
ext.when = { params.tools && params.tools.split(',').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 ${task.ext.prefix}.f1r2.tar.gz" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
pattern: "*{vcf.gz,vcf.gz.tbi,stats}",
saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.id}/${it}" }
]
}
// PAIR_VARIANT_CALLING
//ASCAT
withName: 'ASCAT' {
ext.args = {[
"gender": meta.sex,
"genomeVersion": params.ascat_genome,
"purity": params.ascat_purity,