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Added normalise workflow, some final fixes in variant calling subwork…
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…flows.
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@RaqManzano
RaqManzano committed Aug 30, 2023
1 parent c1bdc0a commit 375cb4e
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Showing 24 changed files with 476 additions and 689 deletions.
6 changes: 3 additions & 3 deletions conf/modules/annotate/annotate.config
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Expand Up @@ -15,17 +15,17 @@

process { // annotate

// VEP TODO: is vep_custom_args working??
// VEP
if (params.tools && params.tools.split(',').contains('vep')) {
withName: 'ENSEMBLVEP_VEP' {
ext.args = { [
(params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_loftee) ? "--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-${params.vep_version}/share/ensembl-vep-${params.vep_version}-0" : '',
(params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '',
(params.vep_spliceregion) ? '--plugin SpliceRegion' : '',
(params.vep_spliceregion) ? "--plugin SpliceRegion" : '',
(params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf',
(params.vep_custom_args) ?: ''
(params.vep_custom_args) ?: ""
].join(' ').trim() }
// If just VEP: <vcf prefix>_VEP.ann.vcf
ext.prefix = { vcf.baseName - ".vcf" + "_VEP.ann" }
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58 changes: 0 additions & 58 deletions conf/modules/consensus/normalise.config
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This file was deleted.

2 changes: 1 addition & 1 deletion conf/modules/gatk4_preprocessing/recalibrate.config
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Expand Up @@ -38,7 +38,7 @@ process { // recalibrate
]
}

withName: '.*:BAM_APPLYBQSR::CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM' {
withName: '.*:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM' {
publishDir = [
enabled: !params.save_output_as_bam,
mode: params.publish_dir_mode,
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69 changes: 39 additions & 30 deletions conf/modules/gatk4_preprocessing/splitncigarreads.config
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Expand Up @@ -15,54 +15,63 @@

process { //splitncigar
// TODO: check SECOND_RUN and suffixes
withName: '.*:SPLITNCIGAR:GATK4_SPLITNCIGARREADS' {
ext.args = ['-rf ReassignOneMappingQuality',
'-RMQF 255 ',
'-RMQT 60',
'-U ALLOW_N_CIGAR_READS'].join(' ').trim()
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/splitncigar/${meta.patient}/${meta.id}/" },
pattern: "*{bam,bai}",
enabled: params.save_align_intermeds // will be saved as CRAM
]
withName: 'GATK4_SPLITNCIGARREADS' {
ext.args = '--create-output-bam-index false'
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.sncr.cram" : "${meta.id}_${intervals.simpleName}.sncr.cram" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('splitncigar')) }
publishDir = [
enabled: !params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/splitncigarreads/${meta.id}/" },
pattern: "*{cram,crai}"
]
}

withName: '.*:SECOND_RUN:GATK_PREPROCESSING:SPLITNCIGAR:GATK4_SPLITNCIGARREADS' {
ext.prefix = {"${meta.id}.sncr"}
ext.args = ['-rf ReassignOneMappingQuality',
'-RMQF 255 ',
'-RMQT 60',
'-U ALLOW_N_CIGAR_READS'].join(' ').trim()
ext.args = '--create-output-bam-index false'
ext.prefix = { "${meta.id}.sncr.cram" }
ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('splitncigar')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/splitncigar/${meta.patient}/${meta.id}/" },
path: { "${params.outdir}/preprocessing/splitncigarreads/${meta.id}/" },
pattern: "*{bam,bai}",
enabled: params.save_align_intermeds // will be saved as CRAM
]
}

withName: ".*:PREPARE_SECOND_RUN:MERGE_ALIGN:INDEX_MERGE_BAM" {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/" },
pattern: "*.{bai,csi}",
saveAs: { params.save_bam_mapped ? "second_run/${meta.patient}/${meta.id}/${it}" : null },
enabled: params.save_align_intermeds
]
withName: ".*:PREPARE_SECOND_RUN:MERGE_ALIGN:INDEX_MERGE_BAM" {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/" },
pattern: "*.{bai,csi}",
saveAs: { params.save_bam_mapped ? "second_run/${meta.patient}/${meta.id}/${it}" : null },
enabled: params.save_align_intermeds
]

}
}

withName: '.*:SPLITNCIGAR:SAMTOOLS_INDEX' {
withName: '.*:BAM_SPLITNCIGARREADS:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM' {
ext.args = params.bam_csi_index ? '-c' : ''
publishDir = [
path: { "${params.outdir}/preprocessing/splitncigar/${meta.patient}/${meta.id}/" },
path: { "${params.outdir}/preprocessing/splitncigarreads/${meta.id}/" },
mode: params.publish_dir_mode,
pattern: "*.{bai,csi}",
enabled: params.save_align_intermeds
pattern: "*{recal.cram,recal.cram.crai}",
enabled: !params.save_output_as_bam,
]
}

withName: '.*:BAM_SPLITNCIGARREADS:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM' {
ext.prefix = { "${meta.id}.sncr" }
ext.when = { meta.num_intervals > 1 }
publishDir = [
enabled: !params.save_output_as_bam,
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/splitncigarreads/${meta.id}/" },
pattern: "*cram"
]
}




}
54 changes: 54 additions & 0 deletions conf/modules/normalise/vt.config
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@@ -0,0 +1,54 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.
----------------------------------------------------------------------------------------
*/

// VT

process { // vt

withName: 'VT_DECOMPOSE'{
ext.args = ""
ext.prefix = { vcf.baseName - ".vcf.gz" + ".dec" }
publishDir = [
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/vt/${meta.id}" },
pattern: "*.dec.stats"
],
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.variantcaller}/${meta.id}" },
pattern: {"*{vcf.gz,vcf.gz.tbi}"}
enabled: false
]
]
}

withName: 'VT_NORMALISE'{
ext.args = {"-n"}
ext.prefix = { vcf.baseName - ".vcf.gz" + ".norm" }
publishDir = [
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.variantcaller}/${meta.id}" },
pattern: "*{vcf.gz,vcf.gz.tbi}",
],
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/vt/${meta.id}" },
pattern: {"*.stats"},
enabled: true
]
]
}

}
21 changes: 10 additions & 11 deletions conf/modules/variant_calling/manta.config
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Expand Up @@ -14,15 +14,14 @@
// MANTA

process { // manta
if (params.tools && params.tools.split(',').contains('manta')) {
withName: 'MANTA_SOMATIC' {
ext.args = {params.wes || meta.status >= 2 ? "--exome" : "" }
ext.prefix = { "${meta.id}.manta" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/manta/${meta.id}" },
pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'MANTA_SOMATIC' {
ext.args = {params.wes || meta.status >= 2 ? "--exome" : "" }
ext.prefix = { "${meta.id}.manta" }
ext.when = { params.tools && params.tools.split(',').contains('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}"
]
}
}
}
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