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@maxulysse
maxulysse committed Mar 4, 2025
1 parent 346a6a7 commit d48306b
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Showing 3 changed files with 38 additions and 38 deletions.
66 changes: 33 additions & 33 deletions conf/modules.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ process {

process {

withName: 'NFCORE_RNAVAR:.*:CAT_FASTQ' {
withName: 'NFCORE_RNAVAR.*CAT_FASTQ' {
publishDir = [
path: { "${params.outdir}/fastq" },
mode: params.publish_dir_mode,
Expand All @@ -33,23 +33,23 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:STAR_GENOMEGENERATE' {
withName: 'NFCORE_RNAVAR.*STAR_GENOMEGENERATE' {
ext.args = params.read_length ? "--sjdbOverhang ${params.read_length - 1}" : ''
}

withName: 'NFCORE_RNAVAR:.*:STAR_INDEXVERSION' {
withName: 'NFCORE_RNAVAR.*STAR_INDEXVERSION' {
publishDir = [
enabled: false
]
}

withName: 'NFCORE_RNAVAR:.*:PREPARE_GENOME:UNTAR' {
withName: 'NFCORE_RNAVAR.*PREPARE_GENOME:UNTAR' {
publishDir = [
enabled: false
]
}

withName: 'NFCORE_RNAVAR:.*:REMOVE_UNKNOWN_REGIONS' {
withName: 'NFCORE_RNAVAR.*REMOVE_UNKNOWN_REGIONS' {
ext.prefix = { "${meta.id}.exon" }
publishDir = [
path: { "${params.outdir}/genome" },
Expand All @@ -59,7 +59,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:STAR_GENOMEGENERATE' {
withName: 'NFCORE_RNAVAR.*STAR_GENOMEGENERATE' {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
Expand All @@ -68,7 +68,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:GFFREAD' {
withName: 'NFCORE_RNAVAR.*GFFREAD' {
ext.args = '--keep-exon-attrs -F -T'
publishDir = [
path: { "${params.outdir}/genome" },
Expand All @@ -78,7 +78,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:GTF2BED' {
withName: 'NFCORE_RNAVAR.*GTF2BED' {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
Expand All @@ -87,7 +87,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:SAMTOOLS_FAIDX' {
withName: 'NFCORE_RNAVAR.*SAMTOOLS_FAIDX' {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
Expand All @@ -96,7 +96,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:GATK4_CREATESEQUENCEDICTIONARY' {
withName: 'NFCORE_RNAVAR.*GATK4_CREATESEQUENCEDICTIONARY' {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
Expand All @@ -110,7 +110,7 @@ process {

process {

withName: 'NFCORE_RNAVAR:.*:MULTIQC' {
withName: 'NFCORE_RNAVAR.*MULTIQC' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
path: { "${params.outdir}/reports"},
Expand All @@ -120,7 +120,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:FASTQC' {
withName: 'NFCORE_RNAVAR.*FASTQC' {
ext.args = '--quiet'
publishDir = [
enabled: false
Expand All @@ -132,7 +132,7 @@ process {
process {

// UMITOOLS_EXTRACT
withName: 'NFCORE_RNAVAR:.*:UMITOOLS_EXTRACT' {
withName: 'NFCORE_RNAVAR.*UMITOOLS_EXTRACT' {
ext.args = { [
params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
params.umitools_bc_pattern ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
Expand All @@ -143,7 +143,7 @@ process {

// ALIGN_STAR

withName: 'NFCORE_RNAVAR:.*:STAR_ALIGN' {
withName: 'NFCORE_RNAVAR.*STAR_ALIGN' {
ext.args = { [
'--outSAMtype BAM SortedByCoordinate',
'--readFilesCommand zcat',
Expand Down Expand Up @@ -181,7 +181,7 @@ process {

process {

withName: 'NFCORE_RNAVAR:.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
withName: 'NFCORE_RNAVAR.*ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
ext.prefix = {"${meta.id}.aligned"}
publishDir = [
path: { "${params.outdir}/preprocessing/${meta.id}" },
Expand All @@ -191,7 +191,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
withName: 'NFCORE_RNAVAR.*ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
ext.args = params.bam_csi_index ? '-c' : ''
ext.prefix = {"${meta.id}.aligned"}
publishDir = [
Expand All @@ -202,11 +202,11 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:GATK4_BEDTOINTERVALLIST' {
withName: 'NFCORE_RNAVAR.*GATK4_BEDTOINTERVALLIST' {
publishDir = [ enabled: false ]
}

withName: 'NFCORE_RNAVAR:.*:GATK4_INTERVALLISTTOOLS' {
withName: 'NFCORE_RNAVAR.*GATK4_INTERVALLISTTOOLS' {
ext.args = [
'--SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW',
'--UNIQUE true',
Expand All @@ -216,7 +216,7 @@ process {
publishDir = [ enabled: false ]
}

withName: 'NFCORE_RNAVAR:.*:PICARD_MARKDUPLICATES' {
withName: 'NFCORE_RNAVAR.*PICARD_MARKDUPLICATES' {
ext.args = [
'--ASSUME_SORTED true',
'--VALIDATION_STRINGENCY LENIENT',
Expand All @@ -239,7 +239,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
withName: 'NFCORE_RNAVAR.*BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
ext.args = params.bam_csi_index ? '-c' : ''
ext.prefix = {"${meta.id}.md"}
publishDir = [
Expand All @@ -250,20 +250,20 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:SPLITNCIGAR:GATK4_SPLITNCIGARREADS' {
withName: 'NFCORE_RNAVAR.*SPLITNCIGAR:GATK4_SPLITNCIGARREADS' {
ext.args = '--create-output-bam-index false'
ext.prefix = { "${meta.id}.splitncigarreads" }
}

withName: 'NFCORE_RNAVAR:.*:SPLITNCIGAR:SAMTOOLS_INDEX' {
withName: 'NFCORE_RNAVAR.*SPLITNCIGAR:SAMTOOLS_INDEX' {
ext.args = params.bam_csi_index ? '-c' : ''
}

withName: 'NFCORE_RNAVAR:.*:SPLITNCIGAR:.*' {
withName: 'NFCORE_RNAVAR.*SPLITNCIGAR:*' {
publishDir = [ enabled: false ]
}

withName: 'NFCORE_RNAVAR:.*:SAMTOOLS_STATS|SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS' {
withName: 'NFCORE_RNAVAR.*SAMTOOLS_STATS|SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS' {
publishDir = [
path: { "${params.outdir}/reports/stats/${meta.id}" },
mode: params.publish_dir_mode,
Expand All @@ -277,12 +277,12 @@ process {
// BASE RECALIBRATION PROCESS
process {

withName: 'NFCORE_RNAVAR:.*:GATK4_BASERECALIBRATOR' {
withName: 'NFCORE_RNAVAR.*GATK4_BASERECALIBRATOR' {
ext.args = '--use-original-qualities'
publishDir = [ enabled: false ]
}

withName: 'NFCORE_RNAVAR:.*:RECALIBRATE:APPLYBQSR' {
withName: 'NFCORE_RNAVAR.*RECALIBRATE:APPLYBQSR' {
ext.args = [
'--use-original-qualities',
'--add-output-sam-program-record'
Expand All @@ -296,7 +296,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:RECALIBRATE:SAMTOOLS_INDEX' {
withName: 'NFCORE_RNAVAR.*RECALIBRATE:SAMTOOLS_INDEX' {
ext.args = params.bam_csi_index ? '-c' : ''
ext.prefix = {"${meta.id}.recal"}
publishDir = [
Expand All @@ -313,7 +313,7 @@ process {

process {

withName: 'NFCORE_RNAVAR:.*:GATK4_HAPLOTYPECALLER' {
withName: 'NFCORE_RNAVAR.*GATK4_HAPLOTYPECALLER' {
ext.args = [
'--dont-use-soft-clipped-bases',
'--create-output-variant-index true',
Expand All @@ -323,15 +323,15 @@ process {
publishDir = [ enabled: false ]
}

withName: 'NFCORE_RNAVAR:.*:GATK4_MERGEVCFS' {
withName: 'NFCORE_RNAVAR.*GATK4_MERGEVCFS' {
ext.prefix = {"${meta.id}.haplotypecaller"}
publishDir = [
path: { "${params.outdir}/variant_calling/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "*.{vcf.gz}"
]
}
withName: 'NFCORE_RNAVAR:.*:GATK4_COMBINEGVCFS' {
withName: 'NFCORE_RNAVAR.*GATK4_COMBINEGVCFS' {
ext.prefix = {"${meta.id}.haplotypecaller"}
publishDir = [
path: { "${params.outdir}/variant_calling/${meta.id}" },
Expand All @@ -340,7 +340,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:TABIX_TABIX' {
withName: 'NFCORE_RNAVAR.*TABIX_TABIX' {
ext.args = params.bam_csi_index ? '--csi' : ''
ext.prefix = {"${meta.id}.haplotypecaller"}
publishDir = [
Expand All @@ -350,7 +350,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:GATK4_VARIANTFILTRATION' {
withName: 'NFCORE_RNAVAR.*GATK4_VARIANTFILTRATION' {
ext.prefix = {"${meta.id}.haplotypecaller.filtered"}
ext.args = [
params.gatk_vf_window_size ? "--cluster-window-size $params.gatk_vf_window_size" : '',
Expand All @@ -365,7 +365,7 @@ process {
]
}

withName: 'NFCORE_RNAVAR:.*:GATK4_BEDTOINTERVALLIST' {
withName: 'NFCORE_RNAVAR.*GATK4_BEDTOINTERVALLIST' {
ext.args = '--DROP_MISSING_CONTIGS TRUE'
}
}
6 changes: 3 additions & 3 deletions conf/modules/annotate.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
process {

// SNPEFF
withName: 'NFCORE_RNAVAR:.*:SNPEFF_SNPEFF' {
withName: 'NFCORE_RNAVAR.*SNPEFF_SNPEFF' {
ext.args = { '-nodownload -canon -v' }
ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' }
publishDir = [
Expand All @@ -30,7 +30,7 @@ process {
}

// VEP
withName: 'NFCORE_RNAVAR:.*:ENSEMBLVEP_VEP' {
withName: 'NFCORE_RNAVAR.*ENSEMBLVEP_VEP' {
ext.args = { [
"--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html",
(params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
Expand Down Expand Up @@ -85,7 +85,7 @@ process {
}

// ALL ANNOTATION TOOLS
withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' {
withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL.*(TABIX_BGZIPTABIX|TABIX_TABIX)' {
ext.prefix = { input.name - '.vcf' }
publishDir = [
mode: params.publish_dir_mode,
Expand Down
4 changes: 2 additions & 2 deletions conf/modules/prepare_cache.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
process {

// SNPEFF
withName: 'NFCORE_RNAVAR:.*:SNPEFF_DOWNLOAD' {
withName: 'NFCORE_RNAVAR.*SNPEFF_DOWNLOAD' {
ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge')) }
publishDir = [
mode: params.publish_dir_mode,
Expand All @@ -25,7 +25,7 @@ process {
}

// VEP
withName: 'NFCORE_RNAVAR:.*:ENSEMBLVEP_DOWNLOAD' {
withName: 'NFCORE_RNAVAR.*ENSEMBLVEP_DOWNLOAD' {
ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge')) }
ext.args = { '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' }
publishDir = [
Expand Down

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