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exclude versions.yml from published results. remove enabled:true stat…
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…ements from publishDirs.
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TCLamnidis committed Nov 29, 2024
1 parent 038ab3d commit 9ae8415
Showing 1 changed file with 25 additions and 26 deletions.
51 changes: 25 additions & 26 deletions conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ process {
publishDir = [
path: { "${params.outdir}/preprocessing/fastqc_raw/" },
mode: params.publish_dir_mode,
pattern: '*[!versions.yml]',
]
}

Expand All @@ -57,6 +58,7 @@ process {
publishDir = [
path: { "${params.outdir}/preprocessing/fastqc_processed/" },
mode: params.publish_dir_mode,
pattern: '*[!versions.yml]',
]
}

Expand All @@ -76,6 +78,7 @@ process {
publishDir = [
path: { "${params.outdir}/preprocessing/falco_raw/" },
mode: params.publish_dir_mode,
pattern: '*[!versions.yml]',
]
}

Expand All @@ -86,6 +89,7 @@ process {
publishDir = [
path: { "${params.outdir}/preprocessing/falco_processed/" },
mode: params.publish_dir_mode,
pattern: '*[!versions.yml]',
]
}

Expand Down Expand Up @@ -704,7 +708,8 @@ process {
ext.prefix = { "${meta.sample_id}_${meta.library_id}_${meta.reference}" }
publishDir = [
path: { "${params.outdir}/mapstats/preseq" },
mode: params.publish_dir_mode
mode: params.publish_dir_mode,
pattern: '*[!versions.yml]',
]
}

Expand All @@ -722,7 +727,8 @@ process {
ext.prefix = { "${meta.sample_id}_${meta.library_id}_${meta.reference}" }
publishDir = [
path: { "${params.outdir}/mapstats/preseq" },
mode: params.publish_dir_mode
mode: params.publish_dir_mode,
pattern: '*[!versions.yml]',
]
}

Expand All @@ -742,7 +748,8 @@ process {
ext.prefix = { "${meta.sample_id}_${meta.reference}_depth" }
publishDir = [
path: { "${params.outdir}/mapstats/bedtools" },
mode: params.publish_dir_mode
mode: params.publish_dir_mode,
pattern: '*[!versions.yml]',
]
}

Expand All @@ -752,7 +759,8 @@ process {
ext.prefix = { "${meta.sample_id}_${meta.reference}_breadth" }
publishDir = [
path: { "${params.outdir}/mapstats/bedtools" },
mode: params.publish_dir_mode
mode: params.publish_dir_mode,
pattern: '*[!versions.yml]',
]
}

Expand Down Expand Up @@ -1066,9 +1074,9 @@ process {
withName: 'QUALIMAP_BAMQC_WITHBED|QUALIMAP_BAMQC_NOBED' {
tag = { "${meta.reference}|${meta.sample_id}" }
publishDir = [
path: { "${params.outdir}/mapstats/qualimap/${meta.reference}/${meta.sample_id}/}" },
path: { "${params.outdir}/mapstats/qualimap/${meta.reference}/" },
mode: params.publish_dir_mode,
enabled: true
pattern: '*[!versions.yml]',
]
}

Expand All @@ -1086,7 +1094,7 @@ process {
publishDir = [
path: { "${params.outdir}/damage_estimation/damageprofiler/" },
mode: params.publish_dir_mode,
enabled: true
pattern: '*[!versions.yml]'
]
}

Expand Down Expand Up @@ -1250,8 +1258,7 @@ process {
publishDir = [
path: { "${params.outdir}/genotyping/" },
mode: params.publish_dir_mode,
enabled: true,
pattern: '*.{geno,snp,ind}'
pattern: '*.{geno,snp,ind}',
]
}

Expand All @@ -1262,8 +1269,7 @@ process {
publishDir = [
path: { "${params.outdir}/genotyping/" },
mode: params.publish_dir_mode,
enabled: true,
pattern: '*.{tsv}'
pattern: '*.{tsv}',
]
}

Expand All @@ -1285,9 +1291,9 @@ process {
].join(' ').trim()
ext.prefix = { "${meta.sample_id}_${meta.reference}_realigned" }
publishDir = [
enabled: params.genotyping_gatk_ug_keeprealignbam,
path: { "${params.outdir}/genotyping/IndelRealigner" },
mode: params.publish_dir_mode,
enabled: params.genotyping_gatk_ug_keeprealignbam,
pattern: '*.{bam,bai}'
]
}
Expand All @@ -1306,8 +1312,7 @@ process {
publishDir = [
path: { "${params.outdir}/genotyping/" },
mode: params.publish_dir_mode,
enabled: true,
pattern: '*.vcf.gz'
pattern: '*.vcf.gz',
]
}

Expand All @@ -1318,8 +1323,7 @@ process {
publishDir = [
path: { "${params.outdir}/genotyping/" },
mode: params.publish_dir_mode,
enabled: true,
pattern: '*.vcf.gz.tbi'
pattern: '*.vcf.gz.tbi',
]
}

Expand All @@ -1336,8 +1340,7 @@ process {
publishDir = [
path: { "${params.outdir}/genotyping/" },
mode: params.publish_dir_mode,
enabled: true,
pattern: '*.{vcf.gz,vcf.gz.tbi}'
pattern: '*.{vcf.gz,vcf.gz.tbi}',
]
}

Expand All @@ -1352,8 +1355,7 @@ process {
publishDir = [
path: { "${params.outdir}/genotyping/" },
mode: params.publish_dir_mode,
enabled: true,
pattern: '*.vcf.gz'
pattern: '*.vcf.gz',
]
}

Expand All @@ -1364,8 +1366,7 @@ process {
publishDir = [
path: { "${params.outdir}/genotyping/" },
mode: params.publish_dir_mode,
enabled: true,
pattern: '*.vcf.gz.tbi'
pattern: '*.vcf.gz.tbi',
]
}

Expand All @@ -1375,8 +1376,7 @@ process {
publishDir = [
path: { "${params.outdir}/genotyping/" },
mode: params.publish_dir_mode,
enabled: true,
pattern: '*.txt'
pattern: '*.txt',
]
}

Expand All @@ -1395,8 +1395,7 @@ process {
publishDir = [
path: { "${params.outdir}/genotyping/" },
mode: params.publish_dir_mode,
enabled: true,
pattern: '*.{glf,beagle}.gz'
pattern: '*.{glf,beagle}.gz',
]
}
}

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