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Update modules.config #1099

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merged 4 commits into from
Nov 30, 2024
Merged

Update modules.config #1099

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53ef005
put fastp results in own directory
TCLamnidis Nov 29, 2024
d36dee2
Put adapter removal results in own directory
TCLamnidis Nov 29, 2024
038ab3d
fix bam_filtering result directory name. Minor formatting changes
TCLamnidis Nov 29, 2024
9ae8415
exclude versions.yml from published results. remove enabled:true stat…
TCLamnidis Nov 29, 2024
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75 changes: 37 additions & 38 deletions conf/modules.config
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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 All @@ -103,13 +107,13 @@ process {
ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
publishDir = [
[
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/preprocessing/fastp" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.preprocessing_savepreprocessedreads
],
[
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/preprocessing/fastp" },
mode: params.publish_dir_mode,
pattern: '*.{log,html,json}'
]
Expand All @@ -133,13 +137,13 @@ process {
ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
publishDir = [
[
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/preprocessing/fastp" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.preprocessing_savepreprocessedreads
],
[
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/preprocessing/fastp" },
mode: params.publish_dir_mode,
pattern: '*.{log,html,json}'
]
Expand All @@ -165,13 +169,13 @@ process {
ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
publishDir = [
[
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/preprocessing/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.preprocessing_savepreprocessedreads
],
[
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/preprocessing/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.settings'
]
Expand Down Expand Up @@ -199,13 +203,13 @@ process {
ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
publishDir = [
[
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/preprocessing/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.preprocessing_savepreprocessedreads
],
[
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/preprocessing/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.settings'
]
Expand All @@ -216,7 +220,7 @@ process {
tag = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }
ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }
publishDir = [
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/preprocessing/adapterremoval" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.preprocessing_savepreprocessedreads
Expand Down Expand Up @@ -335,7 +339,7 @@ process {
tag = { "${meta.sample_id}_${meta.library_id}_${meta.reference}" }
ext.prefix = { "${meta.sample_id}_${meta.library_id}_${meta.reference}" }
publishDir = [
path: { "${params.outdir}/preprocessing" },
path: { "${params.outdir}/bam_filtering/" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.preprocessing_savepreprocessedreads
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 @@ -862,7 +870,7 @@ process {
path: { "${params.outdir}/damage_manipulation/" },
mode: params.publish_dir_mode,
pattern: '*.{bai,csi}'
]
]
}

//
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 @@ -1115,7 +1123,7 @@ process {
ext.prefix = { "${meta2.id}_samtoolsdepth" }
ext.args = '-aa -q30 -Q30 -H'
publishDir = [
enabled: false
enabled: false
]
}

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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