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cannot exclude with glob patterns
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@maxulysse
maxulysse committed Nov 9, 2023
1 parent 47e219a commit 7c8b399
Showing 1 changed file with 34 additions and 46 deletions.
80 changes: 34 additions & 46 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,7 @@ process {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

Expand All @@ -54,8 +53,7 @@ process {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

Expand All @@ -64,17 +62,15 @@ process {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

withName: 'HISAT2_EXTRACTSPLICESITES' {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

Expand All @@ -83,8 +79,7 @@ process {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

Expand All @@ -93,53 +88,47 @@ process {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

withName: 'GTF2BED' {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

withName: 'GTF_GENE_FILTER' {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

withName: 'CUSTOM_GETCHROMSIZES' {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}

withName: 'CAT_FASTQ' {
publishDir = [
path: { "${params.outdir}/fastq" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_merged_fastq ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_merged_fastq ? filename : null }
]
}
}
Expand All @@ -151,8 +140,7 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}",
saveAs: { params.save_reference ? it : null }
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
]
}
}
Expand Down Expand Up @@ -203,7 +191,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
publishDir = [
path: { "${params.outdir}/${params.trimmer}/fastqc" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand Down Expand Up @@ -488,7 +476,7 @@ if (!params.skip_alignment) {
publishDir = [
path: { "${params.outdir}/${params.aligner}/bigwig" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand All @@ -504,7 +492,7 @@ if (!params.skip_alignment) {
publishDir = [
path: { "${params.outdir}/${params.aligner}/bigwig" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand All @@ -520,7 +508,7 @@ if (!params.skip_alignment) {
publishDir = [
path: { "${params.outdir}/${params.aligner}/stringtie" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand Down Expand Up @@ -574,31 +562,31 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml,!*_meta_info.json}"
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
]
}

withName: '.*:QUANTIFY_STAR_SALMON:SALMON_TX2GENE' {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT' {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*' {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand Down Expand Up @@ -763,7 +751,7 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand Down Expand Up @@ -851,7 +839,7 @@ if (!params.skip_alignment && !params.skip_qc) {
publishDir = [
path: { "${params.outdir}/${params.aligner}/qualimap" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand Down Expand Up @@ -902,15 +890,15 @@ if (!params.skip_alignment && !params.skip_qc) {
publishDir = [
path: { "${params.outdir}/${params.aligner}/featurecounts" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'MULTIQC_CUSTOM_BIOTYPE' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/featurecounts" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand All @@ -922,7 +910,7 @@ if (!params.skip_alignment && !params.skip_qc) {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand All @@ -934,7 +922,7 @@ if (!params.skip_alignment && !params.skip_qc) {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand Down Expand Up @@ -1023,7 +1011,7 @@ if (!params.skip_alignment && !params.skip_qc) {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand All @@ -1037,7 +1025,7 @@ if (!params.skip_alignment && !params.skip_qc) {
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
mode: params.publish_dir_mode,
pattern: '*.txt',
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
],
[
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/pdf" },
Expand All @@ -1060,7 +1048,7 @@ if (!params.skip_alignment && !params.skip_qc) {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand All @@ -1077,7 +1065,7 @@ if (!params.skip_multiqc) {
params.skip_alignment? '' : "/${params.aligner}"
].join('') },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand All @@ -1094,31 +1082,31 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
publishDir = [
path: { "${params.outdir}/${params.pseudo_aligner}" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml,!*_meta_info.json}"
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
]
}

withName: '.*:QUANTIFY_SALMON:SALMON_TX2GENE' {
publishDir = [
path: { "${params.outdir}/${params.pseudo_aligner}" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:QUANTIFY_SALMON:SALMON_TXIMPORT' {
publishDir = [
path: { "${params.outdir}/${params.pseudo_aligner}" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:QUANTIFY_SALMON:SALMON_SE_.*' {
publishDir = [
path: { "${params.outdir}/${params.pseudo_aligner}" },
mode: params.publish_dir_mode,
pattern: "{!versions.yml}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
Expand Down

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