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Use eval output for tool versions #1115

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Use eval output for tool versions #1115

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4e84d37
Use cmd output for tool versions
bentsherman Nov 15, 2023
8734ccb
Merge branch 'dev' into cmd-output
bentsherman Nov 15, 2023
e68f451
Fix failing process
bentsherman Nov 15, 2023
f79e09d
Remove references to versions.yml in config
bentsherman Dec 12, 2023
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95 changes: 37 additions & 58 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,7 @@ def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').colle
process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]

withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
Expand All @@ -41,7 +40,7 @@ process {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
saveAs: { filename -> params.save_reference ? filename : null }
]
}

Expand All @@ -53,7 +52,7 @@ process {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
saveAs: { filename -> params.save_reference ? filename : null }
]
}

Expand All @@ -62,15 +61,15 @@ process {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
saveAs: { filename -> params.save_reference ? filename : null }
]
}

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

Expand All @@ -79,7 +78,7 @@ process {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
saveAs: { filename -> params.save_reference ? filename : null }
]
}

Expand All @@ -88,7 +87,7 @@ process {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
saveAs: { filename -> params.save_reference ? filename : null }
]
}

Expand All @@ -97,23 +96,23 @@ process {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
saveAs: { filename -> params.save_reference ? filename : null }
]
}

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

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

Expand All @@ -122,23 +121,23 @@ process {
publishDir = [
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
saveAs: { filename -> params.save_reference ? filename : null }
]
}

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

withName: 'CAT_FASTQ' {
publishDir = [
path: { "${params.outdir}/fastq" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_merged_fastq ? filename : null }
saveAs: { params.save_merged_fastq ? filename : null }
]
}
}
Expand All @@ -150,7 +149,7 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
publishDir = [
path: { "${params.outdir}/genome/index" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
saveAs: { filename -> params.save_reference ? filename : null }
]
}
}
Expand Down Expand Up @@ -200,8 +199,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
ext.args = '--quiet'
publishDir = [
path: { "${params.outdir}/${params.trimmer}/fastqc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand Down Expand Up @@ -485,8 +483,7 @@ if (!params.skip_alignment) {
ext.prefix = { "${meta.id}.forward" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/bigwig" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

Expand All @@ -501,8 +498,7 @@ if (!params.skip_alignment) {
ext.prefix = { "${meta.id}.reverse" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/bigwig" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand All @@ -517,8 +513,7 @@ if (!params.skip_alignment) {
].join(' ').trim() }
publishDir = [
path: { "${params.outdir}/${params.aligner}/stringtie" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand Down Expand Up @@ -572,32 +567,29 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
saveAs: { filename -> filename.endsWith('_meta_info.json') ? null : filename }
]
}

withName: '.*:QUANTIFY_STAR_SALMON:TX2GENE' {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

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

withName: '.*:QUANTIFY_STAR_SALMON:SE_.*' {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand Down Expand Up @@ -760,8 +752,7 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
withName: '.*:QUANTIFY_RSEM:RSEM_MERGE_COUNTS' {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand Down Expand Up @@ -847,8 +838,7 @@ if (!params.skip_alignment && !params.skip_qc) {
withName: 'QUALIMAP_RNASEQ' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/qualimap" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand Down Expand Up @@ -898,16 +888,14 @@ if (!params.skip_alignment && !params.skip_qc) {
].join(' ').trim() }
publishDir = [
path: { "${params.outdir}/${params.aligner}/featurecounts" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

withName: 'MULTIQC_CUSTOM_BIOTYPE' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/featurecounts" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand All @@ -918,8 +906,7 @@ if (!params.skip_alignment && !params.skip_qc) {
withName: '.*:BAM_RSEQC:RSEQC_BAMSTAT' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand All @@ -930,8 +917,7 @@ if (!params.skip_alignment && !params.skip_qc) {
withName: '.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand Down Expand Up @@ -1019,8 +1005,7 @@ if (!params.skip_alignment && !params.skip_qc) {
withName: '.*:BAM_RSEQC:RSEQC_READDISTRIBUTION' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand All @@ -1033,8 +1018,7 @@ if (!params.skip_alignment && !params.skip_qc) {
[
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
mode: params.publish_dir_mode,
pattern: '*.txt',
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
pattern: '*.txt'
],
[
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/pdf" },
Expand All @@ -1056,8 +1040,7 @@ if (!params.skip_alignment && !params.skip_qc) {
withName: '.*:BAM_RSEQC:RSEQC_TIN' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand All @@ -1074,8 +1057,7 @@ if (!params.skip_multiqc) {
"${params.outdir}/multiqc",
params.skip_alignment? '' : "/${params.aligner}"
].join('') },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand All @@ -1093,7 +1075,7 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
publishDir = [
path: { "${params.outdir}/${params.pseudo_aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
saveAs: { filename -> filename.endsWith('_meta_info.json') ? null : filename }
]
}
}
Expand All @@ -1106,7 +1088,7 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') {
publishDir = [
path: { "${params.outdir}/${params.pseudo_aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.run_info.json') || filename.endsWith('.log') ? null : filename }
saveAs: { filename -> filename.endsWith('.run_info.json') || filename.endsWith('.log') ? null : filename }
]
}
}
Expand All @@ -1117,25 +1099,22 @@ if (!params.skip_pseudo_alignment) {
withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE' {
publishDir = [
path: { "${params.outdir}/${params.pseudo_aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMPORT' {
ext.prefix = { "${quant_type}.merged" }
publishDir = [
path: { "${params.outdir}/${params.pseudo_aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*' {
publishDir = [
path: { "${params.outdir}/${params.pseudo_aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}
}
Expand Down
7 changes: 1 addition & 6 deletions modules/local/bedtools_genomecov/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ process BEDTOOLS_GENOMECOV {
output:
tuple val(meta), path("*.forward.bedGraph"), emit: bedgraph_forward
tuple val(meta), path("*.reverse.bedGraph"), emit: bedgraph_reverse
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('bedtools'), cmd("bedtools --version | sed -e 's/bedtools v//g'"), emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -44,10 +44,5 @@ process BEDTOOLS_GENOMECOV {
-strand - \\
$args \\
| bedtools sort > ${prefix_reverse}.bedGraph

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
}
7 changes: 1 addition & 6 deletions modules/local/cat_additional_fasta/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ process CAT_ADDITIONAL_FASTA {
output:
path "${name}.fasta", emit: fasta
path "${name}.gtf" , emit: gtf
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('python'), cmd("python --version | sed 's/Python //g'"), emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -33,10 +33,5 @@ process CAT_ADDITIONAL_FASTA {

cat $fasta $add_fasta > ${name}.fasta
cat $gtf ${add_fasta.baseName}.gtf > ${name}.gtf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
}
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