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Remove empty outdirs #1612

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merged 3 commits into from
Aug 5, 2024
Merged

Remove empty outdirs #1612

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56828b9
remove empty output directories
FriederikeHanssen Aug 5, 2024
96b4a87
Update CHANGELOG.md
FriederikeHanssen Aug 5, 2024
e48d9bd
fix linting
FriederikeHanssen Aug 5, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -40,6 +40,7 @@ Loametjåhkkå is another one of the main peaks of the Pårte massif.
- [#1570](https://github.com/nf-core/sarek/pull/1570) - Remove duplicated notes in FASTQC output docs
- [#1596](https://github.com/nf-core/sarek/pull/1596) - Fix haplotypecaller tests
- [#1597](https://github.com/nf-core/sarek/pull/1597) - Fix deepvariant tests
- [#1612](https://github.com/nf-core/sarek/pull/1612) - Remove empty output directories

### Removed

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8 changes: 4 additions & 4 deletions conf/modules/prepare_genome.config
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Expand Up @@ -39,9 +39,9 @@ process {
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/cnvkit" },
path: { "${params.outdir}/reference" },
pattern: "*{bed}",
saveAs: { params.save_reference || params.build_only_index ? it : null }
saveAs: { params.save_reference || params.build_only_index ? "cnvkit/${it}" : null }
]
}

Expand All @@ -50,9 +50,9 @@ process {
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/cnvkit" },
path: { "${params.outdir}/reference" },
pattern: "*{cnn}",
saveAs: { params.save_reference || params.build_only_index ? it : null }
saveAs: { params.save_reference || params.build_only_index ? "cnvkit/${it}" : null }
]
}

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12 changes: 6 additions & 6 deletions conf/modules/prepare_intervals.config
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Expand Up @@ -23,28 +23,28 @@ process {
withName: 'CREATE_INTERVALS_BED' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/intervals" },
path: { "${params.outdir}/reference" },
pattern: "*bed",
saveAs: { params.save_reference || params.build_only_index ? it : null }
saveAs: { params.save_reference || params.build_only_index ? "intervals/${it}" : null }
]
}

withName: 'GATK4_INTERVALLISTTOBED' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/intervals" },
path: { "${params.outdir}/reference" },
pattern: "*bed",
saveAs: { params.save_reference || params.build_only_index ? it : null }
saveAs: { params.save_reference || params.build_only_index ? "intervals/${it}" : null }
]
}

withName: 'TABIX_BGZIPTABIX_INTERVAL_SPLIT|TABIX_BGZIPTABIX_INTERVAL_COMBINED' {
ext.prefix = {"${meta.id}"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/intervals" },
path: { "${params.outdir}/reference" },
pattern: "*bed.gz",
saveAs: { params.save_reference || params.build_only_index ? it : null }
saveAs: { params.save_reference || params.build_only_index ? "intervals/${it}" : null }
]
}
}
4 changes: 2 additions & 2 deletions conf/modules/trimming.config
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Expand Up @@ -32,10 +32,10 @@ process {
pattern: "*.{html,json,log}"
],
[
path: { "${params.outdir}/preprocessing/fastp/${meta.sample}/" },
path: { "${params.outdir}/preprocessing/" },
mode: params.publish_dir_mode,
pattern: "*.fastp.fastq.gz",
saveAs: { params.save_trimmed || params.save_split_fastqs ? it : null }
saveAs: { params.save_trimmed || params.save_split_fastqs ? "fastp/${meta.sample}/${it}" : null }
]
]
}
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4 changes: 2 additions & 2 deletions subworkflows/local/bam_variant_calling_cnvkit/main.nf
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Expand Up @@ -37,8 +37,8 @@ workflow BAM_VARIANT_CALLING_CNVKIT {

versions = versions.mix(CNVKIT_BATCH.out.versions)
versions = versions.mix(CNVKIT_GENEMETRICS.out.versions)
versions = versions.mix( CNVKIT_CALL.out.versions)
versions = versions.mix( CNVKIT_EXPORT.out.versions)
versions = versions.mix(CNVKIT_CALL.out.versions)
versions = versions.mix(CNVKIT_EXPORT.out.versions)
emit:
cnv_calls_raw = CNVKIT_CALL.out.cns // channel: [ meta, cns ]
cnv_calls_export = CNVKIT_EXPORT.out.output // channel: [ meta, export_format ]
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