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Tidy up umitools/ umicollapse config
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‎workflows/rnaseq/nextflow.config‎

Lines changed: 58 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -134,14 +134,49 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
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]
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}
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// Use the same umi_dedup prefix for umitools and umicollapse
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withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMI(COLLAPSE|TOOLS)_TRANSCRIPTOME:UMI(COLLAPSE|TOOLS_DEDUP)' {
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ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
141+
}
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// Publishing logic for umitools:
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withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
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publishDir = [
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[
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path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
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mode: params.publish_dir_mode,
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pattern: '*.bam',
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saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
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],
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[
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path: { "${params.outdir}/${params.aligner}/umitools/transcriptomic_dedup_log" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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],
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[
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path: { "${params.outdir}/${params.aligner}/umitools" },
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mode: params.publish_dir_mode,
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pattern: '*.tsv'
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]
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]
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}
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166+
// Publishing logic for umicollapse
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168+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_TRANSCRIPTOME:UMICOLLAPSE' {
169+
publishDir = [
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[
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path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
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mode: params.publish_dir_mode,
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pattern: '*.bam',
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saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
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],
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[
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path: { "${params.outdir}/${params.aligner}/umicollapse/transcriptomic_dedup_log" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
@@ -231,64 +266,49 @@ if (!params.skip_alignment) {
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].join(' ').trim()}
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}
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269+
// Use the same umi_dedup prefix for umitools and umicollapse
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withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMI(COLLAPSE|TOOLS)_GENOME:UMI(COLLAPSE|TOOLS_DEDUP)' {
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ext.prefix = { "${meta.id}.umi_dedup.sorted" }
236-
publishDir = [
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[
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path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
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mode: params.publish_dir_mode,
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pattern: '*.bam',
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saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
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]
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]
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}
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246-
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:UMICOLLAPSE' {
247-
publishDir = [
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[
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path: { "${params.outdir}/${params.aligner}/umicollapse/genomic_dedup_log" },
250-
mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
275+
// Publishing logic for umitools:
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256-
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_TRANSCRIPTOME:UMICOLLAPSE' {
277+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
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publishDir = [
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[
259-
path: { "${params.outdir}/${params.aligner}/umicollapse/transcriptomic_dedup_log" },
280+
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
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mode: params.publish_dir_mode,
261-
pattern: '*.log'
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]
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]
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}
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266-
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS' {
267-
publishDir = [
282+
pattern: '*.bam',
283+
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
284+
],
268285
[
269286
path: { "${params.outdir}/${params.aligner}/umitools/genomic_dedup_log" },
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mode: params.publish_dir_mode,
271288
pattern: '*.log'
289+
],
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[
291+
path: { "${params.outdir}/${params.aligner}/umitools" },
292+
mode: params.publish_dir_mode,
293+
pattern: '*.tsv'
272294
]
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]
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}
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276-
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS' {
298+
// Publishing logic for umicollapse
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300+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:UMICOLLAPSE' {
277301
publishDir = [
278302
[
279-
path: { "${params.outdir}/${params.aligner}/umitools/transcriptomic_dedup_log" },
303+
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
280304
mode: params.publish_dir_mode,
281-
pattern: '*.log'
305+
pattern: '*.bam',
306+
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
282307
],
283-
]
284-
}
285-
286-
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_(GEN|TRANSCRIPT)OME:UMITOOLS' {
287-
publishDir = [
288308
[
289-
path: { "${params.outdir}/${params.aligner}/umitools" },
309+
path: { "${params.outdir}/${params.aligner}/umicollapse/genomic_dedup_log" },
290310
mode: params.publish_dir_mode,
291-
pattern: '*.tsv'
311+
pattern: '*.log'
292312
]
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]
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}
@@ -297,10 +317,10 @@ if (!params.skip_alignment) {
297317
ext.args = { params.bam_csi_index ? '-c' : '' }
298318
ext.prefix = { "${meta.id}.umi_dedup.sorted" }
299319
publishDir = [
300-
path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
320+
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
301321
mode: params.publish_dir_mode,
302322
pattern: '*.{bai,csi}',
303-
saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
323+
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
304324
]
305325
}
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