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Final outputpath fixes
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grst committed Jan 26, 2024
1 parent ede1ee9 commit e707e28
Showing 1 changed file with 35 additions and 9 deletions.
44 changes: 35 additions & 9 deletions conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -73,15 +73,15 @@ process {
]
]
}
withName: '.*:.*:FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
ext.args = '--quiet'
publishDir = [
path: { "${params.outdir}/fastqc/raw" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: '.*:.*:FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
ext.args = '--quiet'
publishDir = [
path: { "${params.outdir}/fastqc/trimmed" },
Expand Down Expand Up @@ -166,7 +166,7 @@ process {
ext.args = { meta.single_end ? "--algo ${params.umitools_method} --two-pass" : "--method ${params.umitools_method} --two-pass --paired --remove-unpaired --remove-chimeric" }
ext.prefix = { "${meta.id}.umi_dedup.sorted" }
publishDir = [
path: { "${params.outdir}/bam_deduplicated" },
path: { "${params.outdir}/umi_dedup/bam_deduplicated" },
mode: params.publish_dir_mode,
pattern: '*.bam',
enabled: (
Expand All @@ -178,6 +178,7 @@ process {
publishDir = [
path: { "${params.outdir}/umi_dedup/fastq_deduplicated" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: (
params.save_umi_intermeds
)
Expand All @@ -189,7 +190,8 @@ process {
//
withName: 'MIRTRACE_RUN' {
publishDir = [
path: { "${params.outdir}/mirtrace" },
//"mirtrace" already part of the published folder
path: { "${params.outdir}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand Down Expand Up @@ -237,14 +239,30 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:(BOWTIE_MAP_MATURE|BAM_STATS_MATURE).*' {
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE' {
publishDir = [
path: { "${params.outdir}/mirna_quant/bam/mature" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:(BOWTIE_MAP_HAIRPIN|BAM_STATS_HAIRPIN).*' {
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:.*' {
ext.prefix = { "${meta.id}.sorted" }
publishDir = [
path: { "${params.outdir}/mirna_quant/bam/mature" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_HAIRPIN' {
publishDir = [
path: { "${params.outdir}/mirna_quant/bam/hairpin" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:.*' {
ext.prefix = { "${meta.id}.sorted" }
publishDir = [
path: { "${params.outdir}/mirna_quant/bam/hairpin" },
mode: params.publish_dir_mode,
Expand All @@ -265,9 +283,17 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_SEQCLUSTER' {
publishDir = [
path: { "${params.outdir}/mirna_quant/bam/seqcluster" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'MIRTOP_QUANT' {
publishDir = [
path: { "${params.outdir}/mirna_quant/mirtop" },
//mirtop already part of the output folder
path: { "${params.outdir}/mirna_quant/" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand Down Expand Up @@ -302,9 +328,9 @@ process {
}
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME' {
publishDir = [
path: { "${params.outdir}/unmapped/bam" },
path: { "${params.outdir}/genome_quant/bam" },
mode: params.publish_dir_mode,
pattern: "unmapped/*.gz"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand Down

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