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Remove versioned_outdir param #33

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merged 1 commit into from
Feb 8, 2024
Merged

Remove versioned_outdir param #33

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2 changes: 1 addition & 1 deletion modules/provenance.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ process collect_provenance {

executor 'local'

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_*_provenance.yml", mode: 'copy'
publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_*_provenance.yml", mode: 'copy'

input:
tuple val(sample_id), path(provenance_files)
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22 changes: 11 additions & 11 deletions modules/tbprofiler.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process fastp {

tag { sample_id }

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_fastp.{json,csv}", mode: 'copy'
publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_fastp.{json,csv}", mode: 'copy'

input:
tuple val(sample_id), path(reads_1), path(reads_2)
Expand Down Expand Up @@ -40,8 +40,8 @@ process tbprofiler {

tag { sample_id }

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_tbprofiler*.{csv,json}"
publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_tbprofiler*.{bam,bam.bai,vcf}", enabled: !params.rename_ref
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_tbprofiler*.{csv,json}"
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_tbprofiler*.{bam,bam.bai,vcf}", enabled: !params.rename_ref

input:
tuple val(sample_id), path(reads_1), path(reads_2)
Expand Down Expand Up @@ -126,7 +126,7 @@ process rename_ref_in_alignment {

tag { sample_id }

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_tbprofiler*.{bam,bam.bai}", enabled: params.rename_ref, saveAs: { x -> x.replace("_renamed", "") }
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_tbprofiler*.{bam,bam.bai}", enabled: params.rename_ref, saveAs: { x -> x.replace("_renamed", "") }

input:
tuple val(sample_id), path(alignment)
Expand All @@ -145,7 +145,7 @@ process rename_ref_in_variants {

tag { sample_id }

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_tbprofiler*.vcf", enabled: params.rename_ref, saveAs: { x -> x.replace("_renamed", "") }
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_tbprofiler*.vcf", enabled: params.rename_ref, saveAs: { x -> x.replace("_renamed", "") }

input:
tuple val(sample_id), path(variants)
Expand All @@ -163,7 +163,7 @@ process qualimap_bamqc {

tag { sample_id }

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_qualimap_alignment_qc.csv"
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_qualimap_alignment_qc.csv"

input:
tuple val(sample_id), file(alignment)
Expand Down Expand Up @@ -194,7 +194,7 @@ process snpit {

tag { sample_id }

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_snpit_unchecked.tsv"
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_snpit_unchecked.tsv"

conda "$baseDir/environments/snpit.yml"

Expand Down Expand Up @@ -226,7 +226,7 @@ process check_snpit_against_tbprofiler {

executor 'local'

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_snpit.tsv"
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_snpit.tsv"

input:
tuple val(sample_id), path(snpit_results), path(tbprofiler_report_json)
Expand Down Expand Up @@ -292,7 +292,7 @@ process plot_coverage {

conda "$baseDir/environments/seaborn.yml"

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_coverage_plot.png"
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_coverage_plot.png"

input:
tuple val(sample_id), path(depths), path(resistance_genes_bed)
Expand Down Expand Up @@ -323,7 +323,7 @@ process generate_low_coverage_bed {

tag { sample_id }

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_low_coverage_regions.bed"
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_low_coverage_regions.bed"

input:
tuple val(sample_id), path(depths)
Expand All @@ -345,7 +345,7 @@ process calculate_gene_coverage {

tag { sample_id }

publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_resistance_gene_coverage.csv"
publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_resistance_gene_coverage.csv"

input:
tuple val(sample_id), path(depths), path(resistance_genes_bed)
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1 change: 0 additions & 1 deletion nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@ params {
min_af_used_for_prediction = 0.1
ref_name = 'NC_000962.3'
rename_ref = false
versioned_outdir = false
outdir = 'results'
pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
Expand Down