Remove --versioned_outdir param

BCCDC-PHL · May 16, 2024 · 226b632 · 226b632
1 parent d014d32
commit 226b632
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Showing 8 changed files with 9 additions and 10 deletions.
diff --git a/modules/bakta.nf b/modules/bakta.nf
@@ -4,7 +4,7 @@ process bakta {
 
     errorStrategy 'ignore'
 
-    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}*.{gbk,gff,json,log}", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}*.{gbk,gff,json,log}", mode: 'copy'
 
     input:
     tuple val(sample_id), path(assembly), val(assembler), val(assembly_mode)

diff --git a/modules/fastp.nf b/modules/fastp.nf
@@ -2,7 +2,7 @@ process fastp {
 
     tag { sample_id }
 
-    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_fastp.json", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_fastp.json", mode: 'copy'
 
     input:
     tuple val(sample_id), path(reads)
@@ -40,7 +40,7 @@ process fastp_json_to_csv {
 
     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: "${sample_id}_fastp.csv", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_fastp.csv", mode: 'copy'
 
     input:
     tuple val(sample_id), path(fastp_json)

diff --git a/modules/long_read_qc.nf b/modules/long_read_qc.nf
@@ -60,7 +60,7 @@ process merge_nanoq_reports {
 
     executor 'local'
 
-    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_nanoq.csv", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_nanoq.csv", mode: 'copy'
 
     input:
     tuple val(sample_id), path(nanoq_pre_filter), path(nanoq_post_filter)
@@ -82,7 +82,7 @@ process bandage {
     executor 'local'
     errorStrategy 'ignore'
 
-    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_bandage.png", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_bandage.png", mode: 'copy'
 
     input:
     tuple val(sample_id), path(assembly_graph), val(assembler), val(assembly_mode)

diff --git a/modules/prokka.nf b/modules/prokka.nf
@@ -4,7 +4,7 @@ process prokka {
 
     errorStrategy 'ignore'
 
-    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_prokka.{gbk,gff}", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_prokka.{gbk,gff}", mode: 'copy'
 
     input:
     tuple val(sample_id), path(assembly), val(assembler), val(assembly_mode)

diff --git a/modules/provenance.nf b/modules/provenance.nf
@@ -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)

diff --git a/modules/quast.nf b/modules/quast.nf
@@ -41,7 +41,7 @@ process parse_quast_report {
 
     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: "${sample_id}_${assembler}_${assembly_mode}_quast.csv", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_quast.csv", mode: 'copy'
 
     input:
     tuple val(sample_id), path(quast_report), val(assembler), val(assembly_mode)

diff --git a/modules/unicycler.nf b/modules/unicycler.nf
@@ -2,7 +2,7 @@ process unicycler {
 
     tag { sample_id + ' / ' + assembly_mode }
 
-    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_unicycler_${assembly_mode}.{fa,gfa,log}", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_unicycler_${assembly_mode}.{fa,gfa,log}", mode: 'copy'
 
     input:
     tuple val(sample_id), path(reads), val(assembly_mode)

diff --git a/nextflow.config b/nextflow.config
@@ -23,7 +23,6 @@ params {
     filtlong_min_length = 1000
     filtlong_keep_percent = 90
     samplesheet_input = 'NO_FILE'
-    versioned_outdir = false
     pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
     pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
 }