From 7549e07d74dc5f88a32e7cb037b8be044af03444 Mon Sep 17 00:00:00 2001
From: Dan Fornika <dfornika@gmail.com>
Date: Tue, 20 Feb 2024 14:36:38 -0800
Subject: [PATCH] Remove versioned_outdir param

---
 modules/mlst.nf       |  6 +++---
 modules/provenance.nf |  2 +-
 modules/quast.nf      | 41 +++++++++++++++++++++++++----------------
 nextflow.config       |  1 -
 4 files changed, 29 insertions(+), 21 deletions(-)

diff --git a/modules/mlst.nf b/modules/mlst.nf
index 4b1f507..12697f5 100644
--- a/modules/mlst.nf
+++ b/modules/mlst.nf
@@ -2,7 +2,7 @@ process mlst {
 
     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: "${sample_id}_mlst.json"
+    publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_mlst.json"
 
     input:
     tuple val(sample_id), path(assembly)
@@ -40,8 +40,8 @@ process parse_alleles {
     
     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: "${sample_id}_alleles.csv"
-    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_sequence_type.csv"
+    publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_alleles.csv"
+    publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_sequence_type.csv"
 
     input:
     tuple val(sample_id), path(mlst_csv), path(mlst_json)
diff --git a/modules/provenance.nf b/modules/provenance.nf
index 966b423..e1286fa 100644
--- 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
index 012db10..acc9ba9 100644
--- a/modules/quast.nf
+++ b/modules/quast.nf
@@ -3,26 +3,35 @@ process quast {
     tag { sample_id }
 
     input:
-      tuple val(sample_id), path(assembly)
+    tuple val(sample_id), path(assembly)
 
     output:
-      tuple val(sample_id), path("${sample_id}_quast.tsv"), emit: tsv
-      tuple val(sample_id), path("${sample_id}_quast_provenance.yml"), emit: provenance
+    tuple val(sample_id), path("${sample_id}_quast.tsv"), emit: tsv
+    tuple val(sample_id), path("${sample_id}_quast_provenance.yml"), emit: provenance
 
     script:
-      """
-      printf -- "- process_name: quast\\n" > ${sample_id}_quast_provenance.yml
-      printf -- "  tool_name: quast\\n  tool_version: \$(quast --version | cut -d ' ' -f 2 | tr -d 'v')\\n" >> ${sample_id}_quast_provenance.yml
-
-      quast --threads ${task.cpus} \
+    """
+    printf -- "- process_name: quast\\n"                  >> ${sample_id}_quast_provenance.yml
+    printf -- "  tools:\\n"                               >> ${sample_id}_quast_provenance.yml
+    printf -- "    - tool_name: quast\\n"                 >> ${sample_id}_quast_provenance.yml
+    printf -- "      tool_version: \$(quast --version | cut -d ' ' -f 2 | tr -d 'v')\\n" >> ${sample_id}_quast_provenance.yml
+    printf -- "      parameters:\\n"                      >> ${sample_id}_quast_provenance.yml
+    printf -- "        - parameter: --space-efficient\\n" >> ${sample_id}_quast_provenance.yml
+    printf -- "          value: null\\n"                  >> ${sample_id}_quast_provenance.yml
+    printf -- "        - parameter: --fast\\n"            >> ${sample_id}_quast_provenance.yml
+    printf -- "          value: null\\n"                  >> ${sample_id}_quast_provenance.yml
+    printf -- "        - parameter: --min-contig\\n"      >> ${sample_id}_quast_provenance.yml
+    printf -- "          value: 0\\n"                     >> ${sample_id}_quast_provenance.yml
+
+    quast --threads ${task.cpus} \
         --space-efficient \
 	--fast \
 	--min-contig 0 \
         ${assembly}  \
 	--output-dir ${sample_id}
 
-      mv ${sample_id}/transposed_report.tsv ${sample_id}_quast.tsv
-      """
+    mv ${sample_id}/transposed_report.tsv ${sample_id}_quast.tsv
+    """
 }
 
 process parse_quast_report {
@@ -31,16 +40,16 @@ 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: "${sample_id}_quast.csv", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_quast.csv", mode: 'copy'
 
     input:
-      tuple val(sample_id), path(quast_report)
+    tuple val(sample_id), path(quast_report)
 
     output:
-      tuple val(sample_id), path("${sample_id}_quast.csv")
+    tuple val(sample_id), path("${sample_id}_quast.csv")
 
     script:
-      """
-      parse_quast_report.py ${quast_report} > ${sample_id}_quast.csv
-      """
+    """
+    parse_quast_report.py ${quast_report} > ${sample_id}_quast.csv
+    """
 }
diff --git a/nextflow.config b/nextflow.config
index 0b8a6c8..04a0308 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -18,7 +18,6 @@ params {
   minid = 95
   mincov = 10
   minscore = 50
-  versioned_outdir = false
   pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
   pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
 }