Tag outputs with assembler name (#15)

BCCDC-PHL · Dec 1, 2021 · 7b2c6f6 · 7b2c6f6
1 parent 0c7c16b
commit 7b2c6f6
Show file tree

Hide file tree

Showing 6 changed files with 35 additions and 34 deletions.
diff --git a/modules/bakta.nf b/modules/bakta.nf
@@ -5,22 +5,22 @@ process bakta {
     publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}*.{gbk,gff,json,log}", mode: 'copy'
 
     input:
-      tuple val(sample_id), path(assembly)
+      tuple val(sample_id), path(assembly), val(assembler)
 
     output:
-      tuple val(sample_id), path("${sample_id}_bakta.gbk"), emit: gbk
-      tuple val(sample_id), path("${sample_id}_bakta.gff"), emit: gff
-      tuple val(sample_id), path("${sample_id}_bakta.json"), emit: json
-      tuple val(sample_id), path("${sample_id}_bakta.log"), emit: log
-      tuple val(sample_id), path("${sample_id}_bakta_provenance.yml"), emit: provenance
+      tuple val(sample_id), path("${sample_id}_${assembler}_bakta.gbk"), emit: gbk
+      tuple val(sample_id), path("${sample_id}_${assembler}_bakta.gff"), emit: gff
+      tuple val(sample_id), path("${sample_id}_${assembler}_bakta.json"), emit: json
+      tuple val(sample_id), path("${sample_id}_${assembler}_bakta.log"), emit: log
+      tuple val(sample_id), path("${sample_id}_${assembler}_bakta_provenance.yml"), emit: provenance
 
     script:
       """
-      printf -- "- tool_name: bakta\\n  tool_version: \$(bakta --version | cut -d ' ' -f 2)\\n" > ${sample_id}_bakta_provenance.yml
+      printf -- "- tool_name: bakta\\n  tool_version: \$(bakta --version | cut -d ' ' -f 2)\\n" > ${sample_id}_${assembler}_bakta_provenance.yml
       bakta --db ${params.bakta_db} --threads ${task.cpus} --compliant --keep-contig-headers --locus-tag ${sample_id} --prefix "${sample_id}" ${assembly}
-      cp ${sample_id}.gff3 ${sample_id}_bakta.gff
-      cp ${sample_id}.gbff ${sample_id}_bakta.gbk
-      cp ${sample_id}.json ${sample_id}_bakta.json
-      cp ${sample_id}.log ${sample_id}_bakta.log
+      cp ${sample_id}.gff3 ${sample_id}_${assembler}_bakta.gff
+      cp ${sample_id}.gbff ${sample_id}_${assembler}_bakta.gbk
+      cp ${sample_id}.json ${sample_id}_${assembler}_bakta.json
+      cp ${sample_id}.log ${sample_id}_${assembler}_bakta.log
       """
 }
diff --git a/modules/prokka.nf b/modules/prokka.nf
@@ -2,21 +2,21 @@ process prokka {
 
     tag { sample_id }
 
-    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_prokka.{gbk,gff}", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_prokka.{gbk,gff}", mode: 'copy'
 
     input:
-      tuple val(sample_id), path(assembly)
+      tuple val(sample_id), path(assembly), val(assembler)
 
     output:
-      tuple val(sample_id), path("${sample_id}_prokka.gbk"), emit: gbk
-      tuple val(sample_id), path("${sample_id}_prokka.gff"), emit: gff
-      tuple val(sample_id), path("${sample_id}_prokka_provenance.yml"), emit: provenance
+      tuple val(sample_id), path("${sample_id}_${assembler}_prokka.gbk"), emit: gbk
+      tuple val(sample_id), path("${sample_id}_${assembler}_prokka.gff"), emit: gff
+      tuple val(sample_id), path("${sample_id}_${assembler}_prokka_provenance.yml"), emit: provenance
 
     script:
       """
-      printf -- "- tool_name: prokka\\n  tool_version: \$(prokka --version 2>&1 | cut -d ' ' -f 2)\\n" > ${sample_id}_prokka_provenance.yml
+      printf -- "- tool_name: prokka\\n  tool_version: \$(prokka --version 2>&1 | cut -d ' ' -f 2)\\n" > ${sample_id}_${assembler}_prokka_provenance.yml
       prokka --cpus ${task.cpus} --compliant --locustag ${sample_id} --centre "BCCDC-PHL" --prefix "${sample_id}" ${assembly}
-      cp ${sample_id}/${sample_id}.gbk ${sample_id}_prokka.gbk
-      cp ${sample_id}/${sample_id}.gff ${sample_id}_prokka.gff
+      cp ${sample_id}/${sample_id}.gbk ${sample_id}_${assembler}_prokka.gbk
+      cp ${sample_id}/${sample_id}.gff ${sample_id}_${assembler}_prokka.gff
       """
 }
diff --git a/modules/quast.nf b/modules/quast.nf
@@ -2,22 +2,20 @@ process quast {
 
     tag { sample_id }
 
-    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_quast.tsv", mode: 'copy'
-
-    cpus 2
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_quast.tsv", mode: 'copy'
 
     input:
-      tuple val(sample_id), path(assembly)
+      tuple val(sample_id), path(assembly), val(assembler)
 
     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("${sample_id}_${assembler}_quast.tsv"), val(assembler), emit: tsv
+      tuple val(sample_id), path("${sample_id}_${assembler}_quast_provenance.yml"), emit: provenance
 
     script:
       """
-      printf -- "- tool_name: quast\\n  tool_version: \$(quast --version | cut -d ' ' -f 2)\\n" > ${sample_id}_quast_provenance.yml
+      printf -- "- tool_name: quast\\n  tool_version: \$(quast --version | cut -d ' ' -f 2)\\n" > ${sample_id}_${assembler}_quast_provenance.yml
       quast --threads ${task.cpus} ${assembly} --space-efficient --fast --output-dir ${sample_id}
-      mv ${sample_id}/transposed_report.tsv ${sample_id}_quast.tsv
+      mv ${sample_id}/transposed_report.tsv ${sample_id}_${assembler}_quast.tsv
       """
 }
 
@@ -27,16 +25,16 @@ process parse_quast_report {
 
     executor 'local'
 
-    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_quast.json", mode: 'copy'
+    publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_quast.json", mode: 'copy'
 
     input:
-      tuple val(sample_id), path(quast_report)
+      tuple val(sample_id), path(quast_report), val(assembler)
 
     output:
-      tuple val(sample_id), path("${sample_id}_quast.json")
+      tuple val(sample_id), path("${sample_id}_${assembler}_quast.json")
 
     script:
       """
-      parse_quast_report.py ${quast_report} > ${sample_id}_quast.json
+      parse_quast_report.py ${quast_report} > ${sample_id}_${assembler}_quast.json
       """
 }
diff --git a/modules/shovill.nf b/modules/shovill.nf
@@ -9,7 +9,7 @@ process shovill {
       tuple val(sample_id), path(reads_1), path(reads_2)
 
     output:
-      tuple val(sample_id), path("${sample_id}_shovill.fa"), emit: assembly
+      tuple val(sample_id), path("${sample_id}_shovill.fa"), val("shovill"), emit: assembly
       tuple val(sample_id), path("${sample_id}_shovill.log"), emit: log
       tuple val(sample_id), path("${sample_id}_shovill_provenance.yml"), emit: provenance
 

diff --git a/modules/unicycler.nf b/modules/unicycler.nf
@@ -8,7 +8,7 @@ process unicycler {
       tuple val(sample_id), path(reads_1), path(reads_2)
 
     output:
-      tuple val(sample_id), path("${sample_id}_unicycler.fa"), emit: assembly
+      tuple val(sample_id), path("${sample_id}_unicycler.fa"), val("unicycler"), emit: assembly
       tuple val(sample_id), path("${sample_id}_unicycler.gfa"), emit: assembly_graph
       tuple val(sample_id), path("${sample_id}_unicycler.log"), emit: log
       tuple val(sample_id), path("${sample_id}_unicycler_provenance.yml"), emit: provenance

diff --git a/nextflow.config b/nextflow.config
@@ -35,6 +35,9 @@ profiles {
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 process {
+  withName: quast {
+    cpus = 2
+  }
   withName: fastp {
     cpus = 4
   }
@@ -57,7 +60,7 @@ process {
 manifest {
   author = 'Dan Fornika'
   name = 'BCCDC-PHL/routine-assembly'
-  version = '0.2.0'
+  version = '0.2.1'
   description = 'BCCDC-PHL Routine Assembly'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'