Re-add getSoftwareName

nf-core · Aug 13, 2021 · 3abdf96 · 3abdf96
1 parent ed5ea08
commit 3abdf96
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Showing 2 changed files with 9 additions and 2 deletions.
diff --git a/modules/fastqc/functions.nf b/modules/fastqc/functions.nf
@@ -2,6 +2,13 @@
 //  Utility functions used in nf-core DSL2 module files
 //
 
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
 //
 // Extract name of module from process name using $task.process
 //

diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getProcessName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -9,7 +9,7 @@ process FASTQC {
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getProcessName(task.process).toLowerCase(), meta:meta, publish_by_meta:['id']) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {