modules_nanopore.config: output concatenated Nanopore reads to ${outd…

…ir}/fastq (#43)
peterk87 · Aug 16, 2023 · 85afe8d · 85afe8d
1 parent e3d8b5a
commit 85afe8d
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Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/conf/modules_nanopore.config b/conf/modules_nanopore.config
@@ -11,6 +11,17 @@ process {
     ]
   }
 
+  withName: 'CAT_NANOPORE_FASTQ' {
+    ext.args = ''
+    publishDir = [
+      [
+        path: { "${params.outdir}/fastq" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+      ]
+    ]
+  }
+
   withName: 'IRMA' {
     publishDir = [
       [

diff --git a/modules/local/misc.nf b/modules/local/misc.nf
@@ -1,5 +1,3 @@
-include { getSoftwareName; fluPrefix } from './functions'
-
 process CAT_NANOPORE_FASTQ {
   tag "${meta.id}"
   label 'process_low'