update fastqc config

nf-core · Oct 18, 2023 · dd97948 · dd97948
1 parent e6a0b75
commit dd97948
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -87,14 +87,6 @@ process {
     }
 }
 
-if (!(params.skip_fastqc)) {
-    process {
-        withName: '.*:FASTQC_FASTP:FASTQC_.*' {
-            ext.args = '--quiet'
-        }
-    }
-}
-
 if (!params.skip_fastp) {
     process {
         withName: 'FASTP' {
@@ -130,6 +122,14 @@ if (!params.skip_fastp) {
 
     if (!params.skip_fastqc) {
         process {
+            withName: '.*:.*:FASTQC_FASTP:FASTQC_RAW' {
+                ext.args = '--quiet'
+                publishDir = [
+                    path: { "${params.outdir}/fastqc/raw" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
             withName: '.*:.*:FASTQC_FASTP:FASTQC_TRIM' {
                 ext.args = '--quiet'
                 publishDir = [