Combine output and project param

genepi · Apr 21, 2024 · 1b7d4ca · 1b7d4ca
1 parent 8f2f79a
commit 1b7d4ca
Show file tree

Hide file tree

Showing 3 changed files with 11 additions and 6 deletions.
diff --git a/modules/local/annotate.nf b/modules/local/annotate.nf
@@ -1,6 +1,6 @@
 process ANNOTATE {
 
-    publishDir "${params.output}", mode: 'copy'
+    publishDir "${params.pubDir}", mode: 'copy'
 
     input:
     path variants_ch

diff --git a/tests/test_single_bam.config b/tests/test_single_bam.config
@@ -11,6 +11,5 @@
 params {
     project         = "test-job"
     files           = "$projectDir/tests/data/bam/*.bam"
-    output          = "out"
 }
 
diff --git a/workflows/mtdna_server_2.nf b/workflows/mtdna_server_2.nf
@@ -1,18 +1,24 @@
 println "Welcome to ${params.service.name} ${workflow.manifest.version}"
 println "(c) ${workflow.manifest.author}"
 requiredParams = [
-    'project', 'files', 'output'
+    'project', 'files'
 ]
 
 for (param in requiredParams) {
     if (params[param] == null) {
         exit 1, "Parameter ${param} is required."
     }
 }   
-
+
+if(params.output == null) {
+    params.pubDir = "output/${params.project}"
+} else {
+    params.pubDir = params.output
+}
+
 if (params.output_reports == null || params.output_auxiliary == null ) {
-    params.output_reports = params.output
-    params.output_auxiliary = params.output    
+    params.output_reports = params.pubDir
+    params.output_auxiliary = params.pubDir    
 }
 
 include { INDEX } from '../modules/local/index'