Make publishDir more flexible

software/fastqc/main.nf

@@ -1,4 +1,6 @@
 nextflow.preview.dsl = 2
+def MODULE = "fastqc"
+params.fastqc_publish_dir = "${params.out_dir}/$MODULE"
 
 process FASTQC {
     input:
@@ -9,10 +11,10 @@ process FASTQC {
         path "*.zip", emit: report // e.g. for MultiQC later
         path "*.version.txt", emit: version
 
-    container 'docker.pkg.github.com/nf-core/fastqc'
+    container "docker.pkg.github.com/nf-core/$module"
     conda "${moduleDir}/environment.yml"
 
-    publishDir "${params.out_dir}", mode: params.publish_dir_mode
+    publishDir "${params.fastqc_publish_dir}/$name", mode: params.publish_dir_mode
 
     script:
         """

software/fastqc/meta.yml

@@ -14,8 +14,20 @@ tools:
         overrepresented sequences.
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+params:
+  - out_dir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output filese into `$out_dir/MODULE_NAME`
+  - fastqc_publish_dir:
+      type: string
+      description: |
+        Override the automatically generated output directory.
+  - publish_dir_mode:
+      type: string
+      description: Set the publishDir mode (e.g. copy, link, ...)
 input:
-    -
   - name:
       type: string
       description: Sample identifier
@@ -23,7 +35,6 @@ input:
       type: file
       description: Input FastQ file, or pair of files
 output:
-    -
   - report:
       type: file
       description: FastQC report