Give finishing touches after the review

software/multiqc/main.nf

@@ -24,9 +24,8 @@ process MULTIQC {
 
     script:
     def software = getSoftwareName(task.process)
-    def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
     """
-    multiqc -f $options.args $custom_config .
+    multiqc -f $options.args .
-     multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
+    multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
     """
 }

software/multiqc/meta.yml

@@ -33,14 +33,18 @@ input:
         description: |
             List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
 output:
-    - data:
-        type: dir
-        description: MultiQC data dir
-        pattern: "multiqc_data"
     - report:
         type: file
         description: MultiQC report file
         pattern: "multiqc_report.html"
+    - data:
+        type: dir
+        description: MultiQC data dir
+        pattern: "multiqc_data"
+    - plots:
+        type: file
+        description: Plots created by MultiQC
+        pattern: "*_data"
     - version:
         type: file
         description: File containing software version
@@ -48,3 +52,4 @@ output:
 authors:
     - "@abhi18av"
     - "@bunop"
+    - "@drpatelh"

tests/software/multiqc/main.nf

@@ -5,14 +5,11 @@ nextflow.enable.dsl = 2
 include { MULTIQC } from '../../../software/multiqc/main.nf' addParams(options: [publish_dir: 'test_multiqc'])
 include { test_paired_end } from '../fastqc/main.nf' addParams(options: [publish_dir: 'test_paired_end'])
 
-ch_multiqc_config = file("$launchDir/tests/software/multiqc/multiqc_config.yml", checkIfExists: true)
-
 workflow test_multiqc {
     test_paired_end()
 
     input = [
-        ch_multiqc_config
+        test_paired_end.out.zip.collect { it[1] }.ifEmpty([])
-            .mix(test_paired_end.out.zip.collect { it[1] }.ifEmpty([]))
     ]
 
     MULTIQC(*input)