Update the tests for MultiQC

.github/workflows/multiqc.yml

@@ -26,5 +26,12 @@ jobs:
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
 
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.x"
+    - name: Install dependencies
+      run: python -m pip install --upgrade pip pytest-workflow
+
     # Test the module
-    - run: nextflow run ./software/multiqc/test/ -profile docker
+    - run: pytest --tag multiqc --symlink --wt 2

software/multiqc/main.nf

@@ -2,31 +2,29 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options = initOptions(params.options)
+def options    = initOptions(params.options)
 
 process MULTIQC {
     tag "multiqc"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda(params.enable_conda ? "bioconda::multiqc=1.9" : null)
-    container "quay.io/biocontainers/multiqc:1.9--py_1"
+    conda     (params.enable_conda ? "bioconda::multiqc=1.9" : null)
+    container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
 
     input:
-    path(generic_report)
+    tuple val(meta), path(reads)
 
+    
     output:
-    path "multiqc_data", emit: dir
-    path "multiqc_report.html", emit: html
-    path "*.version.txt", emit: version
+    path "*multiqc_report.html", emit: report
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
 
     script:
-    def software = getSoftwareName(task.process)
-
     """
-    multiqc .
-    multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
+    multiqc -f $options.args .
     """
 }

tests/software/multiqc/main.nf

@@ -10,10 +10,10 @@ workflow test_multiqc {
     def input = []
 
     input = [[id: 'test'], // meta map
-             [file("${launchDir}/tests/data/fastqc/test_1.fastq.html", checkIfExists: true),
-              file("${launchDir}/tests/data/fastqc/test_1.fastq.zip", checkIfExists: true),
-              file("${launchDir}/tests/data/fastqc/test_2.fastq.html", checkIfExists: true),
-              file("${launchDir}/tests/data/fastqc/test_2.fastq.zip", checkIfExists: true)]]
+             [file("${launchDir}/tests/data/fastqc/test_1_fastqc.html", checkIfExists: true),
+              file("${launchDir}/tests/data/fastqc/test_1_fastqc.zip", checkIfExists: true),
+              file("${launchDir}/tests/data/fastqc/test_2_fastqc.html", checkIfExists: true),
+              file("${launchDir}/tests/data/fastqc/test_2_fastqc.zip", checkIfExists: true)]]
 
     MULTIQC(input)
 }

tests/software/multiqc/test.yml

@@ -3,7 +3,4 @@
   tags:
     - multiqc
   files:
-    - path: output/test_multiqc/test_fastqc.html
-      md5sum: 7027e72c3e55292c1567f12e02565e3b
-    - path: output/test_multiqc/test_fastqc.html
-      md5sum: 7027e72c3e55292c1567f12e02565e3b
+    - path: output/test_multiqc/multiqc_report.html