Fix multiqc tests

.github/filters.yml

@@ -49,6 +49,7 @@ gffread:
   - tests/software/gffread/**
 
 multiqc:
+  - software/fastqc/**
   - software/multiqc/**
   - tests/software/multiqc/**
 

tests/software/multiqc/main.nf

@@ -2,15 +2,15 @@
 
 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'])
+include { FASTQC  } from '../../../software/fastqc/main.nf'  addParams( options: [:] )
+include { MULTIQC } from '../../../software/multiqc/main.nf' addParams( options: [:] )
 
 workflow test_multiqc {
-    test_paired_end()
-
-    input = [
-        test_paired_end.out.zip.collect { it[1] }.ifEmpty([])
-    ]
-
-    MULTIQC(*input)
+    
+    def input = []
+    input = [ [ id: 'test', single_end: false ],
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+    FASTQC  ( input )
+    MULTIQC ( FASTQC.out.zip.collect { it[1] } )
 }

tests/software/multiqc/test.yml

@@ -1,7 +1,7 @@
 - name: multiqc
-  command: nextflow run ./tests/software/multiqc/ -entry test_multiqc -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/multiqc -entry test_multiqc -c tests/config/nextflow.config
   tags:
     - multiqc
   files:
-    - path: output/test_multiqc/multiqc_report.html
+    - path: output/multiqc/multiqc_report.html