Add tests for fastqc module

.gitignore

@@ -1,6 +1,6 @@
 .nextflow*
 work/
 results/
-./data
+test_output/
 .DS_Store
 *.code-workspace

software/fastqc/main.nf

@@ -3,21 +3,21 @@ nextflow.preview.dsl = 2
 process FASTQC {
     input:
         tuple val(name), path(reads)
-        val (fastqc_args)
-        val (outputdir)
 
     output:
         tuple val(name), path ("*fastqc*"), emit: all
         path "*.zip", emit: report // e.g. for MultiQC later
+        path "*.version.txt", emit: version
 
-    container 'quay.io/biocontainers/fastqc:0.11.8--2'
+    container 'docker.pkg.github.com/nf-core/fastqc'
+    // see https://github.com/nextflow-io/nextflow/issues/1674
+    conda "../environment.yml"
 
-    publishDir "$outputdir",
-        mode: "copy", overwrite: true
+    publishDir "${params.out_dir}", mode: params.publish_dir_mode
 
     script:
         """
-        fastqc $fastqc_args -q -t 2 $reads
-        fastqc --version &> fastqc.version.txt
+        fastqc ${params.fastqc_args} -t ${task.cpus} $reads
+        fastqc --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > fastqc.version.txt
         """
 }

software/fastqc/test/data/test_R1.fastq.gz

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R1.fastq.gz

software/fastqc/test/data/test_R2.fastq.gz

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R2.fastq.gz

software/fastqc/test/data/test_single_end.fastq.gz

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_single_end.fastq.gz

software/fastqc/test/main.nf

@@ -1,21 +1,31 @@
 #!/usr/bin/env nextflow
 nextflow.preview.dsl = 2
 
-params.outdir = "."             // gets set in nextflow.config file (as './results/fastqc')
+params.out_dir = "test_output"
 params.fastqc_args = ''
-params.verbose = false
+params.publish_dir_mode = "copy"
 
-// TODO: check the output files in some way
-// include '../../../tests/functions/check_process_outputs.nf'
-include '../main.nf'
+include { FASTQC } from '../main.nf'
 
-// Define input channels
-ch_read_files = Channel 
-    .fromFilePairs('../../../test-datasets/test*{1,2}.fastq.gz',size:-1)
-    // .view()  // to check whether the input channel works
-
-// Run the workflow
-workflow {
-    FASTQC (ch_read_files, params.outdir, params.fastqc_args, params.verbose)
-    // .check_output()
+/**
+ * Test if FASTQC runs with single-end data
+ */
+workflow test_single_end {
+    input_files = Channel.fromPath("data/test_single_end.fastq.gz")
+                    .map {f -> [f.baseName, f]}
+    input_files.view()
+    FASTQC(input_files)
+}
+
+/**
+ * Test if FASTQC runs with paired end data
+ */
+workflow test_paired_end {
+    input_files = Channel.fromFilePairs("data/test_R{1,2}.fastq.gz")
+    FASTQC(input_files)
+}
+
+workflow {
+    test_single_end()
+    test_paired_end()
 }

software/fastqc/test/nextflow.config

@@ -1,2 +0,0 @@
-// docker.enabled = true
-params.outdir = './results/fastqc'