FastQC: actually run a test

nf-core/module_testing/check_process_outputs.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+nextflow.preview.dsl = 2
+
+cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
+
+process check_output {
+    input:
+    val x from cheers
+
+    script:
+    """
+    echo '$x world!'
+    """
+}

tools/fastqc/main.nf

@@ -1,15 +1,15 @@
 process fastqc {
-    tag "$sample_id"
+    tag "FastQC - $sample_id"
     publishDir "${params.outdir}/fastqc", mode: 'copy',
         saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
 
-    container: 'quay.io/biocontainers/fastqc:0.11.8--2'
+    container 'quay.io/biocontainers/fastqc:0.11.8--2'
 
     input:
-    set val(sample_id), file(reads)
+    tuple sample_id, path(reads)
 
     output:
-    file "*_fastqc.{zip,html}"
+    path "*_fastqc.{zip,html}"
 
     script:
     """

tools/fastqc/test/main.nf

@@ -1,13 +1,21 @@
 #!/usr/bin/env nextflow
-echo true
+nextflow.preview.dsl = 2
+include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../main.nf' params(params)
 
-cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
+// Define input channels
+readPaths = [
+  ['SRR389222_sub1', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz']],
+  ['SRR389222_sub2', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']],
+  ['SRR389222_sub3', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz']]
+]
+Channel
+  .from(readPaths)
+  .map { row -> [ row[0], [row[1][0]]] }
+  .set { ch_read_files }
 
-process sayHello {
+// Run the workflow
-  input:
+workflow {
-    val x from cheers
+    fastqc(ch_read_files)
-  script:
+    // .check_output()
-    """
-    echo '$x world!'
-    """
 }

tools/fastqc/test/nextflow.config

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

tools/samtools/index/main.nf

@@ -1,13 +1,13 @@
 process samtools_index {
     tag "${bam.baseName}"
 
-    container: 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
+    container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
 
     input:
-    set file(bam)
+    path(bam)
 
     output:
-    file "*.sorted.bam"
+    path "*.sorted.bam"
 
     script:
     def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'

tools/samtools/sort/main.nf

@@ -1,13 +1,13 @@
 process samtools_index {
     tag "${bam.baseName}"
 
-    container: 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
+    container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
 
     input:
-    set file(bam)
+    path(bam)
 
     output:
-    file "*.bam.bai"
+    path "*.bam.bai"
 
     script:
     """

tools/trim_galore/main.nf

@@ -7,15 +7,15 @@ process fastqc {
             else filename
         }
 
-    container: 'quay.io/biocontainers/trim-galore:0.6.5--0'
+    container 'quay.io/biocontainers/trim-galore:0.6.5--0'
 
     input:
-    set val(sample_id), file(reads)
+    tuple sample_id, path(reads)
 
     output:
-    set val(name), file("*fq.gz")
+    tuple name, path("*fq.gz")
-    file "*trimming_report.txt"
+    path "*trimming_report.txt"
-    file "*_fastqc.{zip,html}"
+    path "*_fastqc.{zip,html}"
 
     script:
     c_r1 = clip_r1 > 0 ? "--clip_r1 ${clip_r1}" : ''