Merge pull request #37 from ewels/master

Cutadapt - merge tests into one

software/cutadapt/main.nf

@@ -14,7 +14,7 @@ process cutadapt {
     reverse_fq = "trimmed_2.fastq"
 
 
-    if (params.singleEnd) {
+    if (params.single_end) {
         processing = """
                     cutadapt \
                         -j ${task.cpus} \
@@ -32,14 +32,10 @@ process cutadapt {
                         --pair-filter=any \
                         --output ${forward_fq} \
                         --paired-output ${reverse_fq} ${reads}
-
-
                     """
     }
 
-    version = """
-    cutadapt --version &> v_cutadapt.txt
-    """
+    version = "cutadapt --version &> v_cutadapt.txt"
 
     return processing + version
 }

software/cutadapt/test/main.nf

@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+nextflow.preview.dsl = 2
+include '../main.nf' params(params)
+
+// Define input channels
+paired_end_input = Channel.fromFilePairs('../../../test-datasets/tools/cutadapt/input/*_{1,2}.fastq' )
+
+// TODO: params.single_end is set to false in nextflow config
+// But most of this module is not functional currently anyway....
+single_end_input = Channel.from([
+        ['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'],
+        ['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'],
+        ['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'],
+        ['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz']
+    ]).map { row -> [ row[0], [ file(row[1]) ] ] }
+
+// Run the workflow
+workflow {
+    cutadapt(paired_end_input)
+    cutadapt(single_end_input)
+}

software/cutadapt/test/nextflow.config

@@ -1,9 +1,9 @@
 docker.enabled = true
 params.outdir = './results'
 
-params{    
-    //preprocessing options
+params{
+    // Preprocessing options
     cutadapt_min_length = 40
     cutadapt_min_quality = 25
-    singleEnd = true
+    single_end = false
 }

software/cutadapt/test_paired/main.nf

@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl = 2
-include '../main.nf' params(params)
-
-// Define input channels
-
-Channel
-  .fromFilePairs('../../../test-datasets/tools/cutadapt/input/*_{1,2}.fastq' )
-  .set { ch_read_files }
-
-// Run the workflow
-workflow {
-    cutadapt(ch_read_files)
-}

software/cutadapt/test_paired/nextflow.config

@@ -1,9 +0,0 @@
-docker.enabled = true
-params.outdir = './results'
-
-params{    
-    //preprocessing options
-    cutadapt_min_length = 40
-    cutadapt_min_quality = 25
-    singleEnd = false
-}

software/cutadapt/test_single/main.nf

@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl = 2
-include '../main.nf' params(params)
-
-// Define input channels
-
-readPaths = [
-  ['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'],
-  ['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'],
-  ['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'],
-  ['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz']
-]
-Channel
-  .from(readPaths)
-  .map { row -> [ row[0], [ file(row[1]) ] ] }
-  .set { ch_read_files }
-
-// Run the workflow
-workflow {
-    cutadapt(ch_read_files)
-}