From f36902b9afc01ccfaed50acdc37e74d3da1e1206 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 17:09:06 +0200
Subject: [PATCH] Cutadapt - merge tests into one

---
 software/cutadapt/main.nf                     |  8 ++-----
 software/cutadapt/test/main.nf                | 21 +++++++++++++++++++
 .../{test_single => test}/nextflow.config     |  6 +++---
 software/cutadapt/test_paired/main.nf         | 14 -------------
 software/cutadapt/test_paired/nextflow.config |  9 --------
 software/cutadapt/test_single/main.nf         | 21 -------------------
 6 files changed, 26 insertions(+), 53 deletions(-)
 create mode 100644 software/cutadapt/test/main.nf
 rename software/cutadapt/{test_single => test}/nextflow.config (64%)
 delete mode 100644 software/cutadapt/test_paired/main.nf
 delete mode 100644 software/cutadapt/test_paired/nextflow.config
 delete mode 100644 software/cutadapt/test_single/main.nf

diff --git a/software/cutadapt/main.nf b/software/cutadapt/main.nf
index 734b30b1..52dc2a3a 100644
--- a/software/cutadapt/main.nf
+++ b/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
 }
diff --git a/software/cutadapt/test/main.nf b/software/cutadapt/test/main.nf
new file mode 100644
index 00000000..2ab4529b
--- /dev/null
+++ b/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)
+}
diff --git a/software/cutadapt/test_single/nextflow.config b/software/cutadapt/test/nextflow.config
similarity index 64%
rename from software/cutadapt/test_single/nextflow.config
rename to software/cutadapt/test/nextflow.config
index 4b805ff3..888e1ec8 100644
--- a/software/cutadapt/test_single/nextflow.config
+++ b/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
 }
diff --git a/software/cutadapt/test_paired/main.nf b/software/cutadapt/test_paired/main.nf
deleted file mode 100644
index 46d0fdc6..00000000
--- a/software/cutadapt/test_paired/main.nf
+++ /dev/null
@@ -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)
-}
diff --git a/software/cutadapt/test_paired/nextflow.config b/software/cutadapt/test_paired/nextflow.config
deleted file mode 100644
index 08e52203..00000000
--- a/software/cutadapt/test_paired/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-docker.enabled = true
-params.outdir = './results'
-
-params{    
-    //preprocessing options
-    cutadapt_min_length = 40
-    cutadapt_min_quality = 25
-    singleEnd = false
-}
diff --git a/software/cutadapt/test_single/main.nf b/software/cutadapt/test_single/main.nf
deleted file mode 100644
index 657e2428..00000000
--- a/software/cutadapt/test_single/main.nf
+++ /dev/null
@@ -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)
-}