From 490eca706c3d2ecc52395d977e5fe29145eba60c Mon Sep 17 00:00:00 2001
From: Piotr Faba <piotr.faba@ardigen.com>
Date: Fri, 6 Mar 2020 13:23:12 +0000
Subject: [PATCH] single and paired end supported

---
 tools/cutadapt/main.nf                        | 42 +++++++++++++------
 tools/cutadapt/test/main.nf                   | 22 ----------
 tools/cutadapt/test_paired/main.nf            | 14 +++++++
 tools/cutadapt/test_paired/nextflow.config    |  9 ++++
 tools/cutadapt/test_single/main.nf            | 21 ++++++++++
 .../{test => test_single}/nextflow.config     |  1 +
 6 files changed, 75 insertions(+), 34 deletions(-)
 delete mode 100644 tools/cutadapt/test/main.nf
 create mode 100644 tools/cutadapt/test_paired/main.nf
 create mode 100644 tools/cutadapt/test_paired/nextflow.config
 create mode 100644 tools/cutadapt/test_single/main.nf
 rename tools/cutadapt/{test => test_single}/nextflow.config (87%)

diff --git a/tools/cutadapt/main.nf b/tools/cutadapt/main.nf
index 432eccb4..bdd444af 100644
--- a/tools/cutadapt/main.nf
+++ b/tools/cutadapt/main.nf
@@ -4,24 +4,42 @@ process cutadapt {
     container 'quay.io/biocontainers/cutadapt:1.16--py27_1'
 
     input:
-    tuple sample_id, file(input_forward_fq), file(input_reverse_fq)
+    tuple val(sample_id), file(reads)
 
     output:
-    tuple sample_id, file(forward_fq), file(reverse_fq)
+    tuple sample_id, file("trimmed_*.fastq")
 
     script:
-    forward_fq = "trimmed_forward.fastq"
-    reverse_fq = "trimmed_reverse.fastq"
+    forward_fq = "trimmed_1.fastq"
+    reverse_fq = "trimmed_2.fastq"
 
-    """
-    cutadapt \
-			-j ${task.cpus} \
-			-q $params.cutadapt_min_quality \
-			--minimum-length $params.cutadapt_min_length \
-			--pair-filter=any \
-			--output ${forward_fq} \
-			--paired-output ${reverse_fq} '${input_forward_fq}' '${input_reverse_fq}'
     
+    if (params.singleEnd) {
+        processing = """
+                    cutadapt \
+		            	-j ${task.cpus} \
+		            	-q $params.cutadapt_min_quality \
+		            	--minimum-length $params.cutadapt_min_length \
+		            	--output ${forward_fq} \
+		            	${reads}
+                    """
+    } else {
+        processing = """
+                    cutadapt \
+		            	-j ${task.cpus} \
+		            	-q $params.cutadapt_min_quality \
+		            	--minimum-length $params.cutadapt_min_length \
+		            	--pair-filter=any \
+		            	--output ${forward_fq} \
+		            	--paired-output ${reverse_fq} ${reads}
+            
+                    
+                    """
+    }
+
+    version = """
     cutadapt --version &> v_cutadapt.txt
     """
+
+    return processing + version
 }
diff --git a/tools/cutadapt/test/main.nf b/tools/cutadapt/test/main.nf
deleted file mode 100644
index 69c1eef8..00000000
--- a/tools/cutadapt/test/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl = 2
-include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
-include '../main.nf' params(params)
-
-// Define input channels
-readPaths = [
-  [ sample: 'SRR4238351', 
-    R1: '../../../test-datasets/tools/cutadapt/input/SRR396636.sra_1.fastq', 
-    R2: '../../../test-datasets/tools/cutadapt/input/SRR396636.sra_2.fastq'
-  ]
-]
-Channel
-  .from(readPaths)
-  .map { row -> tuple( row.sample_name, file(row.R1.trim()), file(row.R2.trim()) ) }
-  .set { ch_read_files }
-
-// Run the workflow
-workflow {
-    cutadapt(ch_read_files)
-    // .check_output()
-}
diff --git a/tools/cutadapt/test_paired/main.nf b/tools/cutadapt/test_paired/main.nf
new file mode 100644
index 00000000..46d0fdc6
--- /dev/null
+++ b/tools/cutadapt/test_paired/main.nf
@@ -0,0 +1,14 @@
+#!/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/tools/cutadapt/test_paired/nextflow.config b/tools/cutadapt/test_paired/nextflow.config
new file mode 100644
index 00000000..08e52203
--- /dev/null
+++ b/tools/cutadapt/test_paired/nextflow.config
@@ -0,0 +1,9 @@
+docker.enabled = true
+params.outdir = './results'
+
+params{    
+    //preprocessing options
+    cutadapt_min_length = 40
+    cutadapt_min_quality = 25
+    singleEnd = false
+}
diff --git a/tools/cutadapt/test_single/main.nf b/tools/cutadapt/test_single/main.nf
new file mode 100644
index 00000000..96947ad0
--- /dev/null
+++ b/tools/cutadapt/test_single/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+nextflow.preview.dsl = 2
+include '../main.nf' params(params)
+
+// Define input channels
+
+readPaths = [
+  ['SRR4238351', '../../../test-datasets/tools/fastqc/input/SRR4238351_subsamp.fastq.gz'],
+  ['SRR4238355', '../../../test-datasets/tools/fastqc/input/SRR4238355_subsamp.fastq.gz'],
+  ['SRR4238359', '../../../test-datasets/tools/fastqc/input/SRR4238359_subsamp.fastq.gz'],
+  ['SRR4238379', '../../../test-datasets/tools/fastqc/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)
+}
diff --git a/tools/cutadapt/test/nextflow.config b/tools/cutadapt/test_single/nextflow.config
similarity index 87%
rename from tools/cutadapt/test/nextflow.config
rename to tools/cutadapt/test_single/nextflow.config
index b1c505a7..4b805ff3 100644
--- a/tools/cutadapt/test/nextflow.config
+++ b/tools/cutadapt/test_single/nextflow.config
@@ -5,4 +5,5 @@ params{
     //preprocessing options
     cutadapt_min_length = 40
     cutadapt_min_quality = 25
+    singleEnd = true
 }