the module is working in test

test-datasets

@@ -1 +1 @@
-Subproject commit e5fef88994b8d34c7bf4b07116e5f7a330d2ee3b
+Subproject commit be215c0874e2485f0d8e12a6f0addf08f2cd08df

tools/cutadapt/main.nf

@@ -7,9 +7,12 @@ process cutadapt {
     tuple sample_id, file(input_forward_fq), file(input_reverse_fq)
 
     output:
-    tuple sample_id, file(output_forward_fq), file(output_reverse_fq)
+    tuple sample_id, file(forward_fq), file(reverse_fq)
 
     script:
+    forward_fq = "trimmed_forward.fastq"
+    reverse_fq = "trimmed_reverse.fastq"
+
     """
     cutadapt \
 			-j ${task.cpus} \
@@ -17,7 +20,7 @@ process cutadapt {
 			--minimum-length $params.cutadapt_min_length \
 			--pair-filter=any \
 			--output ${forward_fq} \
-			--paired-output ${reverse_fq} '$input_forward_fq' '$input_reverse_fq'
+			--paired-output ${reverse_fq} '${input_forward_fq}' '${input_reverse_fq}'
     
     cutadapt --version &> v_cutadapt.txt
     """

tools/cutadapt/test/main.nf

@@ -0,0 +1,22 @@
+#!/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()
+}

tools/cutadapt/test/nextflow.config

@@ -0,0 +1,8 @@
+docker.enabled = true
+params.outdir = './results'
+
+params{    
+    //preprocessing options
+    cutadapt_min_length = 40
+    cutadapt_min_quality = 25
+}