FastQ Screen works with E coli paired-end test file

tools/fastq_screen/main.nf

@@ -9,7 +9,9 @@ process FASTQ_SCREEN {
     input:
 	    tuple val(name), path(reads)
 		val (outputdir)
-		val (fastq_screen_args)
+		// fastq_screen_args are best passed in to the workflow in the following manner:
+		// --fastq_screen_args="--subset 200000 --force"
+		val (fastq_screen_args)  
 		val (verbose)
 
 	output:
@@ -21,8 +23,9 @@ process FASTQ_SCREEN {
 		mode: "link", overwrite: true
 
     script:
-		fastq_screen_args = fastq_screen_args.replaceAll(/'/,"")
-
+		println(name)
+		println(reads)
+		println(outputdir)
 		if (verbose){
 			println ("[MODULE] FASTQ SCREEN ARGS: "+ fastq_screen_args)
 		}

tools/fastq_screen/test/main.nf

@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+nextflow.preview.dsl = 2
+
+params.outdir = "."
+params.fastq_screen_args = ''
+// fastq_screen_args are best passed in to the workflow in the following manner:
+// --fastq_screen_args="--subset 200000 --force"
+
+params.verbose = false
+
+if (params.verbose){
+    println ("[WORKFLOW] FASTQ SCREEN ARGS ARE: " + params.fastq_screen_args)
+}
+
+// TODO: include '../../../nf-core/module_testing/check_process_outputs.nf'
+include '../main.nf'
+
+// Define input channels
+
+ch_read_files = Channel 
+  .fromFilePairs('../../../test-datasets/Ecoli*{1,2}.fastq.gz',size:-1)
+  // .view()  // to check whether the input channel works
+
+// Run the workflow
+workflow {
+    main:
+        FASTQ_SCREEN(ch_read_files, params.outdir, params.fastq_screen_args, params.verbose)
+
+    // TODO .check_output()
+}

tools/fastq_screen/test/nextflow.config

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