Merge pull request #24 from FelixKrueger/fastq_screen

Added FastQ Screen module

tools/fastq_screen/main.nf

@@ -0,0 +1,38 @@
+nextflow.preview.dsl=2
+
+process FASTQ_SCREEN {
+	
+	// depending on the number of genomes and the type of genome (e.g. plants!), memory needs to be ample!
+	// label 'bigMem'
+	// label 'multiCore'
+
+    input:
+	    tuple val(name), path(reads)
+		val (outputdir)
+		// 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:
+	    path "*png",  emit: png
+	    path "*html", emit: html
+		path "*txt",  emit: report
+
+	publishDir "$outputdir",
+		mode: "link", overwrite: true
+
+    script:
+		println(name)
+		println(reads)
+		println(outputdir)
+		if (verbose){
+			println ("[MODULE] FASTQ SCREEN ARGS: "+ fastq_screen_args)
+		}
+
+	"""
+	module load fastq_screen
+	fastq_screen $fastq_screen_args $reads
+	"""
+
+}

tools/fastq_screen/meta.yml

@@ -0,0 +1,31 @@
+name: FastQ Screen
+description: Run FastQ Screen on sequenced reads for Species Identification
+keywords:
+    - Quality Control
+    - Species Screen
+    - Contamination
+tools:
+    - fastqc:
+        description: |
+            FastQ Screen allows you to screen a library of sequences in
+            FastQ format against a set of sequence databases so you can
+            see if the composition of the library matches with what you expect.
+        homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
+        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/_build/html/index.html
+input:
+    -
+        - sample_id:
+            type: string
+            description: Sample identifier
+        - reads:
+            type: file
+            description: Input FastQ file
+output:
+    -
+        - report:
+            type: file
+            description: FastQ Screen report
+            pattern: *_screen.{txt,html,png}
+            optional_pattern: *_screen.bisulfite_orientation.png
+authors:
+    - @FelixKrueger

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'