From f8916eb9b53b9ab7c425d239c2a8d77338322794 Mon Sep 17 00:00:00 2001
From: FelixKrueger <felix.krueger@babraham.ac.uk>
Date: Mon, 16 Mar 2020 14:17:38 +0000
Subject: [PATCH] FastQC module is working and now accepting arguments

---
 tools/fastqc/main.nf              | 45 +++++++++++++++++++++----------
 tools/fastqc/meta.yml             |  6 +++--
 tools/fastqc/test/main.nf         | 25 +++++++++--------
 tools/fastqc/test/nextflow.config |  4 +--
 4 files changed, 49 insertions(+), 31 deletions(-)
 mode change 100644 => 100755 tools/fastqc/test/main.nf

diff --git a/tools/fastqc/main.nf b/tools/fastqc/main.nf
index 65ba5981..83956ae8 100644
--- a/tools/fastqc/main.nf
+++ b/tools/fastqc/main.nf
@@ -1,20 +1,37 @@
-process fastqc {
-    tag "FastQC - $sample_id"
-    publishDir "${params.outdir}/fastqc", mode: 'copy',
-        saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
+nextflow.preview.dsl = 2
 
-    container 'quay.io/biocontainers/fastqc:0.11.8--2'
+process FASTQC {	
+    
+    // tag "FastQC - $sample_id"
 
-    input:
-    tuple sample_id, path(reads)
+	input:
+	    tuple val(name), path(reads)
+		val (outputdir)
+        // fastqc_args are best passed into the workflow in the following manner:
+        // --fastqc_args="--nogroup -a custom_adapter_file.txt"
+		val (fastqc_args)
+		val (verbose)
 
-    output:
-    path "*_fastqc.{zip,html}"
+	output:
+	    tuple val(name), path ("*fastqc*"), emit: all
+		path "*.zip",                       emit: report // e.g. for MultiQC later
+	
+    // container 'quay.io/biocontainers/fastqc:0.11.8--2' 
 
-    script:
-    """
-    fastqc -q $reads
+	publishDir "$outputdir",
+		mode: "copy", overwrite: true
+
+	script:
+
+		if (verbose){
+			println ("[MODULE] FASTQC ARGS: " + fastqc_args)
+		}
+
+		"""
+		module load fastqc
+		fastqc $fastqc_args -q -t 2 $reads
+
+        fastqc --version &> fastqc.version.txt
+		"""
 
-    fastqc --version &> fastqc.version.txt
-    """
 }
diff --git a/tools/fastqc/meta.yml b/tools/fastqc/meta.yml
index 0d5afc23..0d67f866 100644
--- a/tools/fastqc/meta.yml
+++ b/tools/fastqc/meta.yml
@@ -16,7 +16,7 @@ tools:
         documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
 input:
     -
-        - sample_id:
+        - name:
             type: string
             description: Sample identifier
         - reads:
@@ -29,4 +29,6 @@ output:
             description: FastQC report
             pattern: *_fastqc.{zip,html}
 authors:
-    - @ewels
+    - 
+        - @ewels
+        - @FelixKrueger
diff --git a/tools/fastqc/test/main.nf b/tools/fastqc/test/main.nf
old mode 100644
new mode 100755
index c349bbe8..9ec2d338
--- a/tools/fastqc/test/main.nf
+++ b/tools/fastqc/test/main.nf
@@ -1,22 +1,21 @@
 #!/usr/bin/env nextflow
 nextflow.preview.dsl = 2
-include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
-include '../main.nf' params(params)
+
+params.outdir = "."             // gets set in nextflow.config file (as './results/fastqc')
+params.fastqc_args = ''
+params.verbose = false
+
+// TODO: check the output files in some way
+// include '../../../nf-core/module_testing/check_process_outputs.nf'
+include '../main.nf'
 
 // 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][0]) ] ] }
-  .set { ch_read_files }
+ch_read_files = Channel 
+    .fromFilePairs('../../../test-datasets/test*{1,2}.fastq.gz',size:-1)
+    // .view()  // to check whether the input channel works
 
 // Run the workflow
 workflow {
-    fastqc(ch_read_files)
+    FASTQC (ch_read_files, params.outdir, params.fastqc_args, params.verbose)
     // .check_output()
 }
diff --git a/tools/fastqc/test/nextflow.config b/tools/fastqc/test/nextflow.config
index c137a138..e28180ad 100644
--- a/tools/fastqc/test/nextflow.config
+++ b/tools/fastqc/test/nextflow.config
@@ -1,2 +1,2 @@
-docker.enabled = true
-params.outdir = './results'
+// docker.enabled = true
+params.outdir = './results/fastqc'