From 223077e5a665e7374f317733fb3756db7774ff39 Mon Sep 17 00:00:00 2001
From: FelixKrueger <felix.krueger@babraham.ac.uk>
Date: Tue, 17 Mar 2020 21:46:21 +0000
Subject: [PATCH 1/3] MultiQC module and test workflow

---
 tools/multiqc/main.nf              | 32 ++++++++++++++++++++++
 tools/multiqc/test/main.nf         | 44 ++++++++++++++++++++++++++++++
 tools/multiqc/test/nextflow.config |  2 ++
 3 files changed, 78 insertions(+)
 create mode 100644 tools/multiqc/main.nf
 create mode 100755 tools/multiqc/test/main.nf
 create mode 100644 tools/multiqc/test/nextflow.config

diff --git a/tools/multiqc/main.nf b/tools/multiqc/main.nf
new file mode 100644
index 00000000..6fe1daac
--- /dev/null
+++ b/tools/multiqc/main.nf
@@ -0,0 +1,32 @@
+nextflow.preview.dsl=2
+
+process MULTIQC {
+	
+    // tag "FastQC - $sample_id"
+    
+    input:
+	    path (file)
+		val (outdir)
+		val (multiqc_args)
+        // multiqc_args are best passed into the workflow in the following manner:
+        // --multiqc_args="--exlude STAR --title custom_report_title"
+		val (verbose)
+
+	output:
+	    path "*html",       emit: html
+
+	publishDir "${outdir}/multiqc",
+		mode: "copy", overwrite: true
+
+    script:
+
+		if (verbose){
+			println ("[MODULE] MULTIQC ARGS: " + multiqc_args)
+		}
+
+		"""
+		module load multiqc
+		multiqc $multiqc_args -x work . 
+		"""
+
+}
\ No newline at end of file
diff --git a/tools/multiqc/test/main.nf b/tools/multiqc/test/main.nf
new file mode 100755
index 00000000..6e630211
--- /dev/null
+++ b/tools/multiqc/test/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+nextflow.preview.dsl=2
+
+params.outdir = "."
+params.verbose = false
+params.multiqc_args = ''
+
+// include '../../../nf-core/module_testing/check_process_outputs.nf'
+include '../main.nf'
+
+if (params.verbose){
+    println ("[WORKFLOW] MULTIQC ARGS: "          + params.multiqc_args)
+}
+
+multiqc_ch = Channel
+  .fromPath( ['../../../test-datasets/*trimming_report.txt','../../../test-datasets/*fastqc.zip','../../../test-datasets/*screen.txt','../../../test-datasets/*bowtie2_stats.txt'] )
+  .collect()   // collect() flattens all channels to single list
+  // .view()   // view the files in the channel
+  
+
+// Run the workflow
+workflow {
+
+    main:
+        // This is an example workflow for real reads aligned with Bowtie2. Just for illustration purposes
+        
+        // FASTQC          (file_ch, params.outdir, params.fastqc_args, params.verbose)
+        // FASTQ_SCREEN    (file_ch, params.outdir, params.fastq_screen_args, params.verbose)
+        // TRIM_GALORE     (file_ch, params.outdir, params.trim_galore_args, params.verbose)
+        // FASTQC2         (TRIM_GALORE.out.reads, params.outdir, params.fastqc_args, params.verbose)
+        // BOWTIE2         (TRIM_GALORE.out.reads, params.outdir, params.bowtie2_args, params.verbose)
+     
+        // merging channels for MultiQC
+        // multiqc_ch = FASTQC.out.report.mix(
+        //     TRIM_GALORE.out.report,
+        //     FASTQ_SCREEN.out.report,
+        //     FASTQC2.out.report,
+        //     BOWTIE2.out.stats,
+        // ).collect()     
+
+        MULTIQC                          (multiqc_ch, params.outdir, params.multiqc_args, params.verbose)
+
+        // .check_output() TODO
+}
\ No newline at end of file
diff --git a/tools/multiqc/test/nextflow.config b/tools/multiqc/test/nextflow.config
new file mode 100644
index 00000000..63c458ca
--- /dev/null
+++ b/tools/multiqc/test/nextflow.config
@@ -0,0 +1,2 @@
+// docker.enabled = true
+params.outdir = './results'

From 974c6168d6dd45bdc505234117e505adaa417966 Mon Sep 17 00:00:00 2001
From: FelixKrueger <felix.krueger@babraham.ac.uk>
Date: Wed, 18 Mar 2020 10:06:38 +0000
Subject: [PATCH 2/3] Added short description of MultiQC

---
 tools/multiqc/meta.yml | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 tools/multiqc/meta.yml

diff --git a/tools/multiqc/meta.yml b/tools/multiqc/meta.yml
new file mode 100644
index 00000000..04e9ca42
--- /dev/null
+++ b/tools/multiqc/meta.yml
@@ -0,0 +1,26 @@
+name: MultiQC
+description: Aggregate results from bioinformatics analyses across many samples into a single report
+keywords:
+    - QC
+    - bioinformatics tools
+    - Beautiful stand-alone HTML report
+tools:
+    - fastqc:
+        description: |
+            MultiQC searches a given directory for analysis logs and compiles a HTML report.
+            It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+        homepage: https://multiqc.info/
+        documentation: https://multiqc.info/docs/
+input:
+    -
+        - reads:
+            type: file
+            description: List of report file(s)
+output:
+    -
+        - multiqc_report:
+            type: file
+            description: MultiQC report
+            pattern: *multiqc*.html
+authors:
+    - @FelixKrueger

From 5aaacf8173c5f3fce1961bfffef307b0a6164596 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 11 Jul 2020 13:25:51 +0200
Subject: [PATCH 3/3] Update tools/multiqc/main.nf

---
 tools/multiqc/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tools/multiqc/main.nf b/tools/multiqc/main.nf
index 6fe1daac..493497c1 100644
--- a/tools/multiqc/main.nf
+++ b/tools/multiqc/main.nf
@@ -25,8 +25,7 @@ process MULTIQC {
 		}
 
 		"""
-		module load multiqc
 		multiqc $multiqc_args -x work . 
 		"""
 
-}
\ No newline at end of file
+}