From b56a0322ab984cd4bdfeebb507c55a91904de9b4 Mon Sep 17 00:00:00 2001
From: Abhinav Sharma <abhi18av@users.noreply.github.com>
Date: Tue, 8 Dec 2020 18:57:14 +0530
Subject: [PATCH] Apply suggestions from code review by @drpatelh

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/multiqc/main.nf       | 14 +++++++-------
 software/multiqc/meta.yml      |  8 ++++----
 tests/software/fastqc/main.nf  |  2 +-
 tests/software/multiqc/main.nf |  6 ++----
 4 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/software/multiqc/main.nf b/software/multiqc/main.nf
index b682b583..80dfb0c5 100644
--- a/software/multiqc/main.nf
+++ b/software/multiqc/main.nf
@@ -5,28 +5,28 @@ params.options = [:]
 def options    = initOptions(params.options)
 
 process MULTIQC {
-    tag "multiqc"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: '') }
 
-    conda(params.enable_conda ? "bioconda::multiqc=1.9" : null)
+    conda     (params.enable_conda ? "bioconda::multiqc=1.9" : null)
     container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
 
     input:
-    path multiqc_config
-    path multiqc_custom_config
-    path('fastqc/*')
+    path multiqc_files
 
     output:
     path "*multiqc_report.html", emit: report
-    path "*_data", emit: data
-    path "*_plots", optional: true, emit: plots
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
+    path "*.version.txt"       , emit: version
 
     script:
+    def software = getSoftwareName(task.process)
     def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
     """
     multiqc -f $options.args $custom_config .
+     multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
     """
 }
diff --git a/software/multiqc/meta.yml b/software/multiqc/meta.yml
index 9d2c2dde..4fac4394 100644
--- a/software/multiqc/meta.yml
+++ b/software/multiqc/meta.yml
@@ -28,16 +28,16 @@ params:
             Run the module with Conda using the software specified
             via the `conda` directive
 input:
-    - generic_report:
+    - multiqc_files:
         type: file
         description: |
-            List of report, for example the html and zip output of FastQC
+            List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
 output:
-    - dir:
+    - data:
         type: dir
         description: MultiQC data dir
         pattern: "multiqc_data"
-    - html:
+    - report:
         type: file
         description: MultiQC report file
         pattern: "multiqc_report.html"
diff --git a/tests/software/fastqc/main.nf b/tests/software/fastqc/main.nf
index 7885c903..27411a17 100644
--- a/tests/software/fastqc/main.nf
+++ b/tests/software/fastqc/main.nf
@@ -31,6 +31,6 @@ workflow test_paired_end {
 
     emit:
     html = FASTQC_PE.out.html
-    zip = FASTQC_PE.out.zip
+    zip  = FASTQC_PE.out.zip
 
 }
diff --git a/tests/software/multiqc/main.nf b/tests/software/multiqc/main.nf
index 8bc429c6..ab25e8c3 100644
--- a/tests/software/multiqc/main.nf
+++ b/tests/software/multiqc/main.nf
@@ -6,15 +6,13 @@ include { MULTIQC } from '../../../software/multiqc/main.nf' addParams(options:
 include { test_paired_end } from '../fastqc/main.nf' addParams(options: [publish_dir: 'test_paired_end'])
 
 ch_multiqc_config = file("$launchDir/tests/software/multiqc/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
 
 workflow test_multiqc {
     test_paired_end()
 
     input = [
-        ch_multiqc_config,
-        ch_multiqc_custom_config.collect().ifEmpty([]),
-        test_paired_end.out.zip.collect { it[1] }.ifEmpty([])
+        ch_multiqc_config
+            .mix(test_paired_end.out.zip.collect { it[1] }.ifEmpty([]))
     ]
 
     MULTIQC(*input)