From 0fe8b6cb7439567722809d68ab97f1faefd3e18b Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@uni-tuebingen.de>
Date: Mon, 20 Aug 2018 17:45:31 +0200
Subject: [PATCH] Add missing deepTools output for MultiQC/Report

---
 bin/scrape_software_versions.py | 2 ++
 main.nf                         | 1 +
 2 files changed, 3 insertions(+)

diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
index ba6e83ed5..eb7eb55c5 100755
--- a/bin/scrape_software_versions.py
+++ b/bin/scrape_software_versions.py
@@ -14,6 +14,7 @@
     'Picard MarkDuplicates': ['v_markduplicates.txt', r"([\d\.]+)-SNAPSHOT"],
     'Samtools': ['v_samtools.txt', r"samtools (\S+)"],
     'featureCounts': ['v_featurecounts.txt', r"featureCounts v(\S+)"],
+    'deepTools': ['v_deeptools.txt', r"bamCoverage (\S+)"],
     'StringTie': ['v_stringtie.txt', r"(\S+)"],
     'Preseq': ['v_preseq.txt', r"Version: (\S+)"],
     'RSeQC': ['v_rseqc.txt', r"read_duplication.py ([\d\.]+)"],
@@ -32,6 +33,7 @@
 results['featureCounts'] = '<span style="color:#999999;\">N/A</span>'
 results['StringTie'] = '<span style="color:#999999;\">N/A</span>'
 results['Preseq'] = '<span style="color:#999999;\">N/A</span>'
+results['deepTools'] = '<span style="color:#999999;\">N/A</span>'
 results['RSeQC'] = '<span style="color:#999999;\">N/A</span>'
 results['MultiQC'] = '<span style="color:#999999;\">N/A</span>'
 
diff --git a/main.nf b/main.nf
index 68afeca2b..a1abc371c 100644
--- a/main.nf
+++ b/main.nf
@@ -1055,6 +1055,7 @@ process get_software_versions {
     stringtie --version &> v_stringtie.txt
     preseq &> v_preseq.txt
     read_duplication.py --version &> v_rseqc.txt
+    echo \$(bamCoverage --version 2>&1) > v_deeptools.txt
     featureCounts -v &> v_featurecounts.txt
     picard MarkDuplicates --version &> v_markduplicates.txt  || true
     samtools --version &> v_samtools.txt