Software scraping fix

Author: jfy133

CHANGELOG.md

@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - General code cleanup and standardisation of parameters with no default setting
 - [#750](https://github.com/nf-core/eager/issues/750) - Fixed piped commands requesting the same number of CPUs at each command step
 - [#757](https://github.com/nf-core/eager/issues/757) - Removed confusing 'Data Type' variable from MultiQC workflow summary (not consistent with TSV input)
+- [#759](https://github.com/nf-core/eager/pull/759) - Fixed malformed software scraping regex that resulted in N/A in MultiQC report
 
 ### `Dependencies`
 

bin/scrape_software_versions.py

@@ -16,7 +16,7 @@
     'Bowtie2': ['v_bowtie2.txt', r"bowtie2-([0-9]+\.[0-9]+\.[0-9]+) -fdebug"],
     'Qualimap': ['v_qualimap.txt', r"QualiMap v.(\S+)"],
     'GATK HaplotypeCaller': ['v_gatk.txt', r" v(\S+)"],
-    #'GATK UnifiedGenotyper': ['v_gatk3_5.txt', r"version (\S+)"],
+    'GATK UnifiedGenotyper': ['v_gatk3.txt', r"(\S+)"],
     'bamUtil' : ['v_bamutil.txt', r"Version: (\S+);"],
     'fastP': ['v_fastp.txt', r"([\d\.]+)"],
     'DamageProfiler' : ['v_damageprofiler.txt', r"DamageProfiler v(\S+)"],
@@ -37,7 +37,7 @@
     'kraken':['v_kraken.txt', r"Kraken version (\S+)"],
     'eigenstrat_snp_coverage':['v_eigenstrat_snp_coverage.txt',r"(\S+)"],
     'mapDamage2':['v_mapdamage.txt',r"(\S+)"],
-    'bbduk':['v_bbduk.txt',r"(\S+)"]
+    'bbduk':['v_bbduk.txt',r"(.*)"]
 }
 
 results = OrderedDict()

main.nf

@@ -2939,6 +2939,7 @@ process get_software_versions {
     qualimap --version &> v_qualimap.txt 2>&1 || true
     preseq &> v_preseq.txt 2>&1 || true
     gatk --version 2>&1 | head -n 1 > v_gatk.txt 2>&1 || true
+    gatk3 --version 2>&1 > v_gatk3.txt 2>&1 || true
     freebayes --version &> v_freebayes.txt 2>&1 || true
     bedtools --version &> v_bedtools.txt 2>&1 || true
     damageprofiler --version &> v_damageprofiler.txt 2>&1 || true
@@ -2957,7 +2958,7 @@ process get_software_versions {
     pileupCaller --version &> v_sequencetools.txt 2>&1 || true
     bowtie2 --version | grep -a 'bowtie2-.* -fdebug' > v_bowtie2.txt || true
     eigenstrat_snp_coverage --version | cut -d ' ' -f2 >v_eigenstrat_snp_coverage.txt || true
-    mapDamage2 --version > v_mapdamage.txt || true
+    mapDamage --version > v_mapdamage.txt || true
     bbduk.sh | grep 'Last modified' | cut -d' ' -f 3-99 > v_bbduk.txt || true
 
     scrape_software_versions.py &> software_versions_mqc.yaml