Fix software versioning

Author: jfy133

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - [#824](https://github.com/nf-core/eager/issues/824) Fixes large memory footprint of bedtools coverage calculation.
 - [#822](https://github.com/nf-core/eager/issues/822) Fixed post-adapterremoval trimmed files not being lane-merged and included in downstream analyses
+- Fixed a couple of software version reporting commands
 
 ### `Dependencies`
 

bin/scrape_software_versions.py

@@ -9,13 +9,13 @@
     "FastQC": ["v_fastqc.txt", r"FastQC v(\S+)"],
     "MultiQC": ["v_multiqc.txt", r"multiqc, version (\S+)"],
     'AdapterRemoval':['v_adapterremoval.txt', r"AdapterRemoval ver. (\S+)"],
-    'Picard MarkDuplicates': ['v_markduplicates.txt', r"(\S+)"],
+    'Picard MarkDuplicates': ['v_markduplicates.txt', r"Version:(\S+)"],
     'Samtools': ['v_samtools.txt', r"samtools (\S+)"],
     'Preseq': ['v_preseq.txt', r"Version: (\S+)"],
     'BWA': ['v_bwa.txt', r"Version: (\S+)"], 
     '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 HaplotypeCaller': ['v_gatk.txt', r"The Genome Analysis Toolkit \(GATK\) v(\S+)"],
     'GATK UnifiedGenotyper': ['v_gatk3.txt', r"(\S+)"],
     'bamUtil' : ['v_bamutil.txt', r"Version: (\S+);"],
     'fastP': ['v_fastp.txt', r"([\d\.]+)"],

main.nf

@@ -3088,7 +3088,7 @@ process get_software_versions {
     ( exec 7>&1; picard MarkDuplicates --version 2>&1 >&7 | grep -v '/' >&2 ) 2> v_markduplicates.txt || true
     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
+    gatk --version 2>&1 | grep '(GATK)' > v_gatk.txt 2>&1 || true
     gatk3 --version 2>&1 | head -n 1 > v_gatk3.txt 2>&1 || true
     freebayes --version &> v_freebayes.txt 2>&1 || true
     bedtools --version &> v_bedtools.txt 2>&1 || true