From d6ef7253b899cbe1fae035ea14a464d32e316955 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Mon, 31 May 2021 21:41:15 +0200 Subject: [PATCH] Software scraping fix --- CHANGELOG.md | 1 + bin/scrape_software_versions.py | 4 ++-- main.nf | 3 ++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b7fdfe363..eb85bd4ba 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py index 5c9c0da9c..74d4ab0be 100755 --- a/bin/scrape_software_versions.py +++ b/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() diff --git a/main.nf b/main.nf index 256dc93e6..b0c3e0d3b 100644 --- a/main.nf +++ b/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