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Software version fix #760

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Merged
jfy133 merged 1 commit into from
May 31, 2021
Merged

Software version fix #760

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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`

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4 changes: 2 additions & 2 deletions bin/scrape_software_versions.py
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Expand Up @@ -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+)"],
Expand All @@ -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()
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3 changes: 2 additions & 1 deletion main.nf
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Expand Up @@ -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
Expand All @@ -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
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