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Fix malformed software version regex #759

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jfy133 wants to merge 23 commits into from
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Fix malformed software version regex #759

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da6bea8
Fix malformed software version regex
jfy133 May 28, 2021
6dc290f
Update Changelog
jfy133 May 28, 2021
f4c3af6
Merge branch 'dev' into software_version_fix
jfy133 May 28, 2021
b775bd0
Adding debugging for GHA
jfy133 May 31, 2021
8f7f26b
More samtools debugging
jfy133 May 31, 2021
71b7dfd
Verbosity is a newer thing...
jfy133 May 31, 2021
c48e51e
Replace shell with script black
jfy133 May 31, 2021
c7daf36
Hehehehe forgot to change script variable assignement
jfy133 May 31, 2021
56c1373
Try changing samtools version
jfy133 May 31, 2021
2464080
Oops wrong
jfy133 May 31, 2021
551220a
Try moving BAM filtering to separate CI test
jfy133 May 31, 2021
b0bf1ba
Fix indent
jfy133 May 31, 2021
03e0e1a
More debugging
jfy133 May 31, 2021
234386c
Try replacing -o with redirect for samtools filter
jfy133 May 31, 2021
52c6f18
Fix bam filter command
jfy133 May 31, 2021
87a523c
filter bam auto-produces file names...
jfy133 May 31, 2021
24934b3
Get artefact to find reason for failure
jfy133 Jun 1, 2021
63f5fed
Fix issue with dodgy character
jfy133 Jun 1, 2021
e1841a8
Set up to allways upload artefact and sep. MALT
jfy133 Jun 1, 2021
4623198
Add file
jfy133 Jun 1, 2021
dd4869c
Merge branch 'dev' into software_version_fix
jfy133 Jun 1, 2021
953367f
Make sure ZIP should also be always run
jfy133 Jun 1, 2021
2722592
Merge branch 'software_version_fix' of github.com:nf-core/eager into …
jfy133 Jun 1, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#751](https://github.com/nf-core/eager/pull/751) - Added missing label to mtnucratio
- 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
- [#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 @@ -2940,6 +2940,7 @@ 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 @@ -2958,7 +2959,7 @@ 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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