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Fix RunMultiQC error #657

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szilvajuhos merged 2 commits into from
Oct 1, 2018
Merged

Fix RunMultiQC error #657

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040b37d
ensure that all tools give out versions
maxulysse Sep 26, 2018
0fc2252
update CHANGELOG
maxulysse Sep 26, 2018
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- [#646](https://github.com/SciLifeLab/Sarek/pull/646) - Update [`pathfindr`](https://github.com/NBISweden/pathfindr) submodule

### `Fixed`

- [#657](https://github.com/SciLifeLab/Sarek/pull/657) - Fix `RunMultiQC.nf` bug

## [2.2.0] - Skårki - 2018-09-21

### `Added`
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28 changes: 14 additions & 14 deletions runMultiQC.nf
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Expand Up @@ -50,28 +50,28 @@ process GetVersionAll {
publishDir directoryMap.multiQC, mode: 'link'

input:
file(versions) from Channel.fromPath("${directoryMap.version}/*").collect()
file(versions) from Channel.fromPath("${directoryMap.version}/*").collect().ifEmpty(file ("empty"))

output:
file ("tool_versions_mqc.yaml") into versionsForMultiQC
file ("tool_versions_mqc.yaml") into versionsForMultiQC

when: !params.noReports

script:
"""
bcftools version > v_bcftools.txt
bcftools version > v_bcftools.txt 2>&1 || true
bwa &> v_bwa.txt 2>&1 || true
configManta.py --version > v_manta.txt
configureStrelkaGermlineWorkflow.py --version > v_strelka.txt
echo "${params.version}" &> v_sarek.txt
echo "${workflow.nextflow.version}" &> v_nextflow.txt
fastqc -v > v_fastqc.txt
freebayes --version > v_freebayes.txt
gatk ApplyBQSR --help 2>&1 | grep Version: > v_gatk.txt
multiqc --version &> v_multiqc.txt
qualimap --version &> v_qualimap.txt
samtools --version &> v_samtools.txt
vcftools --version > v_vcftools.txt
configManta.py --version > v_manta.txt 2>&1 || true
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@alneberg alneberg Sep 26, 2018

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Will be much harder to spot errors with MultiQC if we ignore all potential version fetching errors, no?

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@maxulysse maxulysse Sep 27, 2018

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I guess it doesn't really matter, because, if a tool is failing, it will be seen when we're really using the tool, not when we want to check its version.
Worst case scenario here, we won't have it display properly.

configureStrelkaGermlineWorkflow.py --version > v_strelka.txt 2>&1 || true
echo "${params.version}" &> v_sarek.txt 2>&1 || true
echo "${workflow.nextflow.version}" &> v_nextflow.txt 2>&1 || true
fastqc -v > v_fastqc.txt 2>&1 || true
freebayes --version > v_freebayes.txt 2>&1 || true
gatk ApplyBQSR --help 2>&1 | grep Version: > v_gatk.txt 2>&1 || true
multiqc --version &> v_multiqc.txt 2>&1 || true
qualimap --version &> v_qualimap.txt 2>&1 || true
samtools --version &> v_samtools.txt 2>&1 || true
vcftools --version &> v_vcftools.txt 2>&1 || true

scrape_tool_versions.py &> tool_versions_mqc.yaml
"""
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