Automatic restart & General csv file updates#562
Merged
FriederikeHanssen merged 32 commits intonf-core:devfrom Jun 9, 2022
Merged
Automatic restart & General csv file updates#562FriederikeHanssen merged 32 commits intonf-core:devfrom
FriederikeHanssen merged 32 commits intonf-core:devfrom
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maxulysse
reviewed
Jun 9, 2022
maxulysse
reviewed
Jun 9, 2022
| withName: 'BCFTOOLS_STATS'{ | ||
| ext.when = { !(params.skip_tools && params.skip_tools.contains('bcftools')) } | ||
| ext.prefix = { meta.type ? "${meta.variantcaller}_${vcf.baseName.minus(".vcf")}_${meta.type}" : "${meta.variantcaller}_${vcf.baseName.minus(".vcf")}" } | ||
| ext.prefix = { "${vcf.baseName.minus(".vcf")}" } |
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then why minus(".vcf") if basename here?
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here baseName removes .gz and then vcf is still left
Using simpleName would remove also anything after a dot in the regular filename
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will comment this better for future us
FriederikeHanssen
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Test on actual data ran through |
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This PR adds automatic restart when no
--input+ any step butmappingis specified. In addition, the way the csvs are written is changed:When multiple variantcallers are selected it looks something like this:
file.name, to ensure compatibility even when prefixes inmodules.configor the modules themselves are changed, i.e. custom configs or upstream updates that would lead to multiple points of adaptation.outdir/csv/Other changes:
typeis not needed anymore. The file name for annotation are retrieved from the vcf directly and not custom build. This also ensures that annotated and called vcf files have a similar file name structure to ease postprocessing when searching for files.target_bedand adapt docs forintervalsPR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).