Changing the names of the pbsv output #19
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vagkaratzas
requested changes
Feb 19, 2025
| include { PBSV_DISCOVER } from '../../../modules/nf-core/pbsv/discover/main' | ||
| include { PBSV_CALL } from '../../../modules/nf-core/pbsv/call/main' | ||
| include { BCFTOOLS_INDEX } from '../../../modules/nf-core/bcftools/index/main' | ||
| include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_SV } from '../../../modules/nf-core/bcftools/index/main' |
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If a module is only called once within the same subworkflow, you don't have to rename it. You can select it in the modules.config file with a less generic selector like this:
withName: '.*:BAM_SV_VARIANT_CALLING:BCFTOOLS_INDEX' {
ext.prefix = { "${meta.id}.pbsv" }
}
| ext.prefix = {"${meta.id}.pbsv"} | ||
| } | ||
| } | ||
|
|
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Since the prefixes are changing, I guess the generated files will also change names. Be sure to also update the output files in the output.md doc.
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).