qc and preprocessing nf-core subworkflow added#59
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Joon-Klaps
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Dec 2, 2025
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Minor detail regarding the MMseqs modules
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| // TODO remove if unused | ||
| // include { MMSEQS_SEARCH } from '../modules/nf-core/mmseqs/search/main' | ||
| // include { MTMALIGN_ALIGN } from '../modules/nf-core/mtmalign/align/main' | ||
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Looking more in depth, the modules themselves aren't even used in the pipeline?
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Other people have left them there...so for now, until I figure out what they want to do with them for the first release, I've just commented ;)
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Thanks @Joon-Klaps ! |
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Closes #7
Combination of
seqkitandseqfutools similar to the proteinfamilies pipeline.seqfu_statsoutput example:seqkitpre-processing option examples (found in modules.config):PR checklist
nf-core pipelines lint).nf-test test */local --profile=~test,dockerfor all new local tests).nf-test test */local --profile=~test,docker,debug).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).docs/images/proteinannotator-metromap.light.excalidraw.pnganddocs/images/proteinannotator-metromap.light.excalidraw.png(edit the light version only, then export and turn on dark mode) are both updated (use the excalidraw website or VS Code plugin to edit)