Release 3.0.0 #277
Release 3.0.0 #277
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…ation of mhc binding for peptides without functionality, runs through with stub
New structure of mhc binding subworkflow
Fix stub run in mhc binding subworkflow with new template
Initial setup of netmhcpan module
…n external tools import
…. Breaks the current main workflow structure, which needs to be adjust in future PRs
Add initial draft of netmhciipan module
… ci tests. mhcflurry fetches models from server, and if multiple tests spawn in parallel, the server doesn't respond anymore
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I cannot fix the CI tests for nf-core download on Edit: Discussion here: https://nfcore.slack.com/archives/C04QR0T3G3H/p1745924266198209 |
assets/supported_alleles.json
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These are all the supported mhc alleles of all mhc binding predictors (netmhc(ii)pan, mhcflurry, mhcnuggets(ii)). Unfortunately, non of the tools provide sufficient tooling such that I could check their supported alleles. This file is loaded in the prepare_prediction_input.nf. To filter out non-supported mhc alleles that the user provided.
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is this specific to a genome in particular?
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Yes. Every human has 6 HLA class I alleles (3 maternal, 3 paternal). Currently afaik over 1k HLA class I allele variants are known. For HLA class II alleles it is even more complex. That results in having such a big amount of HLA alleles in that file
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https://hla.alleles.org/pages/nomenclature/naming_alleles/ if you want to know more
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Release PR feedback
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Thank you already for the reviews @kubranarci @famosab @maxulysse! 🙏🏼 Not quite sure how to handle the new CodeQL failiing tests, since I included the ci.yml from the dev template. I started a discussion here: https://nfcore.slack.com/archives/CE5LG7WMB/p1746538936390669 Edit: TL;DR: We should ignore the failing tests. |
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Would be great to get approves from @famosab and @maxulysse until Friday 🙏🏼 Thank you again |
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Its a nit pick but I would introduce a Dependencies section where you denote old and new software versions when modules are being updated :) maybe you can start this beginning with pipeline version 3.0.0
Major release: Comprehensive restructure of pipeline #205
Most important changes:
syfpeithi--toolsare:mhcflurry(default),mhcnuggets,mhcnuggetsii,netmhcpan,netmhciipanepaa.pyinto a subworkflowMHC_BINDING_PREDICTION, which allows simple addition of future predictorsmhcgnomesand supported alleles for each predictor are stored inassets/supported_alleles.jsonepaa.pyandEPYTOPE_PREDICTION_VARto only be used with variants. Output:tsvof peptides from variants. Use--fasta_outputto generate additional variant-based protein fasta fileFASTA2PEPTIDES)--wide_format_output<outdir>/predictions/<meta.id>/<meta.id>.tsvto<outdir>/predictions/<meta.id>.tsvPR checklist
nf-core 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).