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Add supported_alleles.json to handle supported alleles per predictor #262

Merged
merged 1 commit into from
Jan 29, 2025
Merged

Add supported_alleles.json to handle supported alleles per predictor #262

merged 1 commit into from
Jan 29, 2025

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jonasscheid
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@jonasscheid jonasscheid commented Jan 28, 2025 •
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This is a tricky one. Each predictor has its own set (and mostly its own HLA type nomenclature), which they support. This PR introduces a json file assets/supported_alleles.json, which is loaded in the the mhc-binding-subworkflow. This file contains the normalized HLA annotations produced by mhcgnomes (a.k.a the official HLA nomenclature by IMGT e.g.HLA-A*02:01). mhcgnomes allows users to provide a variety of (inofficial) HLA types (e.g. A0201, A*01:01 etc.), which hopefully reduces the frustrating part of finding the correct HLA nomenclature. If you are still unsure how the proper nomenclature looks like, please look at assets/supported_alleles.json

Some small adjustments were sneaked into this PR, e.g. MHCNUGGETSII (class 2) gets its own process and file/allele handling.

Last step before aligning with the devbranch will be to reduce the complexity of handling netmhc tools and the associated imports. There won't be support for multiple versions of netmhcpan and netmhciipan anymore due to models being outdated and maintenance reasons.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/epitopeprediction branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Jan 28, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 97d7b63

+| ✅ 222 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-28 17:49:07

@jonasscheid jonasscheid merged commit eef4be2 into nf-core:mhc-binding-subworkflow Jan 29, 2025
3 of 18 checks passed
@jonasscheid jonasscheid deleted the handle-supported-alleles branch January 29, 2025 06:51
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