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Add initial mhcflurry module #253

Merged
merged 5 commits into from
Dec 17, 2024
Merged

Add initial mhcflurry module #253

merged 5 commits into from
Dec 17, 2024

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jonasscheid
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@jonasscheid jonasscheid commented Dec 16, 2024 •
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Add initial mhcflurry module #215 #205

  • Download functionality is implemented in the module itself and will be only called once. Models are always stored in ~/.local/share/mhcflurry/<release>. Unfortunately, that cannot be changed
  • MHCflurry presentation_percentile is used as metric to define a binder ( see Paper )
  • Newest 2.1.4 version is currently not usable via conda due to dependency issues
  • Check for supported alleles will be implemented in future PRs
  • Tests will be implemented in future PRs

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.
  • README.md is updated (including new tool citations and authors/contributors).

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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 Dec 16, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0610c87

+| ✅ 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 2024-12-17 07:11:20

@jonasscheid jonasscheid merged commit 67bc3a2 into nf-core:mhc-binding-subworkflow Dec 17, 2024
5 of 18 checks passed
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@jonasscheid @nf-core-bot