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Update epytope and Ensembl reference handling #213

Merged
merged 19 commits into from
Oct 11, 2023
Merged

Update epytope and Ensembl reference handling #213

merged 19 commits into from
Oct 11, 2023

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christopher-mohr
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@christopher-mohr christopher-mohr commented Oct 3, 2023 •
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This

  • updates the epytope version to the most recent and custom container
  • changes the Ensembl (biomart) reference handling, the default reference is now the most recent for GRCh37 and GRCh38 respectively. In addition, users can now provide any valid Ensembl reference (archive) version.
  • changes the parameter name and description of the Ensembl reference parameter
  • moves the handling of the parameter from the python script to modules.config
  • ensures that methods from epytope are used if available and remove corresponding code in epaa.py

Note
The handling of the most recent Ensembl (biomart) version is now possible due to the functionality in epytope available with the most recent version. This was implemented in a way to be as adaptive as possible to DB schema changes on the Ensembl BioMart side (retrieval of field names via API etc), however with old archive versions (e.g. 2014 and 2018) there are still issues due to inconsistencies on the Ensembl side.

I will still update to the most recent template to make the linting checks happy. :)

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>).
  • 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).

@christopher-mohr christopher-mohr added enhancement New feature or request do not merge labels Oct 3, 2023
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github-actions bot commented Oct 3, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 747341b

+| ✅ 160 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowEpitopeprediction.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-11 18:45:36

@christopher-mohr christopher-mohr mentioned this pull request Oct 3, 2023
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jonasscheid
jonasscheid requested changes Oct 9, 2023
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Thanks for incorporating this 🚀
I only see some minor rendering issues, else lgtm

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@christopher-mohr christopher-mohr merged commit e0d2ab9 into nf-core:dev Oct 11, 2023
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@christopher-mohr christopher-mohr deleted the update_pipeline_and_fix_biomart_con branch October 11, 2023 20:07
@christopher-mohr christopher-mohr mentioned this pull request Nov 6, 2023
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@jonasscheid jonasscheid jonasscheid approved these changes

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