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Allele data can also be used via internet link in sample sheet #211

Merged
merged 3 commits into from
Aug 31, 2023
Merged

Allele data can also be used via internet link in sample sheet #211

merged 3 commits into from
Aug 31, 2023

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alina-bauer
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@alina-bauer alina-bauer commented Aug 31, 2023 •
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Now allele data as an internet link can also be used in pipeline.
Restoring the functionality of the previous PR.

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).

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github-actions bot commented Aug 31, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 89259c6

+| ✅ 159 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-31 08:22:27

jonasscheid
jonasscheid approved these changes Aug 31, 2023
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Local runs run through except grch38 -> #208

@jonasscheid jonasscheid merged commit 6700180 into nf-core:dev Aug 31, 2023
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@christopher-mohr
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Just two comments:

  • the pipeline does not accept .alleles files anymore now. Might not be necessary, just important to note that the behavior of the pipeline is changed.
  • why do you want to handle "remotely stored" files manually in the python script? The file staging is done by the pipeline/nextflow functionality anyway.

@alina-bauer
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I will write it in my backlog.. the .alleles file will follow soon.
Yes I didn't have that in mind.. the file staging by nextflow is much easier, this functionality will follow soon together with the yet not used allele check.

@christopher-mohr
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I will write it in my backlog.. the .alleles file will follow soon. Yes I didn't have that in mind.. the file staging by nextflow is much easier, this functionality will follow soon together with the yet not used allele check.

Thanks for the feedback!

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@jonasscheid jonasscheid jonasscheid approved these changes

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@alina-bauer @christopher-mohr @jonasscheid