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Check sample sheet uses Row Checker class #209

Merged
merged 11 commits into from
Aug 29, 2023
Merged

Check sample sheet uses Row Checker class #209

merged 11 commits into from
Aug 29, 2023

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alina-bauer
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@alina-bauer alina-bauer commented Aug 22, 2023 •
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The RowChecker class we could use to check the basic validity of the input.

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 22, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 18507f6

+| ✅ 159 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-29 12:23:10

@alina-bauer alina-bauer reopened this Aug 22, 2023
@alina-bauer
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The test_grch38_variant_tsv probably fails because of a key error in the ensemble database. This is the same problem as in PR #200.

jonasscheid
jonasscheid requested changes Aug 22, 2023
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Some minor things, otherwise LGTM 👍🏼

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christopher-mohr
christopher-mohr reviewed Aug 23, 2023
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@alina-bauer alina-bauer marked this pull request as ready for review August 29, 2023 11:25
@jonasscheid jonasscheid merged commit 50812f9 into nf-core:dev Aug 29, 2023
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@jonasscheid jonasscheid jonasscheid approved these changes

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@alina-bauer @christopher-mohr @jonasscheid