8000 Fix unique variant annotation field handling #136 by jonasscheid · Pull Request #135 · nf-core/epitopeprediction · GitHub
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Fix unique variant annotation field handling #136 #135

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Merged
merged 4 commits into from
Feb 8, 2022
Merged

Fix unique variant annotation field handling #136 #135

merged 4 commits into from
Feb 8, 2022

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jonasscheid
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@jonasscheid jonasscheid commented Feb 8, 2022 •
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Minor change:
Some variants in SnpEff (v.4.3t) contain a LOF flag, which altered the dynamic structure of variant annotations. Since most variants do not have this flag, it caused an error. In general, the pipeline crashes, when a variant has metadata, which other variants don't have.

This PR closes #136

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.
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github-actions bot commented Feb 8, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 0b116bb

+| ✅ 140 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-02-08 14:54:05

marissaDubbelaar
marissaDubbelaar approved these changes Feb 8, 2022
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LGTM

christopher-mohr
christopher-mohr requested changes 8000 Feb 8, 2022
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Some of the checks/tests do not pass at the moment (the external tools and markdownlint is fine but the rest should pass).

We should also mention, that this fixes the general case where one (or more) variant has annotated metadata which is not available for others, like LOF in this case.

It would also be good to add it to the CHANGELOG.

ggabernet
ggabernet approved these changes Feb 8, 2022
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Same points as above but otherwise looks good to me

@jonasscheid jonasscheid changed the title Avoid erroneous LOF annotation of SnpEff Fix #136 Feb 8, 2022
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Also the changelog should be updated 👍

@jonasscheid jonasscheid changed the title Fix #136 Allow variants with unique annotation fields Feb 8, 2022
christopher-mohr
christopher-mohr requested changes Feb 8, 2022
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@jonasscheid jonasscheid changed the title Allow variants with unique annotation fields Fix unique variant annotation field handling #136 Feb 8, 2022
christopher-mohr
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LGTM!

@christopher-mohr christopher-mohr merged commit e9fed37 into nf-core:dev Feb 8, 2022
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Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install markdownlint-cli
  • Fix the markdown errors
    • Automatically: markdownlint . --fix
    • Manually resolve anything left from markdownlint .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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@ggabernet ggabernet ggabernet approved these changes

@christopher-mohr christopher-mohr christopher-mohr approved these changes

@marissaDubbelaar marissaDubbelaar marissaDubbelaar approved these changes

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