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Update documentation around VEP and snpEff cache #1222

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Merged
adamrtalbot merged 16 commits into from
Sep 12, 2023
Merged

Update documentation around VEP and snpEff cache #1222

adamrtalbot merged 16 commits into from
Sep 12, 2023

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@adamrtalbot adamrtalbot commented Sep 11, 2023 •
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Changes:

  • Changed order to start with motivation then become more specific
  • Try to introduce the topic of the cache before describing how to use it.
  • Add an additional catch for missing directories within --vep_cache and --snpeff_cache.

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/sarek 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).

@adamrtalbot
Update documentation around VEP and snpEff cache
dcb3268 
Changes:
 - Changed order to start with motivation then become more specific
 - Try to introduce the topic of the cache before describing how to use it.
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github-actions bot commented Sep 11, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a236eab

+| ✅ 140 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-12 15:41:31

maxulysse
maxulysse reviewed Sep 11, 2023
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maxulysse commented Sep 11, 2023

Can you update CHANGELOG

FriederikeHanssen
FriederikeHanssen reviewed Sep 11, 2023
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FriederikeHanssen
FriederikeHanssen reviewed Sep 11, 2023
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FriederikeHanssen
FriederikeHanssen reviewed Sep 11, 2023
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Awesome ❤️ every time I read it it gets more and more clear. Some small suggestions when reading through it, but looks great already

adamrtalbot
adamrtalbot commented Sep 12, 2023
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adamrtalbot
adamrtalbot commented Sep 12, 2023
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adamrtalbot
adamrtalbot commented Sep 12, 2023
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@maxulysse @adamrtalbot
Update docs/usage.md
a236eab 
Co-authored-by: Adam Talbot <[email protected]>
@adamrtalbot adamrtalbot merged commit 767e4af into nf-core:dev Sep 12, 2023
@adamrtalbot adamrtalbot deleted the cache_docs_improvements branch September 12, 2023 16:31
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

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@adamrtalbot @maxulysse @FriederikeHanssen