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Merge template updates up to 2.14.1 #243

Merged
merged 11 commits into from
May 16, 2024
Merged

Merge template updates up to 2.14.1 #243

merged 11 commits into from
May 16, 2024

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christopher-mohr
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@christopher-mohr christopher-mohr commented May 15, 2024 •
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  • Merging the last two template updates
  • Add check if protein information available from BioMart

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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 May 15, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 16d714a

+| ✅ 202 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-16 06:16:32

@christopher-mohr
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Ensembl most recent BioMart version currently unavailable, therefore the grch38 test fails:

Server Status
The Ensembl websites and REST servers are currently unavailable as we apply updates. Our archive sites, FTP site and public MySQL servers are unaffected. Please try again shortly.

jonasscheid
jonasscheid requested changes May 15, 2024
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LGTM, thanks! Only adjusting the changelog date and name remains

CHANGELOG.md Outdated Show resolved Hide resolved
@christopher-mohr @jonasscheid
Update CHANGELOG.md
fe02f4d 
Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
@christopher-mohr
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LGTM, thanks! Only adjusting the changelog date and name remains

I will still check the issue with GRCH38 which does not seem to be (solely) caused by the Ensembl unavailability.

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In the meantime, Ensembl replied and confirmed that there are currently some issues with the most recent BioMart version. What happened is that the protein field/table we are using to retrieve protein information was/is currently not accessible and therefore no information is available in the df.

I added a check to make sure that the information is only accessed if available.

@jonasscheid jonasscheid merged commit 0282263 into nf-core:dev May 16, 2024
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@christopher-mohr christopher-mohr deleted the merge-template-update-2-14-1 branch May 16, 2024 08:16
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