Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Conversation

christopher-mohr
Copy link
Collaborator

@christopher-mohr christopher-mohr commented May 15, 2024 •
edited
Loading

  • 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented May 15, 2024 •
edited
Loading

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
Copy link
Collaborator Author

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
View reviewed changes
Copy link
Contributor

@jonasscheid jonasscheid left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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 <[email protected]>
@christopher-mohr
Copy link
Collaborator Author

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.

@christopher-mohr
Copy link
Collaborator Author

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
17 checks passed
@christopher-mohr christopher-mohr deleted the merge-template-update-2-14-1 branch May 16, 2024 08:16
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jonasscheid jonasscheid jonasscheid approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@christopher-mohr @jonasscheid @nf-core-bot