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

fix annoying PRESEQ failure #382

Closed
wants to merge 3 commits into from
Closed

fix annoying PRESEQ failure #382

wants to merge 3 commits into from

Conversation

bounlu
Copy link

@bounlu bounlu commented Feb 22, 2024

Fixes #161

@bounlu bounlu requested a review from a team as a code owner February 22, 2024 09:08
@github-actions GitHub Actions
Copy link

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @bounlu,

It looks like this pull-request is has been made against the nf-core/methylseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/methylseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@bounlu bounlu changed the base branch from master to dev February 22, 2024 14:47
@github-actions GitHub Actions
Copy link

github-actions bot commented Feb 27, 2024 •
edited
Loading

nf-core lint overall result: Failed ❌

Posted for pipeline commit 415f8ab

+| ✅ 167 tests passed       |+
#| ❔   5 tests were ignored |#
-| ❌   8 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowMethylseq.groovy
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-27 08:45:57

ewels
ewels requested changes Feb 28, 2024
View reviewed changes
Copy link
Member

@ewels ewels left a comment

Choose a reason for hiding this comment

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

Please submit this upstream, to the nf-core modules repo. Direct link to the equivalent file is here. Once it's merged there we can update the module in this pipeline.

This preseq lcextrap module is used by at least 6 different pipelines (see https://nf-co.re/modules/preseq_lcextrap), so fixing it upstream improves all of them:

included in:
atacseq, chipseq, cutandrun, methylseq, nascent, rnaseq

Thanks,

Phil

@ewels
Copy link
Member

ewels commented Feb 28, 2024

Leaving the PR open here until a new one is opened in the modules repo, just so that the change doesn't get lost.

@ewels
Copy link
Member

ewels commented Mar 8, 2024

@bounlu please shout if you don't intend to submit this upstream, so that someone else can take the task. It'd be nice to get this improvement into the pipeline.

@bounlu
Copy link
Author

bounlu commented Mar 8, 2024

It would be great if someone else do it. Thanks.

@maxulysse
Copy link
Member

nf-core/modules#5091

@maxulysse
Copy link
Member

@bounlu the module has been updated upstream.
Now you just need to run nf-core modules update preseq/lcextrap on your PR and push the changes

@ewels ewels mentioned this pull request Mar 22, 2024
Merged
@ewels
Copy link
Member

ewels commented Mar 22, 2024

PR in #390

@ewels ewels closed this Mar 22, 2024
@ewels ewels deleted the fix_preseq branch March 22, 2024 09:12
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ewels ewels ewels requested changes

@FelixKrueger FelixKrueger Awaiting requested review from FelixKrueger FelixKrueger is a code owner automatically assigned from nf-core/methylseq

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

Successfully merging this pull request may close these issues.

Preseq failing most of the time
4 participants
@bounlu @ewels @maxulysse @edmundmiller