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

Bugfix/figure creation #129

Merged
merged 2 commits into from
Aug 7, 2024
Merged

Bugfix/figure creation #129

merged 2 commits into from
Aug 7, 2024

Conversation

tillenglert
Copy link
Collaborator

While checking the pipeline again especially downstream analysis, I realised only one of the chosen alleles is used in plotting, instead of all. The reason was the input structures of the processes: PLOT_ENTITY_BINDING_RATIOS and PLOT_SCORE_DISTRIBUTION. They both had two single item inputs: path alleles and path conditions alongside the multi item input: path(prep_scores) which contains one file for each allele. I'm not quite sure what change broke the process, but it is only executed once (as intended by nextflow). Therefore adding an each to the multi item input fixes the behaviour.

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/metapep 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 Aug 6, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 890b4a1

+| ✅ 196 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-06 12:56:45

skrakau
skrakau approved these changes Aug 7, 2024
View reviewed changes
Copy link
Member

@skrakau skrakau left a comment

Choose a reason for hiding this comment

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

LGTM!

@tillenglert tillenglert merged commit 8923d02 into nf-core:dev Aug 7, 2024
21 checks passed
@tillenglert tillenglert deleted the bugfix/figure_creation branch August 16, 2024 10:07
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@skrakau skrakau skrakau 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.
2 participants
@tillenglert @skrakau