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

Oncomplete fix #1460

Draft
wants to merge 2 commits into
base: dev
Choose a base branch
from
Draft

Oncomplete fix #1460

wants to merge 2 commits into from

Conversation

robsyme
Copy link
Contributor

@robsyme robsyme commented Nov 29, 2024 •
edited
Loading

Note: This PR is not intended to be merged, it just serves as an executable example of the upstream changes in nf-core/tools and nf-core/modules.

The onComplete handler currently calls the toList() operator on a queue channel, but by the time the onComplete handler is called, the channels have all been emptied, and this operator will hang forever.

This fix moves the transformation of the queue channel into a value channel (which is safe to use inside the onComplete block) and also cleans up the attachMultiqcReport function.

The actual PRs that need to be merged are:

@robsyme robsyme changed the base branch from master to dev November 29, 2024 22:17
@nf-core nf-core deleted a comment from github-actions bot Nov 29, 2024
@github-actions GitHub Actions
Copy link

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4773e58

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-29 22:17:52

@robsyme robsyme self-assigned this Nov 30, 2024
@robsyme robsyme marked this pull request as draft November 30, 2024 20:01
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees

@robsyme robsyme

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@robsyme