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

Update to nf-test 0.9.2 #284

Merged
merged 6 commits into from
Nov 4, 2024
Merged

Update to nf-test 0.9.2 #284

merged 6 commits into from
Nov 4, 2024

Conversation

atrigila
Copy link
Contributor

@atrigila atrigila commented Nov 4, 2024

Update CI nf-test to latest version that fixes the issue of failed tests when they were empty during sharding.
Additionally, I updated nf-core modules and subworkflows.

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/demultiplex 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).

@atrigila atrigila requested a review from a team as a code owner November 4, 2024 19:07
@atrigila atrigila requested review from matthdsm and removed request for a team November 4, 2024 19:07
@github-actions GitHub Actions
Copy link

github-actions bot commented Nov 4, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4da452b

+| ✅ 203 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.5.2
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-04 21:46:21

nschcolnicov
nschcolnicov approved these changes Nov 4, 2024
View reviewed changes
Copy link
Contributor

@nschcolnicov nschcolnicov left a comment

Choose a reason for hiding this comment

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

LGTM, please pull from dev before merging

@atrigila atrigila merged commit dc17d88 into nf-core:dev Nov 4, 2024
15 checks passed
@atrigila atrigila mentioned this pull request Nov 5, 2024
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@nschcolnicov nschcolnicov nschcolnicov approved these changes

@matthdsm matthdsm Awaiting requested review from matthdsm matthdsm is a code owner automatically assigned from nf-core/demultiplex

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
@atrigila @nschcolnicov