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

Add psueudoaligner pipeline level tests to test suite #1279

Merged
merged 4 commits into from
Apr 10, 2024
Merged

Add psueudoaligner pipeline level tests to test suite #1279

merged 4 commits into from
Apr 10, 2024

Conversation

adamrtalbot
Copy link
Contributor

@adamrtalbot adamrtalbot commented Apr 9, 2024 •
edited
Loading

Adds pseudoaligner tests in the same format as #1272
Removes existing CI tests

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/rnaseq 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).

@adamrtalbot adamrtalbot added this to the nf-test milestone Apr 9, 2024
@github-actions GitHub Actions
Copy link

github-actions bot commented Apr 9, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4299d47

+| ✅ 167 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 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 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 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!

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-10 09:33:54

@adamrtalbot adamrtalbot merged commit f3aec8b into nf-core:dev Apr 10, 2024
184 checks passed
@adamrtalbot adamrtalbot deleted the pseudo_aligners_nftest branch April 10, 2024 10:16
@adamrtalbot adamrtalbot mentioned this pull request Jun 20, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@maxulysse maxulysse maxulysse approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
nf-test
Development

Successfully merging this pull request may close these issues.
2 participants
@adamrtalbot @maxulysse