Skip to content

Feature/fix tests#15

Merged
KateSakharova merged 14 commits into
devfrom
feature/kate-fix
Oct 29, 2025
Merged

Feature/fix tests#15
KateSakharova merged 14 commits into
devfrom
feature/kate-fix

Conversation

@KateSakharova

@KateSakharova KateSakharova commented Oct 28, 2025 •
edited
Loading

Copy link
Copy Markdown
Contributor

Fix templates issues
General pipeline test is still broken - we will need to modify it anyway after another PRs, ignore for now

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/seqsubmit branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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 Bot commented Oct 28, 2025 •
edited
Loading

Copy link
Copy Markdown

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ba0276d

+| ✅ 201 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  25 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline 2. Present QC for raw reads (MultiQC)
  • 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 README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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!
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-10-29 09:51:07

@KateSakharova KateSakharova changed the title Feature/kate fix Feature/fix tests Oct 28, 2025
ochkalova
ochkalova approved these changes Oct 29, 2025
View reviewed changes

@ochkalova ochkalova left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

Thanks for solving test problem 👍🏻

Comment thread .nf-core.yml Outdated
KateSakharova and others added 3 commits October 29, 2025 10:45
@KateSakharova
return main
4437a04
@KateSakharova @ochkalova
Update .nf-core.yml
974f3dc 
Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>
@KateSakharova
return main more
ba0276d
@KateSakharova KateSakharova merged commit 1de7f16 into dev Oct 29, 2025
6 checks passed
@KateSakharova KateSakharova deleted the feature/kate-fix branch October 29, 2025 09:51
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@ochkalova ochkalova ochkalova 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

@KateSakharova @ochkalova