Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Test full 100 genomes #174

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
Merged
erikrikarddaniel merged 3 commits into from
Nov 27, 2025
Merged

Test full 100 genomes #174

erikrikarddaniel merged 3 commits into from
Nov 27, 2025

Conversation

@erikrikarddaniel
Copy link
Member

@erikrikarddaniel erikrikarddaniel commented Nov 27, 2025

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/magmap 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).
  • 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).

Modify the test_full so it uses 100 abundant genomes rather than try to identify genomes.

@nf-core-bot
Copy link
Member

nf-core-bot commented Nov 27, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@github-actions
Copy link

github-actions bot commented Nov 27, 2025 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3a08e45

+| ✅ 241 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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: If you use nf-core/magmap for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX Add bibliography of tools and data used in your pipeline
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-11-27 12:25:22

danilodileo
danilodileo approved these changes Nov 27, 2025
View reviewed changes
Copy link
Collaborator

@danilodileo danilodileo left a comment

Choose a reason for hiding this comment

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

LGTM

@erikrikarddaniel erikrikarddaniel merged commit a8d27c2 into nf-core:dev Nov 27, 2025
7 checks passed
@erikrikarddaniel erikrikarddaniel deleted the test-full-100-genomes branch November 27, 2025 13:35
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@danilodileo danilodileo danilodileo 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.

3 participants

@erikrikarddaniel @nf-core-bot @danilodileo