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

Crop overview multiqc #36

Merged
merged 7 commits into from
Dec 15, 2023
Merged

Crop overview multiqc #36

merged 7 commits into from
Dec 15, 2023

Conversation

kbestak
Copy link
Collaborator

@kbestak kbestak commented Dec 11, 2023 •
edited
Loading

MultiQC now shows crop overview if create_training_subset param is true. Added leftover versions. Gitpod container is nf-core/gitpod:dev instead of latest so that nf-test does not have to be updated manually each time.

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!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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
Copy link

github-actions bot commented Dec 11, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8bd15fd

+| ✅ 158 tests passed       |+
!| ❗  11 tests had warnings |!

❗ 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 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 main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-15 09:06:09

@FloWuenne
Copy link
Collaborator

Is this readyforreview @kbestak ?

@kbestak
Copy link
Collaborator Author

kbestak commented Dec 14, 2023 •
edited
Loading

It is ready for review, but before merging I'll make the quick tower.yml update #37

FloWuenne
FloWuenne approved these changes Dec 15, 2023
View reviewed changes
Copy link
Collaborator

@FloWuenne FloWuenne left a comment

Choose a reason for hiding this comment

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

LGTM!

@FloWuenne FloWuenne merged commit 3a0b2ef into dev Dec 15, 2023
@FloWuenne FloWuenne deleted the crop_overview_multiqc branch December 15, 2023 12:07
This was referenced Dec 15, 2023
Closed
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FloWuenne FloWuenne FloWuenne 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
@kbestak @FloWuenne