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

Nf core template merge 2.13 (manual) #32

Merged
merged 11 commits into from
Feb 22, 2024
Merged

Nf core template merge 2.13 (manual) #32

merged 11 commits into from
Feb 22, 2024

Conversation

pinin4fjords
Copy link
Member

@pinin4fjords pinin4fjords commented Feb 22, 2024 •
edited

In this PR:

  • Resolve template merge conflicts
  • Switch some of the workflow structure to be more similar to newer nf-core/rnaseq
  • Switch to @adamrtalbot 's CI wizardry

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/riboseq 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>).
  • 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

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @pinin4fjords,

It looks like this pull-request is has been made against the nf-core/riboseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/riboseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@pinin4fjords pinin4fjords changed the base branch from master to dev February 22, 2024 13:42
@pinin4fjords pinin4fjords changed the title Nf core template merge 2.13 (jon manual) Nf core template merge 2.13 (manual) Feb 22, 2024
@github-actions GitHub Actions
Copy link

github-actions bot commented Feb 22, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c4a7509

+| ✅ 184 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  18 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: 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
  • 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: If applicable, make list of people who have also contributed
  • 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 output.md: Write this documentation describing your workflow's output
  • 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 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-22 17:36:59

@pinin4fjords pinin4fjords mentioned this pull request Feb 22, 2024
Closed
maxulysse
maxulysse reviewed Feb 22, 2024
View reviewed changes
modules.json Outdated Show resolved Hide resolved
maxulysse
maxulysse approved these changes Feb 22, 2024
View reviewed changes
Copy link
Member

@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

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

apart from the previous comments it looks pretty good

adamrtalbot
adamrtalbot approved these changes Feb 22, 2024
View reviewed changes
Copy link

@adamrtalbot adamrtalbot left a comment

Choose a reason for hiding this comment

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

Good job, this is a big one!

@pinin4fjords
Copy link
Member Author

Thanks for reviews @maxulysse @adamrtalbot !

@pinin4fjords pinin4fjords merged commit 9a91d22 into dev Feb 22, 2024
85 checks passed
@pinin4fjords pinin4fjords deleted the nf-core-template-merge-2.13_jon branch February 22, 2024 18:18
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

@adamrtalbot adamrtalbot adamrtalbot 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.

None yet
4 participants
@pinin4fjords @maxulysse @adamrtalbot @nf-core-bot