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

Adress issues from review #469

Merged
merged 31 commits into from
Oct 14, 2024
Merged

Adress issues from review #469

merged 31 commits into from
Oct 14, 2024

Conversation

apeltzer
Copy link
Member

@apeltzer apeltzer commented Oct 8, 2024

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/smrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

@apeltzer apeltzer added this to the 2.4.0 milestone Oct 8, 2024
@github-actions GitHub Actions
Copy link

github-actions bot commented Oct 8, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5254dae

+| ✅ 243 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-13 21:17:40

@apeltzer
Copy link
Member Author

apeltzer commented Oct 8, 2024

@nf-core-bot fix linting

@atrigila atrigila mentioned this pull request Oct 8, 2024
Merged
8 tasks
@atrigila
Copy link
Contributor

atrigila commented Oct 8, 2024

I can't reproduce the error:

CI:
image
Gitpod:
image

@apeltzer
Copy link
Member Author

apeltzer commented Oct 8, 2024

CI not working now because of the template v.3.0.0 release. I'm afraid we need to merge thta one in too :-(

@apeltzer
Copy link
Member Author

Likely Need to merge in 3.0.1 First and then work on this

@apeltzer
Copy link
Member Author

Mergen in dev with Template Channels so that wie can fix anything remaining here and then push everything to dev. Hopefully that should do the Trick and we‘re there then .)

@apeltzer
Copy link
Member Author

Issue with template will be fixed today with nf-core/tools 3.0.2 —> we should merge that in here directly then.

@apeltzer
Copy link
Member Author

Ok next steps would be merging #474 to this PR's branch. Then merging this one to dev and ultimately then making the release after updating the changelog date appropriately :)

@nf-core-bot
Copy link
Member

⚠️ Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.1.
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.

@apeltzer apeltzer enabled auto-merge October 14, 2024 08:27
@apeltzer
Copy link
Member Author

Ok should be fine to go

maxulysse
maxulysse reviewed Oct 14, 2024
View reviewed changes
.gitignore Show resolved Hide resolved
maxulysse
maxulysse approved these changes Oct 14, 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.

minor comments

@apeltzer apeltzer merged commit 4ca8cb1 into dev Oct 14, 2024
10 checks passed
mashehu
mashehu approved these changes Oct 14, 2024
View reviewed changes
CITATIONS.md Show resolved Hide resolved
nextflow.config Show resolved Hide resolved
subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf Show resolved Hide resolved
subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf Show resolved Hide resolved
@apeltzer apeltzer deleted the adress-issues branch October 14, 2024 08:52
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mashehu mashehu mashehu approved these changes

@maxulysse maxulysse maxulysse 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.
6 participants
@apeltzer @atrigila @nf-core-bot @maxulysse @mashehu @nschcolnicov