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

316 update cellranger modules to latest nf coremodules versions #317

Merged
merged 5 commits into from
Apr 16, 2024
Merged

316 update cellranger modules to latest nf coremodules versions #317

merged 5 commits into from
Apr 16, 2024

Conversation

fmalmeida
Copy link
Contributor

@fmalmeida fmalmeida commented Apr 16, 2024 •
edited
Loading

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/scrnaseq 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>).
  • 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).

@fmalmeida fmalmeida requested a review from grst April 16, 2024 10:22
@fmalmeida fmalmeida self-assigned this Apr 16, 2024
@fmalmeida fmalmeida linked an issue Apr 16, 2024 that may be closed by this pull request
Update cellranger modules to latest nf-core/modules versions #316
Closed
@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 @fmalmeida,

It looks like this pull-request is has been made against the nf-core/scrnaseq 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/scrnaseq 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!

@fmalmeida fmalmeida changed the base branch from master to dev April 16, 2024 10:23
@fmalmeida fmalmeida requested a review from apeltzer April 16, 2024 10:23
@github-actions GitHub Actions
Copy link

github-actions bot commented Apr 16, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 984c101

+| ✅ 171 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-16 11:06:32

grst
grst reviewed Apr 16, 2024
View reviewed changes
Copy link
Member

@grst grst left a comment

Choose a reason for hiding this comment

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

Any idea why the download test might be failing?

conf/modules.config Outdated
@@ -98,7 +98,7 @@ if(params.aligner == "cellranger") {
path: "${params.outdir}/${params.aligner}/count",
mode: params.publish_dir_mode
]
ext.args = {"--chemistry ${meta.chemistry} " + (meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : '')}
ext.args = {"--chemistry ${meta.chemistry} --create-bam false " + (meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : '')}
Copy link
Member

Choose a reason for hiding this comment

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

Why? E.g. RNA velocity analysis relies on this, I'd expect a couple of users complain about this being default all of a sudden.

Copy link
Contributor Author

Choose a reason for hiding this comment

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

New version of cellranger requires this parameter to be used.

Did not know it was used by other workflows. Should I default to true or make a parameter?

Copy link
Member

Choose a reason for hiding this comment

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

I see. A parameter would be nice, but I don't mind setting to true and following up on this separately.

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Now defaulting to true. Anyways, users can still overwrite if needed as it is a ext.args. So, we can consider having a param later upon request.

@fmalmeida
Copy link
Contributor Author

Any idea why the download test might be failing?

No idea actually, it just worked fine in gitpod.

@grst
Copy link
Member

grst commented Apr 16, 2024

Ok, I just restarted it, maybe it was random 🤞

@grst grst merged commit 7c15e0a into dev Apr 16, 2024
11 checks passed
@grst grst deleted the 316-update-cellranger-modules-to-latest-nf-coremodules-versions branch April 16, 2024 11:28
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@grst grst grst left review comments

@apeltzer apeltzer apeltzer approved these changes

Assignees

@fmalmeida fmalmeida

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Update cellranger modules to latest nf-core/modules versions
3 participants
@fmalmeida @grst @apeltzer