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

Update diagram #266

Merged
merged 1 commit into from
Sep 30, 2024
Merged

Update diagram #266

merged 1 commit into from
Sep 30, 2024

Conversation

atrigila
Copy link
Contributor

Closes #261

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/demultiplex 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).

@atrigila atrigila requested a review from a team as a code owner September 30, 2024 12:02
@atrigila atrigila requested review from kobelavaerts and removed request for a team September 30, 2024 12:02
@github-actions GitHub Actions
Copy link

github-actions bot commented Sep 30, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4d9e18b

+| ✅ 190 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.5.1
  • 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 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 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-30 12:03:43

@grst
Copy link
Member

grst commented Sep 30, 2024

What about cellranger? Wouldn't that be a completely separate demultiplexing route?

@apeltzer
Copy link
Member

It's hard to see but mkfastq is the cell ranger part no? Although I think that's not compatible with samshee I am afraid ...

@grst
Copy link
Member

grst commented Sep 30, 2024

ah, got it. Not sure about samshee... it should still use an illumina samplesheet, no?

@atrigila
Copy link
Contributor Author

In the code we run samshee in three demultiplexers:

demultiplex/workflows/demultiplex.nf

Line 96 in 17cde5d

if (!("samshee" in skip_tools) && (params.demultiplexer in ["bcl2fastq", "bclconvert", "mkfastq"])){

I used that as reference.

@apeltzer
Copy link
Member

Then all fine 😉😎

@atrigila atrigila merged commit 3562e9e into nf-core:dev Sep 30, 2024
9 checks passed
@atrigila atrigila mentioned this pull request Oct 3, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@apeltzer apeltzer apeltzer approved these changes

@kobelavaerts kobelavaerts Awaiting requested review from kobelavaerts kobelavaerts is a code owner automatically assigned from nf-core/demultiplex

@nschcolnicov nschcolnicov Awaiting requested review from nschcolnicov

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
@atrigila @grst @apeltzer