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Update diagram #266

Merged
merged 1 commit into from
Sep 30, 2024
Merged

Update diagram #266

merged 1 commit into from
Sep 30, 2024

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atrigila
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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
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github-actions bot commented Sep 30, 2024 •
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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
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grst commented Sep 30, 2024

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

@apeltzer
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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
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grst commented Sep 30, 2024

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

@atrigila
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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
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Then all fine 😉😎

@atrigila atrigila merged commit 3562e9e into nf-core:dev Sep 30, 2024
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@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

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3 participants
@atrigila @grst @apeltzer