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Cellranger 10XV4 #348

Merged
merged 7 commits into from
Jul 30, 2024
Merged

Cellranger 10XV4 #348

merged 7 commits into from
Jul 30, 2024

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nick-youngblut
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Added support for 10XV4 (SC3Pv4). This includes:

  • updating protocols.json
  • adding the 10X V4 barcode whitelist
  • updating the docs

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
    • nf-core schema build fails due to: --fasta: Not in pipeline parameters & --gtf: Not in pipeline parameters.
  • 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).

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@grst grst mentioned this pull request Jul 29, 2024
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@grst grst changed the base branch from master to dev July 29, 2024 09:12
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github-actions bot commented Jul 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 34f4be7

+| ✅ 204 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 2.14.1
  • Run at 2024-07-30 07:05:54

grst
grst approved these changes Jul 29, 2024
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Many thanks for working on this! Looks mostly good to me, could you please

  • update the CHANGELOG
  • reset the kallistobustools module (nf-core doesn't allow modification of modules installed from nf-core/modules, they have to be updated centrally in the modules repository). You can follow up on that separately - the pattern is only documentation and has no effect on the pipeline functionality.

modules/nf-core/kallistobustools/count/meta.yml Outdated
@@ -47,7 +47,7 @@ input:
- technology:
type: string
description: String value defining the sequencing technology used.
pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}"
pattern: "{10XV1,10XV2,10XV3,10XV4,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}"
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This change would need to be made in nf-core/modules and then be pulled into the pipeline using nf-core modules update.

@nick-youngblut
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@grst for "update the CHANGELOG", is this sufficient:

## v2.7.1 - 2024-07-29

- Add 10XV4 chemistry

I can also bump the version to 2.7.1 throughout the codebase: nextflow.config & multiqc_config.yml

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grst commented Jul 29, 2024

Don't worry about the version, I'll do that when making a patch release

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grst commented Jul 30, 2024

@nf-core-bot fix linting

@grst grst merged commit 5f11686 into nf-core:dev Jul 30, 2024
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@nick-youngblut nick-youngblut deleted the cellranger_10XV4 branch July 30, 2024 14:31
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@nick-youngblut @grst @nf-core-bot