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Updates cellranger_vdj #305

Merged
merged 6 commits into from
Feb 27, 2024
Merged

Updates cellranger_vdj #305

merged 6 commits into from
Feb 27, 2024

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ggabernet
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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/airrflow 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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github-actions bot commented Feb 16, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit afa4c1d

+| ✅ 205 tests passed       |+
#| ❔   7 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-20 15:02:56

@ggabernet ggabernet requested a review from mapo9 February 20, 2024 19:26
ggabernet
ggabernet commented Feb 20, 2024
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CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- [#294](https://github.com/nf-core/airrflow/pull/294) Merge template updates nf-core/tools v2.11.1
- [#299](https://github.com/nf-core/airrflow/pull/299) Add profile for common NEB and TAKARA protocols
- Add possibility to merge multi-lane samples when starting from fastq files
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@mapo9 I added the possibility to merge multi-lane samples for Bulk, and to send multi-lane samples to the same cellranger vdj process, as Cellranger can handle them directly.

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that's great thanks!

ggabernet
ggabernet commented Feb 20, 2024
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nextflow.config
@@ -120,7 +120,6 @@ params {
// Single cell raw input options
// -----------------------
reference_10x = null
sc_raw = false
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Not needed if setting the param library_generation_protocol == "sc_10X_genomics"

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sure, we can leave it out and add library_generation_protocols for the mixcr single cell analysis as well

ggabernet
ggabernet commented Feb 20, 2024
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subworkflows/local/sc_raw_input.nf
ch_sc_reference
)
ch_versions = ch_versions.mix(CELLRANGER_VDJ.out.versions)
ch_sc_reference.collect()
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@mapo9 this one is important, if combining a channel with multiple input files, with one that only contains 1 file, e.g. the reference here, one needs to use the .collect() method for the reference, as otherwise the CELLRANGER_VDJ process will only be executed once for one sample at random.

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👍

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thanks! fixing this behaviour would've taken me hours probably

mapo9
mapo9 approved these changes Feb 27, 2024
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lgtm, thanks for the changes!

@ggabernet ggabernet merged commit a0ad699 into nf-core:cellranger_vdj Feb 27, 2024
22 of 28 checks passed
@ggabernet ggabernet deleted the cellranger_vdj branch November 27, 2024 01:10
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@mapo9 mapo9 mapo9 approved these changes

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@ggabernet @mapo9