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feat(cellranger count and multi): Add create-bam option to cellranger count and multi pipelines #387

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merged 8 commits into from
Nov 22, 2024
Merged

feat(cellranger count and multi): Add create-bam option to cellranger count and multi pipelines #387

merged 8 commits into from
Nov 22, 2024

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kopichris
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This PR is related to issue #384 posted by @nick-youngblut.

The primary purpose of this pull request is to allow users to set the --create-bam parameter within the cellranger count and cellranger multi pipelines. This is an important parameter because the BAM files produced by cellranger can take up a considerable amount of disk space and computational resources, even for a small number of samples. By allowing users to set this parameter manually, we allow them finer control over how the pipeline is executed and what is provided as output.

PR checklist

  • This comment contains a description of changes (with reason).
  • 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>).
  • CHANGELOG.md is updated.

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 2.14.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@kopichris
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Hi @grst, anything else needed on my end before the PR can be reviewed? Thank you in advance for your time and consideration.

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grst commented Oct 30, 2024

Would be great if you could look into those merge conflicts. Otherwise I'll look into it as soon as I find some time.

grst
grst reviewed Oct 30, 2024
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grst
grst reviewed Nov 6, 2024
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github-actions bot commented Nov 7, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 750e644

+| ✅ 217 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 3.0.2
  • Run at 2024-11-18 13:41:16

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grst commented Nov 18, 2024

@nf-core-bot fix linting

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grst approved these changes Nov 18, 2024
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LGTM

@kopichris
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Hi @grst,

I really appreciate it, thank you so much for your time and assistance with this pull request!

Best,
Chris

@grst grst merged commit 2d0015e into nf-core:dev Nov 22, 2024
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@grst grst mentioned this pull request Dec 2, 2024
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@kopichris @nf-core-bot @grst