feat(cellranger count and multi): Add create-bam option to cellranger count and multi pipelines #387
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… count and multi pipelines
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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. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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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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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
reviewed
Oct 30, 2024
nextflow.config
Outdated
| @@ -43,6 +43,7 @@ params { | |||
| // Cellranger parameters | |||
| skip_cellranger_renaming = false | |||
| cellranger_index = null | |||
| cellranger_create_bam = true | |||
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What do you think of unifying this into a single parameter that supports all aligners that create bams (i.e. the different cellrangers and starsolo)?
E.g. in #rnaseq this is called --save_align_intermeds
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Happy to unify these flags into a single parameter for those aligners that create bams. I'll review the rnaseq pipeline to get a better idea about how this was implemented. Thank you again for your direction and support on this pull request.
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Now is this parameter called --create-bam or --save_align_intermeds? Either is fine with me, but it should be consistent everywhere.
Other than that, this is exactly what I had in mind. Can you implement the flag also for cellranger multi and cellranger arc?
…lignment files are saved for CellRanger and STAR
grst
reviewed
Nov 6, 2024
Co-authored-by: Gregor Sturm <[email protected]>
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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-bamparameter within thecellranger countandcellranger multipipelines. 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
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.