Cell Ranger wrapper

[mschecht]

Hi Snakemake community! 👋

I'm developing a Snakemake workflow that uses 10x Genomics' Cell Ranger for preprocessing single-cell RNA-seq data, and I'd love to contribute a wrapper for cellranger count (and possibly others) to the wrappers repository.

Since Cell Ranger is not available on any Conda channel due to licensing restrictions, would it be acceptable to include a note like this in the meta.yaml?

note: |
  This wrapper requires Cell Ranger to be installed and available in the system PATH.
  You can download it from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest

Let me know if this approach sounds good—happy to open a PR if so. Thanks!

[fgvieira]

Hi @mschecht and thanks for your interest in snakemake wrappers!

As far as I can see, there is an outdated version of cellranger in conda, but the code seems to be open source on GitHub. Have you tried compiling the code on GitHub? If so, do you think it would be possible to create a new recipe in (e.g.) bioconda?

[mschecht]

Hi @fgvieira, thanks for the quick reply!

You're right — while the code for Cell Ranger is available on GitHub, it’s distributed under a license that appears compatible with Bioconda’s open-source requirements. I assume that's why the package is so old on conda.

Nexflow nf-core/scrnaseq also makes this disclamer:

That said, if there's interest in a Snakemake wrapper for Cell Ranger, I’d be happy to contribute one that assumes the user has installed the software manually (e.g., via the official tarball from 10x). Let me know if that would be helpful!

[fgvieira]

I think it would be great to have a wrapper for cell Ranger!

If I understand you correctly, it is possible to have it on bioconda, no? If so, I'd say the best way would be to first create a recipe on bioconda, and then make a wrapper with that bioconda environment. However, you can also just make the wrapper and add a note that the user has to either:

• have cellrranger installed locally
• use a docker image (like they do in nf-core)