fix: detect cellranger version to determine output file paths dynamically and automatically#9
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dlaehnemann wants to merge 1 commit intomainfrom
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…tect this for determining where outputs end up
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Just to clarify: are you waiting on a review from a user like me, or someone else (e.g. someone more familiar with "official" snakemake workflows? I've successfully used your main branch with cellranger v9 through Is it helpful if I try to do the same with this branch? I have to look again at the documentation but I think EDIT I'm trying. snakedeploy deploy-workflow https://github.com/snakemake-workflows/cellranger-multi . --branch fix/account-for-different-output-file-paths-with-cellranger-10-0-0 |
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I'm confused. It seems to have crashed in the `post-deploy.sh' script. Needless to say that not even the 'results' subdirectory was created. I ran: nohup snakemake --cores all --sdm conda apptainer --default-resources runtime=720 and this is the content of my |
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Hey @kevinrue, sorry, this pull request is not near being ready. There's too many other workflows and projects that have gotten in the way, so far. So unless you need some functionality that is only available in |
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And the failure you are seeing in the |
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It seems like the output file path in
cellranger multijust randomly changed for some files from version9.0.1to version10.0.0. So we have to make the workflow even more complicated. I filed an issue for reference here:10XGenomics/cellranger#267
First, we need to record the installed version of cellranger, to be able to detect this version reliably upon starting the workflow, to then determine where outputs end up. 🤯