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Add custom/tabulartogseacls #2606
Add custom/tabulartogseacls #2606
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@nvnieuwk thanks for the review- think we should be good here too now :-) |
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Looks good here too! 🚀
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Docs people! Docs!
@jfy133 Ok, no cookies for me. But docs fixed! Thanks for the review. |
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Almost there, but I would still allow complete flexibility by not requiring a specific meta
element
(You can blame @FriederikeHanssen for this, I used to be more flexible with metas
but she's convinced me now ;) )
Co-authored-by: James A. Fellows Yates <[email protected]>
Appreciate the review @jfy133 |
Creates a module for building .cls files of the type consumed by GSEA from sample metadata tables in either CSV or TSV format, with output like:
This is essentially a description of the classes in a column of a sample sheet so that differential gene set analysis can be undertaken.
The necessary column(variable) is currently taken from the meta (which will gel with efforts in the differentialabundance workflow), but it can be passed outside the meta if that would be preferable.
The module does not currently consume the matrix itself, but the samples metadata file which assumed to be in synch with the appropriate matrices (which we separately ensure in the differential abundance workflow).
PR checklist
versions.yml
file.label
PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware