Upgrade simpleaf to 0.19.0 #7405
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update simpleaf modules
restructure simpleaf quant output
update linting
DongzeHE
approved these changes
Feb 4, 2025
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PR checklist
Update to simpleaf 0.19.0.
simpleaf/index now can build an index from a reference probe set CSV file or a reference feature barcode CSV file.
simpleaf/quant now exports the h5ad version of the count matrix.
This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the module conventions in the contribution docs
If necessary, include test data in your PR.
Remove all TODO statements.
Emit the
versions.ymlfile.Follow the naming conventions.
Follow the parameters requirements.
Follow the input/output options guidelines.
Add a resource
label[ x] Use BioConda and BioContainers if possible to fulfil software requirements.
Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
nf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda