Fix cellranger multi handling of crispr data #7175
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fmalmeida
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Dec 11, 2024
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Hi @svigneau ,
Thanks for the code work here 😄
There are few things before we can consider it done.
- We have to skip conda checks as highlighted by @famosab here
- Now that the test-datasets for
crisprare available, we must also include the nf-test run forcrispr. Can you add that?
Other than that, it is good.
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PR checklist
Closes #7174
nf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularityThe proposed changes are described in issue 7174 and intended to fix a bug that prevents handling of CRISPR data when using
cellranger multiwith gene expression and CRISPR libraries.The addition of a test dataset with CRISPR data has been requested in PR 1415. A dedicated test for CRISPR data handling by
cellranger multiwill be submitted in a separate PR once the test dataset is approved.I removed testing using
condaprofile from the checklist because running it leads to the following error related to a different module:CELLRANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead.