In #184, we completed the script for normalizing CITE-seq data. In this PR, I do the remaining task we need for prepping Gawad data, which is to update the integration_input_dir column in the library metadata. I confirmed that, with this change, the project runs through the snakemake pipeline as well without errors with: snakemake -c1 --use-conda --configfile config/config-scpca.yaml --config groups_to_integrate=["SCPCP000007"].
Closes #181
In #184, we completed the script for normalizing CITE-seq data. In this PR, I do the remaining task we need for prepping Gawad data, which is to update the
integration_input_dircolumn in the library metadata. I confirmed that, with this change, the project runs through the snakemake pipeline as well without errors with:snakemake -c1 --use-conda --configfile config/config-scpca.yaml --config groups_to_integrate=["SCPCP000007"].