To run the workflow, download the input data using 00_download_data.sh. It includes case and control studies count matrix with its own barcode and gene files. Also include enfisema gene set file and marker associated to cell identities file.
Then, execute 01_run_default.sh. You can previous observe what is going to be executed using 00_dry_run.sh. The default settings are already established. To modify them, check config info.
Example of use:
snakemake --use-conda -c 1