theislab/mubind-benchmark

snakemake and notebook results for mubind package (weekly results )

mubind (snakemake)

Snakemake pipeline related to mubind main repository.

Test

To test that the pipeline is running properly, as a small test, please execute config_test.yaml

snakemake -c 1 --printshellcmds --configfile config_test.yaml --nolock

The parameter -c indicates that only one core is used.

Full pipeline

Run until the data preparation step

snakemake -c 5 --printshellcmds --configfile config.yaml --until data_prepare --nolock

Fit model preparation step

snakemake -c 5 --printshellcmds --configfile config.yaml --until fit_model --nolock

This is useful once the datasets are prepared, to only define GPU nodes if using --cluster