Below is the structure of the results directory. Pathways will be populated with parameters set in the params file. An example of a parameters file is found in the demo params.
sc_nf_diffexpression
├── differential_expression
│ ├── covariate_to_test_1
│ │ ├── [files: merged differential results]
│ │ ├── [plots: results]
│ │ ├── cell_label=cluster_1
│ │ │ ├── method=package::resolution::method___formula=cov_1pluscov_2pluscov_3
│ │ │ │ ├── [files: differential results]
│ │ │ │ ├── gsea_method-gsea_config_1=value::gsea_config_2=value::gsea_config_3=value::...::db=databases::signed
│ │ │ │ ├── gsea_method-gsea_config_1=value::gsea_config_2=value::gsea_config_3=value::...::db=databases::unsigned
│ │ │ │ ... etc. ...
│ │ │ ├── method=package::resolution::method___formula=cov_1pluscov_2pluscov_3__proportion_covs-cluster
│ │ │ ... etc. ...
│ │ ├── cell_label=cluster_2
│ │ ... etc. ...
│ ├── covariate_to_test_2
│ ... etc. ...