Get a drake plan for a specific analysis type.

These functions are internally loading and binding a smaller plans (subplans) into full plans. All of them are using get_common_subplan(), get_cluster_markers_subplan(), and get_contrasts_subplan().

get_single_sample_plan() uses get_input_qc_subplan() and get_norm_clustering_subplan().

get_integration_plan() uses get_integration_subplan() and get_int_clustering_subplan().

Usage

get_single_sample_plan(cfg, cfg_pipeline = NULL)

get_integration_plan(cfg, cfg_pipeline = NULL)

Arguments

cfg

• For get_single_sample_plan(): A list of config lists returned by load_single_sample_configs().

• For get_integration_plan(): A list of config lists returned by load_integration_configs().

cfg_pipeline

One of:

• A scdrake_list object: pipeline config (see load_pipeline_config()) obtained from pipeline.yaml file located in a pipeline config directory

• NULL: the config will be loaded using the path defined in the scdrake_pipeline_config_dir option

Value

drake::drake_plan()