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Config processing.

Source: R/config_process_common.R, R/config_process_integration.R, R/config_process_single_sample.R
process_config.Rd

These functions are responsible for checking and processing of config parameters. The most important steps are:

  • Setting up the pipeline parameters, such as drake targets and cache, parallel processing, etc.

  • Extracting a path to SQLite database file from gene annotation package.

  • Conversion of relative paths (to project's root directory) to absolute and putting some paths under a base output directory.

  • Checking and processing of CLUSTER_MARKERS_SOURCES, CONTRASTS_SOURCES, and INTEGRATION_SOURCES parameters.

Usage

.process_pipeline_config(cfg)

.process_main_config(cfg)

.process_cluster_markers_config(cfg, other_variables)

.process_contrasts_config(cfg, other_variables)

.prepare_cell_annotation_sources_params(
  cell_annotation_sources,
  cell_annotation_default_params
)

.process_integration_config(cfg, other_variables)

.process_int_clustering_config(cfg, other_variables)

.process_input_qc_config(cfg, other_variables)

.process_norm_clustering_config(cfg, other_variables)

Arguments

cfg

A named list with pipeline parameters.

other_variables

A list of variables in whose environment the yaml_file will be evaluated, see details in load_config().

cell_annotation_sources

A named list.

cell_annotation_default_params

A named list with default parameters.

Value

A modified cfg.