process_config: Config processing.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Config processing.

Description

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.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.