get_subplan_common: Get a 'drake' subplan common to all pipelines.

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

Get a drake subplan common to all pipelines.

Description

A subplan for storing configs and runtime information.

A subplan for cluster_markers stage.

A subplan for contrasts stage (differential expression).

Usage

get_common_subplan(
  cfg_pipeline,
  cfg_main,
  pipeline_type_ = c("single_sample", "integration")
)

get_cluster_markers_subplan(cfg, cfg_pipeline, cfg_main)

get_contrasts_subplan(cfg, cfg_pipeline, cfg_main)

Arguments

cfg_pipeline	A scdrake_list object: pipeline config (see load_pipeline_config()) obtained from pipeline.yaml file located in pipeline config directory.
cfg_main	A list of general parameters (loaded from ⁠00_main.yaml⁠ from single-sample or integration config directory).
pipeline_type_	A character scalar indicating the type of pipeline. Based on the pipeline type, some targets depend on different targets.
cfg	A list of parameters for this stage (from single-sample or integration config directory, loaded from e.g. cluster_markers.yaml, etc.).

Details

The pipeline_type target is defined in the plan returned from get_common_subplan().

Value

drake::drake_plan()

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.