get_subplan_single_sample: Get a 'drake' plan for a stage of single-sample pipeline.

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 plan for a stage of single-sample pipeline.

Description

A plan for 01_input_qc stage.

A plan for 02_norm_clustering stage. The following subplans are included:

• get_clustering_graph_subplan(), get_clustering_kmeans_subplan(), get_clustering_sc3_subplan()

  • Bound together with get_clustering_subplan()

• get_cell_annotation_subplan()

• get_dimred_plots_other_vars_subplan()

Usage

get_input_qc_subplan(cfg, cfg_pipeline, cfg_main)

get_norm_clustering_subplan(cfg, cfg_pipeline, cfg_main)

Arguments

cfg	A list of parameters for this stage (loaded from single-sample config directory, e.g. ⁠01_input_qc.yaml⁠, etc.).
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 config directory).

Value

drake::drake_plan()

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