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

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On {scdrake} load or attach (?), several environment variables are read and corresponding options() are set. Those are mainly variables controlling paths to config directories. See get_scdrake_options() for more details and list of used environment variables.

We can take the SCDRAKE_SINGLE_SAMPLE_CONFIG_DIR environment variable as an example:

• If it is set, the scdrake_single_sample_config_dir option is set on {scdrake} load or attach.
• It it is not set, a default value "config/single_sample" will be used for the option above. You can see that the default value is consistent with the file structure of a newly initialized {scdrake} project.
• Value of the scdrake_single_sample_config_dir option is the default one for many {scdrake} functions, e.g. update_single_sample_configs(dir = getOption("scdrake_pipeline_config_dir"), ...) or run_single_sample(dir = getOption("scdrake_pipeline_config_dir"), ...).

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Environment variables are mainly used in _drake_single_sample.R and _drake_integration.R scripts. Those are scripts sourced by {drake} in a fresh new R session via {callr} when you call e.g. run_single_sample_r(). For this reason, environment variables are the only way how to pass dynamic parameters into such scripts. In case of {scdrake}, the most important are paths to directories with config files, which carry analysis/pipeline-specific parameters.

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