Run csMR Step 3 — csMR_step3

Run the csMR Snakemake workflow with R_HOME and R_LIBS explicitly set from the target csMR conda environment.

Usage

csMR_step3_run(
  repo_dir = "~/Project/software/csMR",
  config_file = "./output/csMR/step2_config/config.yml",
  jobs = NULL,
  forcerun = NULL,
  work_flow.snakefile = NULL,
  env_name = "csMR",
  conda = Sys.which("conda"),
  dry_run = FALSE,
  log_file = NULL
)

Arguments

repo_dir: csMR repository directory.
config_file: Config file path.
jobs: Number of Snakemake jobs. If NULL, run with bare -j and let Snakemake use all available cores.
forcerun: Optional Snakemake targets/rules to force-run. Default NULL means no --forcerun is added.
work_flow.snakefile: Snakemake workflow file path. If NULL, use file.path(repo_dir, "work_flow.snakefile").
env_name: Conda env name.
conda: Path to conda.
dry_run: Whether to run --dry-run.
log_file: Optional log file path.

Value

A list with command (copyable shell command), status, log_file, r_lib, and r_home. Output streams to console in real time and is also saved to log_file.

Details

The first four arguments (repo_dir, config_file, jobs, forcerun) are the most commonly adjusted by users in routine runs.

Examples

if (FALSE) { # \dontrun{
csMR_step3_run(repo_dir = "~/Project/software/csMR", jobs = NULL, dry_run = TRUE)
} # }