suppressPackageStartupMessages(library(GetoptLong))
enforce = FALSE
execute = TRUE
prefix = ""
email = NULL
submitby = "qsub"
GetoptLong("config=s", "A configuration R script. Check the help page of `load_config()`
function to find out how to properly set one.",
"enforce!", "Enforce to run all jobs (by default FALSE)",
"execute!", "Whether submit jobs to clusters (by default FALSE)",
"email=s", "Email address the messages should be sent to",
"submitby=s", "which job system. (by default qsub)",
"prefix=s", "job prefix",
head = "",
foot = "",
script_name = "-e \"epik.cmd::epik()\" run_pipeline")
library(epik.cmd)
epik_pipeline(config, prefix = prefix, email = email, enforce = enforce, submit_by = submitby)
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