Run non-mutating project and runtime preflight checks

This optional comprehensive preflight is useful on a new cluster, after the submission environment changes, or before an expensive run. doctor_project() checks configuration, scheduler commands, container runtime, enabled-stage files, project storage, and the job-tracking database. It is not required before run_project() and does not submit work, create directories, or modify the configuration.

Usage

doctor_project(input, steps = NULL, deep = FALSE, quiet = FALSE)

Arguments

input

A project configuration object, YAML file, or project directory.

steps

Optional stages to check. By default all enabled stages are used.

deep

Also initialize Python and check optional postprocessing modules.

quiet

Suppress the printed report.

Value

A bg_project_doctor object with an ok flag and a checks data frame.