Add a Step to an Existing Workflow

Usage

add_workflow_step(wf_summary, step_tmpl, sbatch_opts = NULL, step_name = NULL)

Arguments

wf_summary: The workflow summary object
step_tmpl: A step template function, see the Step Template section for details.
sbatch_opts: A named list of sbatch options to overwrite or complement the default ones (default = NULL). (see the SBATCH Options section for details).
step_name: An optional name for the step

Value

The updated workflow summary

Step Template

A step template is a function factory used to simplify the setup of a step. The slurmworkflow package provides several simple ones like step_tmpl_bash_script that takes a bash script to be run as argument or step_tmpl_r_script that takes an R script to be run as argument with an optional setup_script to load the required modules beforehand.

SBATCH Options

The sbatch_opts named list accepts all existing arguments to sbatch. It only works with the long form (e.g. "job-name" instead of "J"). The full list of arguments is available in the sbacth documentation. Some arguments like "mem", "mem-per-cpu" and "mem-per-gpu" are mutually exclusive, providing multiple of them will result in an error. However, if one is set at the creation of the workflow in default_sbatch_opts (e.g. "mem") and another at the addition of a step in sbatch_opts (e.g. "mem-per-gpu"), the second one will be used.

Examples

if (FALSE) {
wf <- add_workflow_step(
  step_tmpl_r_script(r_script = "R/abce-abc.R", setup_script = "loadR.sh"),
  sbatch_opts = list(
    "mem-per-cpu" = "4G",
    "cpus-per-task" = 28,
    "time" = 500
  ),
  step_name = "abc"
)
}