rerun: Re-run a pipeline in case of hardware or software failures.

In flowr: Streamlining Design and Deployment of Complex Workflows

Description

• hardware no change required, simple rerun: rerun(x=flow_wd)

• software either a change to flowmat or flowdef has been made: rerun(x=flow_wd, mat = new_flowmat, def = new_flowdef)

NOTE:

flow_wd: flow working directory, same input as used for status

Usage

rerun(x, ...)

## S3 method for class 'character'
rerun(x, ...)

## S3 method for class 'flow'
rerun(
  x,
  mat,
  def,
  start_from,
  samplename,
  execute = TRUE,
  kill = TRUE,
  select,
  ignore,
  verbose = opts_flow$get("verbose"),
  ...
)

Arguments

x	flow working directory
...	passed onto to_flow
mat	(optional) flowmat fetched from previous submission if missing. For more information regarding the format refer to to_flowmat
def	(optional) flowdef fetched from previous submission if missing. For more information regarding the format refer to to_flowdef
start_from	(required) which job to start from, this is a job name.
samplename	(optional) If flowmat contains multiple samples, provide the samplename, corresponding to the flow working directory provided.
execute	[logical] whether to execute or not
kill	(optional) logical indicating whether to kill the jobs from the previous execution of flow.
select	(optional) select a subset of jobs to rerun [character vector]
ignore	(optional) ignore a subset of jobs to rerun [character vector]
verbose	A numeric value indicating the amount of messages to produce. Values are integers varying from 0, 1, 2, 3, .... Please refer to the verbose page for more details. opts_flow$get("verbose")

Details

This function fetches details regarding the previous execution from the flow working directory (flow_wd).

It reads the flow object from the flow_details.rds file, and extracts flowdef and flowmat from it using to_flowmat and to_flowdef functions.

Using new flowmat OR flowdef for re-run:

Optionally, if either of flowmat or flowdef are supplied; supplied ones are used instead of those extracted from previous submission.

This functions efficiently updates job details of the latest submission into the previous file; thus information regarding previous job ids and their status is not lost.

Examples

## Not run: 

# 
rerun(wd = wd, fobj = fobj, execute = TRUE, kill = TRUE)


## End(Not run)

flowr documentation built on March 3, 2021, 1:12 a.m.