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

rerun {flowr} | R Documentation

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

### 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)

[Package flowr version 0.9.10 Index]