flowr (version 0.9.11)

kill: Kill all jobs submitted to the computing platform, for one or multiple flows

Description

NOTE:

This requires files which are created at the end of the submit_flow command.

Even if you want to kill the flow, its best to let submit_flow do its job, when done simply use kill(flow_wd). If submit_flow is interrupted, files like flow_details.rds etc are not created, thus flowr looses the association of jobs with flow instance and cannot monitor, kill or re-run the flow.

Usage

kill(x, ...)
# S3 method for character
kill(x, force = FALSE, ...)
# S3 method for flow
kill(
  x,
  kill_cmd,
  verbose = opts_flow$get("verbose"),
  jobid_col = "job_sub_id",
  ...
)

Arguments

x

either path to flow wd or object of class flow

...

not used

force

You need to set force=TRUE, to kill multiple flows. This makes sure multiple flows are NOT killed by accident.

kill_cmd

The command used to kill. flowr tries to guess this commands, as defined in the detect_kill_cmd(). Supplying it here; for custom platforms.

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")

jobid_col

Advanced use. The column name in 'flow_details.txt' file used to fetch jobids to kill

Examples

# NOT RUN {
# }
# NOT RUN {
## example for terminal
## flowr kill_flow x=path_to_flow_directory
## In case path matches multiple folders, flowr asks before killing
kill(x='fastq_haplotyper*')
 Flowr: streamlining workflows
 found multiple wds:
 /fastq_haplotyper-MS132-20150825-16-24-04-0Lv1PbpI
 /fastq_haplotyper-MS132-20150825-17-47-52-5vFIkrMD
 Really kill all of them ? kill again with force=TRUE

## submitting again with force=TRUE will kill them:
kill(x='fastq_haplotyper*', force = TRUE)
# }