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In order for Nextflow to play nicely in managed environments, we need to avoid using System.exit calls, and the recently depreciated exit() Nextflow function.
For problems with pipeline execution, we can use the error() Nextflow function, however there is no equivalent for exiting cleanly if we just want to stop without any problems.
Usage scenario
Example current usage of exit 0 in nf-core pipelines, after printing usage information to the terminal:
if (params.help) {
log.info paramsHelp("nextflow run my_pipeline --input input_file.csv")
exit 0
}
Suggest implementation
Equivalent of error() but with exit code 0 and no terminal output. Any supplied strings should not be coloured red.
The text was updated successfully, but these errors were encountered:
Seems like we should just modify exit() to throw a special type of exception instead of System.exit(). That way all the nf-core pipelines will just start using it.
The ScriptRunner could handle this special exception by cancelling the session instead of re-throwing the error.
New feature
In order for Nextflow to play nicely in managed environments, we need to avoid using
System.exit
calls, and the recently depreciatedexit()
Nextflow function.For problems with pipeline execution, we can use the
error()
Nextflow function, however there is no equivalent for exiting cleanly if we just want to stop without any problems.Usage scenario
Example current usage of
exit 0
in nf-core pipelines, after printing usage information to the terminal:Suggest implementation
Equivalent of
error()
but with exit code0
and no terminal output. Any supplied strings should not be coloured red.The text was updated successfully, but these errors were encountered: