Passing option flags to qsub

[Neil Tedeschi]

Hi,

I am working on a univa grid engine cluster.   I need to call qsub with the -b n flag:

    qsub -b n .command.run

nextflow calls qsub as follows:

    qsub -terse .command.run

Is there a way I can have nextflow pass the needed flags to its call of qsub?

Thanks,

Neil

[Paolo Di Tommaso]

Try using clusterOptions 

https://www.nextflow.io/docs/latest/process.html?#clusteroptions

--
You received this message because you are subscribed to the Google Groups "Nextflow" group.
To unsubscribe from this group and stop receiving emails from it, send an email to nextflow+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/nextflow/e2b00998-33fa-4546-87b3-91ba2784936dn%40googlegroups.com.

[Neil Tedeschi]

That does not seem to work.  Setting clusterOptions = '-b n' sets the option in the .command.run file.  Unfortunately, I need to set the flag before .command.run is read by qsub.  Without -b n, qsub does not read the file as a script and therefore does not read the options.

[Paolo Di Tommaso]

Therefore cannot be provided via Nextflow. A trick can consist of creating a wrapper script named `qsub` that passthrough the original command and prepend that flag. 

To view this discussion on the web visit https://groups.google.com/d/msgid/nextflow/9fcc5604-134e-4492-a4e3-465bad35a1a6n%40googlegroups.com.

[Neil Tedeschi]

The trick worked.  Thank you.