bentsherman
commented
2 months ago If it's a directive in the job script, you should be able to add it via clusterOptions:
// nextflow.config
process.clusterOptions = '-S /bin/bash'We could potentially add it to Nextflow here: https://github.com/nextflow-io/nextflow/blob/5a37e6177f7a0e02b2af922768a0df5984b07b7b/modules/nextflow/src/main/groovy/nextflow/executor/SgeExecutor.groovy#L39-L88
The UGE and SGE executors are identical under the hood. As long as this -S option is the same across all Grid Engine variants it should be fine, but I would try the clusterOptions approach first and see if it works for you.
caldodge
New feature
Nextflow scripts appear to use bash features (like array variables), but some schedulers (UGE, in this case) default to /bin/sh, causing array variable code to fail. Can a parameter be added, so that in a config file users can specify /bin/bash as the shell to the scheduler?
Usage scenario
Usage case is batch operation of nextflow scripts which use bash-specific features.
Suggest implementation
Sorry, I'm not a nextflow expert. Since there are already parameters which are translated into scheduler directives, it would be a simple matter of adding another parameter ("shell", perhaps), and adding code to translate that to a scheduler directive ("#$ -S /bin/bash"). If someone could identify the code which does this translation, I would try tackling it myself.