feature request: Make "/bin/bash" configurable

[stianlagstad]

I would like to make /bin/bash configurable, either through setting an environment variable or through setting a configuration value. Would a PR for this be welcome? Is there anyone I should discuss this with first? Or are there things I should know before I start?

One complicating factor I'm aware of is that there may be a need to use one shell on the host system (or the external worker, such as a GCP batch instance), and a different shell inside of the docker/singularity container. Maybe there would be need of two environment variables.

Prior work and comments on this:

• Issue: https://github.com/nextflow-io/nextflow/issues/1598. The issue suggests to use /usr/bin/env bash instead of bin/bash, but was rejected. Note the comment from Paolo: "The only solution that I can see is to make the shell path configurable via config setting (env var or config file) which defaults to /bin/bash and the user can change as needed."
• PR: https://github.com/nextflow-io/nextflow/pull/2341. A PR which suggested to change /bin/bash to /usr/bin/env bash. This was not accepted, and closed, due to the previous discussion in the above link.

My main motivations for this idea are:

1. To be able to use nextflow on systems where /bin/bash is not available, and where users can't easily setup a symlink or similar.
2. Get more reproducible workflows, as we can control which version of bash is used.
3. To avoid the many duplicate hardcoded strings "/bin/bash" present in the nextflow repository. Running the command find . -name "*.groovy" -type f -exec grep -o "/bin/bash" {} + | wc -l on the current master branch gives 106 results. If there were (many) fewer of these, then other packaging tools would be able to package nextflow and write a small patch which changes the occurrences of these strings.

Any input is appreciated. Thank you!

[bentsherman]

Excluding tests, there are about 15 hardcoded references to /bin/bash, most of them related to launching the .command.run script on a particular executor

I believe the launcher script has certain assumptions baked in around bash, so it would make sense to point to a different version of bash but not necessarily a different shell

It could make sense as an environment variable or a config option such as executor.bash