Is it possible to add a command before bash in nxf_trace() of .command.run?

[lishengting]

Just as showed in above picture.
Is it possible to add /path/to/stat_tool before /bin/bash，or even replace /bin/bash by another software written by myself?

Thanks!

[robsyme]

Absolutely! There are in fact a couple of ways.

You might consider adding it in the shebang line of the script block.

process Demo {
    script:
    """
    #!/path/to/stat_tool
    echo 'Hello world!'
    """
}

Nextflow will detect the shebang line and adjust the .command.run statement accordingly:

nxf_launch() {
   /path/to/stat_tool /private/tmp/lishengting/work/a7/9f73aef2239268b6a44213553372cc/.command.sh
}

You can also adjust the interpreter with the shell process directive (documentation here):

process Demo {
    debug true
    shell '/path/to/stat_tool', '--extra-args', 'if_necessary'

    script:
    "echo 'Hello world!'"
}

Of course, because this is a process directive it can also be overridden via configuration. You might have a nextflow.config file that includes:

process {
  withName: Demo {
    shell = '/path/to/stat_tool'
  }
}

[lishengting]

That's very convenient.
Thanks a lot!