Option -C doesn't (seem to) work

[tjcreedy]

Bug report

If I run any nextflow command specifying a config file with -c, it works fine, but if I switch to -C it gives an error. Am I missing something about how the -C option should work?

Expected behavior and actual

Nextflow should run using only the specified config file and no other config files; instead, it gives an error.

Steps to reproduce the problem

touch test.config
nextflow run hello -c test.config # runs fine
nextflow run hello -C test.config # error

Program output

Unknown option: -C -- Check the available commands and options and syntax with 'help'

Environment

• Nextflow version: 23.10.0.5889
• Java version: openjdk 21-internal 2023-09-19
• Operating system: Pop!_OS 22.04 LTS (also tested on Ubuntu 22.04 and 20.04)
• Bash version: 5.1.16(1)

[bentsherman]

This is because -c and -C are top-level options, not run options, however -c is also secretly supported by the run command as a convenience. This should work:

nextflow -C test.config run hello

[mpiersonsmela]

I ran into this problem too. This is NOT listed anywhere in the documentation and switching from -c to -C broke a lot of stuff for me until I found this on Github.