Nextflow won't work when running from private repo and main script is not named "main.nf"

Bug report

Expected behavior and actual behavior

When running nextflow on a private repo with a main script called other than main.nf, it fails, complaining that the resource main.nf was not found.

If manifest.mainScript = "my_script.nf" is added to the nextflow.config file, it works.

# nextflow.config
params {
    skip_step = false
}
manifest {
    mainScript = "my_script.nf"
}

But if this same line is added by including another config file into the main one, it won't work.

# nextflow.config
params {
    skip_step = false
}
includeConfig 'manifest.config'

# manifest.config
manifest {
    mainScript = "my_script.nf"
}

Steps to reproduce the problem

1. Set up a git provider (e.g. GitHub) and save it to the $HOME/.nextflow/scm file.
2. Create a minimal nextflow.config file (optional).
3. Create a minimal script named my_script.nf.
4. Save it to a new private repo on your git provider (e.g. GitHub)
5. Run the following command:

nextflow run https://github.com/my_user/my_repo.git -main-script my_script.nf

Program output

N E X T F L O W  ~  version 23.10.0
Pulling sralchemab/test_repo ...
Remote resource not found: https://api.github.com/repos/sralchemab/test_repo/contents/main.nf

Here's the nextflow.log file.

Additional context

If I run it locally, it works as expected.

Environment

• Nextflow version: 23.10.0
• Java version: openjdk 17.0.9-internal 2023-10-17
• Operating system: Amazon Linux 2023
• Bash version: zsh 5.8.1 (x86_64-amazon-linux-gnu)

Start by reproducing the private-repository command with nextflow.config, manifest.config, and -main-script my_script.nf, then inspect the private GitHub retrieval and included-configuration paths. Done means the command locates my_script.nf when manifest.mainScript is supplied through an included config, without requesting main.nf.