-stub-run as first option causes failure

[keiranmraine]

Bug report

Expected behavior and actual behavior

The order of Nextflow run options shouldn't matter.

For a local configuration with a test profile defined, specifying the -stub-run or -stub option prior to -profile <profile> results in an error.

Steps to reproduce the problem

https://github.com/cynapse-ccri/ExpansionHunter/releases/tag/0.3.0

Works:

$ nextflow run -profile test -stub-run main.nf

Fails:

$ nextflow run -stub-run -profile test main.nf

Program output

N E X T F L O W  ~  version 22.10.3
Pulling nextflow-io/true ...
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/nextflow-io/true/contents/nextflow.config
Remote resource not found: https://api.github.com/repos/nextflow-io/true/contents/main.nf

Working .nextflow.log
Failing .nextflow.log

Environment

• Nextflow version: 22.10.3
• Java version: openjdk 17.0.5 2022-10-1
• Operating system: Debian GNU/Linux 11 (bullseye) (GitHub codespace)
• Bash version: GNU bash, version 5.1.4(1)-release (x86_64-pc-linux-gnu)

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[setshabaTaukobong]

Hi, Im seeing the same issue on my side. Has this been resolved?

[bentsherman]

I think this has to do with how the CLI options are parsed. With the run command you should always specify the pipeline first, e.g. run main.nf [options]. If you don't, it may fail in certain cases.

This issue should be fixed with the new CLI (#3600)

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.