Running pipelines from a git-repo with a main.nf doesnt work

[ekageyama]

Bug report

Here is a minimal pipeline with a main.nf and a nextflow config inside a subdirectory
https://github.com/ekageyama/nextflow_sub/tree/main

Expected behavior and actual behavior

nextflow run https://github.com/ekageyama/nextflow_sub.git -main-script pipeline/main.nf

or

nextflow run https://github.com/ekageyama/nextflow_sub/pipeline/
should work

Program output

Can't find git repository config file -- Repository may be corrupted: /Users/kageyamj/.nextflow/assets/ekageyama/nextflow_sub`
Or

WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/ekageyama/nextflow_sub/pipeline//contents/nextflow.config
Remote resource not found: https://api.github.com/repos/ekageyama/nextflow_sub/pipeline//contents/main.nf```

Environment

• Nextflow version: 24.04.4
• Java version: 22.0.2
• Operating system: macOS
• Bash version: zsh 5.9 (x86_64-apple-darwin23.0)