git submodule USERAUTH fail when private repositories

[huguesfontenelle]

Bug report

My repository is private.
It has a submodule which is also private.
I specify the credentials in SCM configuration file.
nextflow pull repo/pipeline
pulls the pipeline but not the submodule.

Expected behavior and actual behavior

(Submodules should be authenticated)

Steps to reproduce the problem

(By definition, it is a bit difficult to share private repositories)

Program output

$ nextflow pull repo/pipeline 
Checking repo/pipeline ...
git@github.com:repo/data.git: USERAUTH fail

Where repo/data is included as a submodule in repo/pipeline.

Environment

• Nextflow version: 19.01.0
• Java version: 11.0.2
• Operating system: macOS

Additional context

Contents of .gitmodules:

[submodule "data"]
	path = data
	url = git@github.com:repo/data.git
	branch = dev

Note: changing the authentication from git to https, ie changing the url to https://github.com/repo/data.git and making data pubic works. Obviously.

[rspreafico-vir]

Confirming this with 19.0.0.modules-draft10-SNAPSHOT, with the caveat that in my case it does not attempt to download the submodules. (for me too, both parent and child repo are private)

This will become a more important issues when Nextflow modules are finalized, since a natural way to distribute modules will be through git submodule.

[czotti]

Same here I have a pipeline with a bin folder which is a git submodule and I face an error like:

UnknownHostKey: hostname. RSA key fingerprint is XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX

Could be really nice to have.

[huguesfontenelle]

I think this is solved in #1205, released in v19.07.0