tests: Add test case for cross-organization subwf

[jvfe]

Strangely it is passing at the moment, it seems the install command returns a passing exit code regardless of installing all modules.

• Addresses Add test case for subworkflow with different module remotes #2

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[muffato]

You mean it's passing locally ? I can't see any action run here on GitHub CI

[muffato]

Ah, that's because Actions are turned off by default on forked repositories.

I've now enabled them, but probably they will only kick in next time there's a commit on this branch.

[jvfe]

Ah, that's because Actions are turned off by default on forked repositories.

Ooh ok that makes sense, I had tested it locally.
Either way, I just manually submitted the action and it does show what I said: https://github.com/sanger-tol/nf-core-tools/actions/runs/9661393766/job/26649018814
Another test failed (not related to my changes, it's just changelog/bump issues), but mine succeeds.

I'll test the actual subworkflow install command manually (outside of the test) and capture the exit code, but that seems like it's returning a 0 even when it doesn't install every component.

[jvfe]

Yep, that's definitely the case, when running:

nf-core subworkflows --git-remote https://github.com/jvfe/test-subworkflow-remote install hic_bwamem2

and then getting the exit code:

echo $?

it returns 0.

[jvfe]

Yep, that's definitely the case, when running:

nf-core subworkflows --git-remote https://github.com/jvfe/test-subworkflow-remote install hic_bwamem2

and then getting the exit code:

echo $?

it returns 0.

Apparently this is expected (discussed here). So the way to go is to check for the missing module in the module json list, which is what 568363a does.

[jvfe]

Yep, now it's failing as expected: https://github.com/sanger-tol/nf-core-tools/actions/runs/9717099844/job/26822060543
For some reason the actions are not running automatically, I'll check this later.

[muffato]

Looks fine.

Yep, now it's failing as expected: https://github.com/sanger-tol/nf-core-tools/actions/runs/9717099844/job/26822060543 For some reason the actions are not running automatically, I'll check this later.

Yep, I'm wondering too !

Also, if the return value of install(...) is not an indicator of success/failure, why is it checked in other parts of tests/subworkflows/install.py ? If something's indeed not right, make it an issue on the nf-core repo.

[jvfe]

Looks fine.

Yep, now it's failing as expected: https://github.com/sanger-tol/nf-core-tools/actions/runs/9717099844/job/26822060543 For some reason the actions are not running automatically, I'll check this later.

Yep, I'm wondering too !

Also, if the return value of install(...) is not an indicator of success/failure, why is it checked in other parts of tests/subworkflows/install.py ? If something's indeed not right, make it an issue on the nf-core repo.

Thanks! I've now created the issue. I was hesitant to create it at first since given the conversation on slack I thought it was something expected.

Yeah and I'm not sure why the CI wasn't running, but I just sent some dummy commits and now it runs. I tried to change the base branch for this PR to see if that was the reason behind it (like if maybe it just runs the CI for PRs against the main branch), but apparently not.

[jvfe]

Apparently the issue with the modules test failing is unrelated to my changes, because, after some local testing, I could see it also fails in the master branch. Given that's the case, I'll be merging this then.