Add nftests custom modules

[nschcolnicov]

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[famosab]

You will also need to remove the modules from the pytest config file. Afterwards we should be good to go :)

https://github.com/nf-core/modules/blob/816ff3b787af7e12e75a7d95f76b631f474853ee/tests/config/pytest_modules.yml#L112C1-L120C53

[nschcolnicov]

There is a linting error:

But running the command suggested nf-core modules lint --fix reveals that the changes that it is expecting are not correct, it tries to convert all of the output channels into map type:

What do you think about this? @famosab

[famosab]

Huh that is interesting can you commit the "fixed" yaml files and push them to this PR so I can have a look?

[nschcolnicov]

Huh that is interesting can you commit the "fixed" yaml files and push them to this PR so I can have a look?

Take a look: eb84fde

[famosab]

We are almost done :)

[famosab]

see comment above

[nschcolnicov]

It seems that I'm no longer able to push to this branch:

@famosab @mirpedrol Do you know what could be wrong?

[famosab]

@nschcolnicov I think you should be able to push again :)

[SPPearce]

The docker CI runners should be working now.

[SPPearce]

Just a linting issue on one of the modules, then should be good to merge.

[nschcolnicov]

Just a linting issue on one of the modules, then should be good to merge.

Thank you for looking into this. The linting error seems to be a bug. After running the suggested command:
nf-core modules lint --fix custom/matrixfilter
We get that the meta.yml is updated with inaccurate values, output files get labeled as map, among other things:

[famosab]

I have seen this error before, its already an issue on nf-core/tools. I would suggest to fix it manually:

 ╭─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────╮
│                      ╷                          ╷                            │
│ Module name          │ File path                │ Test message               │
│╶─────────────────────┼──────────────────────────┼───────────────────────────╴│
│ custom/matrixfilter  │ modules/nf-core/custom/… │ Module meta.yml does not   │
│                      │                          │ match main.nf. Outputs     │
│                      │                          │ should contain:            │
│                      │                          │ {'filtered': ['meta',      │
│                      │                          │ '.filtered.tsv'], 'tests': │
│                      │                          │ ['meta', '.tests.tsv'],    │
│                      │                          │ 'session_info': ['meta',   │
│                      │                          │ '*R_sessionInfo.log'],     │
│                      │                          │ 'versions':                │
│                      │                          │ ['versions.yml']} Run      │
│                      │                          │ nf-core modules lint --fix │
│                      │                          │ to update the meta.yml     │
│                      │                          │ file.                      │
│                      ╵                          ╵                            │
╰──────────────────────────────────────────────────────────────────────────────╯

[famosab]

Looks good to me mostly. Wondering why the tests fail though...

[SPPearce]

Looks good to me mostly. Wondering why the tests fail though...

Think the runners are having a bad day again...

[atrigila]

Looks good to me! I agree with opening a new ticket with the suggestion so this new nf-tests can move forward :)

Stale