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]

I think the update was needed because we changed one of the outputs per my request. But why --fix now does these kind of replacements also seems off to me. @mashehu @mirpedrol what do you guys think? is that expected behavior and should we just manually revert these changes or is something wrong with tools?

[mirpedrol]

Changing the name of the output and using *R_sessionInfo.log is the right change but replacing the type and description is not! We saw the same with other modules, it must be a weird bug with the --fix command, you can revert this.
And the same for the other outputs where this happened, like filtered.csv and tests.csv

[famosab]

We are almost done :)

[famosab]

there was a new convention recently, maybe you can update to adhere to that: https://nf-co.re/docs/guidelines/components/modules#configuration-of-extargs-in-tests

[nschcolnicov]

Just to make sure, you are requesting me to pass the values that I'm providing via ext.args using params instead of the actual value? Didn't you correct me to do it this way on a previous comment? https://github.com/nf-core/modules/pull/7201/files/816ff3b787af7e12e75a7d95f76b631f474853ee#r1888548704 Want to make sure I'm doing it the exact way you are suggesting

[famosab]

If I did then I am sorry. But what is meant is that the params that you need to pass are written directly in the nf.test file which makes its directly understandable for other people that look at your tests and then they do not have to go through multiple nextflow.config files.

[nschcolnicov]

No, sorry, you are right, I was wrong both times, I just wasn't understanding how you wanted me to structure the config, I think I have now understood and addressed the issues, let me know what you think @famosab 😄

[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 :)

[nschcolnicov]

@famosab Tests should be passing but the docker_self_hosted one is having an issue, I don't think it is related to my changes though. I see they all fail with this error:
touch: cannot touch '.command.trace': Permission denied
Also linting still fails due to the issue where it wants to have everything in the meta.yml converted to meta type.

[famosab]

@nschcolnicov I think there are still issues with the CI-runners. Maybe you can check slack in the next few days to see if that gets resolved.

[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]

One more (small) thing - I would ask you to update your links so that they follow the convention and look like this:

file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)

[famosab]

That also means that all the test-datasets that you need must be present on the modules branch of the test-datasets repository. I know that there will be some restructuring around the test-datasets so maybe it makes sense to have them present there so they do not get lost and the tests stop working. I can review a PR over at the test-datasets repo when you add them.