create ASCAT nf tests and remove pytest

[mauro-saporita]

PR checklist

Closes #5170

nf-test not working - pytest runs as expected but the nf-test I've created returns the following error: Path value cannot be null

• 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

[FriederikeHanssen]

It would be nice if we could keep this info somewhere for local testing on input file changes. maybe we can add a readme here

[mauro-saporita]

Good point! I'm going to save it in a readme; where do you suggest I should save it? In modules/nf-core/ascat/tests?

[FriederikeHanssen]

I think that is a good palce

[FriederikeHanssen]

can you add a check for the version?

[mauro-saporita]

Added; but unfortunately the test doesn't work, I get the following error: Path value cannot be null

[FriederikeHanssen]

when you ru the module manually do you get a versions file?

[mauro-saporita]

I get the error when it runs { assert process.success } so it doesn't run the test at all - could be something wrong with the way I declare the inputs?

                input[1] = []
                input[2] = []
                input[3] = []
                input[4] = []
                input[5] = []
                input[6] = []

[mauro-saporita]

the pytest runs with the following:

ASCAT_SIMPLE ( input , [], [], [], [], [], [])

[mauro-saporita]

Path value cannot be null issue solved by @sateeshperi - but test still not working

[mauro-saporita]

@maxulysse let's hold a bit on this PR; tests are not working yet 😣

[famosab]

Can you also update the path as in #5281 ? :)

[famosab]

@mauro-saporita Do you still have time to work on the proposed changes?

[mauro-saporita]

@mauro-saporita Do you still have time to work on the proposed changes?

I'm sorry lately I've been off the radar; busy with some other projects. I can work on this issue in June unless someone else would like to take it in the next week Hackathon event.

[famosab]

@mauro-saporita I added the loci and allele files for WGS (maybe we need some for WES as well?): nf-core/test-datasets#1239

[famosab]

Maybe you can add these paths to the nf test code and then run the tests on your machine. If that works we can add the files to the test_data and update the paths.

[famosab]

Just to test it out:

Suggested change

	input[1] = []
	input[2] = []
	input[1] = [path('https://raw.githubusercontent.com/nf-core/test-datasets/d677699283dbbeb51876d1bb3c18fb687d1db4ea/data/genomics/homo_sapiens/illumina/ascat/G1000_alleles_WGS_hg38/G1000_alleles_hg38_chr21.txt')]
	input[2] = [path('https://raw.githubusercontent.com/nf-core/test-datasets/d677699283dbbeb51876d1bb3c18fb687d1db4ea/data/genomics/homo_sapiens/illumina/ascat/G1000_loci_WGS_hg38/G1000_loci_hg38_chr21.txt')]

[famosab]

Suggested change

	input[1] = []
	input[2] = []
	input[1] = [path('https://raw.githubusercontent.com/nf-core/test-datasets/d677699283dbbeb51876d1bb3c18fb687d1db4ea/data/genomics/homo_sapiens/illumina/ascat/G1000_alleles_WGS_hg38/G1000_alleles_hg38_chr21.txt')]
	input[2] = [path('https://raw.githubusercontent.com/nf-core/test-datasets/d677699283dbbeb51876d1bb3c18fb687d1db4ea/data/genomics/homo_sapiens/illumina/ascat/G1000_loci_WGS_hg38/G1000_loci_hg38_chr21.txt')]