PURGEDUPS_PURGEDUPS migration to nf-test

[TomHarrop]

PR checklist

Closes #7674

• 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

[SPPearce]

There is no snapshot output?
Can you add a stub to the module, and a corresponding test please.

[TomHarrop]

Thanks, I think those are done.

[TomHarrop]

@SPPearce looks like that issue using --stub is discussed here: nextflow-io/nextflow#5456

 Cannot invoke method clone() on null object

The conda test segfaults, not sure if this matters as both the container tests pass.

    > Command error:
    >   .command.sh: line 2:  1960 Segmentation fault      (core dumped) calcuts test.PB.stat > test.cutoffs 2> >(tee test.calcuts.log >&2)

[SPPearce]

That generally means you need to add stubs to the other modules you are using to setup the tests, can you try doing that in this PR please

[TomHarrop]

Oh great, thanks for the tip. It's just the failing conda tests now.

[SPPearce]

Hmm, your snapshot is empty though, are you sure the tool is making output on docker and singularity?

[TomHarrop]

Thanks @SPPearce , that should be fixed now. It was an issue with the way the input had been specified for pytest.

[awgymer]

CALCUTS conda tests are failing with a segmentation fault, but separately the other module conda tests are failing because of a discrepancy in the versions.yml.

It looks like the conda version should be the same as that in the biocontainers images but I can't test it locally to see what the actual output and difference is

[SPPearce]

The version is being returned as 1.25 or 1.26 between the different container methods

[famosab]

Yeah conda returns 1.2.6 while docker returns 1.2.5

[famosab]

Lets swap to seqera containers I would suggest?

Docker: community.wave.seqera.io/library/purge_dups:1.2.6--1966ab26985f9f67
Singularity: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8a/8afcc1222a0512a4fae7a7e7315ccfc841f3578df600b99d3dc563c3a8361352/data

[famosab]

@TomHarrop I do not have write access to your fork but this is what you need to replace:

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8a/8afcc1222a0512a4fae7a7e7315ccfc841f3578df600b99d3dc563c3a8361352/data':
        'community.wave.seqera.io/library/purge_dups:1.2.6--1966ab26985f9f67' }"

[TomHarrop]

@famosab if you want to suggest those changes I will accept them - that way your commit is tracked.

Otherwise LMK if you want me to just make the change.

Thanks!

[SPPearce]

@famosab if you want to suggest those changes I will accept them - that way your commit is tracked.

Otherwise LMK if you want me to just make the change.

Thanks!

Just make the change yourself please, I'm sure Famke won't mind it isn't in her name on the commit.

[TomHarrop]

OK done, hope that was the file you were referring to.

[famosab]

Could you also re-run nf-test? :) And update the snaps?

[SPPearce]

Also you should remove the entry in the tests/config/pytest_modules.yml file to stop the pytest from running.

[TomHarrop]

Also you should remove the entry in the tests/config/pytest_modules.yml file to stop the pytest from running.

I think I did, just not for the other submodules.

[famosab]

There is #8472 and #8471 which might need to be merged first for this to work :)