add_module_arriba_visualisation

[peterpru]

This PR adds the module ARRIBA/VISUALISATION

PR checklist

Closes #XXX

• [x] This comment contains a description of changes (with reason).
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] If you've added a new tool - have you followed the module conventions in the contribution docs
• [x] If necessary, include test data in your PR.
• [x] Remove all TODO statements.
• [x] Emit the versions.yml file.
• [x] Follow the naming conventions.
• [x] Follow the parameters requirements.
• [x] Follow the input/output options guidelines.
• [x] Add a resource label
• [x] 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:
  • [x] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [x] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [x] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

[SPPearce]

Hi @peterpru , I updated this PR, but couldn't push it back to your branch. I pushed it to a new branch on the main repo: https://github.com/nf-core/modules/tree/add-arriba-visualisation/modules/nf-core/arriba/visualisation

[peterpru]

When I run the tests, docker fails, but conda and singularity succeed:

Adding the following to the nextflow.config file makes docker succeed, but then singularity fails, saying it cannot have both singularity and docker active.

docker {    
    enabled = true
    fixOwnership = true
    runOptions = '--platform=linux/amd64'
}

[fellen31]

Could you run UNTAR with https://github.com/suhrig/arriba/releases/download/v2.4.0/arriba_v2.4.0.tar.gz as input, instead of ARRIBA_DOWNLOAD in setup?

[fellen31]

Maybe just uploading known_fusions, cytobands and a smaller version of protein_domains to test-data, and inputting those to ARRIBA_VISUALISATION is easiest in this case? If that's why you need ARRIBA_DOWNLOAD/UNTAR.

[peterpru]

Added this instead, I realised the other part forced the activation of docker even while trying to run singularity:

docker {
    runOptions = '--platform=linux/amd64'
}

[SPPearce]

Added this instead, I realised the other part forced the activation of docker even while trying to run singularity:

docker {
    runOptions = '--platform=linux/amd64'
}

Hmmm, I think this should already be specified by default: https://github.com/nf-core/modules/blob/bb21d916a55074acbb48cedc282242077e4ad9b9/tests/config/nf-test.config#L38C5-L39C5

[peterpru]

Added this instead, I realised the other part forced the activation of docker even while trying to run singularity:

docker {
    runOptions = '--platform=linux/amd64'
}

Hmmm, I think this should already be specified by default: https://github.com/nf-core/modules/blob/bb21d916a55074acbb48cedc282242077e4ad9b9/tests/config/nf-test.config#L38C5-L39C5

I agree, it looks like it is in there already. However, the docker test failed without it.

[fellen31]

@peterpru I can't see ARRIBA_VISUALISATION running in the tests at all? https://github.com/nf-core/modules/actions/runs/10365583027/job/28693132891?pr=4192#step:14:46

[SPPearce]

@peterpru , do you need a hand here?

[peterpru]

@peterpru , do you need a hand here?

If you want to, I appreciate it. I will not be able to work on it again before November.

[peterpru]

Closing due to time constraints.