add nirvana

[FriederikeHanssen]

requires nf-core/test-datasets#1830

This PR adds Nirvana, an annotation tool developped by Illumina

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
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• 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

[jonasscheid]

LGTM, only fix linter complains :)

[FriederikeHanssen]

Somehow the Singularity container does not work. It has Nirvana not in the path and is missing some dotnet symlink :confused_husky:

not sure why, given that both the conda recipe and docker container work

[maxulysse]

LGTM

[jonasscheid]

I wanted to suggest using the galaxy container, but there is none. Also not on quay. But why is nirvana in bioconda but not quay/galaxy 🤔

[adamrtalbot]

Is the cache_prefix a path or a specific string within the path?

[FriederikeHanssen]

If the data looks like this:

❯ tree
.
├── Cache
│   └── SARS-CoV-2
│       ├── SARS-CoV-2.polyphen.ndb
│       ├── SARS-CoV-2.sift.ndb
│       └── SARS-CoV-2.transcripts.ndb
├── References
│   └── SARS-CoV-2.ASM985889v3.dat
└── SupplementaryAnnotation
    └── SARS-CoV-2
        ├── SARS-COV-2_AllFreq.nsa
        ├── SARS-COV-2_AllFreq.nsa.idx
        ├── SARS-COV-2_AllFreq.nsa.schema
        ├── SARS-CoV-2_ProteinDomains.nsi
        └── SARS-CoV-2_ProteinDomains.nsi.schema

then the cache is ./Cache/SARS-CoV-2/ and thecache_prefix is SARS-CoV-2 (here the one that is the prefix of the filename), so it overall is resolved to ./Cache/SARS-CoV-2/SARS-CoV-2.

I am not certain we can enforce people to match the prefix on the actual files with the folder name. I have not seen more Nirvana caches to check how this normally looks like. Alternatively, we could possible stage in the files and somehow extract the cache prefix to build the path, but it feels brittle

[adamrtalbot]

Alternatively, we could possible stage in the files and somehow extract the cache prefix to build the path, but it feels brittle

I think we should do this at the workflow level, so I'm fine with this.