Metaspace submit

[Bisho2122]

PR checklist

Closes #7878
Closes #8087

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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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
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    • 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

[Bisho2122]

I migrated this PR #8087 to this one.

[itrujnara]

This module has come a long way, and now it's very close to being ready. I have one minor remark, and I still want the other reviewers from the previous take to see this one.

[SPPearce]

Do we not want meta maps here?

[SPPearce]

? Which of these would be the real use case?

[Bisho2122]

I get the confusion. I think secrets has to be defined by the user using nextflow secrets set METASPACE_API_KEY "USER_API_KEY". I was trying to mimic the setup from sentieon modules (https://github.com/nf-core/modules/blob/9fe7867a4f012db581d7bd560228ded1074eb0e5/modules/nf-core/sentieon/dedup/tests/nextflow.config).

So it can be tested locally without the need to use nextflow secrets by just export api key as environment variable. Or it could be set by nextflow secrets. Both should work.

[Bisho2122]

My PR for a bioconda recipe was recently merged and now we have a bioconda package (https://anaconda.org/bioconda/metaspace2020). So no more linting issues :)