Epytope switch in process peptide_prediction

[jonasscheid]

The new release of epytope (v3.0.0) provides an altered prediction structure due to the incorporation of rank metrics.
This PR aims to embed the new prediction structure in the epaa.py script, which is called by the PEPTIDE_PREDICTION process.

Related issues:
#54
#130

PR checklist

• 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/epitopeprediction branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[christopher-mohr]

I will have a look. 👍
Could you also please change conda and the containers in the process here. Should be bioconda::epytope and quay.io/biocontainers/epytope. I think you might have to specify the tag as well. If it works the test should pass as well.

[christopher-mohr]

There was a permission problem with the bioconda container which is fixed now. The container can now be pulled from http://quay.io/biocontainers/epytope:3.0.0--pyh5e36f6f_0.

[christopher-mohr]

Some things that need to be changed but overall it looks good. 👍

[christopher-mohr]

LGTM! Some of the tests are failing because of an epytope issue which will be solved in the new release.