Update Fred2 from version 2.0.6 to 2.0.7

[skrakau]

Update Fred2.

Maybe we can improve the changelog in another PR.

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 necessary, also make a PR on the nf-core/epitopeprediction branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/epitopeprediction/tree/master/.github/CONTRIBUTING.md

[skrakau]

The CI failed because 1) #39 should have waited until Fred2 was updated to 2.0.7 (thought we updated this already) and 2) just realised that I only added the mouse alleles to methods in ANN.py, but not to syfpeithi in PSSM.py. Thus this should be updated in Fred2, and for this pipeline for now the test_peptides_h2 should be run using MHCNuggets (or MHCFlurry)

[christopher-mohr]

Thanks @skrakau! Currently there are not mouse PSSMs for Syfpeithi in FRED2, therefore we should make sure that only mhcflurry and mhcnuggets is used with mouse alleles (can be done in a separate PR). Could you just change the test accordingly in this PR please? I will take care about the changelog with the template merge.

[skrakau]

Ah forgot, makes sense then.

[christopher-mohr]

The test will be adapted in a separate PR.