Add hiv resistance detection

[svarona]

Description of changes

• Added sierra-local HIVdb software for resistance and codon mutations detection
• Added codfreq for codon frequency calculation
• Created reporting .csv files
• Added documentation to README
• Added documentation to output.md
• Added documentation to usage.md
• Added software credits
• Added hiv tests
• Added HIV resistance reports
• Updated metro-map

Related issues:

• Add HIV resistance detection subworkflow #548

Fixed issues:

• Add sierra-local #549
• Add codfreq for codon frequency calculation #550
• Generate reporting .csv files #551
• add documentation #554
• Generate HTML reports #552
• Add HIV resistance to the metro-map #553

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/viralrecon branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• 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).

[svarona]

Can you also update the metro-map including hiv res?

Yes! I wanted to show you the proposal before commiting it! We can see it tomorrow in our meeting!