DSL-2 conversion, update IRMA to v1.0.2

[peterk87]

Changes

• Update IRMA to version 1.0.2
• Removed reads param. Users need to specify a sample sheet with input param instead. Sample sheet can be tab-delimited (TSV) or CSV and must have a header line and 3 columns (sample name, FASTQ path/URL to forward reads, FASTQ path/URL to reverse reads).
• Add IRMA params
  • irma_module: IRMA module (default: FLU-utr)
  • keep_ref_deletions: set consensus sequence deletion by ambiguation (i.e. replace ref seq with Ns) (default: true)
• Add BLAST subtyping params:
  • pident_threshold: % identity threshold (default: 0.85)
  • min_aln_length: min alignment length (default: 50)
• Convert to DSL-2
• Replace Azure Pipelines CI with GitHub Actions CI
• add nextflow_schema.json and lib/ helper nf-core Jar file and Groovy scripts for params validation, printing help
• Use nf-core modules where possible
• Use nf-core module style for all processes

PR checklist

• [X] Ensure the test suite passes (nextflow run . -profile test,docker).
• [X] Usage Documentation in docs/usage.md is updated.
• [X] Output Documentation in docs/output.md is updated.
• [X] CHANGELOG.md is updated.
• [X] README.md is updated (including new tool citations and authors/contributors).

[github-actions[bot]]

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

• Install markdownlint-cli
  • On Mac: brew install markdownlint-cli
  • Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
• Fix the markdown errors
  • Automatically: markdownlint . --config .github/markdownlint.yml --fix
  • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment :+1:

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!