DSL2: metagenomics

[ilight1542]

TODOS:

• Ensure files passed to metagenomics profiling are identifiable with outputted names (eg should be able to distinguish mapped, vs unmapped to ref (if user selects 'all': do we want to merge these and just use the raw sequencing reads --> this i think is the expected behavior but not always working?)
• Finish testing for maltextract @merszym
• Finish testing of various input parameters to ensure proper behavior for outputted files (ensure no overwriting of files is occurring with ext.prefix (!!)
• Test malt parallel execution (multiple independent submissions)
• Test warning and parameter combo checks implemented in eager.nf
• Add any necessary warnings or errors for parameter combos for metagenomics to eager.nf
• Double check documentation is correct, and easy to understand
• Check how single-strand vs double strand mixed input into malt currently behaves -- currently does not flag singlestranded if one sample is singlestranded (this info may be wiped from metamap at mapping step?). Need to check for single sample(!)
• Update that malt keeps Single stranded library prep info for later use in maltextract

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 - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
  • If necessary, also make a PR on the nf-core/eager 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).

[merszym]

@jfy133 @ilight1542 All remaining issues are fixed/documented/updated :)

[jfy133]

There are still some small code clean up that can be done/addressed in a future PR but otherwise this looks good to me to get it in and start fixing everything else in smaller follow up PRs (assuming tests are passing)

[jfy133]

@nf-core-bot fix linting