Add MALT metagenomic classifier functionality

[jfy133]

This begins adding metagenomic classifier functionality to EAGER primarily for pathogen screeening.

The exact classifer can be specified - but currently only MALT is implemented (as precursor for HOPS).

Path in github actions test for database downloading will be pointed to nf-core once nf-core/test-datasets#97

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/eager 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/eager/tree/master/.github/CONTRIBUTING.md

[apeltzer]

Can you update the tests as the PR you mentioned has been merged now? That will then perform a final tests upon which I'm reviewing then - thanks a bunch!

[jfy133]

Can you update the tests as the PR you mentioned has been merged now? That will then perform a final tests upon which I'm reviewing then - thanks a bunch!

Done! I've only added github actions testing though. Let me know if you also want travis a the same time and I'll work out how to add it (it's a little complicated because I have to first download the MALT databsae, as MALT expects a dir rather than files)

[apeltzer]

Needs some more documentation please!

[jfy133]

Needs some more documentation please!

Oops sorry - I thought MALT was merged already! So I just started using the same branch for the next step. The new commit isn't actually working yet ;).

Reflagged as WIP!

[jfy133]

@apeltzer assuming tests go through, this should be ready.

Note, to compensate for the lack of documentation in your last comment - I added lots extra for you to check ;).

[jfy133]

I'm closing this as Im finding problems and it doesn't make sense to run github actions on my personal account and here. Will make a new one onceit's working!