Add metagenomics module

[jfy133]

Is your feature request related to a problem? Please describe.
A standard step of ancient metagenomics work (pathogens, microbiome), is now performing a metagenomic screening i.e. rapid/approximate alignment against a reference database of many genomes at once - typically on the off-target reads of the original host (e.g. host is human, but want to look what bacterial infection killed the person). It would be another good end point of EAGER is a basic OTU table (and some summaries), as initial microbial composition check before downstream analysis outside the scope of EAGER.

This would also be a nice upgrade from EAGER1, for any future publication as it brings EAGER up-to-date with the current state of the aDNA field.

Describe the solution you'd like
Add meta-genomic module.

Suggestions:

• HOPS Pipeline (currently requires a slight modification to the conda recipe to make malt-extract accessible via a environment variable)
• Kraken (@maxibor - would need your input here)

Other things to consider
MALT (used in HOPS) often requires a large amount of MEM/CPUs depending on the database. How to specify this/warn the user?

[apeltzer]

All in V2.1? :-D

[jfy133]

HOPS certainly. It'll be straight forward once Ron has updated the HOPS recipe.

[jfy133]

#284

[apeltzer]

All there in dev, coming with 2.1.0 !

[jfy133]

Re-opening after reconsideration of adding Kraken with @maxibor , which is more accesible tool to wider labs and is pretty commonly used now. Maxime is the expert here so will assign that to him.

[maxibor]

Kraken PR with #355

[jfy133]

Thanks @maxibor !