New module for contamination screening: Sylph

[egreenberg7]

Resolves #1615. I have mostly implemented the addition of Sylph into the nf-core rnaseq pipeline for contamination screening. We may want to wait for Sylphtax to be added to MultiQC and then for that to be updated in the pipeline, see my PR there. Sylph has similar precision and much lower compute requirements than Kraken2/Bracken; the main disadvantage in my eyes is that it cannot do individual read assignments. In any case, I think it would be a very useful tool for contamination screening as an alternative to the Kraken2/Bracken combination and was mentioned as an alternative when that was added (see here).

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[egreenberg7]

A bug that still needs to be dealt with before merging: if Sylph detects no species (primarily for small test files, or maybe incorrect database), it outputs a blank text file that causes sylphtax to crash. We'll have to add some way of checking the sylph output before feeding it to sylph tax I presume. Otherwise, it seems to be working fine.
FIXED

Also, for now I did not put tests of the file extensions for the sylph database/taxonomy in the nextflow schema, but that could be an enhancement.

[pinin4fjords]

Really nice work, thanks!

Yes, let's wait for the MultiQC module (I've nudged Phil but he's crazy busy)

We'll also have to figure out what's going on with the failing tests.

[pinin4fjords]

Let's not do this. There's lots of cases where the params contains unused options, we don't need to warn the user each time.

[egreenberg7]

I'll comment here that this is in line with Kraken2. It is a bit different from params containing unused options in that if a person provides a Sylph database/taxonomy to the the pipeline but contaminant-screening is not set to sylph, then sylph will not run even though the database has been provided. I could making the wording a bit more clear or just follow through and delete it entirely

[pinin4fjords]

Maybe we should delete it from kraken as well then. I think if I'm a user I expect to be able to turn something off an not get warnings about excess params.