Rewrite genome paths

[ewels]

Currently, genome paths are handled in a very inflexible way. Basically, a genome / bowtie / bowtie2 / gtf path has to be specified and each is dealt with manually. This is bad as it's difficult if not impossible to add other types of genome indices (bismark / other aligners) and involves quite a bit of code duplication.

• [x] Allow any @reference tag in the genomes.config file
• [x] Parse these into a single hash so we don't care what the tag was
• [x] Allow pipelines and modules to use the @require_reference <type> tag for anything that's in the hash
• [x] Update pipelines and modules to use this syntax
• [x] Alter modules to check for and include paths in a consistent manner

With this, the current listing and genomes wizard will have to be updated:

• [x] Listing can be much less verbose and more agnostic to tag name
• [x] Wizard should still start by asking for assembly / genome id but then allow any tag
• [x] Wizard should start by iterating through a directory and checking for known indices: .fa, .ebwt, .bt2 files, .gtf files and any other known structure
• [x] This will make wizard way faster and more accurate.
• [x] Confirm each detected path so that we can ignore bogus ones.

[ewels]

Quite a lot of commits for this issue:

• 36fca4a2d1e5ac9b03b9090d44dc866ab9a6e177
• 49143099cf48ec36924e5641759666f4916473b7
• 3e3bca05e8af003922463ee5a6f7b9346f8dfd73
• 2894d7e7a4061ea0ac1e31d91974ae693fdbda8e
• ec44279aea7ce5ca6b148479be4aec6d000c589e
• bd2fca05b06850b5bfecca3426d806210d39e5b0
• 7aa1be32144b93313aec445c232d4f8d32827733
• 845a3738140ced67d9f3f74cfe3f22f670a46692
• cd6b38f373f6c3a0222a2507ee6b914200394686
• df7637ded87569aca04491276dc89d9dadd5677f
• e2bffc6a729c38755821fc2a46436522737735f4
• c2910b7133ac8e8c7bee495b505b220e42fa694e
• fce944df6500594a72eeb64702c070668f2f4581

[ewels]

Written and tested (a bit). Seems to be working nicely. New --add_genome wizard is much much nicer..

[ewels]

I should mention - @stu2, @s-andrews, @FelixKrueger and anyone else who might be using the development fork of Cluster Flow - this update will break your setup (old style reference genomes won't be recognised).

See the readme for instructions on updating. It's a 2 minute job, so shouldn't be a big deal..