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.

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

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

[ewels]

Quite a lot of commits for this issue:

• 36fca4a
• 4914309
• 3e3bca0
• 2894d7e
• ec44279
• bd2fca0
• 7aa1be3
• 845a373
• cd6b38f
• df7637d
• e2bffc6
• c2910b7
• fce944d

[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..