Add a possibility to plug another mapper

[karel-brinda]

• Based on one of the reviewers comments
• A bit tricky – not all mappers can work in 1 command
• The way to go: create a bash script align_to_genome.sh [params] ref.fa query.fa
• Still have to somehow handle passing minimap2 presets to this

Phases:

1. clean the current batch_align.py (copying to deprec for archivation and removing all unused functions so that we modify only the relevant ones)
2. create align_to_genome.sh
3. adjust configuration

Users then can modify align_to_genome.sh if they want to use a custom read mapper (experimentally).

(All this should be relatively simple. If not, we shouldn't implement it.)