FastA indexing + bwa indexing

Should follow more the examples of e.g .viralrecon: 

https://github.com/nf-core/viralrecon/blob/69326f97b1c1d1b8733a0df573cb1f3eff907e6d/main.nf#L163

and `ch_fasta = file(params.fasta)` 

And then use proper 

```
input:
    path fasta from ch_fasta
```