Mode: paired short read (Bowtie2) fails when index is provided as reference fasta file about hostile

[bede]

Hi! Thanks for drawing attention to this, which works today but should be better documented.

Whereas the index parameter accepts a path to a genome in Minimap2 (long read) mode, in Bowtie2 (short read) mode it accepts a path to a precomputed Bowtie2 index, minus the .x.bt2 extension.

So you'll need to build a bowtie2 index (beware, human genome takes 30 mins or so)

bowtie2-build Bos_taurus.ARS-UCD1.3.dna.toplevel.fa bostaurus

And then

hostile clean --fastq1 SRR27845761_1.fastq.gz --fastq2 SRR27845761_2.fastq.gz --threads 10     --index bostaurus

This annoying implementation detail is normally hidden when using standard indexes.

I've updated the readme to make this behaviour clearer.