v1.2.14: Add support for bowtie2 indices as input

⚠️ Intoduces non-backwards compatible changes to the CLI:

• Option -m, --minimap2 becomes -a, --aligner, taking either "minimap2" or "bowtie2" as value
• Option -f, --fasta becomes -g, --genome

Changes in behaviour:

• -g must be a fasta file when using minimap2, and a bowtie2 index prefix when using bowtie2
• A fasta file is created among temporary file when using bowtie2. It is generated from the bt2 index.