Default pipeline create_ref_data -> mappability_bwa does not work properly

[simozacca]

Hi,

The following command

remixt create_ref_data $ref_data_dir

works and ends properly. However, the subsequent command

remixt mappability_bwa $ref_data_dir

fails because bwa does not find the index of the reference genome.

If the default behavior is for generating a mappability file based on bwa alignments, would be possible to add the proper bwa indexing as an additional step in remixt create_ref_data?