Use Minimap2 for scaffolding instead of SortMeRNA

[ppericard]

SortMeRNA is designed to align short reads, Illumina type, and is used as the starting step in MATAM. SortMeRNA is also used to re-align the assembled contigs onto the reference database to perform scaffolding. This is not optimal, and for scaffolding, SortMeRNA should probably be replaced by a more appropriate mapper such as Minimap2.