Fixed a bug in extract_pairs.pl that assumed HiC read pairs only connect (bedtools intersect) two annotations and not more

Replaced bwa mem with mapPacBio.sh from BBMap package, added PlantSat sequence analysis analogically to contigs from Repeat Explorer

processes now moved to modules, test paired data are read into the channel and passed into the pipeline

extended the script to include blast results, assignment to clusters, and the calculation of the matrix