Fixed an error where table n x n filtered down to minimal dimensions of 1 x 1 becomes an integer, however only as a dirty hack with variables that were influenced in the test profile calculations

add option to skip diachromatic processing,
add option to skip align_reads,
remove unused bwa index,
use tuple in prepare_sra.

Testing row and column reordering in TEHeatmap_norm1.R; added exons and PlantSat annotations to analysis

Instead of generating heatmaps, this script now produces a .tab file that can be passed to normalizations and heatmap generation. The tab file is saved in "tab_RE.Rdata" format. However, because it's part of the RepeatExplorer branch of the pipeline, chromosome names and positions are undefined. 

add process CAT_ANNOTATIONS,
prepare shuffled channel.

Fixed errors when matrix for heatmap was too small (less than 2 rows or columns), now gracefully prints an empty image

add repeatexplorer.nf to main pipeline,
rename output for png files.

fixed the bug for the calculation of expected counts of family pairs; moved normalization code into a separate function