v1.1

See merge request !2

Fixed missing apptainer image name
Fixed awk commands (creating temp files instead of editing the file inplace)

Added PAV matrix generation in output/pav. It can be directly used in Panache

Moved reference haplotype to data/haplotypes folder.
Removing reference folder

Added data prep section
Updated Usage section
Still more documentation to do

Added a rule to create 1D and path coverage firgures of each chromosomes in output/figures
Added parameters to config.yml accordingly

Added param fileds in several rules
Added keys in config.yml

Added missing library (os)