Moved from wfmash to ragtag in clustering step

See merge request !3

Updated regex pattern to search for required pattern (<haplotype>#<chromosome|ctg id>).
Updated README

Moved ragtag scaffolding to standalone script (ragtagChromInfer.sh). Snakemake now call this script.
Fixed missing library in inputClustering.py.
Updated Snakefile accordingly

Changed clustering tool from wfmash to ragtag. Test phase ahead.

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)