Update getPanachePAV.sh

See merge request !6

Fixed bug in awk command used to rename columns in final PAV matrix

Update Snakefile

See merge request !5

Removed og file creation

Usage statistics and cleaning

See merge request !4

Changed workflow to use graphList.txt instead of recomputing the list of ouput from clustering checkpoint.
Added .og graph generation in rule pggb_on_chr

Back to old scripts.
apptainer is not available when snakemake is launched from apptainer image

Added -P to odgi commands to get progression logs.

Switched to snakebox and its included snakemake. See : https://forgemia.inra.fr/alexis.mergez/pangratools
Updated README accordingly

Added dynamic threading for get_pav rule

Renamed timeStats.py to usageStats.py.
Updated snakefile accordingly.
Fixed bug in snakefile.
Updated README

Fixed dependance issue with pggb_log_compression missing logs/pggb folder

Added "name" field to customize file names
Added timeStats.py to compute statistics about graph assembler

Added timeStats.py to compute stats on pggb time logs (time cpu usage and memory used) [WIP]

Removed deprecated scripts
Added flags instead of positionnal arguments
Removed deprecated rules in Snakefile

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