Prepare merge for v1.2.0

Massive changes in the code occurred in the version :

• The workflow now use a new version of Snakemake>=8.4.7 that efficiently manage computational resources across multiple nodes using the SLURM executor plugin.
• The workflow got simplified by reducing the code size, unifying rules, and improving clarity with better comments and advanced Snakemake functions.
  • Codbase got reduced from 1726 lines to 1105 and the number of rules got reduced from 48 to 20.
    • Now a script dynamically launch the right hifiasm command
    • Now a script dynamically launch purge_dups or not based on user choice
• New features got added such as QUAST, RagTag and LTR elements identification.
• Many options got added in the workflow to allow user to fine tune the execution
• Resources allocated to each rules got revised
• Greatly increase the verbose of the workflow
• All tools got updated, noticeably hifiasm got upgraded from version 0.16.1 to 0.24.0-r703

local_run.sh

@@ -3,7 +3,7 @@
 ## TMP config to run on the CBIB
 #SBATCH --job-name=asm4pg
 #SBATCH --ntasks=20
-#SBATCH --mem=100G
+#SBATCH --mem=200G
 #SBATCH -o slurm_logs/out_job_%j.out
 #SBATCH -e slurm_logs/err_job_%j.err
 
@@ -20,7 +20,7 @@ run_snakemake() {
             snakemake --use-singularity --singularity-args "-B $SNG_BIND" -j $(nproc) -n 
             ;;
         dag)
-            snakemake --use-singularity --singularity-args "-B $SNG_BIND" -j $(nproc) --dag > dag.dot
+            snakemake --use-singularity --singularity-args "-B $SNG_BIND" -j $(nproc) --rulegraph > dag.dot
             if [ $? -eq 0 ]; then
                 echo "Asm4pg -> DAG has been successfully generated as dag.dot"
             else