Merge branch 'dev' of https://forgemia.inra.fr/alexis.mergez/pan1c into dev

Snakefile

@@ -50,9 +50,13 @@ def which_analysis():
     if config["get_PAV"] == "True": # Adding PAV matrix creation
         analysis_inputs.append("output/pav.matrices")
 
-    if config["get_ASMs_SyRI"] == "True": # Creating SyRI  for each figures 
+    if config["get_ASMs_SyRI"] == "True": # Creating SyRI for each input assembly 
         analysis_inputs.append(
-            expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF),
+            expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF)
+        )
+    if config["get_chrInputs_SyRI"] == "True": # Creating SyRI figures for each PGGB input
+        analysis_inputs.append(
+            expand("output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png", chromosome=CHRLIST)
         )
     if config["run_Quast"] == "True": # Running Quast on input haplotypes
         analysis_inputs.append(
@@ -584,6 +588,7 @@ rule final_graph_tagging:
     output:
         "output/pan1c."+config['name']+".gfa.metadata"
     threads: 1
+    priority: 100
     params:
         app_path=config['app.path'],
         pan_name=config['name']

config.yaml

@@ -27,7 +27,7 @@ get_contig_pos: 'True'
 # Computes Presence Absence Variant matrices for Panache (not recommended; very long)
 get_PAV: 'False'
 # Computes SyRI figures for haplotypes 
-#get_allASM_SyRI: 'False' # All vs all
 get_ASMs_SyRI: 'False' # Haplotype vs Reference
+get_chrInputs_SyRI: 'False' # SyRI on chrInputs
 # Creating final report
 create_report: 'True'

example/config_CICD.yaml

@@ -28,6 +28,7 @@ get_contig_pos: 'True'
 get_PAV: 'False'
 # Computes SyRI figures for haplotypes 
 #get_allASM_SyRI: 'False' # All vs all
-get_ASMs_SyRI: 'False' # Haplotype vs Reference
+get_ASMs_SyRI: 'True' # Haplotype vs Reference
+get_chrInputs_SyRI: 'True' # SyRI on chrInputs
 # Creating final report
 create_report: 'True'