Update Snakefile

Added threads to stats jobs

Snakefile

@@ -202,7 +202,7 @@ rule chromosome_clustering:
         expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
     output:
         temp(expand('data/chrInputs/'+config['name']+'.{chromosome}.fa', chromosome=CHRLIST))
-    threads: 2
+    threads: 1
     params:
         app_path=config["app.path"],
         pan_name=config["name"]
@@ -531,6 +531,7 @@ rule aggregate_graphs_stats:
     output:
         genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
         pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+    threads: 1
     params:
         app_path=config['app.path'],
         pan_name=config['name']
@@ -564,6 +565,7 @@ rule pggb_input_stats:
         flag="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
     output:
         "output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
+    threads: 1
     params:
         app_path=config['app.path'],
         pan_name=config['name']
@@ -576,11 +578,12 @@ rule pggb_input_stats:
 rule core_statistics:
     # Aggregate chrInput, chrGraph and pggb statistics into a single tsv 
     input:
-        chrInputStats="output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
-        chrGraphStats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
+        chrInputStats = "output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
+        chrGraphStats = "output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
     output:
-        tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
-        dir=directory("output/pggb.usage.figs")
+        tsv = "output/stats/pan1c."+config['name']+".core.stats.tsv",
+        dir = directory("output/pggb.usage.figs")
+    threads: 1
     params:
         app_path=config['app.path'],
         pan_name=config['name']
@@ -593,12 +596,7 @@ rule core_statistics:
         """
 
 """
-
-Post-processing section :
-    The graph for each chromosome are made as well as some basic statistics.
-    In this section, more stats are produced but more specifics ones requiring dedicated tools (Panacus, PAVs for Panache ...).
-    It also contains rules to use the graph itself. 
-
+Post-processing section
 """
 rule get_pav:
     # Create PAV matrix readable by panache for a given chromosome scale graph
@@ -694,8 +692,7 @@ def get_report_sections(wildcards):
             haplotype=SAMPLES_NOREF
             )
 
-    return sections
-        
+    return sections      
 
 rule create_pan1c_report:
     # Produces a markdown report of chromosomes graphs