Update Snakefile

Snakefile

@@ -97,6 +97,7 @@ rule ragtag_scaffolding:
         tar="data/hap.ragtagged/{haplotype}.tar.gz"
     threads: 8
     retries: 1
+    priority: 100
     params:
         app_path=config["app.path"]
     log: 
@@ -213,6 +214,7 @@ rule chromosome_clustering:
     output:
         temp(expand('data/chrInputs/'+config['name']+'.{chromosome}.fa', chromosome=CHRLIST))
     threads: 1
+    priority: 100
     params:
         app_path=config["app.path"],
         pan_name=config["name"]
@@ -316,6 +318,7 @@ rule wfmash_on_chr:
         mapping=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.mapping.paf"),
         aln=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf")
     threads: 16
+    priority: 100
     params:
         app_path=config['app.path'],
         segment_length=config['wfmash.segment_length'],
@@ -365,6 +368,7 @@ rule seqwish:
     output:
         temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa")
     threads: 8
+    priority: 100
     params:
         app_path=config['app.path'],
         seqwish=config['seqwish.params']
@@ -393,6 +397,7 @@ rule gfaffix_on_chr:
         gfa=temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.gfa"),
         transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
     threads: 1
+    priority: 100
     params:
         app_path=config['app.path']
     log: 
@@ -416,6 +421,7 @@ rule odgi_postprocessing:
     output:
         gfa='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
     threads: 8
+    priority: 100
     params:
         app_path=config['app.path']
     log: 
@@ -478,6 +484,7 @@ rule generate_graph_list:
     output:
         "data/chrGraphs/graphsList.txt"
     threads: 1
+    priority: 100
     run:
         with open(output[0], "w") as handle:
             for file in input:
@@ -494,6 +501,7 @@ rule graph_squeeze:
         cmd="logs/squeeze/"+config['name']+".squeeze.cmd.log",
         time="logs/squeeze/"+config['name']+".squeeze.time.log",
     threads: 16
+    priority: 100
     params:
         app_path=config['app.path']
     shell: