updates resources

configs/cluster_config.json

@@ -4,6 +4,9 @@
         "partition": "express",
         "cpus-per-task": "{threads}",
         "mem": "8G",
-        "output": "logs/rule_logs/{rule}-%j.log",
+        "output": "logs/rule_logs/{rule}-%j.log"
+    },
+    "mosdepth_coverage": {
+        "partition": "short"
     }
 }

workflow/rules/coverage_analysis.smk

@@ -22,6 +22,8 @@ rule mosdepth_coverage:
         "mosdepth"
     conda:
         str(WORKFLOW_PATH / "configs/env/mosdepth.yaml")
+    threads:
+        4
     params:
         out_prefix = lambda wildcards, output: output['summary'].replace('.mosdepth.summary.txt', ''),
     shell:

workflow/rules/within_species_contamintation.smk

@@ -21,7 +21,7 @@ rule verifybamid:
         svd_prefix = lambda wildcards, input: input['svd'][0].replace(Path(input['svd'][0]).suffix, ''),
         out_prefix = lambda wildcards, output: output['ancestry'].replace('.Ancestry', ''),
     threads:
-        1
+        2
     shell:
         r"""
         verifybamid2 \