Adding allocation information for new deepsomatic rules

OpenOmics · Nov 12, 2024 · 1267ed4 · 1267ed4
1 parent e46097e
commit 1267ed4
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Showing 2 changed files with 13 additions and 6 deletions.
diff --git a/config/cluster/slurm.json b/config/cluster/slurm.json
@@ -84,18 +84,24 @@
         "time": "1-00:00:00",
         "gres": "lscratch:750"
     },
-    "deepsomatic_call_variants": {
+    "deepsomatic_call_variants_gpu": {
         "threads": "16",
         "mem": "60G",
         "partition": "gpu",
         "gres": "gpu:a100:1,lscratch:450",
-        "time": "1-00:00:00"
+        "time": "1-12:00:00"
+    },
+    "deepsomatic_call_variants_cpu": {
+        "threads": "36",
+        "mem": "120G",
+        "gres": "lscratch:450",
+        "time": "3-00:00:00"
     },
     "deepsomatic_postprocess_variants": {
-        "threads": "4",
-        "mem": "64G",
+        "threads": "6",
+        "mem": "72G",
         "time": "1-00:00:00",
-        "gres": "lscratch:256"
+        "gres": "lscratch:450"
     },
     "deepvariant": {
         "threads": "18",

diff --git a/workflow/rules/depreciated.smk b/workflow/rules/depreciated.smk
@@ -148,5 +148,6 @@ rule deepsomatic:
         --sample_name_tumor={params.tumor} {params.normal_name_option} \\
         --output_vcf={output.vcf} \\
         --num_shards={threads} \\
-        --intermediate_results_dir=${{tmp}}
+        --intermediate_results_dir=${{tmp}} \\
+        --vcf_stats_report=false
     """