From 3d06f7debb5841cbf3fde7b1b398e7ed50e71b52 Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Mon, 28 Oct 2024 13:03:43 -0400
Subject: [PATCH] Bumping up clairs-to allocated memory and providing half of
 allocted threads

---
 config/cluster/slurm.json  | 4 ++--
 config/cluster/uge.json    | 2 +-
 workflow/rules/somatic.smk | 8 ++++++--
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/config/cluster/slurm.json b/config/cluster/slurm.json
index 876fb93..e616d80 100644
--- a/config/cluster/slurm.json
+++ b/config/cluster/slurm.json
@@ -76,7 +76,7 @@
         "threads": "24",
         "mem": "64G",
         "time": "1-18:00:00",
-        "gres": "lscratch:800"
+        "gres": "lscratch:1200"
     },
     "deepvariant": {
         "threads": "18",
@@ -297,7 +297,7 @@
         "threads": "24"
     },
     "clairs_tumor_only": {
-        "mem": "64G",
+        "mem": "120G",
         "time" : "1-00:00:00",
         "threads": "24"
     },
diff --git a/config/cluster/uge.json b/config/cluster/uge.json
index febd482..671a18d 100644
--- a/config/cluster/uge.json
+++ b/config/cluster/uge.json
@@ -287,7 +287,7 @@
     "threads": "8"
   },
   "clairs_tumor_only": {
-    "mem": "4G",
+    "mem": "5G",
     "partition": "",
     "threads": "8"
   },
diff --git a/workflow/rules/somatic.smk b/workflow/rules/somatic.smk
index f6e1156..02c69b2 100644
--- a/workflow/rules/somatic.smk
+++ b/workflow/rules/somatic.smk
@@ -50,6 +50,7 @@ def get_normal_pileup_table(wildcards):
         # Runs in tumor-only mode
         return []
 
+
 def get_somatic_tn_callers(wildcards):
     """Returns somatic variants found with tumor-normal variant
     callers. For tumor-normal samples, extra somatic callers 
@@ -706,7 +707,10 @@ rule clairs_tumor_only:
         genome  = config['references']['GENOME'],
         outdir = join(workpath, "clairs", "somatic", "{name}"),
     threads: 
-        int(allocated("threads", "clairs_tumor_only", cluster)),
+        # ClairS-TO over utilizes threads,
+        # testing has shown it over utilizes
+        # around 50% of the threads allocated
+        max(int(int(allocated("threads", "clairs_tumor_only", cluster))/2.0), 2),
     container: config['images']['clairs-to']
     envmodules: config['tools']['rlang']
     shell: """
@@ -789,7 +793,7 @@ rule deepsomatic:
     # mechanism for deletion on exit
     if [ ! -d "{params.tmpdir}" ]; then mkdir -p "{params.tmpdir}"; fi
     tmp=$(mktemp -d -p "{params.tmpdir}")
-    trap 'rm -rf "${{tmp}}"' EXIT
+    trap 'du -sh "${{tmp}}"; rm -rf "${{tmp}}"' EXIT
 
     run_deepsomatic \\
         --model_type={params.dv_model_type} \\