From 9253a8450d6d8c6a502d16066b5ac612952b191e Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Fri, 3 May 2024 10:19:09 +0200
Subject: [PATCH] perf: map circle_map_realign more parallelized, try mem_mb
 dependent on thread number

---
 workflow/rules/circle_map.smk | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflow/rules/circle_map.smk b/workflow/rules/circle_map.smk
index 057c23b..e43a3c7 100644
--- a/workflow/rules/circle_map.smk
+++ b/workflow/rules/circle_map.smk
@@ -41,9 +41,9 @@ rule circle_map_realign:
         "logs/circle-map/{sample}.circles.log",
     conda:
         "../envs/circle_map.yaml"
-    threads: 4
+    threads: 16
     resources:
-        mem_mb=lambda wc, input: input.size_mb * 2.5,
+        mem_mb=lambda wc, threads: threads * 5000,
     shell:
         "Circle-Map Realign "
         " -i {input.candidates_bam} "