From 32251687fdf5d064f1dbaac17bf0d6fbfd92233c Mon Sep 17 00:00:00 2001
From: "christoph.stritt@unibas.ch" <christoph.stritt@unibas.ch>
Date: Tue, 16 Jan 2024 12:18:55 +0100
Subject: [PATCH] added string qutations in cluster config
---
assembly/config/cluster_config.yaml | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
create mode 100644 assembly/config/cluster_config.yaml
diff --git a/assembly/config/cluster_config.yaml b/assembly/config/cluster_config.yaml
new file mode 100644
index 0000000..be06717
--- /dev/null
+++ b/assembly/config/cluster_config.yaml
@@ -0,0 +1,29 @@
+cluster:
+ mkdir -p logs/{rule} &&
+ sbatch
+ --partition={resources.partition}
+ --qos={resources.qos}
+ --cpus-per-task={threads}
+ --mem={resources.mem_mb}
+ --job-name=assemblySMK-{rule}-{wildcards}
+ --output=logs/{rule}/{rule}-{wildcards}-%j.stdout
+ --error=logs/{rule}/{rule}-{wildcards}-%j.stderr
+default-resources:
+ - partition='scicore'
+ - qos='1day'
+ - time=12:00:00
+ - mem_mb=20000
+restart-times: 3
+max-jobs-per-second: 10
+max-status-checks-per-second: 1
+local-cores: 1
+latency-wait: 60
+jobs: 500
+keep-going: True
+rerun-incomplete: True
+printshellcmds: True
+scheduler: greedy
+use-conda: True
+
+
+# https://github.com/jdblischak/smk-simple-slurm
--
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