cluster config again

assembly/cluster/config.yaml

@@ -9,9 +9,9 @@ cluster:
     --output=logs/{rule}/{rule}-{wildcards}-%j.stdout
     --error=logs/{rule}/{rule}-{wildcards}-%j.stderr
 default-resources:
-  - partition=scicore
-  - qos=1day
-  - time=12:00:00
+  - partition='scicore'
+  - qos='1day'
+  - time='12:00:00'
   - mem_mb=20000
 restart-times: 3
 max-jobs-per-second: 10

assembly/config/cluster_config.yaml

-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