diff --git a/assembly/cluster/config.yaml b/assembly/cluster/config.yaml index a8eb21698259a77bfd2a075f95285bb9c955f5ad..e4ec8291c8c7c987c4632272466c1ea09d471d18 100644 --- a/assembly/cluster/config.yaml +++ b/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 diff --git a/assembly/config/cluster_config.yaml b/assembly/config/cluster_config.yaml deleted file mode 100644 index e4f0748ab5776b618c9a0109e0318b0dc3448cd7..0000000000000000000000000000000000000000 --- a/assembly/config/cluster_config.yaml +++ /dev/null @@ -1,29 +0,0 @@ -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