adjust swiss profile to cluster
configfile:
- config/config.yaml
- profiles/swiss/builds.yaml
+ - profiles/nextstrain-scicore/scicore-config.yaml
-cores: 8
keep-going: True
printshellcmds: True
-reason: True
-restart-times: 1
stats: stats.json
+
+# Wait a fixed number of seconds for missing files since the cluster file system
+# can be quite slow and the workflow can fail unnecessarily due to this latency.
+latency-wait: 60
+
+# Cluster-specific settings for resources required by any rule. This file
+# provides default resources for all rules and allows users to specify resources
+# per rule by name. An important resource for the Hutch cluster is the requested
+# "partition". Jobs submitted to the "restart" partition will start running
+# almost immediately, but they may also be killed at any moment when someone
+# else needs those resources. This is analogous to the spot resources on AWS.
+cluster-config: profiles/nextstrain-scicore/cluster.json
+
+cluster: "sbatch --time={cluster.time} --mem={cluster.mem} --cpus-per-task={cluster.n} --qos={cluster.qos}"
+
+jobs: 128
+
+jobscript: profiles/nextstrain-scicore/submit.sh
+
+# Set the name for the job as display in the cluster queue.
+jobname: "{rulename}.{jobid}.sh"
+
+# Set the number of threads (cores, actually) that the tree rule or other rules
+# should use on the cluster. These settings override the hardcoded values in the
+# Snakemake rules.
+set-threads: tree=16
