profile: add virusseq profile

profiles/virusseq-hpc/builds.yaml

@@ -0,0 +1,28 @@
+# -----------------------------------------------------------------------------
+# Builds
+# -----------------------------------------------------------------------------
+
+builds:
+
+  # ---------------------------------------------------------------------------
+  # `virusseq` scans the all public SARS-CoV-2 genomes from Canada
+
+  - name: virusseq
+    metadata: data/virusseq/metadata.tsv
+    sequences: data/virusseq/sequences.fasta
+
+    sc2rf:
+      exclude_negatives: true
+
+    summary:
+      extra_cols:
+        - division
+
+    linelist:
+      geo: "division"
+
+    plot:
+      min_cluster_size: 2
+
+    plot_historical:
+      min_cluster_size: 2

profiles/virusseq-hpc/config.yaml

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+#------------------------------------------------------------------------------#
+# Build Config
+#------------------------------------------------------------------------------#
+configfile:
+  - defaults/parameters.yaml
+  - profiles/virusseq-hpc/builds.yaml
+
+#------------------------------------------------------------------------------#
+# Snakemake config
+#------------------------------------------------------------------------------#
+restart-times: 1
+max-jobs-per-second: 1
+latency-wait: 60
+keep-going: True
+show-failed-logs: True
+rerun-incomplete: True
+printshellcmds: False
+
+#------------------------------------------------------------------------------#
+# System config
+#------------------------------------------------------------------------------#
+
+# Maximum number of jobs to run
+jobs : 20
+
+# Default resources for a SINGLE JOB
+# Divide your total resources by the maximum number of jobs
+default-resources:
+  - cpus=16
+  - mem_mb=16000
+  - time_min=720
+
+# What commands should be run to DISPATCH a job?
+cluster:
+  mkdir -p logs/slurm/{rule} &&
+  sbatch
+    --cpus-per-task={resources.cpus}
+    --mem={resources.mem_mb}
+    --job-name=ncov-recombinant:{rule}:{wildcards}
+    --output=logs/slurm/{rule}/{wildcards}-%j.out
+
+# What commands should be run to CANCEL a job?
+cluster-cancel: scancel