diff resfinder/scripts/wdl/computerome.conf @ 0:55051a9bc58d draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resfinder/scripts/wdl/computerome.conf	Mon Jan 10 20:06:07 2022 +0000
@@ -0,0 +1,49 @@
+# TORQUE as a backend for Cromwell on Computerome
+
+# Here is where you can define the backend providers that Cromwell understands.
+# The default is a local provider.
+# To add additional backend providers, you should copy paste additional backends
+# of interest that you can find in the cromwell.example.backends folder
+# folder at https://www.github.com/broadinstitute/cromwell
+# Other backend providers include SGE, SLURM, Docker, udocker, Singularity. etc.
+# Don't forget you will need to customize them for your particular use case.
+
+backend {
+
+    # Override the default backend.
+    default = TORQUE
+
+    # The list of providers.
+    providers {
+
+        TORQUE {
+
+            # The actor that runs the backend.
+            actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
+
+            # The backend custom configuration.
+            config {
+
+                # Number of concurrent jobs allowed
+                concurrent-job-limit = 500
+
+                # The list of possible runtime custom attributes.
+                runtime-attributes = """
+                String walltime = "1:00:00"
+                Int cpu = 1
+                Float memory_mb = 2048.0
+                String queue = "cge"
+                """
+
+                submit = "qsub -W group_list=${queue} -A ${queue} -N ${job_name} -lwalltime=${walltime},nodes=1:ppn=${cpu},mem=${ceil(memory_mb)}mb -d ${cwd} -o ${out} -e ${err} ${script}"
+
+                kill = "qdel ${job_id}"
+                check-alive = "qstat ${job_id}"
+                job-id-regex = "(\\d+)"
+            }
+
+        }
+
+    }
+
+}