Merge pull request #23 from Sage-Bionetworks-Workflows/runuw

setup job to run UW miRNA samples
Sage-Bionetworks-Workflows · Sep 29, 2020 · f539658 · f539658
2 parents c3461f6 + 5cf4b20
commit f539658
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diff --git a/jobs/uw-dian-mirna/job.json b/jobs/uw-dian-mirna/job.json
@@ -0,0 +1,97 @@
+{
+    "cwl_wf_url": "https://github.com/Sage-Bionetworks-Workflows/dockstore-workflow-rnaseq/tree/v1.1.1",
+    "cwl_args_url": "https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-workflow-rnaseq/master/jobs/uw-dian-mirna/job.json",
+    "alignEndsType": "EndToEnd",
+    "outFilterMismatchNmax": 1,
+    "outFilterMultimapScoreRange": 0,
+    "outFilterMultimapNmax": 10,
+    "outFilterScoreMinOverLread": 0,
+    "outFilterMatchNminOverLread": 0,
+    "outFilterMatchNmin": 16,
+    "alignSJDBoverhangMin": 1000,
+    "alignIntronMax": 1,
+    "index_synapseid": "syn22337116",
+    "nthreads": 15,
+    "synapse_parentid": "syn22863725",
+    "synapse_config": {
+        "class": "File",
+        "path": "/etc/synapse/.synapseConfig"
+    },
+    "synapseid": [
+        "syn22334734",
+        "syn22334735",
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+}
diff --git a/jobs/uw-dian-mirna/options.json b/jobs/uw-dian-mirna/options.json
@@ -0,0 +1,17 @@
+{
+  "zone": "us-east-1a",
+  "cluster_name": "rna-seq-reprocessing-scicomp-toil-cluster-v001",
+  "tmpdir": "/var/lib/toil",
+  "run_name": "uwm",
+  "log_level": "DEBUG",
+  "retry_count": "3",
+  "target_time": "1",
+  "max_nodes": "25",
+  "default_disk": "450G",
+  "node_types": "m5.4xlarge",
+  "node_storage": "500",
+  "preemptable_compensation": "0.5",
+  "rescue_frequency": "9000",
+  "cwl": "mirna_single.cwl"
+}
+