Merge pull request #25 from Sage-Bionetworks-Workflows/icddrb

setup job to run ICDDRB dataset
Sage-Bionetworks-Workflows · Oct 14, 2020 · 45424e6 · 45424e6
2 parents b5a6079 + 4c6055b
commit 45424e6
Show file tree

Hide file tree

Showing 2 changed files with 118 additions and 0 deletions.
diff --git a/jobs/ICDDRB_Paired_Fastq/job.json b/jobs/ICDDRB_Paired_Fastq/job.json
@@ -0,0 +1,101 @@
+{
+    "cwl_wf_url": "https://github.com/Sage-Bionetworks-Workflows/dockstore-workflow-rnaseq/tree/v1.1.3",
+    "cwl_args_url": "https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-workflow-rnaseq/v1.1.3/jobs/ICDDRB_Paired_Fastq/job.json",
+    "index_synapseid": "syn20645801",
+    "synapse_parentid": "syn23283873",
+    "nthreads": 15,
+    "synapse_config": {
+        "class": "File",
+        "path": "/etc/synapse/.synapseConfig"
+    },
+    "synapseid": [
+        "syn22332896",
+        "syn22332892",
+        "syn22332893",
+        "syn22332887",
+        "syn22332881",
+        "syn22332884",
+        "syn22332868",
+        "syn22332874",
+        "syn22332898",
+        "syn22332875",
+        "syn22332885",
+        "syn22332878",
+        "syn22332870",
+        "syn22332861",
+        "syn22332857",
+        "syn22332858",
+        "syn22332853",
+        "syn22332859",
+        "syn22909743",
+        "syn22909748",
+        "syn22909864",
+        "syn22909875",
+        "syn22909870",
+        "syn22909868",
+        "syn22909670",
+        "syn22909717",
+        "syn22909796",
+        "syn22909823",
+        "syn22909808",
+        "syn22909810",
+        "syn22909822",
+        "syn22909769",
+        "syn22909852",
+        "syn22909771",
+        "syn22909851",
+        "syn22909891",
+        "syn22909880",
+        "syn22909940",
+        "syn22909939",
+        "syn22909895",
+        "syn22909931",
+        "syn22909927",
+        "syn22909930"
+    ],
+    "synapseid_2": [
+        "syn22332897",
+        "syn22332877",
+        "syn22332882",
+        "syn22332869",
+        "syn22332890",
+        "syn22332899",
+        "syn22332883",
+        "syn22332895",
+        "syn22332886",
+        "syn22332894",
+        "syn22332876",
+        "syn22332879",
+        "syn22332867",
+        "syn22332856",
+        "syn22332860",
+        "syn22332855",
+        "syn22332854",
+        "syn22992382",
+        "syn22909768",
+        "syn22909760",
+        "syn22909889",
+        "syn22909863",
+        "syn22909878",
+        "syn22909809",
+        "syn22909664",
+        "syn22909883",
+        "syn22909855",
+        "syn22909807",
+        "syn22909724",
+        "syn22909824",
+        "syn22909815",
+        "syn22909757",
+        "syn22909869",
+        "syn22909788",
+        "syn22909762",
+        "syn22909884",
+        "syn22909933",
+        "syn22909941",
+        "syn22909932",
+        "syn22909903",
+        "syn22909929",
+        "syn22909918",
+        "syn22909937"
+    ]
+}
diff --git a/jobs/ICDDRB_Paired_Fastq/options.json b/jobs/ICDDRB_Paired_Fastq/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": "icd",
+  "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": "fastq_paired.cwl"
+}
+