From 77a84d1da595c9e0892cd04babff6b0bdfca979b Mon Sep 17 00:00:00 2001
From: root <root@ip-10-41-24-153.ec2.internal>
Date: Thu, 15 Oct 2020 03:45:53 +0000
Subject: [PATCH] setup job to run CCHMC data

---
 jobs/CCHMC_Paired_Fastq/job.json     | 203 +++++++++++++++++++++++++++
 jobs/CCHMC_Paired_Fastq/options.json |  17 +++
 2 files changed, 220 insertions(+)
 create mode 100644 jobs/CCHMC_Paired_Fastq/job.json
 create mode 100644 jobs/CCHMC_Paired_Fastq/options.json

diff --git a/jobs/CCHMC_Paired_Fastq/job.json b/jobs/CCHMC_Paired_Fastq/job.json
new file mode 100644
index 0000000..426af51
--- /dev/null
+++ b/jobs/CCHMC_Paired_Fastq/job.json
@@ -0,0 +1,203 @@
+{
+    "cwl_wf_url": "https://github.com/Sage-Bionetworks-Workflows/dockstore-workflow-rnaseq/tree/v1.1.4",
+    "cwl_args_url": "https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-workflow-rnaseq/v1.1.4/jobs/CCHMC_Paired_Fastq/job.json",
+    "index_synapseid": "syn20645801",
+    "synapse_parentid": "syn23334104",
+    "nthreads": 15,
+    "synapse_config": {
+        "class": "File",
+        "path": "/etc/synapse/.synapseConfig"
+    },
+    "synapseid": [
+        "syn22164881",
+        "syn22164887",
+        "syn22164890",
+        "syn22164903",
+        "syn22164958",
+        "syn22164882",
+        "syn22164950",
+        "syn22164907",
+        "syn22164923",
+        "syn22164921",
+        "syn22164980",
+        "syn22164895",
+        "syn22164942",
+        "syn22164964",
+        "syn22164880",
+        "syn22164878",
+        "syn22164910",
+        "syn22164920",
+        "syn22164879",
+        "syn22164972",
+        "syn22164939",
+        "syn22165055",
+        "syn22165096",
+        "syn22165043",
+        "syn22165070",
+        "syn22165066",
+        "syn22165104",
+        "syn22165114",
+        "syn22165123",
+        "syn22165137",
+        "syn22165113",
+        "syn22165100",
+        "syn22165093",
+        "syn22165084",
+        "syn22165126",
+        "syn22165069",
+        "syn22165097",
+        "syn22165101",
+        "syn22165076",
+        "syn22165125",
+        "syn22165129",
+        "syn22165142",
+        "syn22165138",
+        "syn22165141",
+        "syn22165146",
+        "syn22165140",
+        "syn22165148",
+        "syn22165175",
+        "syn22165162",
+        "syn22165157",
+        "syn22165151",
+        "syn22165156",
+        "syn22165204",
+        "syn22165195",
+        "syn22165202",
+        "syn22165206",
+        "syn22165201",
+        "syn22165200",
+        "syn22165205",
+        "syn22165214",
+        "syn22165215",
+        "syn22165210",
+        "syn22165248",
+        "syn22165209",
+        "syn22165295",
+        "syn22165220",
+        "syn22165211",
+        "syn22165212",
+        "syn22165213",
+        "syn22165216",
+        "syn22165278",
+        "syn22165267",
+        "syn22165304",
+        "syn22165280",
+        "syn22165290",
+        "syn22165301",
+        "syn22165282",
+        "syn22165265",
+        "syn22165336",
+        "syn22165309",
+        "syn22165340",
+        "syn22165328",
+        "syn22165365",
+        "syn22165321",
+        "syn22165372",
+        "syn22165387",
+        "syn22165364",
+        "syn22165381",
+        "syn22165442",
+        "syn22165476",
+        "syn22165493",
+        "syn22165492",
+        "syn22165501",
+        "syn22165487"
+    ],
+    "synapseid_2": [
+        "syn22164945",
+        "syn22164941",
+        "syn22164995",
+        "syn22164992",
+        "syn22164918",
+        "syn22164935",
+        "syn22164955",
+        "syn22164908",
+        "syn22164953",
+        "syn22164998",
+        "syn22164967",
+        "syn22165007",
+        "syn22164905",
+        "syn22164944",
+        "syn22164916",
+        "syn22164931",
+        "syn22164974",
+        "syn22164911",
+        "syn22164959",
+        "syn22165077",
+        "syn22165072",
+        "syn22165119",
+        "syn22165122",
+        "syn22165121",
+        "syn22165135",
+        "syn22165145",
+        "syn22165139",
+        "syn22165132",
+        "syn22165169",
+        "syn22165149",
+        "syn22165118",
+        "syn22165117",
+        "syn22165116",
+        "syn22165115",
+        "syn22165130",
+        "syn22165108",
+        "syn22165133",
+        "syn22165127",
+        "syn22165124",
+        "syn22165134",
+        "syn22165150",
+        "syn22165186",
+        "syn22165160",
+        "syn22165172",
+        "syn22165184",
+        "syn22165163",
+        "syn22165208",
+        "syn22165181",
+        "syn22165207",
+        "syn22165203",
+        "syn22165190",
+        "syn22165199",
+        "syn22165217",
+        "syn22165219",
+        "syn22165218",
+        "syn22165229",
+        "syn22165221",
+        "syn22165222",
+        "syn22165226",
+        "syn22165253",
+        "syn22165234",
+        "syn22165230",
+        "syn22165370",
+        "syn22165232",
+        "syn22165420",
+        "syn22165302",
+        "syn22165247",
+        "syn22165241",
+        "syn22165246",
+        "syn22165272",
+        "syn22165396",
+        "syn22165385",
+        "syn22165412",
+        "syn22165394",
+        "syn22165402",
+        "syn22165425",
+        "syn22165413",
+        "syn22165397",
+        "syn22165451",
+        "syn22165441",
+        "syn22165473",
+        "syn22165429",
+        "syn22165491",
+        "syn22165435",
+        "syn22165478",
+        "syn22165495",
+        "syn22165499",
+        "syn22165506",
+        "syn22165448",
+        "syn22165471",
+        "syn22165502",
+        "syn22165500",
+        "syn22165498",
+        "syn22165490"
+    ]
+}
diff --git a/jobs/CCHMC_Paired_Fastq/options.json b/jobs/CCHMC_Paired_Fastq/options.json
new file mode 100644
index 0000000..22ba9a7
--- /dev/null
+++ b/jobs/CCHMC_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"
+}
+