Merge pull request #24 from Sage-Bionetworks-Workflows/runbgi

setup job to run merged BGI samples

jobs/BGI_Paired_Fastq/job.json

@@ -0,0 +1,133 @@
+{
+    "cwl_wf_url": "https://github.com/Sage-Bionetworks-Workflows/dockstore-workflow-rnaseq/tree/v1.1.2",
+    "cwl_args_url": "https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-workflow-rnaseq/v1.1.2/jobs/BGI_Paired_Fastq/job.json",
+    "index_synapseid": "syn20645801",
+    "synapse_parentid": "syn23043869",
+    "nthreads": 15,
+    "synapse_config": {
+        "class": "File",
+        "path": "/etc/synapse/.synapseConfig"
+    },
+    "synapseid": [
+        "syn23037162",
+        "syn23037217",
+        "syn23037267",
+        "syn23037321",
+        "syn23037383",
+        "syn23037430",
+        "syn23037498",
+        "syn23037550",
+        "syn23037610",
+        "syn23037666",
+        "syn23037718",
+        "syn23037772",
+        "syn23037833",
+        "syn23037888",
+        "syn23037947",
+        "syn23038003",
+        "syn23038064",
+        "syn23038122",
+        "syn23038175",
+        "syn23038247",
+        "syn23038294",
+        "syn23038340",
+        "syn23038377",
+        "syn23038438",
+        "syn23035272",
+        "syn23036330",
+        "syn23035296",
+        "syn23036197",
+        "syn23036035",
+        "syn23035370",
+        "syn23036085",
+        "syn23035491",
+        "syn23036467",
+        "syn23035391",
+        "syn23036117",
+        "syn23035615",
+        "syn23036145",
+        "syn23035520",
+        "syn23035429",
+        "syn23036569",
+        "syn23036165",
+        "syn23035650",
+        "syn23035954",
+        "syn23035200",
+        "syn23035882",
+        "syn23036432",
+        "syn23035785",
+        "syn23035680",
+        "syn23036605",
+        "syn23036622",
+        "syn23036989",
+        "syn23036694",
+        "syn23036927",
+        "syn23036890",
+        "syn23035104",
+        "syn23036860",
+        "syn23037011",
+        "syn23036664",
+        "syn23035148"
+    ],
+    "synapseid_2": [
+        "syn23037191",
+        "syn23037251",
+        "syn23037289",
+        "syn23037339",
+        "syn23037405",
+        "syn23037455",
+        "syn23037521",
+        "syn23037583",
+        "syn23037634",
+        "syn23037688",
+        "syn23037755",
+        "syn23037801",
+        "syn23037871",
+        "syn23037922",
+        "syn23037975",
+        "syn23038036",
+        "syn23038092",
+        "syn23038149",
+        "syn23038203",
+        "syn23038268",
+        "syn23038325",
+        "syn23038365",
+        "syn23038415",
+        "syn23038465",
+        "syn23035815",
+        "syn23036264",
+        "syn23035848",
+        "syn23036448",
+        "syn23036505",
+        "syn23036356",
+        "syn23036292",
+        "syn23036065",
+        "syn23036524",
+        "syn23036220",
+        "syn23036552",
+        "syn23035563",
+        "syn23035315",
+        "syn23035179",
+        "syn23035222",
+        "syn23035594",
+        "syn23035345",
+        "syn23035751",
+        "syn23036390",
+        "syn23035460",
+        "syn23035250",
+        "syn23035998",
+        "syn23035915",
+        "syn23035698",
+        "syn23036960",
+        "syn23036764",
+        "syn23036835",
+        "syn23037035",
+        "syn23036796",
+        "syn23036642",
+        "syn23037066",
+        "syn23036733",
+        "syn23037109",
+        "syn23035135",
+        "syn23037142"
+    ]
+}

jobs/BGI_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": "bgi",
+  "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"
+}
+