"name":"GATK / exome PE fastq to snp",
"components":{
"extract-reference":{
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"file-select",
"script_parameters":{
"names":[
],
"input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
},
- "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153"
+ "output_name":false
},
"bwa-index":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-index",
"script_parameters":{
"value":"8b6e2c4916133e1d859c9e812861ce13+70",
"required":true
}
- }
+ },
+ "output_name":false
},
"bwa-aln":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-aln",
"script_parameters":{
},
"runtime_constraints":{
"max_tasks_per_node":1
- }
+ },
+ "output_name":false
},
"picard-gatk2-prep":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"picard-gatk2-prep",
"script_parameters":{
},
"runtime_constraints":{
"max_tasks_per_node":1
- }
+ },
+ "output_name":false
},
"GATK2-realign":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-realign",
"script_parameters":{
},
"runtime_constraints":{
"max_tasks_per_node":2
- }
+ },
+ "output_name":false
},
"GATK2-bqsr":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-bqsr",
"script_parameters":{
"value":"7e0a277d6d2353678a11f56bab3b13f2+87",
"required":true
}
- }
+ },
+ "output_name":false
},
"GATK2-merge-call":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-merge-call",
"script_parameters":{
"200"
]
}
- }
+ },
+ "output_name":"Variant calls from UnifiedGenotyper"
}
}
}