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Merge branch '12409-cwl-v1.2' refs #12409
[arvados.git]
/
doc
/
examples
/
pipeline_templates
/
gatk-exome-fq-snp.json
diff --git
a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
index 3668f00ab39dd78fb6ebbeba99ea99a77eac500b..481dda38ca70153dd4cda2154e4754a55eef12f2 100644
(file)
--- a/
doc/examples/pipeline_templates/gatk-exome-fq-snp.json
+++ b/
doc/examples/pipeline_templates/gatk-exome-fq-snp.json
@@
-2,6
+2,8
@@
"name":"GATK / exome PE fastq to snp",
"components":{
"extract-reference":{
"name":"GATK / exome PE fastq to snp",
"components":{
"extract-reference":{
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"file-select",
"script_parameters":{
"names":[
"script":"file-select",
"script_parameters":{
"names":[
@@
-11,9
+13,10
@@
],
"input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
},
],
"input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
},
- "
script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153"
+ "
output_name":false
},
"bwa-index":{
},
"bwa-index":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-index",
"script_parameters":{
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-index",
"script_parameters":{
@@
-24,9
+27,11
@@
"value":"8b6e2c4916133e1d859c9e812861ce13+70",
"required":true
}
"value":"8b6e2c4916133e1d859c9e812861ce13+70",
"required":true
}
- }
+ },
+ "output_name":false
},
"bwa-aln":{
},
"bwa-aln":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-aln",
"script_parameters":{
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-aln",
"script_parameters":{
@@
-48,9
+53,11
@@
},
"runtime_constraints":{
"max_tasks_per_node":1
},
"runtime_constraints":{
"max_tasks_per_node":1
- }
+ },
+ "output_name":false
},
"picard-gatk2-prep":{
},
"picard-gatk2-prep":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"picard-gatk2-prep",
"script_parameters":{
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"picard-gatk2-prep",
"script_parameters":{
@@
-67,9
+74,11
@@
},
"runtime_constraints":{
"max_tasks_per_node":1
},
"runtime_constraints":{
"max_tasks_per_node":1
- }
+ },
+ "output_name":false
},
"GATK2-realign":{
},
"GATK2-realign":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-realign",
"script_parameters":{
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-realign",
"script_parameters":{
@@
-97,9
+106,11
@@
},
"runtime_constraints":{
"max_tasks_per_node":2
},
"runtime_constraints":{
"max_tasks_per_node":2
- }
+ },
+ "output_name":false
},
"GATK2-bqsr":{
},
"GATK2-bqsr":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-bqsr",
"script_parameters":{
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-bqsr",
"script_parameters":{
@@
-118,9
+129,11
@@
"value":"7e0a277d6d2353678a11f56bab3b13f2+87",
"required":true
}
"value":"7e0a277d6d2353678a11f56bab3b13f2+87",
"required":true
}
- }
+ },
+ "output_name":false
},
"GATK2-merge-call":{
},
"GATK2-merge-call":{
+ "repository":"arvados",
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-merge-call",
"script_parameters":{
"script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-merge-call",
"script_parameters":{
@@
-155,7
+168,8
@@
"200"
]
}
"200"
]
}
- }
+ },
+ "output_name":"Variant calls from UnifiedGenotyper"
}
}
}
}
}
}