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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 f84ad3fb5274ebca31f8dca2c62ba0c5f4b4ebee..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":[
@@
-11,10
+13,10
@@
],
"input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
},
],
"input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
},
- "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
- "output_is_persistent":false
+ "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":{
@@
-26,9
+28,10
@@
"required":true
}
},
"required":true
}
},
- "output_
is_persistent
":false
+ "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":{
@@
-51,9
+54,10
@@
"runtime_constraints":{
"max_tasks_per_node":1
},
"runtime_constraints":{
"max_tasks_per_node":1
},
- "output_
is_persistent
":false
+ "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":{
@@
-71,9
+75,10
@@
"runtime_constraints":{
"max_tasks_per_node":1
},
"runtime_constraints":{
"max_tasks_per_node":1
},
- "output_
is_persistent
":false
+ "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":{
@@
-102,9
+107,10
@@
"runtime_constraints":{
"max_tasks_per_node":2
},
"runtime_constraints":{
"max_tasks_per_node":2
},
- "output_
is_persistent
":false
+ "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":{
@@
-124,9
+130,10
@@
"required":true
}
},
"required":true
}
},
- "output_
is_persistent
":false
+ "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":{
@@
-162,7
+169,7
@@
]
}
},
]
}
},
- "output_
is_persistent":true
+ "output_
name":"Variant calls from UnifiedGenotyper"
}
}
}
}
}
}