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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 42ba79df81e8ce34f9730d0e952fc71019af9856..481dda38ca70153dd4cda2154e4754a55eef12f2 100644
(file)
--- a/
doc/examples/pipeline_templates/gatk-exome-fq-snp.json
+++ b/
doc/examples/pipeline_templates/gatk-exome-fq-snp.json
@@
-2,137
+2,174
@@
"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":[
- "human_g1k_v37.fasta.gz", "human_g1k_v37.fasta.fai.gz", "human_g1k_v37.dict.gz"
+ "human_g1k_v37.fasta.gz",
+ "human_g1k_v37.fasta.fai.gz",
+ "human_g1k_v37.dict.gz"
],
"input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
},
],
"input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
},
- "
script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d"
+ "
output_name":false
},
"bwa-index":{
},
"bwa-index":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-index",
"script_parameters":{
"input":{
"output_of":"extract-reference"
},
"bwa_tbz":{
"script":"bwa-index",
"script_parameters":{
"input":{
"output_of":"extract-reference"
},
"bwa_tbz":{
- "optional":false
+ "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+ "required":true
}
}
- }
+ },
+ "output_name":false
},
"bwa-aln":{
},
"bwa-aln":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-aln",
"script_parameters":{
"input":{
"script":"bwa-aln",
"script_parameters":{
"input":{
- "optional":"false"
+ "dataclass":"Collection",
+ "required":"true"
},
"reference_index":{
"output_of":"bwa-index"
},
"samtools_tgz":{
},
"reference_index":{
"output_of":"bwa-index"
},
"samtools_tgz":{
- "optional":false
+ "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
+ "required":true
},
"bwa_tbz":{
},
"bwa_tbz":{
- "optional":false
+ "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+ "required":true
}
},
"runtime_constraints":{
"max_tasks_per_node":1
}
},
"runtime_constraints":{
"max_tasks_per_node":1
- }
+ },
+ "output_name":false
},
"picard-gatk2-prep":{
},
"picard-gatk2-prep":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"picard-gatk2-prep",
"script_parameters":{
"input":{
"script":"picard-gatk2-prep",
"script_parameters":{
"input":{
-
"output_of":"bwa-aln"
+ "output_of":"bwa-aln"
},
"reference":{
"output_of":"extract-reference"
},
"picard_zip":{
},
"reference":{
"output_of":"extract-reference"
},
"picard_zip":{
- "optional":false
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
}
},
"runtime_constraints":{
"max_tasks_per_node":1
}
},
"runtime_constraints":{
"max_tasks_per_node":1
- }
+ },
+ "output_name":false
},
"GATK2-realign":{
},
"GATK2-realign":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-realign",
"script_parameters":{
"input":{
"script":"GATK2-realign",
"script_parameters":{
"input":{
-
"output_of":"picard-gatk2-prep"
+ "output_of":"picard-gatk2-prep"
},
"gatk_bundle":{
},
"gatk_bundle":{
- "optional":false
+ "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+ "required":true
},
"picard_zip":{
},
"picard_zip":{
- "optional":false
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
},
"gatk_tbz":{
},
"gatk_tbz":{
- "optional":false
+ "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "required":true
},
"regions":{
},
"regions":{
- "
optional":true
+ "
value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
},
"region_padding":{
},
"region_padding":{
- "
optional":true
+ "
value":10
}
},
"runtime_constraints":{
"max_tasks_per_node":2
}
},
"runtime_constraints":{
"max_tasks_per_node":2
- }
+ },
+ "output_name":false
},
"GATK2-bqsr":{
},
"GATK2-bqsr":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-bqsr",
"script_parameters":{
"input":{
"script":"GATK2-bqsr",
"script_parameters":{
"input":{
-
"output_of":"GATK2-realign"
+ "output_of":"GATK2-realign"
},
"gatk_bundle":{
},
"gatk_bundle":{
- "optional":false
+ "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+ "required":true
},
"picard_zip":{
},
"picard_zip":{
- "optional":false
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
},
"gatk_tbz":{
},
"gatk_tbz":{
- "optional":false
+ "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "required":true
}
}
- }
+ },
+ "output_name":false
},
"GATK2-merge-call":{
},
"GATK2-merge-call":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-merge-call",
"script_parameters":{
"input":{
"script":"GATK2-merge-call",
"script_parameters":{
"input":{
-
"output_of":"GATK2-bqsr"
+ "output_of":"GATK2-bqsr"
},
"gatk_bundle":{
},
"gatk_bundle":{
- "optional":false
+ "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+ "required":true
},
"picard_zip":{
},
"picard_zip":{
- "optional":false
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
},
"gatk_tbz":{
},
"gatk_tbz":{
- "optional":false
+ "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "required":true
},
"regions":{
},
"regions":{
- "
optional":true
+ "
value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
},
"region_padding":{
},
"region_padding":{
- "
optional":true
+ "
value":10
},
"GATK2_UnifiedGenotyper_args":{
},
"GATK2_UnifiedGenotyper_args":{
- "default":["-stand_call_conf","30.0","-stand_emit_conf","30.0","-dcov","200"]
+ "default":[
+ "-stand_call_conf",
+ "30.0",
+ "-stand_emit_conf",
+ "30.0",
+ "-dcov",
+ "200"
+ ]
}
}
- }
+ },
+ "output_name":"Variant calls from UnifiedGenotyper"
}
}
}
}
}
}