15964: Removing mentions of qr1hi from docs. Cleaning up user guide.

[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
deleted file mode 100644 (file)
index f84ad3f..0000000
--- a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
+++ /dev/null
@@ -1,168 +0,0 @@
-{
- "name":"GATK / exome PE fastq to snp",
- "components":{
-  "extract-reference":{
-   "script":"file-select",
-   "script_parameters":{
-    "names":[
-     "human_g1k_v37.fasta.gz",
-     "human_g1k_v37.fasta.fai.gz",
-     "human_g1k_v37.dict.gz"
-    ],
-    "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
-   },
-   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
-   "output_is_persistent":false
-  },
-  "bwa-index":{
-   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
-   "script":"bwa-index",
-   "script_parameters":{
-    "input":{
-     "output_of":"extract-reference"
-    },
-    "bwa_tbz":{
-     "value":"8b6e2c4916133e1d859c9e812861ce13+70",
-     "required":true
-    }
-   },
-   "output_is_persistent":false
-  },
-  "bwa-aln":{
-   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
-   "script":"bwa-aln",
-   "script_parameters":{
-    "input":{
-     "dataclass":"Collection",
-     "required":"true"
-    },
-    "reference_index":{
-     "output_of":"bwa-index"
-    },
-    "samtools_tgz":{
-     "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
-     "required":true
-    },
-    "bwa_tbz":{
-     "value":"8b6e2c4916133e1d859c9e812861ce13+70",
-     "required":true
-    }
-   },
-   "runtime_constraints":{
-    "max_tasks_per_node":1
-   },
-   "output_is_persistent":false
-  },
-  "picard-gatk2-prep":{
-   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
-   "script":"picard-gatk2-prep",
-   "script_parameters":{
-    "input":{
-     "output_of":"bwa-aln"
-    },
-    "reference":{
-     "output_of":"extract-reference"
-    },
-    "picard_zip":{
-     "value":"687f74675c6a0e925dec619cc2bec25f+77",
-     "required":true
-    }
-   },
-   "runtime_constraints":{
-    "max_tasks_per_node":1
-   },
-   "output_is_persistent":false
-  },
-  "GATK2-realign":{
-   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
-   "script":"GATK2-realign",
-   "script_parameters":{
-    "input":{
-     "output_of":"picard-gatk2-prep"
-    },
-    "gatk_bundle":{
-     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
-     "required":true
-    },
-    "picard_zip":{
-     "value":"687f74675c6a0e925dec619cc2bec25f+77",
-     "required":true
-    },
-    "gatk_tbz":{
-     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
-     "required":true
-    },
-    "regions":{
-     "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
-    },
-    "region_padding":{
-     "value":10
-    }
-   },
-   "runtime_constraints":{
-    "max_tasks_per_node":2
-   },
-   "output_is_persistent":false
-  },
-  "GATK2-bqsr":{
-   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
-   "script":"GATK2-bqsr",
-   "script_parameters":{
-    "input":{
-     "output_of":"GATK2-realign"
-    },
-    "gatk_bundle":{
-     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
-     "required":true
-    },
-    "picard_zip":{
-     "value":"687f74675c6a0e925dec619cc2bec25f+77",
-     "required":true
-    },
-    "gatk_tbz":{
-     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
-     "required":true
-    }
-   },
-   "output_is_persistent":false
-  },
-  "GATK2-merge-call":{
-   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
-   "script":"GATK2-merge-call",
-   "script_parameters":{
-    "input":{
-     "output_of":"GATK2-bqsr"
-    },
-    "gatk_bundle":{
-     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
-     "required":true
-    },
-    "picard_zip":{
-     "value":"687f74675c6a0e925dec619cc2bec25f+77",
-     "required":true
-    },
-    "gatk_tbz":{
-     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
-     "required":true
-    },
-    "regions":{
-     "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
-    },
-    "region_padding":{
-     "value":10
-    },
-    "GATK2_UnifiedGenotyper_args":{
-     "default":[
-      "-stand_call_conf",
-      "30.0",
-      "-stand_emit_conf",
-      "30.0",
-      "-dcov",
-      "200"
-     ]
-    }
-   },
-   "output_is_persistent":true
-  }
- }
-}