Bump versions, change optional=false to required=true, set dataclass

for bwa-aln input.

diff --git a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
index 42ba79df81e8ce34f9730d0e952fc71019af9856..3668f00ab39dd78fb6ebbeba99ea99a77eac500b 100644 (file)
--- a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
+++ b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
@@ -5,39 +5,45 @@
    "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"
    },
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d"
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153"
   },
   "bwa-index":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-index",
    "script_parameters":{
     "input":{
      "output_of":"extract-reference"
     },
     "bwa_tbz":{
-     "optional":false
+     "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+     "required":true
     }
    }
   },
   "bwa-aln":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-aln",
    "script_parameters":{
     "input":{
-     "optional":"false"
+     "dataclass":"Collection",
+     "required":"true"
     },
     "reference_index":{
      "output_of":"bwa-index"
     },
     "samtools_tgz":{
-     "optional":false
+     "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
+     "required":true
     },
     "bwa_tbz":{
-     "optional":false
+     "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+     "required":true
     }
    },
    "runtime_constraints":{
@@ -45,17 +51,18 @@
    }
   },
   "picard-gatk2-prep":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"picard-gatk2-prep",
    "script_parameters":{
     "input":{
-      "output_of":"bwa-aln"
+     "output_of":"bwa-aln"
     },
     "reference":{
      "output_of":"extract-reference"
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     }
    },
    "runtime_constraints":{
@@ -63,26 +70,29 @@
    }
   },
   "GATK2-realign":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-realign",
    "script_parameters":{
     "input":{
-      "output_of":"picard-gatk2-prep"
+     "output_of":"picard-gatk2-prep"
     },
     "gatk_bundle":{
-     "optional":false
+     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+     "required":true
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     },
     "gatk_tbz":{
-     "optional":false
+     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+     "required":true
     },
     "regions":{
-     "optional":true
+     "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
     },
     "region_padding":{
-     "optional":true
+     "value":10
     }
    },
    "runtime_constraints":{
@@ -90,47 +100,60 @@
    }
   },
   "GATK2-bqsr":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-bqsr",
    "script_parameters":{
     "input":{
-      "output_of":"GATK2-realign"
+     "output_of":"GATK2-realign"
     },
     "gatk_bundle":{
-     "optional":false
+     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+     "required":true
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     },
     "gatk_tbz":{
-     "optional":false
+     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+     "required":true
     }
    }
   },
   "GATK2-merge-call":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-merge-call",
    "script_parameters":{
     "input":{
-      "output_of":"GATK2-bqsr"
+     "output_of":"GATK2-bqsr"
     },
     "gatk_bundle":{
-     "optional":false
+     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+     "required":true
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     },
     "gatk_tbz":{
-     "optional":false
+     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+     "required":true
     },
     "regions":{
-     "optional":true
+     "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
     },
     "region_padding":{
-     "optional":true
+     "value":10
     },
     "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"
+     ]
     }
    }
   }