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picard-dedupe.json
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picard-dedupe.json
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{
"inputs": [{
"adapter": {
"position": 9,
"prefix": "READ_NAME_REGEX",
"separator": "="
},
"@id": "#read_name_regex",
"depth": 0,
"schema": ["null", "string"]
}, {
"adapter": {
"position": 9,
"prefix": "SORTING_COLLECTION_SIZE_RATIO",
"separator": "="
},
"@id": "#sorting_collections_size_ratio",
"depth": 0,
"schema": ["null", "int"]
}, {
"adapter": {
"position": 9,
"prefix": "MAX_FILE_HANDLES",
"separator": "="
},
"@id": "#max_file_handles_for_read_ends_map",
"depth": 0,
"schema": ["null", "string"]
}, {
"adapter": {
"position": 9,
"prefix": "MAX_SEQS",
"separator": "="
},
"@id": "#max_sequences_for_disk_read_ends_map",
"depth": 0,
"schema": ["null", "int"]
}, {
"adapter": {
"prefix": "AS",
"separator": "="
},
"@id": "#assume_sorted",
"depth": 0,
"schema": ["null", {
"symbols": ["true", "false"],
"type": "enum",
"name": "assume_sorted"
}]
}, {
"adapter": {
"position": 3,
"prefix": "REMOVE_DUPLICATES",
"separator": "="
},
"@id": "#remove_duplicates",
"depth": 0,
"schema": ["null", {
"symbols": ["true", "false"],
"type": "enum",
"name": "remove_duplicates"
}]
}, {
"adapter": {
"position": 9,
"prefix": "COMMENT",
"separator": "="
},
"@id": "#comment",
"depth": 0,
"schema": ["null", "string"]
}, {
"adapter": {
"position": 9,
"prefix": "PG_NAME",
"separator": "="
},
"@id": "#program_group_name",
"depth": 0,
"schema": ["null", "string"]
}, {
"adapter": {
"position": 9,
"prefix": "PG_COMMAND",
"separator": "="
},
"@id": "#program_group_command_line",
"depth": 0,
"schema": ["null", "string"]
}, {
"adapter": {
"position": 9,
"prefix": "PG_VERSION",
"separator": "="
},
"@id": "#program_group_ver",
"depth": 0,
"schema": ["null", "string"]
}, {
"adapter": {
"position": 10,
"prefix": "PG",
"separator": "="
},
"@id": "#program_record",
"depth": 0,
"schema": ["null", "string"]
}, {
"adapter": {
"position": 6,
"prefix": "VERBOSITY",
"separator": "="
},
"@id": "#verbosity",
"depth": 0,
"schema": ["null", {
"symbols": ["ERROR", "WARNING", "INFO", "DEBUG"],
"type": "enum",
"name": "verbosity"
}]
}, {
"depth": 0,
"@id": "#output_type",
"schema": ["null", {
"symbols": ["BAM", "SAM", "Same as input"],
"type": "enum",
"name": "output_type"
}]
}, {
"adapter": {
"position": 5,
"prefix": "CREATE_INDEX",
"separator": "="
},
"@id": "#create_index",
"depth": 0,
"schema": ["null", {
"symbols": ["True", "False"],
"type": "enum",
"name": "create_index"
}]
}, {
"adapter": {
"position": 4,
"prefix": "QUIET",
"separator": "="
},
"@id": "#quiet",
"depth": 0,
"schema": ["null", {
"symbols": ["True", "False"],
"type": "enum",
"name": "quiet"
}]
}, {
"adapter": {
"position": 4,
"prefix": "VALIDATION_STRINGENCY",
"separator": "="
},
"@id": "#validation_stringency",
"depth": 0,
"schema": ["null", {
"symbols": ["STRICT", "LENIENT", "SILENT"],
"type": "enum",
"name": "validation_stringency"
}]
}, {
"adapter": {
"position": 4,
"prefix": "COMPRESSION_LEVEL",
"separator": "="
},
"@id": "#compression_level",
"depth": 0,
"schema": ["null", "int"]
}, {
"adapter": {
"position": 4,
"prefix": "MAX_RECORDS_IN_RAM",
"separator": "="
},
"@id": "#max_records_in_ram",
"depth": 0,
"schema": ["null", "int"]
}, {
"adapter": {
"position": 9,
"prefix": "OPTICAL_DUPLICATE_PIXEL_DISTANCE",
"separator": "="
},
"@id": "#optical_duplicate_pixel_distance",
"depth": 0,
"schema": ["null", "int"]
}, {
"adapter": {
"prefix": "I",
"separator": "=",
"order": 0
},
"@id": "#input_bam",
"depth": 0,
"schema": ["file"]
}],
"sbg:categories": ["BAM/SAM Processing", "Picard"],
"description": "",
"sbg:sbgMaintained": false,
"sbg:modifiedOn": 1430310590,
"outputs": [{
"adapter": {
"glob": {
"lang": "javascript",
"@type": "Transform",
"value": "{\n filename = $job.inputs.input_bam.path\n\n return filename.split('.').slice(0, filename.split('.').length-1).concat(\"metrics\").join(\".\").replace(/^.*[\\\\\\/]/, '')\n\n}"
},
"metadata": {
"file_type": "txt",
"__inherit__": "input_bam"
}
},
"@id": "#metrics_file",
"depth": 0,
"schema": ["null", "file"]
}, {
"adapter": {
"secondaryFiles": [".bai"],
"glob": {
"lang": "javascript",
"@type": "Transform",
"value": "{\n filename = $job.inputs.input_bam.path\n ext = $job.inputs.output_type\n\nif (ext === \"BAM\")\n{\n return filename.split('.').slice(0, filename.split('.').length-1).concat(\"deduped.bam\").join(\".\").replace(/^.*[\\\\\\/]/, '')\n }\n\nelse if (ext === \"SAM\")\n{\n return filename.split('.').slice(0, filename.split('.').length-1).concat(\"deduped.sam\").join('.').replace(/^.*[\\\\\\/]/, '')\n}\n\nelse \n{\n\treturn filename.split('.').slice(0, filename.split('.').length-1).concat(\"deduped.\"+filename.split('.')[filename.split('.').length-1]).join(\".\").replace(/^.*[\\\\\\/]/, '')\n}\n}"
},
"metadata": {
"file_type": {
"lang": "javascript",
"@type": "Transform",
"value": "$self.split(\".\")[$self.split(\".\").length -1]"
},
"__inherit__": "input_bam"
}
},
"@id": "#deduped_bam",
"depth": 0,
"schema": ["null", "file"]
}],
"sbg:contributors": ["admin", "luka.stojanovic"],
"sbg:validationErrors": ["Union item must be a valid Avro schema: Could not make an Avro Schema object from file.", "Union item must be a valid Avro schema: Could not make an Avro Schema object from file.", "Union item must be a valid Avro schema: Could not make an Avro Schema object from file."],
"sbg:projectId": "836f25c1-4d69-4c0e-96c7-83aeff9b6f9a",
"requirements": [{
"imgTag": "",
"imgRepo": "djordjeklisic/picard_1.126:no_R",
"imgId": "9b6931a56d30",
"@type": "DockerCnt"
}, {
"@type": "CpuRequirement",
"value": 1
}, {
"@type": "MemRequirement",
"value": 1000
}],
"@id": "https://rabix-vayu.sbgenomics.com:11180/v1/apps/luka.stojanovic/picard/picard-dedupe/6/",
"sbg:projectSlug": "luka.stojanovic/picard",
"sbg:revision": 6,
"sbg:latestRevision": 15,
"sbg:createdOn": 1429478809,
"sbg:modifiedBy": "admin",
"sbg:toolkit": "Picard",
"sbg:toolkitVersion": "1.66",
"sbg:tagline": "Read SAM and perform various fix-ups. Currently, the only fix-ups are 1: to soft-clip an alignment …",
"label": "Picard dedupe",
"cliAdapter": {
"stdin": "",
"baseCmd": ["java", "-jar", "/picard-tools-1.126/picard.jar", "MarkDuplicates"],
"argAdapters": [{
"prefix": "M",
"separator": "=",
"order": 4,
"value": {
"lang": "javascript",
"@type": "Transform",
"value": "{\n filename = $job.inputs.input_bam.path\n\n return filename.split('.').slice(0, filename.split('.').length-1).concat(\"metrics\").join(\".\").replace(/^.*[\\\\\\/]/, '')\n\n}"
}
}, {
"prefix": "O",
"separator": "=",
"order": 2,
"value": {
"lang": "javascript",
"@type": "Transform",
"value": "{\n filename = $job.inputs.input_bam.path\n ext = $job.inputs.output_type\n\nif (ext === \"BAM\")\n{\n return filename.split('.').slice(0, filename.split('.').length-1).concat(\"deduped.bam\").join(\".\").replace(/^.*[\\\\\\/]/, '')\n }\n\nelse if (ext === \"SAM\")\n{\n return filename.split('.').slice(0, filename.split('.').length-1).concat(\"deduped.sam\").join('.').replace(/^.*[\\\\\\/]/, '')\n}\n\nelse \n{\n\treturn filename.split('.').slice(0, filename.split('.').length-1).concat(\"deduped.\"+filename.split('.')[filename.split('.').length-1]).join(\".\").replace(/^.*[\\\\\\/]/, '')\n}\n}"
}
}],
"stdout": ""
},
"sbg:revisionsInfo": [{
"sbg:modifiedBy": "luka.stojanovic",
"sbg:modifiedOn": 1429478809,
"sbg:revision": 0
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1429778846,
"sbg:revision": 1
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1429780181,
"sbg:revision": 2
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430310590,
"sbg:revision": 6
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430323751,
"sbg:revision": 7
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430323754,
"sbg:revision": 8
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430324121,
"sbg:revision": 10
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430324069,
"sbg:revision": 9
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430324122,
"sbg:revision": 11
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1429886160,
"sbg:revision": 3
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1429890232,
"sbg:revision": 4
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430210204,
"sbg:revision": 5
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430746559,
"sbg:revision": 12
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430746623,
"sbg:revision": 13
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430746632,
"sbg:revision": 14
}, {
"sbg:modifiedBy": "admin",
"sbg:modifiedOn": 1430746943,
"sbg:revision": 15
}],
"@context": "https://github.com/common-workflow-language/common-workflow-language/blob/draft-1/specification/tool-description.md",
"sbg:createdBy": "luka.stojanovic",
"@type": "CommandLine"
}