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                        {
                            "file_format":{
                                "file_format":"pairs",
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                                "@type":[
                                    "FileFormat",
                                    "Item"
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                                "@id":"/file-formats/pairs/",
                                "display_title":"pairs"
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                            "file_size":9437603652,
                            "experiments":[
                                {
                                    "uuid":"a1ca5c96-995d-41fc-bf05-eaf94db015a7",
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                                        {
                                            "uuid":"107a0688-2ebc-4476-a976-0e720b56c476",
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                                }
                            ],
                            "href":"/files-processed/4DNFI3O8M6SZ/@@download/4DNFI3O8M6SZ.pairs.gz",
                            "@id":"/files-processed/4DNFI3O8M6SZ/",
                            "status":"released",
                            "quality_metric":{
                                "principals_allowed":{
                                    "edit":[
                                        "group.admin"
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                                    "view":[
                                        "system.Everyone"
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                                },
                                "uuid":"0ed018f6-ea53-4162-ac1d-14608db235d8",
                                "@type":[
                                    "QualityMetricPairsqc",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-pairsqc/0ed018f6-ea53-4162-ac1d-14608db235d8/",
                                "Total reads":448184804,
                                "Short cis reads (<20kb)":108447582,
                                "Cis reads (>20kb)":172454574,
                                "Trans reads":167282648,
                                "url":"https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3O8M6SZ/pairsqc_report.html",
                                "display_title":"QualityMetricPairsqc from 2018-06-22"
                            },
                            "file_type":"contact list-replicate",
                            "accession":"4DNFI3O8M6SZ",
                            "uuid":"3d31802a-b928-4f2f-b537-148072e1348f",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "description":"This is an output file of the Hi-C processing pipeline",
                            "experiment_sets":[

                            ],
                            "display_title":"4DNFI3O8M6SZ.pairs.gz"
                        }
                    ]
                },
                "name":"input_pairs",
                "meta":{
                    "global":true,
                    "in_path":true,
                    "type":"data file"
                },
                "source":[
                    {
                        "workflow":"/workflows/023bfb3e-9a8b-42b9-a9d4-216079526f68/",
                        "step":"/workflow-runs-awsem/eb4c644b-5fdc-4194-b6c0-571e04332461/",
                        "name":"filtered_pairs",
                        "for_file":"/files-processed/4DNFIBEV8M9E/"
                    },
                    {
                        "workflow":"/workflows/023bfb3e-9a8b-42b9-a9d4-216079526f68/",
                        "step":"/workflow-runs-awsem/9601c8a9-b15e-4067-87fb-177c9ca5d288/",
                        "name":"filtered_pairs",
                        "for_file":"/files-processed/4DNFI3O8M6SZ/"
                    }
                ]
            },
            {
                "run_data":{
                    "type":"input",
                    "meta":[
                        {
                            "workflow_argument_name":"restriction_file",
                            "ordinal":1,
                            "dimension":"0"
                        }
                    ],
                    "file":[
                        {
                            "file_format":{
                                "uuid":"d13d06cf-218e-4f61-55f0-94f226248b2c",
                                "principals_allowed":{
                                    "edit":[
                                        "group.admin"
                                    ],
                                    "view":[
                                        "system.Everyone"
                                    ]
                                },
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "display_title":"juicer_format_restriction_site_file",
                                "file_format":"juicer_format_restriction_site_file",
                                "@id":"/file-formats/juicer_format_restriction_site_file/"
                            },
                            "file_size":61438460,
                            "experiments":[

                            ],
                            "href":"/files-reference/4DNFI3HVC1SE/@@download/4DNFI3HVC1SE.txt",
                            "@id":"/files-reference/4DNFI3HVC1SE/",
                            "status":"released",
                            "file_type":"restriction sites",
                            "accession":"4DNFI3HVC1SE",
                            "uuid":"62da1021-3c96-4aa5-8a06-e5d6cfe9aab1",
                            "@type":[
                                "FileReference",
                                "File",
                                "Item"
                            ],
                            "description":"restriction sites for DpnII on mm10, juicer-formatted",
                            "filename":"mm10_DpnII.txt",
                            "display_title":"4DNFI3HVC1SE.txt"
                        }
                    ]
                },
                "name":"restriction_file",
                "meta":{
                    "global":true,
                    "in_path":true,
                    "type":"reference file"
                },
                "source":[
                    {
                        "for_file":"/files-reference/4DNFI3HVC1SE/",
                        "name":"restriction_file"
                    }
                ]
            }
        ],
        "name":"/workflow-runs-awsem/5d0e1af2-be6a-41b8-96ad-84eb6a6ab4ba/",
        "meta":{
            "run_status":"complete",
            "analysis_step_types":[
                "processing"
            ],
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
                "Item"
            ],
            "display_title":"hi-c-processing-pairs 0.2.6 run 2018-05-31 17:31:27.900564",
            "date_created":"2018-05-31T17:31:28.108851+00:00",
            "status":"released",
            "workflow":{
                "uuid":"c9e0e6f7-b0ed-4a42-9466-cadc2dd84df0",
                "steps":[
                    {
                        "outputs":[
                            {
                                "target":[
                                    {
                                        "name":"merged_pairs"
                                    },
                                    {
                                        "step":"addfragtopairs",
                                        "name":"input_pairs"
                                    },
                                    {
                                        "step":"cooler",
                                        "name":"pairs"
                                    }
                                ],
                                "name":"merged_pairs",
                                "meta":{
                                    "file_format":"pairs",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                }
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_pairs",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b2c",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"array"
                                },
                                "source":[
                                    {
                                        "name":"input_pairs"
                                    }
                                ]
                            }
                        ],
                        "name":"merge-pairs",
                        "meta":{
                            "analysis_step_types":[
                                "merging"
                            ],
                            "software_used":[
                                "9baf9f73-2d59-4eca-a326-340007b2a8b8"
                            ],
                            "description":"Merging pair files"
                        }
                    },
                    {
                        "outputs":[
                            {
                                "target":[
                                    {
                                        "step":"pairs2hic",
                                        "name":"input_pairs"
                                    }
                                ],
                                "name":"pairs_with_frags",
                                "meta":{
                                    "file_format":"pairs",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                }
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_pairs",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b2c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "step":"merge-pairs",
                                        "name":"merged_pairs"
                                    }
                                ]
                            },
                            {
                                "name":"restriction_file",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-55f0-94f226248b2c",
                                    "global":true,
                                    "type":"reference file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"restriction_file"
                                    }
                                ]
                            },
                            {
                                "name":"donothing",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"nofrag"
                                    }
                                ]
                            }
                        ],
                        "name":"addfragtopairs",
                        "meta":{
                            "analysis_step_types":[
                                "annotation"
                            ],
                            "software_used":[
                                "9baf9f73-2d59-4eca-a326-340007b2a8b8"
                            ],
                            "description":"Adding restriction enzyme site information to the pairs file"
                        }
                    },
                    {
                        "outputs":[
                            {
                                "target":[
                                    {
                                        "step":"cool2mcool",
                                        "name":"input_cool"
                                    }
                                ],
                                "name":"cool",
                                "meta":{
                                    "file_format":"cool",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                }
                            }
                        ],
                        "inputs":[
                            {
                                "name":"pairs",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b2c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "step":"merge-pairs",
                                        "name":"merged_pairs"
                                    }
                                ]
                            },
                            {
                                "name":"chrsizes",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-55f0-93f226248b2c",
                                    "global":true,
                                    "type":"reference file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"chromsizes"
                                    }
                                ]
                            },
                            {
                                "name":"binsize",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"min_res"
                                    }
                                ]
                            },
                            {
                                "name":"ncores",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"nthreads"
                                    }
                                ]
                            },
                            {
                                "name":"max_split",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"max_split_cooler"
                                    }
                                ]
                            }
                        ],
                        "name":"cooler",
                        "meta":{
                            "analysis_step_types":[
                                "aggregation"
                            ],
                            "software_used":[
                                "b43e5d6d-f1a6-4713-9b48-8f5c060dad6c"
                            ],
                            "description":"Merged Pairs file is processed using Cooler"
                        }
                    },
                    {
                        "outputs":[
                            {
                                "target":[
                                    {
                                        "name":"hic"
                                    },
                                    {
                                        "step":"add-hic-normvector-to-mcool",
                                        "name":"input_hic"
                                    }
                                ],
                                "name":"hic",
                                "meta":{
                                    "global":true
                                }
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_pairs",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b2c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "step":"addfragtopairs",
                                        "name":"pairs_with_frags"
                                    }
                                ]
                            },
                            {
                                "name":"chromsizes",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-55f0-93f226248b2c",
                                    "global":true,
                                    "type":"reference file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"chromsizes"
                                    }
                                ]
                            },
                            {
                                "name":"min_res",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"min_res"
                                    }
                                ]
                            },
                            {
                                "name":"higlass",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"higlass"
                                    }
                                ]
                            },
                            {
                                "name":"custom_res",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"custom_res"
                                    }
                                ]
                            },
                            {
                                "name":"maxmem",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"maxmem"
                                    }
                                ]
                            },
                            {
                                "name":"mapqfilter",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"mapqfilter_juicer"
                                    }
                                ]
                            }
                        ],
                        "name":"pairs2hic",
                        "meta":{
                            "analysis_step_types":[
                                "aggregation",
                                "normalization"
                            ],
                            "software_used":[
                                "b0c823f7-ca1e-44fb-b0f6-3eefb19eae46"
                            ],
                            "description":"Merged Pairs file is processed using Juicebox"
                        }
                    },
                    {
                        "outputs":[
                            {
                                "target":[
                                    {
                                        "step":"add-hic-normvector-to-mcool",
                                        "name":"input_mcool"
                                    }
                                ],
                                "name":"mcool",
                                "meta":{
                                    "file_format":"mcool",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                }
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_cool",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-bbf0-91f226248b2c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "step":"cooler",
                                        "name":"cool"
                                    }
                                ]
                            },
                            {
                                "name":"ncores",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"nthreads"
                                    }
                                ]
                            },
                            {
                                "name":"chunksize",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"chunksize"
                                    }
                                ]
                            },
                            {
                                "name":"juicer_res",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"juicer_res"
                                    }
                                ]
                            },
                            {
                                "name":"custom_res",
                                "meta":{
                                    "global":true,
                                    "type":"parameter",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"custom_res"
                                    }
                                ]
                            }
                        ],
                        "name":"cool2mcool",
                        "meta":{
                            "analysis_step_types":[
                                "aggregation",
                                "normalization",
                                "file format conversion"
                            ],
                            "software_used":[
                                "b43e5d6d-f1a6-4713-9b48-8f5c060dad6c"
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                            "description":"Cooler file is converted to mcool"
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                    {
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                            {
                                "target":[
                                    {
                                        "name":"mcool"
                                    },
                                    {
                                        "step":"extract-mcool-normvector-for-juicebox",
                                        "name":"mcool"
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                                ],
                                "name":"mcool_with_hicnorm",
                                "meta":{
                                    "file_format":"mcool",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                }
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_mcool",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-ccf0-91f226248b2c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
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                                "source":[
                                    {
                                        "step":"cool2mcool",
                                        "name":"mcool"
                                    }
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                            },
                            {
                                "name":"input_hic",
                                "meta":{
                                    "file_format":"d13d11cf-218e-4f61-bbf0-91f226248b2c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "step":"pairs2hic",
                                        "name":"hic"
                                    }
                                ]
                            }
                        ],
                        "name":"add-hic-normvector-to-mcool",
                        "meta":{
                            "analysis_step_types":[
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                            ],
                            "software_used":[
                                "c1c772a8-5d1c-4481-8ab7-30729f3f6cb2"
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                            "description":"HiC normalization vector is added to mcooler"
                        }
                    },
                    {
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                            {
                                "target":[
                                    {
                                        "name":"cooler_normvector"
                                    }
                                ],
                                "name":"cooler_normvector",
                                "meta":{
                                    "file_format":"normvector_juicerformat",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                }
                            }
                        ],
                        "inputs":[
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                                "name":"custom_res",
                                "meta":{
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                                "source":[
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                            {
                                "name":"chromsize",
                                "meta":{
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                                    "global":true,
                                    "type":"reference file",
                                    "cardinality":"single"
                                },
                                "source":[
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                                        "name":"chromsizes"
                                    }
                                ]
                            },
                            {
                                "name":"mcool",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-ccf0-91f226248b2c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "step":"add-hic-normvector-to-mcool",
                                        "name":"mcool_with_hicnorm"
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                        ],
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                        "meta":{
                            "analysis_step_types":[
                                "file format conversion"
                            ],
                            "software_used":[
                                "f3907ef2-a9fe-4324-bc54-253a4cd53e3c"
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                            "description":"Extracting HiC normalization vector"
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                    "Item"
                ],
                "@id":"/workflows/c9e0e6f7-b0ed-4a42-9466-cadc2dd84df0/",
                "experiment_types":[
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                "category":[
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                "accession":"4DNWFTKI1QLK",
                "display_title":"Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.6 - 4DNWFTKI1QLK"
            },
            "@id":"/workflow-runs-awsem/5d0e1af2-be6a-41b8-96ad-84eb6a6ab4ba/"
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    }
]
