[
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        "name":"/workflow-runs-awsem/5c7c29ea-5ce1-42fc-a09d-a8f9f80626b4/",
        "meta":{
            "display_title":"workflow_bwa-mem_no_unzip-check v8 run 2019-08-08 01:03:06.639362",
            "status":"in review",
            "run_status":"complete",
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
                "Item"
            ],
            "@id":"/workflow-runs-awsem/5c7c29ea-5ce1-42fc-a09d-a8f9f80626b4/",
            "date_created":"2019-08-27T04:03:40.660199+00:00",
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                "processing"
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                "@type":[
                    "Workflow",
                    "Item"
                ],
                "display_title":"Paired-end reads alignment to reference plus output integrity-check - GAPWF9HYUJB9",
                "accession":"GAPWF9HYUJB9",
                "steps":[
                    {
                        "meta":{
                            "software_used":[
                                "42adeb1b-c46c-4ba8-b191-56036ddcd544"
                            ],
                            "analysis_step_types":[
                                "Align paired-end reads to reference genome"
                            ]
                        },
                        "name":"bwa-mem",
                        "inputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"c13d06cf-218e-4f61-aaf0-91f226248b2c"
                                },
                                "name":"fastq_R1",
                                "source":[
                                    {
                                        "name":"fastq_R1"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"c13d06cf-218e-4f61-aaf0-91f226248b2c"
                                },
                                "name":"fastq_R2",
                                "source":[
                                    {
                                        "name":"fastq_R2"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"reference file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"813b0001-5f3f-4e28-9203-4cdf261e19c4"
                                },
                                "name":"reference",
                                "source":[
                                    {
                                        "name":"reference"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"nthreads",
                                "source":[
                                    {
                                        "name":"nthreads"
                                    }
                                ]
                            }
                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"bam"
                                },
                                "name":"raw_bam",
                                "target":[
                                    {
                                        "name":"raw_bam",
                                        "step":"integrity-check"
                                    }
                                ]
                            }
                        ]
                    },
                    {
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                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
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                            "analysis_step_types":[
                                "Check integrity of output file"
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                        },
                        "name":"integrity-check",
                        "inputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":false,
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                                },
                                "name":"raw_bam",
                                "source":[
                                    {
                                        "name":"raw_bam",
                                        "step":"bwa-mem"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"count",
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"QC",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"raw_bam-check",
                                "target":[
                                    {
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                "category":[
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                "experiment_types":[

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        },
        "inputs":[
            {
                "name":"fastq_R1",
                "source":[
                    {
                        "name":"fastq_R1",
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                ],
                "meta":{
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                    "global":true,
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                "run_data":{
                    "file":[
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                            "display_title":"GAPFIT9HIA1D.fastq.gz",
                            "accession":"GAPFIT9HIA1D",
                            "@type":[
                                "FileFastq",
                                "File",
                                "Item"
                            ],
                            "quality_metric":{
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                                "@type":[
                                    "QualityMetricFastqc",
                                    "QualityMetric",
                                    "Item"
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                                "display_title":"QualityMetricFastqc from 2019-08-27",
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                                "Total Sequences":516716922,
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                            "filename":"888968-UDN193590-P_R1.fastq.gz",
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                    "type":"input",
                    "meta":[
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                            "ordinal":1,
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                "name":"fastq_R2",
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                        "name":"fastq_R2",
                        "for_file":"/files-fastq/GAPFIN16EGPT/"
                    }
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                "meta":{
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                "run_data":{
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                            "@type":[
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                            "quality_metric":{
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                                "Total Sequences":516716922,
                                "display_title":"QualityMetricFastqc from 2019-08-27",
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                            "href":"/files-fastq/GAPFIN16EGPT/@@download/GAPFIN16EGPT.fastq.gz",
                            "filename":"888968-UDN193590-P_R2.fastq.gz",
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                            "ordinal":1,
                            "dimension":"0",
                            "workflow_argument_name":"fastq_R2"
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            },
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                "name":"reference",
                "source":[
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                        "name":"reference",
                        "for_file":"/files-reference/GAPFI4U1HXIY/"
                    }
                ],
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"reference file"
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                "run_data":{
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                            "@id":"/files-reference/GAPFI4U1HXIY/",
                            "uuid":"b24ed5ed-a037-48a0-a938-3fecfb90d0cf",
                            "display_title":"GAPFI4U1HXIY.bwt",
                            "accession":"GAPFI4U1HXIY",
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                                "File",
                                "Item"
                            ],
                            "href":"/files-reference/GAPFI4U1HXIY/@@download/GAPFI4U1HXIY.bwt",
                            "description":"hg38 bwa genome index for CGAP, untarred, uncompressed",
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                                    "Item"
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                                "display_title":"bwt",
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                        {
                            "ordinal":1,
                            "dimension":"0",
                            "workflow_argument_name":"reference"
                        }
                    ]
                }
            }
        ],
        "outputs":[
            {
                "name":"raw_bam",
                "target":[
                    {
                        "name":"raw_bam"
                    },
                    {
                        "name":"input_bam",
                        "step":"/workflow-runs-awsem/935b7578-8d4e-4530-85fa-c7a305f92263/",
                        "for_file":"/files-processed/GAPFITKM4JXJ/"
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                            "uuid":"6d44733a-d8b1-485a-bf1a-f0db43e8b167",
                            "display_title":"GAPFITKM4JXJ.bam",
                            "accession":"GAPFITKM4JXJ",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
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                                "display_title":"QualityMetricBamcheck from 2019-08-27",
                                "@id":"/quality-metrics-bamcheck/b11f7ad5-aadc-4a2a-a5ae-de18214f1b61/",
                                "uuid":"b11f7ad5-aadc-4a2a-a5ae-de18214f1b61",
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                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
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                            "file_format":{
                                "display_title":"bam",
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                    "meta":[
                        {
                            "type":"Output processed file",
                            "format":"/file-formats/bam/",
                            "upload_key":"6d44733a-d8b1-485a-bf1a-f0db43e8b167/4DNFIWMJ1U2F.bam"
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    {
        "name":"/workflow-runs-awsem/935b7578-8d4e-4530-85fa-c7a305f92263/",
        "meta":{
            "display_title":"workflow_readgroups-check v9 run 2019-08-08 22:02:45.321937",
            "status":"in review",
            "run_status":"complete",
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
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            "@id":"/workflow-runs-awsem/935b7578-8d4e-4530-85fa-c7a305f92263/",
            "date_created":"2019-08-27T04:03:53.637995+00:00",
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                ],
                "display_title":"Add read groups plus output integrity-check - GAPWFECVBVP9",
                "accession":"GAPWFECVBVP9",
                "steps":[
                    {
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                            "software_used":[
                                "d7ac4c75-e133-4a8e-a19e-b7e87873cc16"
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                            "analysis_step_types":[
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                            ]
                        },
                        "name":"add-readgroups",
                        "inputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                                },
                                "name":"input_bam",
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"sample_name",
                                "source":[
                                    {
                                        "name":"sample_name"
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                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"nthreads",
                                "source":[
                                    {
                                        "name":"nthreads"
                                    }
                                ]
                            }
                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"bam"
                                },
                                "name":"bam_w_readgroups",
                                "target":[
                                    {
                                        "name":"bam_w_readgroups",
                                        "step":"integrity-check"
                                    }
                                ]
                            }
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                    {
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                                "meta":{
                                    "type":"data file",
                                    "global":false,
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                                },
                                "name":"bam_w_readgroups",
                                "source":[
                                    {
                                        "name":"bam_w_readgroups",
                                        "step":"add-readgroups"
                                    }
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                            {
                                "meta":{
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                                    "global":true,
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                                "name":"count",
                                "source":[
                                    {
                                        "name":"count"
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                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"QC",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"bam_w_readgroups-check",
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                "category":[
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                                    "FileFormat",
                                    "Item"
                                ],
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "file_size":104353020141,
                            "status":"uploaded"
                        }
                    ],
                    "type":"input",
                    "meta":[
                        {
                            "ordinal":1,
                            "dimension":"0",
                            "workflow_argument_name":"input_bam"
                        }
                    ]
                }
            }
        ],
        "outputs":[
            {
                "name":"bam_w_readgroups",
                "target":[
                    {
                        "name":"bam_w_readgroups"
                    },
                    {
                        "name":"input_bams",
                        "step":"/workflow-runs-awsem/5717940c-2550-48b6-a16b-99517e95fc9c/",
                        "for_file":"/files-processed/GAPFIJ7FULOF/"
                    }
                ],
                "meta":{
                    "type":"data file",
                    "global":true,
                    "in_path":true
                },
                "run_data":{
                    "file":[
                        {
                            "@id":"/files-processed/GAPFIJ7FULOF/",
                            "uuid":"90ba71d7-2eee-4437-b3db-4c173be36eff",
                            "display_title":"GAPFIJ7FULOF.bam",
                            "accession":"GAPFIJ7FULOF",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "quality_metric":{
                                "uuid":"e799cd0d-6b0a-490e-ab43-3e8690e09ff4",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "display_title":"QualityMetricBamcheck from 2019-08-27",
                                "@id":"/quality-metrics-bamcheck/e799cd0d-6b0a-490e-ab43-3e8690e09ff4/",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "href":"/files-processed/GAPFIJ7FULOF/@@download/GAPFIJ7FULOF.bam",
                            "description":"Intermediate alingnemnt file",
                            "file_format":{
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@id":"/file-formats/bam/",
                                "file_format":"bam",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "file_type":"intermediate file",
                            "file_size":107920567035,
                            "status":"uploaded"
                        }
                    ],
                    "type":"input",
                    "meta":[
                        {
                            "type":"Output processed file",
                            "format":"/file-formats/bam/",
                            "upload_key":"90ba71d7-2eee-4437-b3db-4c173be36eff/4DNFIUH8H1LS.bam"
                        }
                    ]
                }
            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/5717940c-2550-48b6-a16b-99517e95fc9c/",
        "meta":{
            "display_title":"workflow_merge_bam-check v8 run 2019-08-09 03:50:38.533532",
            "status":"in review",
            "run_status":"complete",
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
                "Item"
            ],
            "@id":"/workflow-runs-awsem/5717940c-2550-48b6-a16b-99517e95fc9c/",
            "date_created":"2019-08-27T04:04:15.004009+00:00",
            "analysis_step_types":[
                "processing"
            ],
            "workflow":{
                "@id":"/workflows/30802d8c-20c3-4eea-82dd-dd34621569c6/",
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "display_title":"Merge bam files plus output integrity-check - GAPWFZL73ZQV",
                "accession":"GAPWFZL73ZQV",
                "steps":[
                    {
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Merge bam input files"
                            ]
                        },
                        "name":"merge",
                        "inputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"array",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                                },
                                "name":"input_bams",
                                "source":[
                                    {
                                        "name":"input_bams"
                                    }
                                ]
                            }
                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"bam"
                                },
                                "name":"merged_bam",
                                "target":[
                                    {
                                        "name":"merged_bam",
                                        "step":"integrity-check"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Check integrity of output file"
                            ]
                        },
                        "name":"integrity-check",
                        "inputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":false,
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                                },
                                "name":"merged_bam",
                                "source":[
                                    {
                                        "name":"merged_bam",
                                        "step":"merge"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"count",
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"QC",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"merged_bam-check",
                                "target":[
                                    {
                                        "name":"merged_bam-check"
                                    }
                                ]
                            }
                        ]
                    }
                ],
                "uuid":"30802d8c-20c3-4eea-82dd-dd34621569c6",
                "category":[
                    "processing"
                ],
                "experiment_types":[

                ]
            }
        },
        "inputs":[
            {
                "name":"input_bams",
                "source":[
                    {
                        "name":"bam_w_readgroups",
                        "step":"/workflow-runs-awsem/935b7578-8d4e-4530-85fa-c7a305f92263/",
                        "for_file":"/files-processed/GAPFIJ7FULOF/",
                        "workflow":"/workflows/548e63a4-1936-4f68-8e8d-8e4658767911/"
                    }
                ],
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "run_data":{
                    "file":[
                        {
                            "@id":"/files-processed/GAPFIJ7FULOF/",
                            "uuid":"90ba71d7-2eee-4437-b3db-4c173be36eff",
                            "display_title":"GAPFIJ7FULOF.bam",
                            "accession":"GAPFIJ7FULOF",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "quality_metric":{
                                "uuid":"e799cd0d-6b0a-490e-ab43-3e8690e09ff4",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "display_title":"QualityMetricBamcheck from 2019-08-27",
                                "@id":"/quality-metrics-bamcheck/e799cd0d-6b0a-490e-ab43-3e8690e09ff4/",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "href":"/files-processed/GAPFIJ7FULOF/@@download/GAPFIJ7FULOF.bam",
                            "description":"Intermediate alingnemnt file",
                            "file_format":{
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@id":"/file-formats/bam/",
                                "file_format":"bam",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "file_type":"intermediate file",
                            "file_size":107920567035,
                            "status":"uploaded"
                        }
                    ],
                    "type":"input",
                    "meta":[
                        {
                            "ordinal":1,
                            "dimension":"0",
                            "workflow_argument_name":"input_bams"
                        }
                    ]
                }
            }
        ],
        "outputs":[
            {
                "name":"merged_bam",
                "target":[
                    {
                        "name":"merged_bam"
                    },
                    {
                        "name":"input_bam",
                        "step":"/workflow-runs-awsem/870a2f3c-7efe-4132-90d4-2f1b518b29e3/",
                        "for_file":"/files-processed/GAPFIWDFRPAO/"
                    }
                ],
                "meta":{
                    "type":"data file",
                    "global":true,
                    "in_path":true
                },
                "run_data":{
                    "file":[
                        {
                            "@id":"/files-processed/GAPFIWDFRPAO/",
                            "uuid":"2900dc6e-49d9-4039-93a4-5e966f28185c",
                            "display_title":"GAPFIWDFRPAO.bam",
                            "accession":"GAPFIWDFRPAO",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-08-27",
                                "uuid":"b54895b6-e062-4b00-ad74-9c730d2936b7",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/b54895b6-e062-4b00-ad74-9c730d2936b7/",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "href":"/files-processed/GAPFIWDFRPAO/@@download/GAPFIWDFRPAO.bam",
                            "description":"Intermediate alingnment file",
                            "file_format":{
                                "display_title":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                "file_format":"bam",
                                "@id":"/file-formats/bam/",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "file_type":"intermediate file",
                            "file_size":105679049244,
                            "status":"uploaded"
                        }
                    ],
                    "type":"input",
                    "meta":[
                        {
                            "type":"Output processed file",
                            "format":"/file-formats/bam/",
                            "upload_key":"2900dc6e-49d9-4039-93a4-5e966f28185c/4DNFIQVVB3W6.bam"
                        }
                    ]
                }
            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/870a2f3c-7efe-4132-90d4-2f1b518b29e3/",
        "meta":{
            "display_title":"workflow_picard-markduplicates-check v9 run 2019-08-09 15:13:57.734602",
            "status":"in review",
            "run_status":"complete",
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
                "Item"
            ],
            "@id":"/workflow-runs-awsem/870a2f3c-7efe-4132-90d4-2f1b518b29e3/",
            "date_created":"2019-08-27T04:04:11.689890+00:00",
            "analysis_step_types":[
                "processing"
            ],
            "workflow":{
                "@id":"/workflows/beb2b340-94ee-4afe-b4e3-66caaf063397/",
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "display_title":"Mark duplicates plus output integrity-check - GAPWFLNQ7XTG",
                "accession":"GAPWFLNQ7XTG",
                "steps":[
                    {
                        "meta":{
                            "software_used":[
                                "586cef39-6505-4bf6-920a-4b26a500d210"
                            ],
                            "analysis_step_types":[
                                "Mark duplicates in bam input file"
                            ]
                        },
                        "name":"MarkDuplicates",
                        "inputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                                },
                                "name":"input_bam",
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"xmx",
                                "source":[
                                    {
                                        "name":"xmx"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"xms",
                                "source":[
                                    {
                                        "name":"xms"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"max_records_in_ram",
                                "source":[
                                    {
                                        "name":"max_records_in_ram"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"duplicate_pixel_distance",
                                "source":[
                                    {
                                        "name":"duplicate_pixel_distance"
                                    }
                                ]
                            }
                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"bam"
                                },
                                "name":"dupmarked_bam",
                                "target":[
                                    {
                                        "name":"dupmarked_bam",
                                        "step":"integrity-check"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"txt"
                                },
                                "name":"duplicate_metrics",
                                "target":[
                                    {
                                        "name":"duplicate_metrics"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Check integrity of output file"
                            ]
                        },
                        "name":"integrity-check",
                        "inputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":false,
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                                },
                                "name":"dupmarked_bam",
                                "source":[
                                    {
                                        "name":"dupmarked_bam",
                                        "step":"MarkDuplicates"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"count",
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"report",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"dupmarked_bam-check",
                                "target":[
                                    {
                                        "name":"dupmarked_bam-check"
                                    }
                                ]
                            }
                        ]
                    }
                ],
                "uuid":"beb2b340-94ee-4afe-b4e3-66caaf063397",
                "category":[
                    "processing"
                ],
                "experiment_types":[

                ]
            }
        },
        "inputs":[
            {
                "name":"input_bam",
                "source":[
                    {
                        "name":"merged_bam",
                        "step":"/workflow-runs-awsem/5717940c-2550-48b6-a16b-99517e95fc9c/",
                        "for_file":"/files-processed/GAPFIWDFRPAO/",
                        "workflow":"/workflows/30802d8c-20c3-4eea-82dd-dd34621569c6/"
                    }
                ],
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "run_data":{
                    "file":[
                        {
                            "@id":"/files-processed/GAPFIWDFRPAO/",
                            "uuid":"2900dc6e-49d9-4039-93a4-5e966f28185c",
                            "display_title":"GAPFIWDFRPAO.bam",
                            "accession":"GAPFIWDFRPAO",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-08-27",
                                "uuid":"b54895b6-e062-4b00-ad74-9c730d2936b7",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/b54895b6-e062-4b00-ad74-9c730d2936b7/",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "href":"/files-processed/GAPFIWDFRPAO/@@download/GAPFIWDFRPAO.bam",
                            "description":"Intermediate alingnment file",
                            "file_format":{
                                "display_title":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                "file_format":"bam",
                                "@id":"/file-formats/bam/",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "file_type":"intermediate file",
                            "file_size":105679049244,
                            "status":"uploaded"
                        }
                    ],
                    "type":"input",
                    "meta":[
                        {
                            "ordinal":1,
                            "dimension":"0",
                            "workflow_argument_name":"input_bam"
                        }
                    ]
                }
            }
        ],
        "outputs":[
            {
                "name":"dupmarked_bam",
                "target":[
                    {
                        "name":"dupmarked_bam"
                    },
                    {
                        "name":"input_bam",
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                    {
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                        "step":"/workflow-runs-awsem/e6e0a412-26f0-432c-a6de-9a29d22b1e92/",
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                            "uuid":"4db03c55-6308-4df2-975a-8f7b2fa6c2a0",
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                            "accession":"GAPFITTEYNY1",
                            "@type":[
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                                "File",
                                "Item"
                            ],
                            "quality_metric":{
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                                "@type":[
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                                "display_title":"QualityMetricBamcheck from 2019-08-27",
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                        "name":"duplicate_metrics"
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                ],
                "meta":{
                    "type":"data file",
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                "run_data":{
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                            "accession":"GAPFIWCCQ8SV",
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                            "file_format":{
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                                    "edit":[
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                            "type":"Output processed file",
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        "name":"/workflow-runs-awsem/e6e0a412-26f0-432c-a6de-9a29d22b1e92/",
        "meta":{
            "display_title":"workflow_sort-bam-check v9 run 2019-08-09 22:27:57.903975",
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                "WorkflowRun",
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                "display_title":"Sort bam file plus output integrity-check - GAPWFIFWUPJP",
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                            "analysis_step_types":[
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                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                                },
                                "name":"input_bam",
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "meta":{
                                    "type":"parameter",
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                                    "cardinality":"single"
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                                "name":"max_memory",
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                                    {
                                        "name":"max_memory"
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                            {
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                                    "type":"parameter",
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                                    "cardinality":"single"
                                },
                                "name":"nthreads",
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                                    {
                                        "name":"nthreads"
                                    }
                                ]
                            }
                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"bam"
                                },
                                "name":"sorted_bam",
                                "target":[
                                    {
                                        "name":"sorted_bam",
                                        "step":"integrity-check"
                                    }
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                                "meta":{
                                    "type":"data file",
                                    "global":false,
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                                },
                                "name":"sorted_bam",
                                "source":[
                                    {
                                        "name":"sorted_bam",
                                        "step":"sort"
                                    }
                                ]
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                            {
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                                    "global":true,
                                    "cardinality":"single"
                                },
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                                    {
                                        "name":"count"
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                        ],
                        "outputs":[
                            {
                                "meta":{
                                    "type":"QC",
                                    "global":true,
                                    "cardinality":"single"
                                },
                                "name":"sorted_bam-check",
                                "target":[
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                                        "name":"sorted_bam-check"
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                                ]
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                "category":[
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                        "for_file":"/files-processed/GAPFITTEYNY1/",
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                            "uuid":"4db03c55-6308-4df2-975a-8f7b2fa6c2a0",
                            "display_title":"GAPFITTEYNY1.bam",
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                                "Item"
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                            "quality_metric":{
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                                "@type":[
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                                "display_title":"QualityMetricBamcheck from 2019-08-27",
                                "@id":"/quality-metrics-bamcheck/1f193066-4eff-48b6-a110-21b7800a7d5a/",
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                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
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                                "uuid":"83502314-1fe0-4566-b4af-465808c705a1",
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                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
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                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"1b8f525f-aecb-4211-9ae5-a2c998b05599"
                                },
                                "name":"known-sites-snp",
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                                        "name":"known-sites-snp"
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                            },
                            {
                                "meta":{
                                    "type":"reference file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"fcc2647d-301b-4888-8d9d-83ea4270309c"
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                                "name":"known-sites-indels",
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                            {
                                "meta":{
                                    "type":"data file",
                                    "global":true,
                                    "cardinality":"single",
                                    "file_format":"txt"
                                },
                                "name":"recalibration_report",
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                "experiment_types":[

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                            ],
                            "quality_metric":{
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                            "href":"/files-processed/GAPFIA7YMOIZ/@@download/GAPFIA7YMOIZ.bam",
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                            "file_format":{
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