[
    {
        "name":"/workflow-runs-awsem/9ef1362f-a319-4ed2-93f7-720a765e5599/",
        "meta":{
            "analysis_step_types":[
                "processing"
            ],
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
                "Item"
            ],
            "@id":"/workflow-runs-awsem/9ef1362f-a319-4ed2-93f7-720a765e5599/",
            "date_created":"2019-11-25T06:01:10.146193+00:00",
            "display_title":"workflow_add-readgroups-check v11 run 2019-11-25 06:01:10.109581",
            "workflow":{
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "@id":"/workflows/1ebf697c-949d-46b2-b9a4-8b1a7699ef1f/",
                "experiment_types":[

                ],
                "accession":"GAPWFBN35DT2",
                "steps":[
                    {
                        "name":"add-readgroups",
                        "meta":{
                            "software_used":[
                                "d7ac4c75-e133-4a8e-a19e-b7e87873cc16"
                            ],
                            "analysis_step_types":[
                                "Add read groups to bam input file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"bam_w_readgroups",
                                "target":[
                                    {
                                        "name":"bam_w_readgroups",
                                        "step":"integrity-check"
                                    }
                                ],
                                "meta":{
                                    "cardinality":"single",
                                    "file_format":"bam",
                                    "type":"data file",
                                    "global":true
                                }
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_bam",
                                "meta":{
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "type":"data file",
                                    "global":true
                                },
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "name":"sample_name",
                                "meta":{
                                    "cardinality":"single",
                                    "global":true,
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"sample_name"
                                    }
                                ]
                            },
                            {
                                "name":"nthreads",
                                "meta":{
                                    "cardinality":"single",
                                    "global":true,
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"nthreads"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "name":"integrity-check",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Check integrity of output file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"bam_w_readgroups-check",
                                "target":[
                                    {
                                        "name":"bam_w_readgroups-check"
                                    }
                                ],
                                "meta":{
                                    "cardinality":"single",
                                    "global":true,
                                    "type":"QC"
                                }
                            }
                        ],
                        "inputs":[
                            {
                                "name":"bam_w_readgroups",
                                "meta":{
                                    "cardinality":"single",
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "type":"data file",
                                    "global":false
                                },
                                "source":[
                                    {
                                        "name":"bam_w_readgroups",
                                        "step":"add-readgroups"
                                    }
                                ]
                            },
                            {
                                "name":"count",
                                "meta":{
                                    "cardinality":"single",
                                    "global":true,
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ]
                    }
                ],
                "display_title":"Add read groups plus output integrity-check - GAPWFBN35DT2",
                "category":[
                    "processing"
                ],
                "uuid":"1ebf697c-949d-46b2-b9a4-8b1a7699ef1f"
            },
            "run_status":"complete",
            "status":"in review"
        },
        "outputs":[
            {
                "name":"bam_w_readgroups",
                "target":[
                    {
                        "name":"bam_w_readgroups"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFI9PUMN3F/",
                        "step":"/workflow-runs-awsem/1acf44d1-d7ce-42be-ba39-31d3c47a93eb/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFI9PUMN3F/",
                        "step":"/workflow-runs-awsem/1acf44d1-d7ce-42be-ba39-31d3c47a93eb/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/38d19a8f-eda7-44db-a3e6-c2c23cc0c43a/",
                                "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"
                                    ]
                                },
                                "uuid":"38d19a8f-eda7-44db-a3e6-c2c23cc0c43a"
                            },
                            "accession":"GAPFI9PUMN3F",
                            "file_size":110764558680,
                            "display_title":"GAPFI9PUMN3F.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"6744d4c8-a0a2-4619-ada4-1f68991fb994",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFI9PUMN3F/",
                            "href":"/files-processed/GAPFI9PUMN3F/@@download/GAPFI9PUMN3F.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/bam/",
                            "type":"Output processed file",
                            "upload_key":"6744d4c8-a0a2-4619-ada4-1f68991fb994/GAPFI9PUMN3F.bam"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":true,
                    "type":"data file"
                }
            },
            {
                "name":"bam_w_readgroups-check",
                "target":[
                    {
                        "name":"bam_w_readgroups-check"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "@type":[
                                "QualityMetricBamcheck",
                                "QualityMetric",
                                "Item"
                            ],
                            "@id":"/quality-metrics-bamcheck/38d19a8f-eda7-44db-a3e6-c2c23cc0c43a/",
                            "accession":null,
                            "display_title":"QualityMetricBamcheck from 2019-11-25",
                            "uuid":"38d19a8f-eda7-44db-a3e6-c2c23cc0c43a",
                            "status":"in review"
                        }
                    ],
                    "meta":[
                        {
                            "type":"Output QC file"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"QC"
                }
            }
        ],
        "inputs":[
            {
                "name":"input_bam",
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "source":[
                    {
                        "name":"raw_bam",
                        "workflow":"/workflows/9e094699-561b-4396-8d6a-ffc45f98c5e1/",
                        "for_file":"/files-processed/GAPFI5V1GIRY/",
                        "step":"/workflow-runs-awsem/d05d398a-0887-4de3-a4cd-a2151b8863f0/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/0cbb2e67-0c45-40a0-9aa0-837ff5dec1a1/",
                                "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"
                                    ]
                                },
                                "uuid":"0cbb2e67-0c45-40a0-9aa0-837ff5dec1a1"
                            },
                            "accession":"GAPFI5V1GIRY",
                            "file_size":109338750489,
                            "display_title":"GAPFI5V1GIRY.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"eca5a9ac-f00a-4279-aab9-3f4ed17015c9",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFI5V1GIRY/",
                            "href":"/files-processed/GAPFI5V1GIRY/@@download/GAPFI5V1GIRY.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "dimension":"0",
                            "workflow_argument_name":"input_bam",
                            "ordinal":1
                        }
                    ],
                    "type":"input"
                }
            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/1acf44d1-d7ce-42be-ba39-31d3c47a93eb/",
        "meta":{
            "analysis_step_types":[
                "processing"
            ],
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
                "Item"
            ],
            "@id":"/workflow-runs-awsem/1acf44d1-d7ce-42be-ba39-31d3c47a93eb/",
            "date_created":"2019-11-25T10:01:28.917978+00:00",
            "display_title":"workflow_picard-MarkDuplicates-check v11 run 2019-11-25 10:01:28.882673",
            "workflow":{
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "@id":"/workflows/beb2b340-94ee-4afe-b4e3-66caaf063397/",
                "experiment_types":[

                ],
                "accession":"GAPWFLNQ7XTG",
                "steps":[
                    {
                        "name":"MarkDuplicates",
                        "meta":{
                            "software_used":[
                                "586cef39-6505-4bf6-920a-4b26a500d210"
                            ],
                            "analysis_step_types":[
                                "Mark duplicates in bam input file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"dupmarked_bam",
                                "meta":{
                                    "file_format":"bam",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "target":[
                                    {
                                        "name":"dupmarked_bam",
                                        "step":"integrity-check"
                                    }
                                ]
                            },
                            {
                                "name":"duplicate_metrics",
                                "meta":{
                                    "file_format":"txt",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "target":[
                                    {
                                        "name":"duplicate_metrics"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "name":"xmx",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"xmx"
                                    }
                                ]
                            },
                            {
                                "name":"xms",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"xms"
                                    }
                                ]
                            },
                            {
                                "name":"max_records_in_ram",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"max_records_in_ram"
                                    }
                                ]
                            },
                            {
                                "name":"duplicate_pixel_distance",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"duplicate_pixel_distance"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "name":"integrity-check",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Check integrity of output file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"dupmarked_bam-check",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"report"
                                },
                                "target":[
                                    {
                                        "name":"dupmarked_bam-check"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"dupmarked_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"dupmarked_bam",
                                        "step":"MarkDuplicates"
                                    }
                                ]
                            },
                            {
                                "name":"count",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ]
                    }
                ],
                "display_title":"Mark duplicates plus output integrity-check - GAPWFLNQ7XTG",
                "category":[
                    "processing"
                ],
                "uuid":"beb2b340-94ee-4afe-b4e3-66caaf063397"
            },
            "run_status":"complete",
            "status":"in review"
        },
        "outputs":[
            {
                "name":"dupmarked_bam",
                "target":[
                    {
                        "name":"dupmarked_bam"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIQHUBRKU/",
                        "step":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIQHUBRKU/",
                        "step":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIQHUBRKU/",
                        "step":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/85de219f-42ae-4ac2-b7ad-62b7d381baed/",
                                "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"
                                    ]
                                },
                                "uuid":"85de219f-42ae-4ac2-b7ad-62b7d381baed"
                            },
                            "accession":"GAPFIQHUBRKU",
                            "file_size":113357235025,
                            "display_title":"GAPFIQHUBRKU.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"3999a31d-d15d-433e-8bdf-88150fbfcbd4",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIQHUBRKU/",
                            "href":"/files-processed/GAPFIQHUBRKU/@@download/GAPFIQHUBRKU.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/bam/",
                            "type":"Output processed file",
                            "upload_key":"3999a31d-d15d-433e-8bdf-88150fbfcbd4/GAPFIQHUBRKU.bam"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":true,
                    "type":"data file"
                }
            },
            {
                "name":"duplicate_metrics",
                "target":[
                    {
                        "name":"duplicate_metrics"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"txt",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@id":"/file-formats/txt/",
                                "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"
                                    ]
                                },
                                "display_title":"txt",
                                "uuid":"0cd4e777-a596-4927-95c8-b07716121aa3"
                            },
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIAST6ER2/",
                            "file_size":3520,
                            "accession":"GAPFIAST6ER2",
                            "display_title":"GAPFIAST6ER2.txt",
                            "uuid":"1625a872-1546-42f7-9689-b77fa0d1d25f",
                            "href":"/files-processed/GAPFIAST6ER2/@@download/GAPFIAST6ER2.txt",
                            "status":"uploaded"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/txt/",
                            "type":"Output processed file",
                            "upload_key":"1625a872-1546-42f7-9689-b77fa0d1d25f/GAPFIAST6ER2.txt"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"data file"
                }
            },
            {
                "name":"dupmarked_bam-check",
                "target":[
                    {
                        "name":"dupmarked_bam-check"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "@type":[
                                "QualityMetricBamcheck",
                                "QualityMetric",
                                "Item"
                            ],
                            "@id":"/quality-metrics-bamcheck/85de219f-42ae-4ac2-b7ad-62b7d381baed/",
                            "accession":null,
                            "display_title":"QualityMetricBamcheck from 2019-11-25",
                            "uuid":"85de219f-42ae-4ac2-b7ad-62b7d381baed",
                            "status":"in review"
                        }
                    ],
                    "meta":[
                        {
                            "type":"Output QC file"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"report"
                }
            }
        ],
        "inputs":[
            {
                "name":"input_bam",
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "source":[
                    {
                        "name":"bam_w_readgroups",
                        "workflow":"/workflows/1ebf697c-949d-46b2-b9a4-8b1a7699ef1f/",
                        "for_file":"/files-processed/GAPFI9PUMN3F/",
                        "step":"/workflow-runs-awsem/9ef1362f-a319-4ed2-93f7-720a765e5599/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/38d19a8f-eda7-44db-a3e6-c2c23cc0c43a/",
                                "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"
                                    ]
                                },
                                "uuid":"38d19a8f-eda7-44db-a3e6-c2c23cc0c43a"
                            },
                            "accession":"GAPFI9PUMN3F",
                            "file_size":110764558680,
                            "display_title":"GAPFI9PUMN3F.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"6744d4c8-a0a2-4619-ada4-1f68991fb994",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFI9PUMN3F/",
                            "href":"/files-processed/GAPFI9PUMN3F/@@download/GAPFI9PUMN3F.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "dimension":"0",
                            "workflow_argument_name":"input_bam",
                            "ordinal":1
                        }
                    ],
                    "type":"input"
                }
            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/",
        "meta":{
            "analysis_step_types":[
                "processing"
            ],
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
                "Item"
            ],
            "@id":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/",
            "date_created":"2019-11-25T21:01:26.578249+00:00",
            "display_title":"workflow_sort-bam-check v11 run 2019-11-25 21:01:26.551370",
            "workflow":{
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "@id":"/workflows/560f5194-cd3a-4799-9b1a-6a2d2c371c89/",
                "experiment_types":[

                ],
                "accession":"GAPWFIFWUPJP",
                "steps":[
                    {
                        "name":"sort",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Sort bam input file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"sorted_bam",
                                "meta":{
                                    "file_format":"bam",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "target":[
                                    {
                                        "name":"sorted_bam",
                                        "step":"integrity-check"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "name":"max_memory",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"max_memory"
                                    }
                                ]
                            },
                            {
                                "name":"nthreads",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"nthreads"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "name":"integrity-check",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Check integrity of output file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"sorted_bam-check",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"QC"
                                },
                                "target":[
                                    {
                                        "name":"sorted_bam-check"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"sorted_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"sorted_bam",
                                        "step":"sort"
                                    }
                                ]
                            },
                            {
                                "name":"count",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ]
                    }
                ],
                "display_title":"Sort bam file plus output integrity-check - GAPWFIFWUPJP",
                "category":[
                    "processing"
                ],
                "uuid":"560f5194-cd3a-4799-9b1a-6a2d2c371c89"
            },
            "run_status":"complete",
            "status":"in review"
        },
        "outputs":[
            {
                "name":"sorted_bam",
                "target":[
                    {
                        "name":"sorted_bam"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFISSWY513/",
                        "step":"/workflow-runs-awsem/5c565340-5f12-4d30-b043-0e4fadcd71f5/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFISSWY513/",
                        "step":"/workflow-runs-awsem/843f2c0d-084e-4f2a-bf3b-693f3dd5a406/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFISSWY513/",
                        "step":"/workflow-runs-awsem/5c565340-5f12-4d30-b043-0e4fadcd71f5/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFISSWY513/",
                        "step":"/workflow-runs-awsem/843f2c0d-084e-4f2a-bf3b-693f3dd5a406/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@id":"/file-formats/bam/",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
                                        "group.read-only-admin",
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                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
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                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
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                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/ded50f6d-a746-466c-abf6-7715fba65da6/",
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                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
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                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
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                                }
                            },
                            "accession":"GAPFISSWY513",
                            "file_size":107514335457,
                            "display_title":"GAPFISSWY513.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"d87b2ea0-d0d3-4e4b-84e5-e32ee572ae96",
                            "status":"uploaded",
                            "@type":[
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                                "File",
                                "Item"
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                            "@id":"/files-processed/GAPFISSWY513/",
                            "href":"/files-processed/GAPFISSWY513/@@download/GAPFISSWY513.bam",
                            "file_type":"intermediate file"
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                    ],
                    "meta":[
                        {
                            "format":"/file-formats/bam/",
                            "type":"Output processed file",
                            "upload_key":"d87b2ea0-d0d3-4e4b-84e5-e32ee572ae96/GAPFISSWY513.bam"
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                },
                "meta":{
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                    "in_path":true,
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                }
            },
            {
                "name":"sorted_bam-check",
                "target":[
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                        "name":"sorted_bam-check"
                    }
                ],
                "run_data":{
                    "file":[
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                            "@type":[
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                                "QualityMetric",
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                            "accession":null,
                            "display_title":"QualityMetricBamcheck from 2019-11-25",
                            "uuid":"ded50f6d-a746-466c-abf6-7715fba65da6",
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                    "meta":[
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                            "type":"Output QC file"
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                "meta":{
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                    "in_path":false,
                    "type":"QC"
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            }
        ],
        "inputs":[
            {
                "name":"input_bam",
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
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                "source":[
                    {
                        "name":"dupmarked_bam",
                        "workflow":"/workflows/beb2b340-94ee-4afe-b4e3-66caaf063397/",
                        "for_file":"/files-processed/GAPFIQHUBRKU/",
                        "step":"/workflow-runs-awsem/1acf44d1-d7ce-42be-ba39-31d3c47a93eb/"
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                "run_data":{
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                                ],
                                "@id":"/file-formats/bam/",
                                "principals_allowed":{
                                    "view":[
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                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
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                                    "edit":[
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                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
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                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/85de219f-42ae-4ac2-b7ad-62b7d381baed/",
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                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
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                                "uuid":"85de219f-42ae-4ac2-b7ad-62b7d381baed"
                            },
                            "accession":"GAPFIQHUBRKU",
                            "file_size":113357235025,
                            "display_title":"GAPFIQHUBRKU.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"3999a31d-d15d-433e-8bdf-88150fbfcbd4",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIQHUBRKU/",
                            "href":"/files-processed/GAPFIQHUBRKU/@@download/GAPFIQHUBRKU.bam",
                            "file_type":"intermediate file"
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                    ],
                    "meta":[
                        {
                            "dimension":"0",
                            "workflow_argument_name":"input_bam",
                            "ordinal":1
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                    ],
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            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/5c565340-5f12-4d30-b043-0e4fadcd71f5/",
        "meta":{
            "analysis_step_types":[
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            "@type":[
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            "@id":"/workflow-runs-awsem/5c565340-5f12-4d30-b043-0e4fadcd71f5/",
            "date_created":"2019-11-26T00:01:30.238768+00:00",
            "display_title":"workflow_gatk-BaseRecalibrator v11 run 2019-11-26 00:01:30.213701",
            "workflow":{
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "@id":"/workflows/455b3056-64ca-4a9b-b546-294b01c9ca92/",
                "experiment_types":[

                ],
                "accession":"GAPWF3LQBB7P",
                "steps":[
                    {
                        "name":"BaseRecalibrator",
                        "meta":{
                            "software_used":[
                                "4ae88fb4-23f2-4939-8852-4644069d14d9"
                            ],
                            "analysis_step_types":[
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                        },
                        "outputs":[
                            {
                                "name":"recalibration_report",
                                "meta":{
                                    "file_format":"txt",
                                    "cardinality":"single",
                                    "type":"data file",
                                    "global":true
                                },
                                "target":[
                                    {
                                        "name":"recalibration_report"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "cardinality":"single",
                                    "type":"data file",
                                    "global":true
                                },
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "name":"reference",
                                "meta":{
                                    "file_format":"5ced774b-a73e-4d1b-8186-d7fbbde7a3c2",
                                    "cardinality":"single",
                                    "type":"reference file",
                                    "global":true
                                },
                                "source":[
                                    {
                                        "name":"reference"
                                    }
                                ]
                            },
                            {
                                "name":"known-sites-snp",
                                "meta":{
                                    "file_format":"1b8f525f-aecb-4211-9ae5-a2c998b05599",
                                    "cardinality":"single",
                                    "type":"reference file",
                                    "global":true
                                },
                                "source":[
                                    {
                                        "name":"known-sites-snp"
                                    }
                                ]
                            },
                            {
                                "name":"known-sites-indels",
                                "meta":{
                                    "file_format":"fcc2647d-301b-4888-8d9d-83ea4270309c",
                                    "cardinality":"single",
                                    "type":"reference file",
                                    "global":true
                                },
                                "source":[
                                    {
                                        "name":"known-sites-indels"
                                    }
                                ]
                            }
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                    }
                ],
                "display_title":"Run gatk BaseRecalibrator - GAPWF3LQBB7P",
                "category":[
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                ],
                "uuid":"455b3056-64ca-4a9b-b546-294b01c9ca92"
            },
            "run_status":"complete",
            "status":"in review"
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        "outputs":[
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                "name":"recalibration_report",
                "target":[
                    {
                        "name":"recalibration_report"
                    },
                    {
                        "name":"recalibration_report",
                        "for_file":"/files-processed/GAPFIJG8GL3V/",
                        "step":"/workflow-runs-awsem/843f2c0d-084e-4f2a-bf3b-693f3dd5a406/"
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                ],
                "run_data":{
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                            "file_format":{
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                                "@id":"/file-formats/txt/",
                                "principals_allowed":{
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                                        "remoteuser.INDEXER"
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                                    "edit":[
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                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
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                                "display_title":"txt",
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                            "@type":[
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                            "@id":"/files-processed/GAPFIJG8GL3V/",
                            "status":"uploaded",
                            "file_size":903902,
                            "accession":"GAPFIJG8GL3V",
                            "display_title":"GAPFIJG8GL3V.txt",
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        "inputs":[
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                "name":"input_bam",
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "source":[
                    {
                        "name":"sorted_bam",
                        "workflow":"/workflows/560f5194-cd3a-4799-9b1a-6a2d2c371c89/",
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                        "step":"/workflow-runs-awsem/2be2ec26-c846-48bd-9e61-4ebdca8a631a/"
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                "run_data":{
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                                        "step":"integrity-check"
                                    }
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                                    "type":"parameter"
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                            "@type":[
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                            "href":"/files-processed/GAPFI9HDXSSI/@@download/GAPFI9HDXSSI.bam",
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                "experiment_types":[

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                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
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                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "name":"xmx",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"xmx"
                                    }
                                ]
                            },
                            {
                                "name":"xms",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"xms"
                                    }
                                ]
                            },
                            {
                                "name":"max_records_in_ram",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"max_records_in_ram"
                                    }
                                ]
                            },
                            {
                                "name":"duplicate_pixel_distance",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"duplicate_pixel_distance"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "name":"integrity-check",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Check integrity of output file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"dupmarked_bam-check",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"report"
                                },
                                "target":[
                                    {
                                        "name":"dupmarked_bam-check"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"dupmarked_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"dupmarked_bam",
                                        "step":"MarkDuplicates"
                                    }
                                ]
                            },
                            {
                                "name":"count",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ]
                    }
                ],
                "display_title":"Mark duplicates plus output integrity-check - GAPWFLNQ7XTG",
                "category":[
                    "processing"
                ],
                "uuid":"beb2b340-94ee-4afe-b4e3-66caaf063397"
            },
            "run_status":"complete",
            "status":"in review"
        },
        "outputs":[
            {
                "name":"dupmarked_bam",
                "target":[
                    {
                        "name":"dupmarked_bam"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIK3FA7LW/",
                        "step":"/workflow-runs-awsem/3d9ad889-925f-439a-a74c-720d47ddede6/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIK3FA7LW/",
                        "step":"/workflow-runs-awsem/3d9ad889-925f-439a-a74c-720d47ddede6/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIK3FA7LW/",
                        "step":"/workflow-runs-awsem/3d9ad889-925f-439a-a74c-720d47ddede6/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/cf55bd29-2c1b-46fc-87c0-7004df5c93fc/",
                                "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"
                                    ]
                                },
                                "uuid":"cf55bd29-2c1b-46fc-87c0-7004df5c93fc"
                            },
                            "accession":"GAPFIK3FA7LW",
                            "file_size":106302914624,
                            "display_title":"GAPFIK3FA7LW.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"74085ab7-de6e-4a90-8b58-a4394d010609",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIK3FA7LW/",
                            "href":"/files-processed/GAPFIK3FA7LW/@@download/GAPFIK3FA7LW.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/bam/",
                            "type":"Output processed file",
                            "upload_key":"74085ab7-de6e-4a90-8b58-a4394d010609/GAPFIK3FA7LW.bam"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":true,
                    "type":"data file"
                }
            },
            {
                "name":"duplicate_metrics",
                "target":[
                    {
                        "name":"duplicate_metrics"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"txt",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@id":"/file-formats/txt/",
                                "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"
                                    ]
                                },
                                "display_title":"txt",
                                "uuid":"0cd4e777-a596-4927-95c8-b07716121aa3"
                            },
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIOIKS654/",
                            "file_size":3527,
                            "accession":"GAPFIOIKS654",
                            "display_title":"GAPFIOIKS654.txt",
                            "uuid":"b8473e3e-31c5-4e8c-b35e-3873ec83a449",
                            "href":"/files-processed/GAPFIOIKS654/@@download/GAPFIOIKS654.txt",
                            "status":"uploaded"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/txt/",
                            "type":"Output processed file",
                            "upload_key":"b8473e3e-31c5-4e8c-b35e-3873ec83a449/GAPFIOIKS654.txt"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"data file"
                }
            },
            {
                "name":"dupmarked_bam-check",
                "target":[
                    {
                        "name":"dupmarked_bam-check"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "@type":[
                                "QualityMetricBamcheck",
                                "QualityMetric",
                                "Item"
                            ],
                            "@id":"/quality-metrics-bamcheck/cf55bd29-2c1b-46fc-87c0-7004df5c93fc/",
                            "accession":null,
                            "display_title":"QualityMetricBamcheck from 2019-11-25",
                            "uuid":"cf55bd29-2c1b-46fc-87c0-7004df5c93fc",
                            "status":"in review"
                        }
                    ],
                    "meta":[
                        {
                            "type":"Output QC file"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"report"
                }
            }
        ],
        "inputs":[
            {
                "name":"input_bam",
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "source":[
                    {
                        "name":"bam_w_readgroups",
                        "workflow":"/workflows/1ebf697c-949d-46b2-b9a4-8b1a7699ef1f/",
                        "for_file":"/files-processed/GAPFILRE7OY6/",
                        "step":"/workflow-runs-awsem/4eb16594-4a41-4ec2-a031-d9f3258dca64/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/310c7958-6f7c-4bab-93fa-c5f3f49f5773/",
                                "uuid":"310c7958-6f7c-4bab-93fa-c5f3f49f5773",
                                "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"
                                    ]
                                }
                            },
                            "accession":"GAPFILRE7OY6",
                            "file_size":103509831000,
                            "display_title":"GAPFILRE7OY6.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"ec82bb3f-a033-4889-9872-14cd948e155b",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFILRE7OY6/",
                            "href":"/files-processed/GAPFILRE7OY6/@@download/GAPFILRE7OY6.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "dimension":"0",
                            "workflow_argument_name":"input_bam",
                            "ordinal":1
                        }
                    ],
                    "type":"input"
                }
            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/3d9ad889-925f-439a-a74c-720d47ddede6/",
        "meta":{
            "analysis_step_types":[
                "processing"
            ],
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
                "Item"
            ],
            "@id":"/workflow-runs-awsem/3d9ad889-925f-439a-a74c-720d47ddede6/",
            "date_created":"2019-11-25T21:01:18.299663+00:00",
            "display_title":"workflow_sort-bam-check v11 run 2019-11-25 21:01:18.274129",
            "workflow":{
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "@id":"/workflows/560f5194-cd3a-4799-9b1a-6a2d2c371c89/",
                "experiment_types":[

                ],
                "accession":"GAPWFIFWUPJP",
                "steps":[
                    {
                        "name":"sort",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Sort bam input file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"sorted_bam",
                                "meta":{
                                    "file_format":"bam",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "target":[
                                    {
                                        "name":"sorted_bam",
                                        "step":"integrity-check"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "name":"max_memory",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"max_memory"
                                    }
                                ]
                            },
                            {
                                "name":"nthreads",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"nthreads"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "name":"integrity-check",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Check integrity of output file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"sorted_bam-check",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"QC"
                                },
                                "target":[
                                    {
                                        "name":"sorted_bam-check"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"sorted_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"sorted_bam",
                                        "step":"sort"
                                    }
                                ]
                            },
                            {
                                "name":"count",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ]
                    }
                ],
                "display_title":"Sort bam file plus output integrity-check - GAPWFIFWUPJP",
                "category":[
                    "processing"
                ],
                "uuid":"560f5194-cd3a-4799-9b1a-6a2d2c371c89"
            },
            "run_status":"complete",
            "status":"in review"
        },
        "outputs":[
            {
                "name":"sorted_bam",
                "target":[
                    {
                        "name":"sorted_bam"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIB7BFZ58/",
                        "step":"/workflow-runs-awsem/3a2b9ffb-6c90-4d65-947e-54817883142c/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIB7BFZ58/",
                        "step":"/workflow-runs-awsem/75c45927-8d80-47aa-ae97-ee8f44ab886d/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIB7BFZ58/",
                        "step":"/workflow-runs-awsem/3a2b9ffb-6c90-4d65-947e-54817883142c/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIB7BFZ58/",
                        "step":"/workflow-runs-awsem/75c45927-8d80-47aa-ae97-ee8f44ab886d/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/3a46b41e-7cb0-4398-ac47-ba8d80b34281/",
                                "principals_allowed":{
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                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                },
                                "uuid":"3a46b41e-7cb0-4398-ac47-ba8d80b34281"
                            },
                            "accession":"GAPFIB7BFZ58",
                            "file_size":100452830720,
                            "display_title":"GAPFIB7BFZ58.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"6577ba40-57ef-40c7-95cb-1557718d3005",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIB7BFZ58/",
                            "href":"/files-processed/GAPFIB7BFZ58/@@download/GAPFIB7BFZ58.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/bam/",
                            "type":"Output processed file",
                            "upload_key":"6577ba40-57ef-40c7-95cb-1557718d3005/GAPFIB7BFZ58.bam"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":true,
                    "type":"data file"
                }
            },
            {
                "name":"sorted_bam-check",
                "target":[
                    {
                        "name":"sorted_bam-check"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "@type":[
                                "QualityMetricBamcheck",
                                "QualityMetric",
                                "Item"
                            ],
                            "@id":"/quality-metrics-bamcheck/3a46b41e-7cb0-4398-ac47-ba8d80b34281/",
                            "accession":null,
                            "display_title":"QualityMetricBamcheck from 2019-11-25",
                            "uuid":"3a46b41e-7cb0-4398-ac47-ba8d80b34281",
                            "status":"in review"
                        }
                    ],
                    "meta":[
                        {
                            "type":"Output QC file"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"QC"
                }
            }
        ],
        "inputs":[
            {
                "name":"input_bam",
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "source":[
                    {
                        "name":"dupmarked_bam",
                        "workflow":"/workflows/beb2b340-94ee-4afe-b4e3-66caaf063397/",
                        "for_file":"/files-processed/GAPFIK3FA7LW/",
                        "step":"/workflow-runs-awsem/f6b45d86-0e42-4504-b3a9-464c613f2f51/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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":[
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                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
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                                    "cardinality":"single"
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                                "name":"recalibrated_bam-check",
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                                    "cardinality":"single",
                                    "type":"QC"
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                        "for_file":"/files-processed/GAPFIOH2AVOD/",
                        "step":"/workflow-runs-awsem/746041de-a167-42bf-9216-e8db6c7aab36/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIOH2AVOD/",
                        "step":"/workflow-runs-awsem/746041de-a167-42bf-9216-e8db6c7aab36/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "uuid":"329cf33f-f30e-4634-a848-8a9a145ecfed",
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@id":"/quality-metrics-bamcheck/329cf33f-f30e-4634-a848-8a9a145ecfed/",
                                "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"
                                    ]
                                },
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ]
                            },
                            "accession":"GAPFIOH2AVOD",
                            "file_size":105563743732,
                            "display_title":"GAPFIOH2AVOD.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"eb793b65-fa13-4d17-931e-267abf10ccc2",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIOH2AVOD/",
                            "href":"/files-processed/GAPFIOH2AVOD/@@download/GAPFIOH2AVOD.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/bam/",
                            "type":"Output processed file",
                            "upload_key":"eb793b65-fa13-4d17-931e-267abf10ccc2/GAPFIOH2AVOD.bam"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":true,
                    "type":"data file"
                }
            },
            {
                "name":"bam_w_readgroups-check",
                "target":[
                    {
                        "name":"bam_w_readgroups-check"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "@type":[
                                "QualityMetricBamcheck",
                                "QualityMetric",
                                "Item"
                            ],
                            "@id":"/quality-metrics-bamcheck/329cf33f-f30e-4634-a848-8a9a145ecfed/",
                            "accession":null,
                            "display_title":"QualityMetricBamcheck from 2019-11-25",
                            "uuid":"329cf33f-f30e-4634-a848-8a9a145ecfed",
                            "status":"in review"
                        }
                    ],
                    "meta":[
                        {
                            "type":"Output QC file"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"QC"
                }
            }
        ],
        "inputs":[
            {
                "name":"input_bam",
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "source":[
                    {
                        "name":"raw_bam",
                        "workflow":"/workflows/9e094699-561b-4396-8d6a-ffc45f98c5e1/",
                        "for_file":"/files-processed/GAPFIH1A1SPG/",
                        "step":"/workflow-runs-awsem/ad95e345-3f42-4717-9ffd-93d80af722a0/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/cba2a229-0844-435c-822b-00f19be400f6/",
                                "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"
                                    ]
                                },
                                "uuid":"cba2a229-0844-435c-822b-00f19be400f6"
                            },
                            "accession":"GAPFIH1A1SPG",
                            "file_size":104192554457,
                            "display_title":"GAPFIH1A1SPG.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"afd716d4-714f-4df3-80be-014269c2821d",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIH1A1SPG/",
                            "href":"/files-processed/GAPFIH1A1SPG/@@download/GAPFIH1A1SPG.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "dimension":"0",
                            "workflow_argument_name":"input_bam",
                            "ordinal":1
                        }
                    ],
                    "type":"input"
                }
            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/746041de-a167-42bf-9216-e8db6c7aab36/",
        "meta":{
            "analysis_step_types":[
                "processing"
            ],
            "@type":[
                "WorkflowRunAwsem",
                "WorkflowRun",
                "Item"
            ],
            "@id":"/workflow-runs-awsem/746041de-a167-42bf-9216-e8db6c7aab36/",
            "date_created":"2019-11-25T10:01:21.316734+00:00",
            "display_title":"workflow_picard-MarkDuplicates-check v11 run 2019-11-25 10:01:21.281177",
            "workflow":{
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "@id":"/workflows/beb2b340-94ee-4afe-b4e3-66caaf063397/",
                "experiment_types":[

                ],
                "accession":"GAPWFLNQ7XTG",
                "steps":[
                    {
                        "name":"MarkDuplicates",
                        "meta":{
                            "software_used":[
                                "586cef39-6505-4bf6-920a-4b26a500d210"
                            ],
                            "analysis_step_types":[
                                "Mark duplicates in bam input file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"dupmarked_bam",
                                "meta":{
                                    "file_format":"bam",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "target":[
                                    {
                                        "name":"dupmarked_bam",
                                        "step":"integrity-check"
                                    }
                                ]
                            },
                            {
                                "name":"duplicate_metrics",
                                "meta":{
                                    "file_format":"txt",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "target":[
                                    {
                                        "name":"duplicate_metrics"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "name":"xmx",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"xmx"
                                    }
                                ]
                            },
                            {
                                "name":"xms",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"xms"
                                    }
                                ]
                            },
                            {
                                "name":"max_records_in_ram",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"max_records_in_ram"
                                    }
                                ]
                            },
                            {
                                "name":"duplicate_pixel_distance",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"duplicate_pixel_distance"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "name":"integrity-check",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Check integrity of output file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"dupmarked_bam-check",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"report"
                                },
                                "target":[
                                    {
                                        "name":"dupmarked_bam-check"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"dupmarked_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"dupmarked_bam",
                                        "step":"MarkDuplicates"
                                    }
                                ]
                            },
                            {
                                "name":"count",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ]
                    }
                ],
                "display_title":"Mark duplicates plus output integrity-check - GAPWFLNQ7XTG",
                "category":[
                    "processing"
                ],
                "uuid":"beb2b340-94ee-4afe-b4e3-66caaf063397"
            },
            "run_status":"complete",
            "status":"in review"
        },
        "outputs":[
            {
                "name":"dupmarked_bam",
                "target":[
                    {
                        "name":"dupmarked_bam"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIIKU363K/",
                        "step":"/workflow-runs-awsem/e73e0b52-27e7-40d5-8019-a484c678c61e/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIIKU363K/",
                        "step":"/workflow-runs-awsem/e73e0b52-27e7-40d5-8019-a484c678c61e/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFIIKU363K/",
                        "step":"/workflow-runs-awsem/e73e0b52-27e7-40d5-8019-a484c678c61e/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/35e411a6-0586-4e4e-a30e-42aa1a5d7b6a/",
                                "principals_allowed":{
                                    "view":[
                                        "group.admin",
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                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                },
                                "uuid":"35e411a6-0586-4e4e-a30e-42aa1a5d7b6a"
                            },
                            "accession":"GAPFIIKU363K",
                            "file_size":108271642249,
                            "display_title":"GAPFIIKU363K.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"76696a96-ffbf-47d6-9f04-3ce233ddb4cb",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIIKU363K/",
                            "href":"/files-processed/GAPFIIKU363K/@@download/GAPFIIKU363K.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/bam/",
                            "type":"Output processed file",
                            "upload_key":"76696a96-ffbf-47d6-9f04-3ce233ddb4cb/GAPFIIKU363K.bam"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":true,
                    "type":"data file"
                }
            },
            {
                "name":"duplicate_metrics",
                "target":[
                    {
                        "name":"duplicate_metrics"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"txt",
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                                    "Item"
                                ],
                                "@id":"/file-formats/txt/",
                                "principals_allowed":{
                                    "view":[
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                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
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                                },
                                "display_title":"txt",
                                "uuid":"0cd4e777-a596-4927-95c8-b07716121aa3"
                            },
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIRKBUASE/",
                            "file_size":3515,
                            "accession":"GAPFIRKBUASE",
                            "display_title":"GAPFIRKBUASE.txt",
                            "uuid":"4191d2e2-a518-448f-8fd5-0c7e134e225f",
                            "href":"/files-processed/GAPFIRKBUASE/@@download/GAPFIRKBUASE.txt",
                            "status":"uploaded"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/txt/",
                            "type":"Output processed file",
                            "upload_key":"4191d2e2-a518-448f-8fd5-0c7e134e225f/GAPFIRKBUASE.txt"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"data file"
                }
            },
            {
                "name":"dupmarked_bam-check",
                "target":[
                    {
                        "name":"dupmarked_bam-check"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "@type":[
                                "QualityMetricBamcheck",
                                "QualityMetric",
                                "Item"
                            ],
                            "@id":"/quality-metrics-bamcheck/35e411a6-0586-4e4e-a30e-42aa1a5d7b6a/",
                            "accession":null,
                            "display_title":"QualityMetricBamcheck from 2019-11-25",
                            "uuid":"35e411a6-0586-4e4e-a30e-42aa1a5d7b6a",
                            "status":"in review"
                        }
                    ],
                    "meta":[
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                            "type":"Output QC file"
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                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"report"
                }
            }
        ],
        "inputs":[
            {
                "name":"input_bam",
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "source":[
                    {
                        "name":"bam_w_readgroups",
                        "workflow":"/workflows/1ebf697c-949d-46b2-b9a4-8b1a7699ef1f/",
                        "for_file":"/files-processed/GAPFIOH2AVOD/",
                        "step":"/workflow-runs-awsem/0ea92f22-30d2-4551-a18a-6233fa1bc324/"
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                ],
                "run_data":{
                    "file":[
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                            "file_format":{
                                "file_format":"bam",
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                                    "Item"
                                ],
                                "@id":"/file-formats/bam/",
                                "principals_allowed":{
                                    "view":[
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                                        "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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "uuid":"329cf33f-f30e-4634-a848-8a9a145ecfed",
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@id":"/quality-metrics-bamcheck/329cf33f-f30e-4634-a848-8a9a145ecfed/",
                                "principals_allowed":{
                                    "view":[
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                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
                                        "project.12a92962-8265-4fc0-b2f8-cf14f05db58b",
                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
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                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                },
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ]
                            },
                            "accession":"GAPFIOH2AVOD",
                            "file_size":105563743732,
                            "display_title":"GAPFIOH2AVOD.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"eb793b65-fa13-4d17-931e-267abf10ccc2",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIOH2AVOD/",
                            "href":"/files-processed/GAPFIOH2AVOD/@@download/GAPFIOH2AVOD.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "dimension":"0",
                            "workflow_argument_name":"input_bam",
                            "ordinal":1
                        }
                    ],
                    "type":"input"
                }
            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/e73e0b52-27e7-40d5-8019-a484c678c61e/",
        "meta":{
            "analysis_step_types":[
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            ],
            "@type":[
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            ],
            "@id":"/workflow-runs-awsem/e73e0b52-27e7-40d5-8019-a484c678c61e/",
            "date_created":"2019-11-25T21:01:14.380994+00:00",
            "display_title":"workflow_sort-bam-check v11 run 2019-11-25 21:01:14.363970",
            "workflow":{
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "@id":"/workflows/560f5194-cd3a-4799-9b1a-6a2d2c371c89/",
                "experiment_types":[

                ],
                "accession":"GAPWFIFWUPJP",
                "steps":[
                    {
                        "name":"sort",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Sort bam input file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"sorted_bam",
                                "meta":{
                                    "file_format":"bam",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "target":[
                                    {
                                        "name":"sorted_bam",
                                        "step":"integrity-check"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":true,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "name":"max_memory",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"max_memory"
                                    }
                                ]
                            },
                            {
                                "name":"nthreads",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"nthreads"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "name":"integrity-check",
                        "meta":{
                            "software_used":[
                                "3f2d3b0e-0365-4212-9468-c16ad9531c4d"
                            ],
                            "analysis_step_types":[
                                "Check integrity of output file"
                            ]
                        },
                        "outputs":[
                            {
                                "name":"sorted_bam-check",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"QC"
                                },
                                "target":[
                                    {
                                        "name":"sorted_bam-check"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"sorted_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "global":false,
                                    "type":"data file",
                                    "cardinality":"single"
                                },
                                "source":[
                                    {
                                        "name":"sorted_bam",
                                        "step":"sort"
                                    }
                                ]
                            },
                            {
                                "name":"count",
                                "meta":{
                                    "global":true,
                                    "cardinality":"single",
                                    "type":"parameter"
                                },
                                "source":[
                                    {
                                        "name":"count"
                                    }
                                ]
                            }
                        ]
                    }
                ],
                "display_title":"Sort bam file plus output integrity-check - GAPWFIFWUPJP",
                "category":[
                    "processing"
                ],
                "uuid":"560f5194-cd3a-4799-9b1a-6a2d2c371c89"
            },
            "run_status":"complete",
            "status":"in review"
        },
        "outputs":[
            {
                "name":"sorted_bam",
                "target":[
                    {
                        "name":"sorted_bam"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFI67T8YV5/",
                        "step":"/workflow-runs-awsem/8779aabd-6efb-4471-8b20-d348de73ccd5/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFI67T8YV5/",
                        "step":"/workflow-runs-awsem/1c6848a3-9d65-4023-a598-d5bfc54fb65b/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFI67T8YV5/",
                        "step":"/workflow-runs-awsem/8779aabd-6efb-4471-8b20-d348de73ccd5/"
                    },
                    {
                        "name":"input_bam",
                        "for_file":"/files-processed/GAPFI67T8YV5/",
                        "step":"/workflow-runs-awsem/1c6848a3-9d65-4023-a598-d5bfc54fb65b/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
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                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/b0ce1bd6-ecdb-44a2-a977-4ae59edf21d1/",
                                "uuid":"b0ce1bd6-ecdb-44a2-a977-4ae59edf21d1",
                                "principals_allowed":{
                                    "view":[
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                                        "institution.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
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                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
                                        "group.admin",
                                        "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"
                                    ]
                                }
                            },
                            "accession":"GAPFI67T8YV5",
                            "file_size":102691366931,
                            "display_title":"GAPFI67T8YV5.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"bafedc46-753b-409a-a76f-cdc3a3065e7d",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFI67T8YV5/",
                            "href":"/files-processed/GAPFI67T8YV5/@@download/GAPFI67T8YV5.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "format":"/file-formats/bam/",
                            "type":"Output processed file",
                            "upload_key":"bafedc46-753b-409a-a76f-cdc3a3065e7d/GAPFI67T8YV5.bam"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":true,
                    "type":"data file"
                }
            },
            {
                "name":"sorted_bam-check",
                "target":[
                    {
                        "name":"sorted_bam-check"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "@type":[
                                "QualityMetricBamcheck",
                                "QualityMetric",
                                "Item"
                            ],
                            "@id":"/quality-metrics-bamcheck/b0ce1bd6-ecdb-44a2-a977-4ae59edf21d1/",
                            "accession":null,
                            "display_title":"QualityMetricBamcheck from 2019-11-25",
                            "uuid":"b0ce1bd6-ecdb-44a2-a977-4ae59edf21d1",
                            "status":"in review"
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                    ],
                    "meta":[
                        {
                            "type":"Output QC file"
                        }
                    ],
                    "type":"input"
                },
                "meta":{
                    "global":true,
                    "in_path":false,
                    "type":"QC"
                }
            }
        ],
        "inputs":[
            {
                "name":"input_bam",
                "meta":{
                    "in_path":true,
                    "global":true,
                    "type":"data file"
                },
                "source":[
                    {
                        "name":"dupmarked_bam",
                        "workflow":"/workflows/beb2b340-94ee-4afe-b4e3-66caaf063397/",
                        "for_file":"/files-processed/GAPFIIKU363K/",
                        "step":"/workflow-runs-awsem/746041de-a167-42bf-9216-e8db6c7aab36/"
                    }
                ],
                "run_data":{
                    "file":[
                        {
                            "file_format":{
                                "file_format":"bam",
                                "@type":[
                                    "FileFormat",
                                    "Item"
                                ],
                                "@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"
                                    ]
                                },
                                "display_title":"bam",
                                "uuid":"d13d06cf-218e-4f61-aaf0-91f226248b3c"
                            },
                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
                                    "QualityMetricBamcheck",
                                    "QualityMetric",
                                    "Item"
                                ],
                                "@id":"/quality-metrics-bamcheck/35e411a6-0586-4e4e-a30e-42aa1a5d7b6a/",
                                "principals_allowed":{
                                    "view":[
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                                        "remoteuser.EMBED",
                                        "remoteuser.INDEXER"
                                    ],
                                    "edit":[
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                                },
                                "uuid":"35e411a6-0586-4e4e-a30e-42aa1a5d7b6a"
                            },
                            "accession":"GAPFIIKU363K",
                            "file_size":108271642249,
                            "display_title":"GAPFIIKU363K.bam",
                            "description":"Intermediate alignment file",
                            "uuid":"76696a96-ffbf-47d6-9f04-3ce233ddb4cb",
                            "status":"uploaded",
                            "@type":[
                                "FileProcessed",
                                "File",
                                "Item"
                            ],
                            "@id":"/files-processed/GAPFIIKU363K/",
                            "href":"/files-processed/GAPFIIKU363K/@@download/GAPFIIKU363K.bam",
                            "file_type":"intermediate file"
                        }
                    ],
                    "meta":[
                        {
                            "dimension":"0",
                            "workflow_argument_name":"input_bam",
                            "ordinal":1
                        }
                    ],
                    "type":"input"
                }
            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/8779aabd-6efb-4471-8b20-d348de73ccd5/",
        "meta":{
            "analysis_step_types":[
                "processing"
            ],
            "@type":[
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                "WorkflowRun",
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            ],
            "@id":"/workflow-runs-awsem/8779aabd-6efb-4471-8b20-d348de73ccd5/",
            "date_created":"2019-11-26T00:01:17.600221+00:00",
            "display_title":"workflow_gatk-BaseRecalibrator v11 run 2019-11-26 00:01:17.575258",
            "workflow":{
                "@type":[
                    "Workflow",
                    "Item"
                ],
                "@id":"/workflows/455b3056-64ca-4a9b-b546-294b01c9ca92/",
                "experiment_types":[

                ],
                "accession":"GAPWF3LQBB7P",
                "steps":[
                    {
                        "name":"BaseRecalibrator",
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                            "software_used":[
                                "4ae88fb4-23f2-4939-8852-4644069d14d9"
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                            "analysis_step_types":[
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                            ]
                        },
                        "outputs":[
                            {
                                "name":"recalibration_report",
                                "meta":{
                                    "file_format":"txt",
                                    "cardinality":"single",
                                    "type":"data file",
                                    "global":true
                                },
                                "target":[
                                    {
                                        "name":"recalibration_report"
                                    }
                                ]
                            }
                        ],
                        "inputs":[
                            {
                                "name":"input_bam",
                                "meta":{
                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
                                    "cardinality":"single",
                                    "type":"data file",
                                    "global":true
                                },
                                "source":[
                                    {
                                        "name":"input_bam"
                                    }
                                ]
                            },
                            {
                                "name":"reference",
                                "meta":{
                                    "file_format":"5ced774b-a73e-4d1b-8186-d7fbbde7a3c2",
                                    "cardinality":"single",
                                    "type":"reference file",
                                    "global":true
                                },
                                "source":[
                                    {
                                        "name":"reference"
                                    }
                                ]
                            },
                            {
                                "name":"known-sites-snp",
                                "meta":{
                                    "file_format":"1b8f525f-aecb-4211-9ae5-a2c998b05599",
                                    "cardinality":"single",
                                    "type":"reference file",
                                    "global":true
                                },
                                "source":[
                                    {
                                        "name":"known-sites-snp"
                                    }
                                ]
                            },
                            {
                                "name":"known-sites-indels",
                                "meta":{
                                    "file_format":"fcc2647d-301b-4888-8d9d-83ea4270309c",
                                    "cardinality":"single",
                                    "type":"reference file",
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                                },
                                "source":[
                                    {
                                        "name":"known-sites-indels"
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                "display_title":"Run gatk BaseRecalibrator - GAPWF3LQBB7P",
                "category":[
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                ],
                "uuid":"455b3056-64ca-4a9b-b546-294b01c9ca92"
            },
            "run_status":"complete",
            "status":"in review"
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        "outputs":[
            {
                "name":"recalibration_report",
                "target":[
                    {
                        "name":"recalibration_report"
                    },
                    {
                        "name":"recalibration_report",
                        "for_file":"/files-processed/GAPFID38UPJ1/",
                        "step":"/workflow-runs-awsem/1c6848a3-9d65-4023-a598-d5bfc54fb65b/"
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                ],
                "run_data":{
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                            "file_format":{
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                                        "remoteuser.INDEXER"
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                                    "edit":[
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                            "@id":"/files-processed/GAPFID38UPJ1/",
                            "status":"uploaded",
                            "file_size":903865,
                            "accession":"GAPFID38UPJ1",
                            "display_title":"GAPFID38UPJ1.txt",
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                            "href":"/files-processed/GAPFID38UPJ1/@@download/GAPFID38UPJ1.txt",
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                    "type":"data file"
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                "source":[
                    {
                        "name":"sorted_bam",
                        "workflow":"/workflows/560f5194-cd3a-4799-9b1a-6a2d2c371c89/",
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                "run_data":{
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                            "file_format":{
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                            "quality_metric":{
                                "display_title":"QualityMetricBamcheck from 2019-11-25",
                                "@type":[
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                                    "QualityMetric",
                                    "Item"
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                            "description":"Intermediate alignment file",
                            "uuid":"bafedc46-753b-409a-a76f-cdc3a3065e7d",
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                            "@type":[
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                            "@id":"/files-processed/GAPFI67T8YV5/",
                            "href":"/files-processed/GAPFI67T8YV5/@@download/GAPFI67T8YV5.bam",
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                    ],
                    "meta":[
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                            "dimension":"0",
                            "workflow_argument_name":"input_bam",
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                        }
                    ],
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            },
            {
                "name":"known-sites-indels",
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                    "type":"reference file"
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                "source":[
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                        "name":"known-sites-indels",
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                            "@id":"/files-reference/GAPFIAX2PPYB/",
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                            "display_title":"GAPFIAX2PPYB.vcf",
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                    "meta":[
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                            "workflow_argument_name":"reference",
                            "ordinal":1
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                    ],
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            }
        ]
    },
    {
        "name":"/workflow-runs-awsem/1f95d4e2-f83d-43aa-b205-68d3dd007311/",
        "meta":{
            "analysis_step_types":[
                "processing"
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            "@type":[
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            "display_title":"workflow_gatk-HaplotypeCaller v11 run 2019-11-26 18:00:51.098249",
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                    "Workflow",
                    "Item"
                ],
                "@id":"/workflows/7fd67e19-3425-45f8-8149-c7cac4278fdb/",
                "experiment_types":[

                ],
                "accession":"GAPG8T65T3X9",
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                            "software_used":[
                                "4ae88fb4-23f2-4939-8852-4644069d14d9"
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                            "analysis_step_types":[
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                            ]
                        },
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                            {
                                "name":"gvcf",
                                "target":[
                                    {
                                        "name":"gvcf"
                                    }
                                ],
                                "meta":{
                                    "cardinality":"single",
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                                "name":"input_bam",
                                "meta":{
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                                    "file_format":"d13d06cf-218e-4f61-aaf0-91f226248b3c",
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                                        "name":"input_bam"
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                                ]
                            },
                            {
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                                    "file_format":"5ced774b-a73e-4d1b-8186-d7fbbde7a3c2",
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                                },
                                "source":[
                                    {
                                        "name":"reference"
                                    }
                                ]
                            },
                            {
                                "name":"regions",
                                "meta":{
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                                    "file_format":"0cd4e777-a596-4927-95c8-b07716121aa3",
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                                "source":[
                                    {
                                        "name":"regions"
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                            },
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                                "name":"threshold",
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                                "name":"ERC",
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                                    "type":"parameter"
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                                "source":[
                                    {
                                        "name":"ERC"
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                                "name":"nthreads",
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                            {
                                "name":"nthreads",
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                                    "type":"parameter"
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                                "name":"vcf-check",
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