example.json

{
   "missing_items" : {
      "tumor_rna_seq_cgl_workflow_3_0_x" : [
         "3398874d-0f93-5737-bf19-32a36c9191dc"
      ],
      "normal_rna_seq_cgl_workflow_3_0_x" : [],
      "normal_sequence" : [],
      "tumor_alignment_qc_report" : [
         "3398874d-0f93-5737-bf19-32a36c9191dc"
      ],
      "tumor_alignment" : [
         "3398874d-0f93-5737-bf19-32a36c9191dc"
      ],
      "normal_germline_variants" : [],
      "normal_alignment" : [],
      "tumor_sequence_qc_report" : [
         "3398874d-0f93-5737-bf19-32a36c9191dc"
      ],
      "normal_sequence_qc_report" : [],
      "tumor_rna_seq_quantification" : [],
      "tumor_sequence" : [],
      "normal_rna_seq_quantification" : [],
      "normal_alignment_qc_report" : [],
      "tumor_somatic_variants" : [
         "3398874d-0f93-5737-bf19-32a36c9191dc"
      ]
   },
   "donor_uuid" : "027a0bd9-5df8-5ab3-815f-af42b0909f6c",
   "flags" : {
      "tumor_alignment" : false,
      "normal_rna_seq_cgl_workflow_3_0_x" : false,
      "normal_sequence" : false,
      "tumor_rna_seq_cgl_workflow_3_0_x" : false,
      "tumor_alignment_qc_report" : false,
      "normal_rna_seq_quantification" : false,
      "tumor_sequence_qc_report" : false,
      "tumor_sequence" : true,
      "tumor_rna_seq_quantification" : true,
      "normal_sequence_qc_report" : false,
      "tumor_somatic_variants" : false,
      "normal_alignment_qc_report" : false,
      "normal_germline_variants" : false,
      "normal_alignment" : false
   },
   "present_items" : {
      "normal_germline_variants" : [],
      "normal_alignment" : [],
      "normal_rna_seq_quantification" : [],
      "tumor_rna_seq_quantification" : [
         "3398874d-0f93-5737-bf19-32a36c9191dc"
      ],
      "tumor_sequence_qc_report" : [],
      "tumor_sequence" : [
         "3398874d-0f93-5737-bf19-32a36c9191dc"
      ],
      "normal_sequence_qc_report" : [],
      "tumor_somatic_variants" : [],
      "normal_alignment_qc_report" : [],
      "normal_rna_seq_cgl_workflow_3_0_x" : [],
      "tumor_rna_seq_cgl_workflow_3_0_x" : [],
      "normal_sequence" : [],
      "tumor_alignment_qc_report" : [],
      "tumor_alignment" : []
   },
   "program" : "Treehouse",
   "timestamp" : "2017-04-10T02:25:05.297843",
   "submitter_donor_primary_site" : "BTO:0000042",
   "project" : "Expression Analysis R",
   "specimen" : [
      {
         "specimen_uuid" : "4cde4028-4112-5996-8e28-a0f806916932",
         "submitter_experimental_design" : "RNA-Seq",
         "samples" : [
            {
               "sample_uuid" : "3398874d-0f93-5737-bf19-32a36c9191dc",
               "analysis" : [
                  {
                     "workflow_version" : "1.0.0",
                     "bundle_uuid" : "6ae93c4b-cf7a-56da-bcff-46597bd45fc5",
                     "analysis_type" : "sequence_upload",
                     "workflow_outputs" : [
                        {
                           "file_path" : "THR14_0320_S01_R1.fq.gz",
                           "file_type" : "fastq.gz"
                        },
                        {
                           "file_type" : "fastq.gz",
                           "file_path" : "THR14_0320_S01_R2.fq.gz"
                        }
                     ],
                     "workflow_name" : "spinnaker"
                  },
                  {
                     "timing_metrics" : {
                        "overall_stop_time_utc" : "2017-04-08T02:11:59.101919",
                        "overall_start_time_utc" : "2017-04-07T16:50:25.641979",
                        "overall_walltime_seconds" : 33693,
                        "step_timing" : {
                           "download" : {
                              "stop_time_utc" : "2017-04-07T16:50:25.641979",
                              "start_time_utc" : "2017-04-07T16:54:56.900477",
                              "walltime_seconds" : 271
                           },
                           "tool_run" : {
                              "stop_time_utc" : "2017-04-07T16:54:56.900509",
                              "walltime_seconds" : 33422,
                              "start_time_utc" : "2017-04-08T02:11:59.101886"
                           }
                        }
                     },
                     "parent_uuids" : [
                        "3398874d-0f93-5737-bf19-32a36c9191dc"
                     ],
                     "workflow_url" : "https://dockstore.org/containers/quay.io/ucsc_cgl/rnaseq-cgl-pipeline",
                     "analysis_type" : "rna_seq_quantification",
                     "host_metrics" : {
                        "vm_instance_mem_gb" : 60,
                        "vm_region" : "us-west-2",
                        "vm_instance_type" : "c4.8xlarge",
                        "vm_instance_cores" : 36,
                        "vm_location" : "aws"
                     },
                     "timestamp" : "2017-04-08T02:11:59.101919",
                     "workflow_params" : {
                        "disable-cutadapt" : "False",
                        "output-basename" : "THR14_0320_S01",
                        "save-bam" : "True",
                        "resume" : "",
                        "work-mount" : "/datastore",
                        "no-clean" : "True",
                        "save-wiggle" : "True",
                        "bamqc" : "True",
                        "cores" : "36"
                     },
                     "version" : "1.0.0",
                     "qc_metrics" : {},
                     "workflow_name" : "quay.io/ucsc_cgl/rnaseq-cgl-pipeline",
                     "workflow_inputs" : [
                        {
                           "file_storage_bundle_id" : "6ae93c4b-cf7a-56da-bcff-46597bd45fc5",
                           "file_storage_bundle_files" : [
                              {
                                 "file_storage_bundle_id" : "6ae93c4b-cf7a-56da-bcff-46597bd45fc5",
                                 "file_storage_id" : "8fba946d-183c-5d53-9c71-e50cde2ad45e",
                                 "file_path" : "THR14_0320_S01_R1.fq.gz",
                                 "file_name" : "sample-paired",
                                 "file_type" : "gz"
                              },
                              {
                                 "file_path" : "THR14_0320_S01_R2.fq.gz",
                                 "file_storage_id" : "fc561654-101c-50b9-b999-c0c4fe1b21fe",
                                 "file_storage_bundle_id" : "6ae93c4b-cf7a-56da-bcff-46597bd45fc5",
                                 "file_type" : "gz",
                                 "file_name" : "sample-paired"
                              }
                           ]
                        },
                        {
                           "file_storage_bundle_id" : "d0117ff1-cf53-43a0-aaab-cb15809fbb49",
                           "file_storage_bundle_files" : [
                              {
                                 "file_storage_bundle_id" : "d0117ff1-cf53-43a0-aaab-cb15809fbb49",
                                 "file_storage_id" : "ca79c317-e410-591f-b802-3a0be6b658b7",
                                 "file_path" : "starIndex_hg38_no_alt.tar.gz",
                                 "file_name" : "star",
                                 "file_type" : "gz"
                              },
                              {
                                 "file_type" : "gz",
                                 "file_name" : "rsem",
                                 "file_storage_id" : "b850460d-23c0-57a4-9d4b-af60726476a5",
                                 "file_path" : "rsem_ref_hg38_no_alt.tar.gz",
                                 "file_storage_bundle_id" : "d0117ff1-cf53-43a0-aaab-cb15809fbb49"
                              },
                              {
                                 "file_storage_bundle_id" : "d0117ff1-cf53-43a0-aaab-cb15809fbb49",
                                 "file_storage_id" : "c92d30f3-2731-56b1-b8e4-41d09b1bb2dc",
                                 "file_path" : "kallisto_hg38.idx",
                                 "file_name" : "kallisto",
                                 "file_type" : "idx"
                              }
                           ]
                        }
                     ],
                     "workflow_outputs" : [
                        {
                           "file_type" : "bam",
                           "file_checksum" : "sha1$7c6cbe39475ef1ab01cccb081af3fdaef2cc1a42",
                           "file_size" : 11102553451,
                           "file_path" : "THR14_0320_S01.sortedByCoord.md.bam"
                        },
                        {
                           "file_type" : "gz",
                           "file_checksum" : "sha1$14f49dac84d4247ca28a2350a51aa5c29333eea3",
                           "file_size" : 99710280,
                           "file_path" : "THR14_0320_S01.tar.gz"
                        },
                        {
                           "file_checksum" : "sha1$7b7e78926bb0ad638963d5eafc427f40bb8da57c",
                           "file_type" : "bg",
                           "file_path" : "THR14_0320_S01.wiggle.bg",
                           "file_size" : 1260036159
                        }
                     ],
                     "workflow_version" : "3.2.1-1",
                     "bundle_uuid" : "99fd920c-70ca-4430-853c-ee395ab1df09"
                  }
               ],
               "submitter_sample_id" : "THR14_0320_S01"
            }
         ],
         "submitter_specimen_type" : "Primary tumour - other",
         "submitter_specimen_id" : "THR14_0320_S01"
      }
   ],
   "submitter_donor_id" : "THR14_0320",
   "center_name" : "THR14",
   "schema_version" : "0.0.3"
}