{
  "resourceType" : "Task",
  "id" : "CQDGTaskLongReadExample",
  "meta" : {
    "profile" : ["https://fhir.cqdg.ca/StructureDefinition/CQDGTask"]
  },
  "text" : {
    "status" : "extensions",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Task CQDGTaskLongReadExample</b></p><a name=\"CQDGTaskLongReadExample\"> </a><a name=\"hcCQDGTaskLongReadExample\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"https://simplifier.net/resolve?scope=hl7.fhir.ca.baseline@1.0.2&amp;canonical=https://fhir.cqdg.ca/StructureDefinition/CQDGTask\">https://fhir.cqdg.ca/StructureDefinition/CQDGTask</a></p></div><blockquote><p><b>Ferlab.bio StructureDefinition/workflow</b></p><ul><li>pipeline: dorado 0.7.2</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sequencing-experiment</b></p><ul><li>experimentalStrategy: <a href=\"CodeSystem-experimental-strategy.html#experimental-strategy-ADAS\">Ferlab.bio CodeSystem/experimental-strategy: ADAS</a> (Adaptive Sampling)</li><li>platform: <a href=\"CodeSystem-sequencing-experiment-platform.html#sequencing-experiment-platform-ONT\">Ferlab.bio CodeSystem/sequencing-experiment-platform: ONT</a> (ONT)</li><li>selection: <a href=\"CodeSystem-sequencing-experiment-selection.html#sequencing-experiment-selection-DIRECT\">Ferlab.bio CodeSystem/sequencing-experiment-selection: DIRECT</a> (Direct)</li><li>source: <a href=\"CodeSystem-sequencing-experiment-source.html#sequencing-experiment-source-GEN\">Ferlab.bio CodeSystem/sequencing-experiment-source: GEN</a> (Genomics)</li><li>profilingResolution: <a href=\"CodeSystem-profiling-resolution.html#profiling-resolution-Bulk\">Ferlab.bio CodeSystem/profiling-resolution: Bulk</a> (Bulk)</li><li>instrumentModel: PromethION 24</li><li>poreType: R10.4.1</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sample</b></p><ul><li>ldmSampleId: LDM24680</li><li>labAliquotId: AliquotID4</li></ul></blockquote><p><b>status</b>: Completed</p><p><b>intent</b>: order</p><p><b>priority</b>: Routine</p><p><b>code</b>: <span title=\"Codes:{https://fhir.cqdg.ca/CodeSystem/bioinfo-analysis-code GBVA}\">Germline Variant Analysis</span></p><p><b>requester</b>: <a href=\"Organization-OrganizationExample.html\">Organization CQDG</a></p><p><b>owner</b>: <a href=\"Organization-OrganizationExample.html\">Organization CQDG</a></p><h3>Inputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Type</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:\">Analysed sample</span></td><td><a href=\"Specimen-SpecimenExample.html\">Submitter Sample ID: SpecimenExample</a></td></tr></table><blockquote><p><b>output</b></p><p><b>type</b>: <span title=\"Codes:{https://fhir.cqdg.ca/CodeSystem/data-type De-Novo-Assembly-Aligned-Reads}\">De Novo Assembly Aligned Reads</span></p><p><b>value</b>: <a href=\"DocumentReference-DocumentReferenceExample1.html\">DocumentReference: status = current; type = Sequencing Data Supplement; category = Genomics; securityLabel = test</a></p></blockquote><blockquote><p><b>output</b></p><p><b>type</b>: <span title=\"Codes:{https://fhir.cqdg.ca/CodeSystem/data-type Methylation-Calls}\">Methylation Calls</span></p><p><b>value</b>: <a href=\"DocumentReference-DocumentReferenceExample2.html\">DocumentReference: status = current; type = Aligned Reads; category = Genomics; securityLabel = test</a></p></blockquote><blockquote><p><b>output</b></p><p><b>type</b>: <span title=\"Codes:{https://fhir.cqdg.ca/CodeSystem/data-type Tandem-Repeats}\">Tandem Repeats (TRs)</span></p><p><b>value</b>: <a href=\"DocumentReference-DocumentReferenceExample2.html\">DocumentReference: status = current; type = Aligned Reads; category = Genomics; securityLabel = test</a></p></blockquote></div>"
  },
  "extension" : [{
    "extension" : [{
      "url" : "pipeline",
      "valueString" : "dorado 0.7.2"
    }],
    "url" : "https://fhir.cqdg.ca/StructureDefinition/workflowExtension"
  },
  {
    "extension" : [{
      "url" : "experimentalStrategy",
      "valueCoding" : {
        "system" : "https://fhir.cqdg.ca/CodeSystem/experimental-strategy",
        "code" : "ADAS",
        "display" : "Adaptive Sampling"
      }
    },
    {
      "url" : "platform",
      "valueCoding" : {
        "system" : "https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-platform",
        "code" : "ONT",
        "display" : "ONT"
      }
    },
    {
      "url" : "selection",
      "valueCoding" : {
        "system" : "https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-selection",
        "code" : "DIRECT",
        "display" : "Direct"
      }
    },
    {
      "url" : "source",
      "valueCoding" : {
        "system" : "https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-source",
        "code" : "GEN",
        "display" : "Genomics"
      }
    },
    {
      "url" : "profilingResolution",
      "valueCoding" : {
        "system" : "https://fhir.cqdg.ca/CodeSystem/profiling-resolution",
        "code" : "Bulk",
        "display" : "Bulk"
      }
    },
    {
      "url" : "instrumentModel",
      "valueString" : "PromethION 24"
    },
    {
      "url" : "poreType",
      "valueString" : "R10.4.1"
    }],
    "url" : "https://fhir.cqdg.ca/StructureDefinition/sequencingExperimentExtension"
  },
  {
    "extension" : [{
      "url" : "ldmSampleId",
      "valueString" : "LDM24680"
    },
    {
      "url" : "labAliquotId",
      "valueString" : "AliquotID4"
    }],
    "url" : "https://fhir.cqdg.ca/StructureDefinition/sampleExtension"
  }],
  "status" : "completed",
  "intent" : "order",
  "priority" : "routine",
  "code" : {
    "coding" : [{
      "system" : "https://fhir.cqdg.ca/CodeSystem/bioinfo-analysis-code",
      "code" : "GBVA",
      "display" : "Germline Variant Analysis"
    }]
  },
  "requester" : {
    "reference" : "Organization/OrganizationExample"
  },
  "owner" : {
    "reference" : "Organization/OrganizationExample"
  },
  "input" : [{
    "type" : {
      "text" : "Analysed sample"
    },
    "valueReference" : {
      "reference" : "Specimen/SpecimenExample",
      "display" : "Submitter Sample ID: SpecimenExample"
    }
  }],
  "output" : [{
    "type" : {
      "coding" : [{
        "system" : "https://fhir.cqdg.ca/CodeSystem/data-type",
        "code" : "De-Novo-Assembly-Aligned-Reads",
        "display" : "De Novo Assembly Aligned Reads"
      }]
    },
    "valueReference" : {
      "reference" : "DocumentReference/DocumentReferenceExample1"
    }
  },
  {
    "type" : {
      "coding" : [{
        "system" : "https://fhir.cqdg.ca/CodeSystem/data-type",
        "code" : "Methylation-Calls",
        "display" : "Methylation Calls"
      }]
    },
    "valueReference" : {
      "reference" : "DocumentReference/DocumentReferenceExample2"
    }
  },
  {
    "type" : {
      "coding" : [{
        "system" : "https://fhir.cqdg.ca/CodeSystem/data-type",
        "code" : "Tandem-Repeats",
        "display" : "Tandem Repeats (TRs)"
      }]
    },
    "valueReference" : {
      "reference" : "DocumentReference/DocumentReferenceExample2"
    }
  }]
}