{
  "id": "lib-process:bioinformatics--wgs-analysis-pipeline",
  "_kind": "LibraryProcess",
  "_file": "generated-library/processes.yaml",
  "_cluster": "generated-library",
  "attributes": {
    "displayName": "specializations/domains/science/bioinformatics/wgs-analysis-pipeline",
    "description": "Whole Genome Sequencing Pipeline - End-to-end pipeline for whole genome sequencing analysis\nincluding read alignment, variant calling, annotation, and quality control. Implements GATK best practices\nwith support for germline and somatic workflows.",
    "libraryPath": "library/specializations/domains/science/bioinformatics/wgs-analysis-pipeline.js",
    "specialization": "bioinformatics",
    "references": [
      "- GATK Best Practices: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows",
      "- BWA-MEM2: https://github.com/bwa-mem2/bwa-mem2",
      "- DeepVariant: https://github.com/google/deepvariant",
      "- VEP Documentation: https://www.ensembl.org/info/docs/tools/vep/index.html",
      "- Genome in a Bottle: https://www.nist.gov/programs-projects/genome-bottle"
    ],
    "example": "const result = await orchestrate('specializations/domains/science/bioinformatics/wgs-analysis-pipeline', {\n  projectName: 'Cancer Genomics Study',\n  sampleIds: ['SAMPLE001', 'SAMPLE002', 'SAMPLE003'],\n  referenceGenome: 'GRCh38',\n  analysisType: 'germline', // 'germline', 'somatic', 'trio'\n  fastqDir: '/data/fastq',\n  outputDir: '/results/wgs'\n});",
    "usesAgents": [
      "general-purpose"
    ]
  },
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        "weight": 1
      }
    },
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      "kind": "lib_requires_skill_area",
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        "weight": 0.7
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    },
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      "kind": "lib_applies_to_domain",
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        "weight": 1
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    },
    {
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      "to": "role:research-engineer",
      "kind": "lib_involves_role",
      "attributes": {
        "weight": 1
      }
    },
    {
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        "weight": 0.7
      }
    },
    {
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      "kind": "lib_implements_workflow",
      "attributes": {
        "weight": 1
      }
    },
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      "kind": "lib_belongs_to_specialization",
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}