full workflow + provenance example

{
  "@context": "https://w3id.org/ro/crate/1.1/context",
  "@graph": [
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
      "about": {"@id": "./"}
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "name": "Workflow Analysis Results",
      "description": "Results from running a bioinformatics workflow",
      "hasPart": [
        {"@id": "workflow.cwl"},
        {"@id": "results/output.bam"},
        {"@id": "inputs/sample.fastq"}
      ]
    },
    {
      "@id": "workflow.cwl",
      "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
      "name": "Alignment Workflow",
      "programmingLanguage": {"@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl"},
      "input": [{"@id": "#sample-param"}],
      "output": [{"@id": "#output-param"}]
    },
    {
      "@id": "#sample-param",
      "@type": "FormalParameter",
      "name": "sample",
      "description": "Input sample FASTQ file"
    },
    {
      "@id": "#output-param",
      "@type": "FormalParameter",
      "name": "aligned_output",
      "description": "Aligned BAM output file"
    },
    {
      "@id": "results/output.bam",
      "@type": "File",
      "name": "Aligned Sequences",
      "description": "Aligned DNA sequences in BAM format",
      "encodingFormat": "application/bam",
      "contentSize": "158292",
      "wasGeneratedBy": {"@id": "#run1"}
    },
    {
      "@id": "inputs/sample.fastq",
      "@type": "File",
      "name": "Input DNA Sequences",
      "description": "Raw DNA sequences in FASTQ format",
      "encodingFormat": "application/fastq"
    },
    {
      "@id": "#run1",
      "@type": "CreateAction",
      "name": "Workflow Run 2023-08-15",
      "description": "Execution of alignment workflow with sample data",
      "agent": {"@id": "https://orcid.org/0000-0002-1825-0097"},
      "object": [
        {"@id": "inputs/sample.fastq"},
        {"@id": "workflow.cwl"}
      ],
      "result": {"@id": "results/output.bam"},
      "startTime": "2023-08-15T08:43:21Z",
      "endTime": "2023-08-15T09:12:05Z"
    },
    {
      "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl",
      "@type": "ComputerLanguage",
      "name": "Common Workflow Language",
      "url": {"@id": "https://www.commonwl.org/"}
    },
    {
      "@id": "https://orcid.org/0000-0002-1825-0097",
      "@type": "Person",
      "name": "Josiah Carberry"
    }
  ]
}