{
    "@context": "https://w3id.org/ro/crate/1.1/context",
    "@graph": [
        {
            "@id": "ro-crate-metadata.json",
            "@type": "CreativeWork",
            "about": {
                "@id": "./"
            },
            "conformsTo": [
                {
                    "@id": "https://w3id.org/ro/crate/1.1"
                },
                {
                    "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
                }
            ]
        },
        {
            "@id": "./",
            "@type": "Dataset",
            "datePublished": "2026-10-21",
            "conformsTo": [
                {
                    "@id": "https://w3id.org/ro/wfrun/process/0.1"
                },
                {
                    "@id": "https://w3id.org/ro/wfrun/workflow/0.1"
                },
                {
                    "@id": "https://w3id.org/ro/wfrun/provenance/0.1"
                },
                {
                    "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
                }
            ],
            "name": "Workflow run of nf-core/provenancereport",
            "description": "Generate reproducible Quarto reports together with an audit trail of inputs, checksums, software versions, runtime environments, and provenance metadata.",
            "hasPart": [
                {
                    "@id": "main.nf"
                },
                {
                    "@id": "https://spdx.org/licenses/MIT"
                },
                {
                    "@id": "README.md"
                },
                {
                    "@id": "nextflow_schema.json"
                },
                {
                    "@id": "nextflow.config"
                },
                {
                    "@id": "review_signoff.md"
                },
                {
                    "@id": "test_full_report.qmd"
                },
                {
                    "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv"
                },
                {
                    "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/nf-core-provenancereport_logo_light.png"
                },
                {
                    "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv"
                },
                {
                    "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/multiqc_config.yml"
                },
                {
                    "@id": "samplesheet.csv"
                },
                {
                    "@id": "test_full_report.qmd"
                },
                {
                    "@id": "review_signoff.md"
                },
                {
                    "@id": "review_signoff.md"
                },
                {
                    "@id": "multiqc_report.csv"
                },
                {
                    "@id": "quartonotebook/test_full_report.qmd"
                },
                {
                    "@id": "quartonotebook/test_full_report.html"
                },
                {
                    "@id": "quartonotebook/artifacts/test_full_summary.tsv"
                },
                {
                    "@id": "quartonotebook/prepared_test_full_report.qmd"
                },
                {
                    "@id": "md5sum/provenancereport.md5"
                },
                {
                    "@id": "multiqc/multiqc_report.html"
                },
                {
                    "@id": "multiqc/multiqc_data"
                }
            ],
            "mainEntity": {
                "@id": "main.nf"
            },
            "mentions": [
                {
                    "@id": "#1724052d-e05b-4de8-a7aa-0dcdfb6d010a"
                },
                {
                    "@id": "#tmp/methods_description_mqc.yaml"
                },
                {
                    "@id": "#tmp/nf_core_provenancereport_software_mqc_versions.yml"
                },
                {
                    "@id": "#tmp/pipeline_outputs_mqc.tsv"
                },
                {
                    "@id": "#tmp/samplesheet.csv"
                },
                {
                    "@id": "#tmp/file_checksums_mqc.tsv"
                },
                {
                    "@id": "#tmp/workflow_summary_mqc.yaml"
                },
                {
                    "@id": "#task/844f614b9c13d637bce832e98bc157d2"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d"
                },
                {
                    "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa"
                },
                {
                    "@id": "#task/f5f6b9f0317275f8972e6c7c4f83ce14"
                },
                {
                    "@id": "#task/2747a7b65e3400f5eff04e71962e8799"
                },
                {
                    "@id": "#task/844f614b9c13d637bce832e98bc157d2/test_full_report.qmd"
                },
                {
                    "@id": "#task/844f614b9c13d637bce832e98bc157d2/prepared_test_full_report.qmd"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/test_full_report.html"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/prepared_test_full_report.qmd"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/params.yml"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/artifacts/test_full_summary.tsv"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/versions.yml"
                },
                {
                    "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa/runtime_environment_mqc.tsv"
                },
                {
                    "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa/r_session_info_mqc.yaml"
                },
                {
                    "@id": "#task/f5f6b9f0317275f8972e6c7c4f83ce14/provenancereport.md5"
                },
                {
                    "@id": "#task/2747a7b65e3400f5eff04e71962e8799/multiqc_report.html"
                },
                {
                    "@id": "#task/2747a7b65e3400f5eff04e71962e8799/multiqc_data"
                },
                {
                    "@id": "#publish/844f614b9c13d637bce832e98bc157d2/test_full_report.qmd"
                },
                {
                    "@id": "#publish/4550c8ef87736d4e662a18ee4556ad2d/test_full_report.html"
                },
                {
                    "@id": "#publish/4550c8ef87736d4e662a18ee4556ad2d/artifacts/test_full_summary.tsv"
                },
                {
                    "@id": "#publish/4550c8ef87736d4e662a18ee4556ad2d/prepared_test_full_report.qmd"
                },
                {
                    "@id": "#publish/f5f6b9f0317275f8972e6c7c4f83ce14/provenancereport.md5"
                },
                {
                    "@id": "#publish/2747a7b65e3400f5eff04e71962e8799/multiqc_report.html"
                },
                {
                    "@id": "#publish/2747a7b65e3400f5eff04e71962e8799/multiqc_data"
                }
            ],
            "license": "https://spdx.org/licenses/MIT"
        },
        {
            "@id": "https://w3id.org/ro/wfrun/process/0.1",
            "@type": "CreativeWork",
            "name": "Process Run Crate",
            "version": "0.1"
        },
        {
            "@id": "https://w3id.org/ro/wfrun/workflow/0.1",
            "@type": "CreativeWork",
            "name": "Workflow Run Crate",
            "version": "0.1"
        },
        {
            "@id": "https://w3id.org/ro/wfrun/provenance/0.1",
            "@type": "CreativeWork",
            "name": "Provenance Run Crate",
            "version": "0.1"
        },
        {
            "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0",
            "@type": "CreativeWork",
            "name": "Workflow RO-Crate",
            "version": "1.0"
        },
        {
            "@id": "main.nf",
            "@type": [
                "File",
                "SoftwareSourceCode",
                "ComputationalWorkflow",
                "HowTo"
            ],
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE"
            },
            "name": "nf-core/provenancereport",
            "description": "Generate reproducible Quarto reports together with an audit trail of inputs, checksums, software versions, runtime environments, and provenance metadata.",
            "programmingLanguage": {
                "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
            },
            "codeRepository": "https://github.com/nf-core/provenancereport",
            "version": "89ed44de8da1788e5f00a6dd95bd72c51ff36dff",
            "license": "MIT",
            "url": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/main.nf",
            "encodingFormat": "application/nextflow",
            "runtimePlatform": "Nextflow 26.04.7",
            "hasPart": [
                {
                    "@id": "#module/QUARTO_PREPARE"
                },
                {
                    "@id": "#module/QUARTO_NOTEBOOK"
                },
                {
                    "@id": "#module/REPORTENVIRONMENT"
                },
                {
                    "@id": "#module/MD5SUM"
                },
                {
                    "@id": "#module/MULTIQC"
                }
            ],
            "input": [
                {
                    "@id": "#param/input"
                },
                {
                    "@id": "#param/notebook"
                },
                {
                    "@id": "#param/document"
                },
                {
                    "@id": "#param/outdir"
                },
                {
                    "@id": "#param/publish_dir_mode"
                },
                {
                    "@id": "#param/plaintext_email"
                },
                {
                    "@id": "#param/monochrome_logs"
                },
                {
                    "@id": "#param/help"
                },
                {
                    "@id": "#param/help_full"
                },
                {
                    "@id": "#param/show_hidden"
                },
                {
                    "@id": "#param/version"
                },
                {
                    "@id": "#param/pipelines_testdata_base_path"
                },
                {
                    "@id": "#param/trace_report_suffix"
                },
                {
                    "@id": "#param/config_profile_name"
                },
                {
                    "@id": "#param/config_profile_description"
                },
                {
                    "@id": "#param/custom_config_version"
                },
                {
                    "@id": "#param/custom_config_base"
                },
                {
                    "@id": "#param/validate_params"
                },
                {
                    "@id": "#param/helpFull"
                },
                {
                    "@id": "#param/showHidden"
                },
                {
                    "@id": "#output/document"
                },
                {
                    "@id": "#output/artifacts"
                },
                {
                    "@id": "#output/reports"
                },
                {
                    "@id": "#output/notebook"
                },
                {
                    "@id": "#output/md5sum"
                },
                {
                    "@id": "#output/multiqc_report"
                }
            ],
            "output": [
                
            ],
            "step": [
                {
                    "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_PREPARE"
                },
                {
                    "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_NOTEBOOK"
                },
                {
                    "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:REPORTENVIRONMENT"
                },
                {
                    "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MD5SUM"
                },
                {
                    "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MULTIQC"
                }
            ]
        },
        {
            "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
            "@type": "ComputerLanguage",
            "name": "Nextflow",
            "identifier": "https://www.nextflow.io/",
            "url": "https://www.nextflow.io/",
            "version": "26.04.7"
        },
        {
            "@id": "main.nf#software-application",
            "@type": "SoftwareApplication",
            "name": "Nextflow 26.04.7"
        },
        {
            "@id": "#module/QUARTO_PREPARE",
            "@type": "SoftwareApplication",
            "name": "quarto_prepare",
            "url": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/modules/local/quarto_prepare/main.nf",
            "hasPart": [
                {
                    "@id": "#module/QUARTO_PREPARE/quarto_prepare"
                }
            ]
        },
        {
            "@id": "#module/QUARTO_NOTEBOOK",
            "@type": "SoftwareApplication",
            "name": "quarto_notebook",
            "url": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/modules/nf-core/quarto/notebook/main.nf",
            "hasPart": [
                {
                    "@id": "#module/QUARTO_NOTEBOOK/quarto"
                },
                {
                    "@id": "#module/QUARTO_NOTEBOOK/papermill"
                }
            ]
        },
        {
            "@id": "#module/REPORTENVIRONMENT",
            "@type": "SoftwareApplication",
            "name": "reportenvironment",
            "url": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/modules/local/reportenvironment/main.nf",
            "hasPart": [
                {
                    "@id": "#module/REPORTENVIRONMENT/reportenvironment"
                }
            ]
        },
        {
            "@id": "#module/MD5SUM",
            "@type": "SoftwareApplication",
            "name": "md5sum",
            "url": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/modules/nf-core/md5sum/main.nf",
            "hasPart": [
                {
                    "@id": "#module/MD5SUM/md5sum"
                }
            ]
        },
        {
            "@id": "#module/MULTIQC",
            "@type": "SoftwareApplication",
            "name": "multiqc",
            "url": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/modules/nf-core/multiqc/main.nf",
            "hasPart": [
                {
                    "@id": "#module/MULTIQC/multiqc"
                }
            ]
        },
        {
            "@id": "#module/QUARTO_PREPARE/quarto_prepare",
            "@type": "SoftwareApplication",
            "name": "quarto_prepare",
            "description": "Prepare a Quarto notebook for runtime package-version capture"
        },
        {
            "@id": "#module/QUARTO_NOTEBOOK/quarto",
            "@type": "SoftwareApplication",
            "name": "quarto",
            "description": "An open-source scientific and technical publishing system."
        },
        {
            "@id": "#module/QUARTO_NOTEBOOK/papermill",
            "@type": "SoftwareApplication",
            "name": "papermill",
            "description": "Parameterize, execute, and analyze notebooks"
        },
        {
            "@id": "#module/REPORTENVIRONMENT/reportenvironment",
            "@type": "SoftwareApplication",
            "name": "reportenvironment",
            "description": "Collect the report process, container, R session information, and Python version"
        },
        {
            "@id": "#module/MD5SUM/md5sum",
            "@type": "SoftwareApplication",
            "name": "md5sum",
            "description": "Create MD5 (128-bit) checksums for each file"
        },
        {
            "@id": "#module/MULTIQC/multiqc",
            "@type": "SoftwareApplication",
            "name": "multiqc",
            "description": "MultiQC searches a given directory for analysis logs and compiles a HTML report.\nIt's a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n"
        },
        {
            "@id": "#param/input",
            "@type": "FormalParameter",
            "additionalType": "File",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "encodingFormat": "text/csv",
            "name": "input",
            "description": "Path to comma-separated file containing ids and file paths to include in the report."
        },
        {
            "@id": "#param/notebook",
            "@type": "FormalParameter",
            "additionalType": "File",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "notebook",
            "description": "Path to a Quarto notebook used to render the provenance report. If unset, the bundled default notebook is used."
        },
        {
            "@id": "#param/document",
            "@type": "FormalParameter",
            "additionalType": "File",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "encodingFormat": "text/markdown",
            "name": "document",
            "description": "Path to a documentation file to track that the provenance report has been reviewed."
        },
        {
            "@id": "#param/outdir",
            "@type": "FormalParameter",
            "additionalType": "Dataset",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "outdir",
            "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure."
        },
        {
            "@id": "#param/publish_dir_mode",
            "@type": "FormalParameter",
            "additionalType": "Text",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "publish_dir_mode",
            "defaultValue": "copy",
            "description": "Method used to save pipeline results to output directory."
        },
        {
            "@id": "#param/plaintext_email",
            "@type": "FormalParameter",
            "additionalType": "Boolean",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "plaintext_email",
            "description": "Send plain-text email instead of HTML."
        },
        {
            "@id": "#param/monochrome_logs",
            "@type": "FormalParameter",
            "additionalType": "Boolean",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "monochrome_logs",
            "description": "Do not use coloured log outputs."
        },
        {
            "@id": "#param/help",
            "@type": "FormalParameter",
            "additionalType": "Boolean",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "help",
            "description": "Display the help message."
        },
        {
            "@id": "#param/help_full",
            "@type": "FormalParameter",
            "additionalType": "Boolean",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "help_full",
            "description": "Display the full detailed help message."
        },
        {
            "@id": "#param/show_hidden",
            "@type": "FormalParameter",
            "additionalType": "Boolean",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "show_hidden",
            "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
        },
        {
            "@id": "#param/version",
            "@type": "FormalParameter",
            "additionalType": "Boolean",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "version",
            "description": "Display version and exit."
        },
        {
            "@id": "#param/pipelines_testdata_base_path",
            "@type": "FormalParameter",
            "additionalType": "Text",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "pipelines_testdata_base_path",
            "defaultValue": "https://raw.githubusercontent.com/nf-core/test-datasets/",
            "description": "Base URL or local path to location of pipeline test dataset files"
        },
        {
            "@id": "#param/trace_report_suffix",
            "@type": "FormalParameter",
            "additionalType": "Text",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "trace_report_suffix",
            "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss."
        },
        {
            "@id": "#param/config_profile_name",
            "@type": "FormalParameter",
            "additionalType": "Text",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "config_profile_name",
            "description": "Institutional config name."
        },
        {
            "@id": "#param/config_profile_description",
            "@type": "FormalParameter",
            "additionalType": "Text",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "config_profile_description",
            "description": "Institutional config description."
        },
        {
            "@id": "#param/custom_config_version",
            "@type": "FormalParameter",
            "additionalType": "Text",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "custom_config_version",
            "defaultValue": "master",
            "description": "Git commit id for Institutional configs."
        },
        {
            "@id": "#param/custom_config_base",
            "@type": "FormalParameter",
            "additionalType": "Text",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "custom_config_base",
            "defaultValue": "https://raw.githubusercontent.com/nf-core/configs/master",
            "description": "Base directory for Institutional configs."
        },
        {
            "@id": "#param/validate_params",
            "@type": "FormalParameter",
            "additionalType": "Boolean",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "validate_params",
            "defaultValue": true,
            "description": "Boolean whether to validate parameters against the schema at runtime"
        },
        {
            "@id": "#param/helpFull",
            "@type": "FormalParameter",
            "additionalType": "Boolean",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "helpFull"
        },
        {
            "@id": "#param/showHidden",
            "@type": "FormalParameter",
            "additionalType": "Boolean",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "showHidden"
        },
        {
            "@id": "#output/document",
            "@type": "FormalParameter",
            "additionalType": "File",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "encodingFormat": "text/csv",
            "name": "document"
        },
        {
            "@id": "#output/artifacts",
            "@type": "FormalParameter",
            "additionalType": "File",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "encodingFormat": "text/csv",
            "name": "artifacts"
        },
        {
            "@id": "#output/reports",
            "@type": "FormalParameter",
            "additionalType": "File",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "encodingFormat": "text/csv",
            "name": "reports"
        },
        {
            "@id": "#output/notebook",
            "@type": "FormalParameter",
            "additionalType": "File",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "encodingFormat": "text/csv",
            "name": "notebook"
        },
        {
            "@id": "#output/md5sum",
            "@type": "FormalParameter",
            "additionalType": "File",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "name": "md5sum"
        },
        {
            "@id": "#output/multiqc_report",
            "@type": "FormalParameter",
            "additionalType": "File",
            "conformsTo": {
                "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
            },
            "encodingFormat": "text/csv",
            "name": "multiqc_report"
        },
        {
            "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_PREPARE",
            "@type": "HowToStep",
            "workExample": {
                "@id": "#module/QUARTO_PREPARE"
            },
            "position": 1
        },
        {
            "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_NOTEBOOK",
            "@type": "HowToStep",
            "workExample": {
                "@id": "#module/QUARTO_NOTEBOOK"
            },
            "position": 2
        },
        {
            "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:REPORTENVIRONMENT",
            "@type": "HowToStep",
            "workExample": {
                "@id": "#module/REPORTENVIRONMENT"
            },
            "position": 3
        },
        {
            "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MD5SUM",
            "@type": "HowToStep",
            "workExample": {
                "@id": "#module/MD5SUM"
            },
            "position": 4
        },
        {
            "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MULTIQC",
            "@type": "HowToStep",
            "workExample": {
                "@id": "#module/MULTIQC"
            },
            "position": 5
        },
        {
            "@id": "main.nf#organize",
            "@type": "OrganizeAction",
            "agent": null,
            "instrument": {
                "@id": "main.nf#software-application"
            },
            "name": "Run of Nextflow 26.04.7",
            "object": [
                {
                    "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_PREPARE"
                },
                {
                    "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_NOTEBOOK"
                },
                {
                    "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:REPORTENVIRONMENT"
                },
                {
                    "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MD5SUM"
                },
                {
                    "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MULTIQC"
                }
            ],
            "result": {
                "@id": "#1724052d-e05b-4de8-a7aa-0dcdfb6d010a"
            },
            "startTime": "2026-10-21T17:40:57.309340703Z",
            "endTime": "2026-10-21T17:50:31.240793602Z"
        },
        {
            "@id": "#1724052d-e05b-4de8-a7aa-0dcdfb6d010a",
            "@type": "CreateAction",
            "agent": null,
            "name": "Nextflow workflow run 1724052d-e05b-4de8-a7aa-0dcdfb6d010a",
            "startTime": "2026-10-21T17:40:57.309340703Z",
            "endTime": "2026-10-21T17:50:31.240793602Z",
            "instrument": {
                "@id": "main.nf"
            },
            "object": [
                {
                    "@id": "#param/input/value"
                },
                {
                    "@id": "#param/notebook/value"
                },
                {
                    "@id": "#param/document/value"
                },
                {
                    "@id": "#param/outdir/value"
                },
                {
                    "@id": "#param/publish_dir_mode/value"
                },
                {
                    "@id": "#param/plaintext_email/value"
                },
                {
                    "@id": "#param/monochrome_logs/value"
                },
                {
                    "@id": "#param/help/value"
                },
                {
                    "@id": "#param/help_full/value"
                },
                {
                    "@id": "#param/show_hidden/value"
                },
                {
                    "@id": "#param/version/value"
                },
                {
                    "@id": "#param/pipelines_testdata_base_path/value"
                },
                {
                    "@id": "#param/trace_report_suffix/value"
                },
                {
                    "@id": "#param/config_profile_name/value"
                },
                {
                    "@id": "#param/config_profile_description/value"
                },
                {
                    "@id": "#param/custom_config_version/value"
                },
                {
                    "@id": "#param/custom_config_base/value"
                },
                {
                    "@id": "#param/validate_params/value"
                },
                {
                    "@id": "#param/helpFull/value"
                },
                {
                    "@id": "#param/showHidden/value"
                },
                {
                    "@id": "#output/document/value"
                },
                {
                    "@id": "#output/artifacts/value"
                },
                {
                    "@id": "#output/reports/value"
                },
                {
                    "@id": "#output/notebook/value"
                },
                {
                    "@id": "#output/md5sum/value"
                },
                {
                    "@id": "#output/multiqc_report/value"
                },
                {
                    "@id": "review_signoff.md"
                },
                {
                    "@id": "test_full_report.qmd"
                },
                {
                    "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv"
                },
                {
                    "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/nf-core-provenancereport_logo_light.png"
                },
                {
                    "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv"
                },
                {
                    "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/multiqc_config.yml"
                },
                {
                    "@id": "samplesheet.csv"
                },
                {
                    "@id": "test_full_report.qmd"
                },
                {
                    "@id": "review_signoff.md"
                }
            ],
            "result": [
                {
                    "@id": "review_signoff.md"
                },
                {
                    "@id": "multiqc_report.csv"
                },
                {
                    "@id": "quartonotebook/test_full_report.qmd"
                },
                {
                    "@id": "quartonotebook/test_full_report.html"
                },
                {
                    "@id": "quartonotebook/artifacts/test_full_summary.tsv"
                },
                {
                    "@id": "quartonotebook/prepared_test_full_report.qmd"
                },
                {
                    "@id": "md5sum/provenancereport.md5"
                },
                {
                    "@id": "multiqc/multiqc_report.html"
                },
                {
                    "@id": "multiqc/multiqc_data"
                }
            ]
        },
        {
            "@id": "https://spdx.org/licenses/MIT",
            "@type": "CreativeWork"
        },
        {
            "@id": "README.md",
            "@type": "File",
            "name": "README.md",
            "description": "The README file of the workflow.",
            "encodingFormat": "text/markdown"
        },
        {
            "@id": "nextflow_schema.json",
            "@type": "File",
            "name": "nextflow_schema.json",
            "description": "The parameter schema of the workflow.",
            "encodingFormat": "application/json"
        },
        {
            "@id": "nextflow.config",
            "@type": "File",
            "name": "Resolved Nextflow configuration",
            "description": "The resolved Nextflow configuration for the workflow run.",
            "encodingFormat": "text/plain"
        },
        {
            "@id": "#param/input/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/input"
            },
            "name": "input",
            "value": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/samplesheet.csv"
        },
        {
            "@id": "#param/notebook/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/notebook"
            },
            "name": "notebook",
            "value": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/test_full_report.qmd"
        },
        {
            "@id": "#param/document/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/document"
            },
            "name": "document",
            "value": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/tests/assets/review_signoff.md"
        },
        {
            "@id": "#param/outdir/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/outdir"
            },
            "name": "outdir",
            "value": "s3://nf-core-awsmegatests/provenancereport/results-89ed44de8da1788e5f00a6dd95bd72c51ff36dff"
        },
        {
            "@id": "#param/publish_dir_mode/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/publish_dir_mode"
            },
            "name": "publish_dir_mode",
            "value": "copy"
        },
        {
            "@id": "#param/plaintext_email/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/plaintext_email"
            },
            "name": "plaintext_email",
            "value": false
        },
        {
            "@id": "#param/monochrome_logs/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/monochrome_logs"
            },
            "name": "monochrome_logs",
            "value": false
        },
        {
            "@id": "#param/help/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/help"
            },
            "name": "help",
            "value": false
        },
        {
            "@id": "#param/help_full/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/help_full"
            },
            "name": "help_full",
            "value": false
        },
        {
            "@id": "#param/show_hidden/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/show_hidden"
            },
            "name": "show_hidden",
            "value": false
        },
        {
            "@id": "#param/version/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/version"
            },
            "name": "version",
            "value": false
        },
        {
            "@id": "#param/pipelines_testdata_base_path/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/pipelines_testdata_base_path"
            },
            "name": "pipelines_testdata_base_path",
            "value": "https://raw.githubusercontent.com/nf-core/test-datasets/"
        },
        {
            "@id": "#param/trace_report_suffix/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/trace_report_suffix"
            },
            "name": "trace_report_suffix",
            "value": "2026-10-21_17-40-47"
        },
        {
            "@id": "#param/config_profile_name/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/config_profile_name"
            },
            "name": "config_profile_name",
            "value": "Full test profile"
        },
        {
            "@id": "#param/config_profile_description/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/config_profile_description"
            },
            "name": "config_profile_description",
            "value": "Full representative test dataset with a custom notebook"
        },
        {
            "@id": "#param/custom_config_version/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/custom_config_version"
            },
            "name": "custom_config_version",
            "value": "master"
        },
        {
            "@id": "#param/custom_config_base/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/custom_config_base"
            },
            "name": "custom_config_base",
            "value": "https://raw.githubusercontent.com/nf-core/configs/master"
        },
        {
            "@id": "#param/validate_params/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/validate_params"
            },
            "name": "validate_params",
            "value": true
        },
        {
            "@id": "#param/helpFull/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/helpFull"
            },
            "name": "helpFull",
            "value": false
        },
        {
            "@id": "#param/showHidden/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#param/showHidden"
            },
            "name": "showHidden",
            "value": false
        },
        {
            "@id": "#output/document/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#output/document"
            },
            "name": "document",
            "value": "document.csv"
        },
        {
            "@id": "#output/artifacts/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#output/artifacts"
            },
            "name": "artifacts",
            "value": "artifacts.csv"
        },
        {
            "@id": "#output/reports/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#output/reports"
            },
            "name": "reports",
            "value": "reports.csv"
        },
        {
            "@id": "#output/notebook/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#output/notebook"
            },
            "name": "notebook",
            "value": "notebook.csv"
        },
        {
            "@id": "#output/md5sum/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#output/md5sum"
            },
            "name": "md5sum",
            "value": "md5sum/provenancereport.md5"
        },
        {
            "@id": "#output/multiqc_report/value",
            "@type": "PropertyValue",
            "exampleOfWork": {
                "@id": "#output/multiqc_report"
            },
            "name": "multiqc_report",
            "value": "multiqc_report.csv"
        },
        {
            "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_PREPARE",
            "@type": "ControlAction",
            "instrument": {
                "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_PREPARE"
            },
            "name": "Orchestrate process NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_PREPARE",
            "object": [
                {
                    "@id": "#task/844f614b9c13d637bce832e98bc157d2"
                }
            ]
        },
        {
            "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_NOTEBOOK",
            "@type": "ControlAction",
            "instrument": {
                "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_NOTEBOOK"
            },
            "name": "Orchestrate process NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_NOTEBOOK",
            "object": [
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d"
                }
            ]
        },
        {
            "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:REPORTENVIRONMENT",
            "@type": "ControlAction",
            "instrument": {
                "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:REPORTENVIRONMENT"
            },
            "name": "Orchestrate process NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:REPORTENVIRONMENT",
            "object": [
                {
                    "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa"
                }
            ]
        },
        {
            "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MD5SUM",
            "@type": "ControlAction",
            "instrument": {
                "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MD5SUM"
            },
            "name": "Orchestrate process NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MD5SUM",
            "object": [
                {
                    "@id": "#task/f5f6b9f0317275f8972e6c7c4f83ce14"
                }
            ]
        },
        {
            "@id": "#process-control/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MULTIQC",
            "@type": "ControlAction",
            "instrument": {
                "@id": "#process-step/NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MULTIQC"
            },
            "name": "Orchestrate process NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MULTIQC",
            "object": [
                {
                    "@id": "#task/2747a7b65e3400f5eff04e71962e8799"
                }
            ]
        },
        {
            "@id": "#tmp/methods_description_mqc.yaml",
            "@type": "CreativeWork",
            "name": "methods_description_mqc.yaml",
            "encodingFormat": "application/yaml"
        },
        {
            "@id": "#tmp/nf_core_provenancereport_software_mqc_versions.yml",
            "@type": "CreativeWork",
            "name": "nf_core_provenancereport_software_mqc_versions.yml",
            "encodingFormat": "application/yaml"
        },
        {
            "@id": "#tmp/pipeline_outputs_mqc.tsv",
            "@type": "CreativeWork",
            "name": "pipeline_outputs_mqc.tsv",
            "encodingFormat": "text/tab-separated-values"
        },
        {
            "@id": "#tmp/samplesheet.csv",
            "@type": "CreativeWork",
            "name": "samplesheet.csv",
            "encodingFormat": "text/csv"
        },
        {
            "@id": "#tmp/file_checksums_mqc.tsv",
            "@type": "CreativeWork",
            "name": "file_checksums_mqc.tsv",
            "encodingFormat": "text/tab-separated-values"
        },
        {
            "@id": "#tmp/workflow_summary_mqc.yaml",
            "@type": "CreativeWork",
            "name": "workflow_summary_mqc.yaml",
            "encodingFormat": "application/yaml"
        },
        {
            "@id": "#task/844f614b9c13d637bce832e98bc157d2",
            "@type": "CreateAction",
            "name": "NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_PREPARE (test_full_report)",
            "instrument": {
                "@id": "#module/QUARTO_PREPARE"
            },
            "agent": null,
            "object": [
                {
                    "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/test_full_report.qmd"
                }
            ],
            "result": [
                {
                    "@id": "#task/844f614b9c13d637bce832e98bc157d2/test_full_report.qmd"
                },
                {
                    "@id": "#task/844f614b9c13d637bce832e98bc157d2/prepared_test_full_report.qmd"
                }
            ],
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d",
            "@type": "CreateAction",
            "name": "NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:RENDER_QUARTO_WITH_PROVENANCE:QUARTO_NOTEBOOK (test_full_report)",
            "instrument": {
                "@id": "#module/QUARTO_NOTEBOOK"
            },
            "agent": null,
            "object": [
                {
                    "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv"
                },
                {
                    "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv"
                },
                {
                    "@id": "#task/844f614b9c13d637bce832e98bc157d2/prepared_test_full_report.qmd"
                }
            ],
            "result": [
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/test_full_report.html"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/prepared_test_full_report.qmd"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/params.yml"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/artifacts/test_full_summary.tsv"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/versions.yml"
                }
            ],
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa",
            "@type": "CreateAction",
            "name": "NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:REPORTENVIRONMENT (report runtime environment)",
            "instrument": {
                "@id": "#module/REPORTENVIRONMENT"
            },
            "agent": null,
            "object": [
                
            ],
            "result": [
                {
                    "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa/runtime_environment_mqc.tsv"
                },
                {
                    "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa/r_session_info_mqc.yaml"
                }
            ],
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#task/f5f6b9f0317275f8972e6c7c4f83ce14",
            "@type": "CreateAction",
            "name": "NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MD5SUM (provenancereport)",
            "instrument": {
                "@id": "#module/MD5SUM"
            },
            "agent": null,
            "object": [
                {
                    "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv"
                },
                {
                    "@id": "#task/844f614b9c13d637bce832e98bc157d2/test_full_report.qmd"
                },
                {
                    "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/test_full_report.html"
                },
                {
                    "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/tests/assets/review_signoff.md"
                },
                {
                    "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv"
                }
            ],
            "result": [
                {
                    "@id": "#task/f5f6b9f0317275f8972e6c7c4f83ce14/provenancereport.md5"
                }
            ],
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#task/2747a7b65e3400f5eff04e71962e8799",
            "@type": "CreateAction",
            "name": "NFCORE_PROVENANCEREPORT:PROVENANCEREPORT:MULTIQC (provenancereport)",
            "instrument": {
                "@id": "#module/MULTIQC"
            },
            "agent": null,
            "object": [
                {
                    "@id": "#tmp/workflow_summary_mqc.yaml"
                },
                {
                    "@id": "#tmp/methods_description_mqc.yaml"
                },
                {
                    "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/nf-core-provenancereport_logo_light.png"
                },
                {
                    "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/multiqc_config.yml"
                },
                {
                    "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa/r_session_info_mqc.yaml"
                },
                {
                    "@id": "#tmp/nf_core_provenancereport_software_mqc_versions.yml"
                },
                {
                    "@id": "#tmp/file_checksums_mqc.tsv"
                },
                {
                    "@id": "#tmp/pipeline_outputs_mqc.tsv"
                },
                {
                    "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa/runtime_environment_mqc.tsv"
                },
                {
                    "@id": "#tmp/samplesheet.csv"
                }
            ],
            "result": [
                {
                    "@id": "#task/2747a7b65e3400f5eff04e71962e8799/multiqc_report.html"
                },
                {
                    "@id": "#task/2747a7b65e3400f5eff04e71962e8799/multiqc_data"
                }
            ],
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#task/844f614b9c13d637bce832e98bc157d2/test_full_report.qmd",
            "@type": "CreativeWork",
            "name": "test_full_report.qmd"
        },
        {
            "@id": "#task/844f614b9c13d637bce832e98bc157d2/prepared_test_full_report.qmd",
            "@type": "CreativeWork",
            "name": "prepared_test_full_report.qmd"
        },
        {
            "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/test_full_report.html",
            "@type": "CreativeWork",
            "name": "test_full_report.html",
            "encodingFormat": "text/html"
        },
        {
            "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/prepared_test_full_report.qmd",
            "@type": "CreativeWork",
            "name": "prepared_test_full_report.qmd"
        },
        {
            "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/params.yml",
            "@type": "CreativeWork",
            "name": "params.yml",
            "encodingFormat": "application/yaml"
        },
        {
            "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/artifacts/test_full_summary.tsv",
            "@type": "CreativeWork",
            "name": "artifacts/test_full_summary.tsv",
            "encodingFormat": "text/tab-separated-values"
        },
        {
            "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/versions.yml",
            "@type": "CreativeWork",
            "name": "versions.yml",
            "encodingFormat": "application/yaml"
        },
        {
            "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa/runtime_environment_mqc.tsv",
            "@type": "CreativeWork",
            "name": "runtime_environment_mqc.tsv",
            "encodingFormat": "text/tab-separated-values"
        },
        {
            "@id": "#task/e4f3dd5153c3a5f1e2ff19b35788dafa/r_session_info_mqc.yaml",
            "@type": "CreativeWork",
            "name": "r_session_info_mqc.yaml",
            "encodingFormat": "application/yaml"
        },
        {
            "@id": "#task/f5f6b9f0317275f8972e6c7c4f83ce14/provenancereport.md5",
            "@type": "CreativeWork",
            "name": "provenancereport.md5"
        },
        {
            "@id": "#task/2747a7b65e3400f5eff04e71962e8799/multiqc_report.html",
            "@type": "CreativeWork",
            "name": "multiqc_report.html",
            "encodingFormat": "text/html"
        },
        {
            "@id": "#task/2747a7b65e3400f5eff04e71962e8799/multiqc_data",
            "@type": "CreativeWork",
            "name": "multiqc_data"
        },
        {
            "@id": "#publish/844f614b9c13d637bce832e98bc157d2/test_full_report.qmd",
            "@type": "CreateAction",
            "name": "publish",
            "instrument": {
                "@id": "main.nf#software-application"
            },
            "object": {
                "@id": "#task/844f614b9c13d637bce832e98bc157d2/test_full_report.qmd"
            },
            "result": {
                "@id": "quartonotebook/test_full_report.qmd"
            },
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#publish/4550c8ef87736d4e662a18ee4556ad2d/test_full_report.html",
            "@type": "CreateAction",
            "name": "publish",
            "instrument": {
                "@id": "main.nf#software-application"
            },
            "object": {
                "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/test_full_report.html"
            },
            "result": {
                "@id": "quartonotebook/test_full_report.html"
            },
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#publish/4550c8ef87736d4e662a18ee4556ad2d/artifacts/test_full_summary.tsv",
            "@type": "CreateAction",
            "name": "publish",
            "instrument": {
                "@id": "main.nf#software-application"
            },
            "object": {
                "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/artifacts/test_full_summary.tsv"
            },
            "result": {
                "@id": "quartonotebook/artifacts/test_full_summary.tsv"
            },
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#publish/4550c8ef87736d4e662a18ee4556ad2d/prepared_test_full_report.qmd",
            "@type": "CreateAction",
            "name": "publish",
            "instrument": {
                "@id": "main.nf#software-application"
            },
            "object": {
                "@id": "#task/4550c8ef87736d4e662a18ee4556ad2d/prepared_test_full_report.qmd"
            },
            "result": {
                "@id": "quartonotebook/prepared_test_full_report.qmd"
            },
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#publish/f5f6b9f0317275f8972e6c7c4f83ce14/provenancereport.md5",
            "@type": "CreateAction",
            "name": "publish",
            "instrument": {
                "@id": "main.nf#software-application"
            },
            "object": {
                "@id": "#task/f5f6b9f0317275f8972e6c7c4f83ce14/provenancereport.md5"
            },
            "result": {
                "@id": "md5sum/provenancereport.md5"
            },
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#publish/2747a7b65e3400f5eff04e71962e8799/multiqc_report.html",
            "@type": "CreateAction",
            "name": "publish",
            "instrument": {
                "@id": "main.nf#software-application"
            },
            "object": {
                "@id": "#task/2747a7b65e3400f5eff04e71962e8799/multiqc_report.html"
            },
            "result": {
                "@id": "multiqc/multiqc_report.html"
            },
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "#publish/2747a7b65e3400f5eff04e71962e8799/multiqc_data",
            "@type": "CreateAction",
            "name": "publish",
            "instrument": {
                "@id": "main.nf#software-application"
            },
            "object": {
                "@id": "#task/2747a7b65e3400f5eff04e71962e8799/multiqc_data"
            },
            "result": {
                "@id": "multiqc/multiqc_data"
            },
            "actionStatus": "http://schema.org/CompletedActionStatus"
        },
        {
            "@id": "review_signoff.md",
            "@type": "File",
            "name": "review_signoff.md",
            "encodingFormat": "text/markdown"
        },
        {
            "@id": "test_full_report.qmd",
            "@type": "File",
            "name": "test_full_report.qmd"
        },
        {
            "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv",
            "@type": "File",
            "name": "metadata.tsv",
            "encodingFormat": "text/tab-separated-values"
        },
        {
            "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/nf-core-provenancereport_logo_light.png",
            "@type": "File",
            "name": "nf-core-provenancereport_logo_light.png",
            "encodingFormat": "image/png"
        },
        {
            "@id": "https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv",
            "@type": "File",
            "name": "counts.tsv",
            "encodingFormat": "text/tab-separated-values"
        },
        {
            "@id": "https://github.com/nf-core/provenancereport/tree/89ed44de8da1788e5f00a6dd95bd72c51ff36dff/assets/multiqc_config.yml",
            "@type": "File",
            "name": "multiqc_config.yml",
            "encodingFormat": "application/yaml"
        },
        {
            "@id": "samplesheet.csv",
            "@type": "File",
            "description": "Input file specified by params.input",
            "encodingFormat": "text/csv"
        },
        {
            "@id": "test_full_report.qmd",
            "@type": "File",
            "description": "Input file specified by params.notebook"
        },
        {
            "@id": "review_signoff.md",
            "@type": "File",
            "description": "Input file specified by params.document",
            "encodingFormat": "text/markdown"
        },
        {
            "@id": "review_signoff.md",
            "@type": "File",
            "name": "review_signoff.md",
            "encodingFormat": "text/markdown"
        },
        {
            "@id": "multiqc_report.csv",
            "@type": "File",
            "name": "multiqc_report.csv",
            "encodingFormat": "text/csv"
        },
        {
            "@id": "quartonotebook/test_full_report.qmd",
            "@type": "File",
            "name": "test_full_report.qmd"
        },
        {
            "@id": "quartonotebook/test_full_report.html",
            "@type": "File",
            "name": "test_full_report.html",
            "encodingFormat": "text/html"
        },
        {
            "@id": "quartonotebook/artifacts/test_full_summary.tsv",
            "@type": "File",
            "name": "test_full_summary.tsv",
            "encodingFormat": "text/tab-separated-values"
        },
        {
            "@id": "quartonotebook/prepared_test_full_report.qmd",
            "@type": "File",
            "name": "prepared_test_full_report.qmd"
        },
        {
            "@id": "md5sum/provenancereport.md5",
            "@type": "File",
            "name": "provenancereport.md5"
        },
        {
            "@id": "multiqc/multiqc_report.html",
            "@type": "File",
            "name": "multiqc_report.html",
            "encodingFormat": "text/html"
        },
        {
            "@id": "multiqc/multiqc_data",
            "@type": "Dataset",
            "name": "multiqc_data"
        }
    ]
}