{
  "@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"
        },
        {
          "@id": "https://www.researchobject.org/ro-crate/1.2-DRAFT/profiles"
        }
      ],
      "about": {
        "@id": "./"
      },
      "creator": {
        "@id": "https://orcid.org/0000-0001-9842-9718"
      },
      "license": {
        "@id": "http://spdx.org/licenses/CC0-1.0"
      }
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "author": [
        {
          "@id": "https://orcid.org/0000-0002-0048-3300"
        },
        {
          "@id": "https://orcid.org/0000-0003-3156-2105"
        },
        {
          "@id": "https://orcid.org/0000-0003-2130-0865"
        },
        {
          "@id": "https://orcid.org/0000-0001-9842-9718"
        }
      ],
      "datePublished": "2023-03-13T10:43:00Z",
      "description": "This is the Profile Crate for Workflow RO-Crate. Workflow RO-Crates are a specialization of RO-Crate for packaging an executable workflow with all necessary documentation. It is aligned with, and intends to strictly extend, the more general Bioschemas ComputationalWorkflow profile.\n\nWorkflowHub uses Workflow RO-Crates as an exchange format for users to upload a packaged workflow.",
      "hasPart": [
        {
          "@id": "index.html"
        },
        {
          "@id": "https://w3id.org/ro/crate/1.1/context"
        },
        {
          "@id": "https://bioschemas.org/ComputationalWorkflow"
        },
        {
          "@id": "https://bioschemas.org/FormalParameter"
        },
        {
          "@id": "http://schema.org/ImageObject"
        },
        {
          "@id": "http://schema.org/HowTo"
        },
        {
          "@id": "licenses/"
        },
        {
          "@id": "languages/"
        },
        {
          "@id": "example/"
        }
      ],
      "mentions": [
        {
          "@id": "https://workflowhub.eu/"
        },
        {
          "@id": "https://pypi.org/project/rocrate/"
        },
        {
          "@id": "https://github.com/inab/WfExS-backend/"
        },
        {
          "@id": "https://github.com/KockataEPich/CheckMyCrate/blob/master/CheckMyCrate/profile_library/ro_crate_1.1_basic.json"
        }
      ],
      "identifier": "https://w3id.org/workflowhub/workflow-ro-crate/1.0",
      "license": {
        "@id": "https://spdx.org/licenses/BSD-3-Clause"
      },
      "name": "Workflow RO-Crate profile",
      "publisher": {
        "@id": "https://w3id.org/workflowhub/"
      },
      "sameAs": {
        "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
      },
      "subjectOf": {
        "@id": "ro-crate-preview.html"
      },
      "version": "1.0.3",
      "workExample": {
        "@id": "example/"
      }
    },
    {
      "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0",
      "@type": "Guide",
      "name": "Workflow RO-Crate profile recommendations",
      "hasPart": [
        {
          "@id": "#use-zip"
        },
        {
          "@id": "#include-ComputationalWorkflow"
        },
        {
          "@id": "#comply-ComputationalWorkflow"
        },
        {
          "@id": "#include-HowTo"
        },
        {
          "@id": "#include-ImageObject"
        }
      ]
    },
    {
      "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl",
      "@type": "ComputerLanguage",
      "alternateName": "CWL",
      "identifier": {
        "@id": "https://w3id.org/cwl/v1.0/"
      },
      "name": "Common Workflow Language",
      "url": {
        "@id": "https://www.commonwl.org/"
      }
    },
    {
      "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy",
      "@type": "ComputerLanguage",
      "identifier": {
        "@id": "https://galaxyproject.org/"
      },
      "name": "Galaxy",
      "url": {
        "@id": "https://galaxyproject.org/"
      }
    },
    {
      "@id": "https://w3id.org/workflowhub/workflow-ro-crate#knime",
      "@type": "ComputerLanguage",
      "identifier": {
        "@id": "https://www.knime.com/"
      },
      "name": "KNIME",
      "url": {
        "@id": "https://www.knime.com/"
      }
    },
    {
      "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
      "@type": "ComputerLanguage",
      "identifier": {
        "@id": "https://www.nextflow.io/"
      },
      "name": "Nextflow",
      "url": {
        "@id": "https://www.nextflow.io/"
      }
    },
    {
      "@id": "https://w3id.org/workflowhub/workflow-ro-crate#snakemake",
      "@type": "ComputerLanguage",
      "identifier": {
        "@id": "https://doi.org/10.1093/bioinformatics/bts480"
      },
      "name": "Snakemake",
      "url": {
        "@id": "https://snakemake.readthedocs.io"
      }
    },
    {
      "@id": "#use-zip",
      "@type": "Recommendation",
      "name": "Use ZIP format",
      "category": "MUST",
      "itemReviewed": {
        "@id": "https://www.nationalarchives.gov.uk/PRONOM/x-fmt/263"
      },
      "reviewBody": "The Workflow RO-Crate MUST be zipped, and SHOULD have the file extension .crate.zip to be recognized by WorkflowHub. The ro-crate-metadata.json file SHOULD be directly in the root of the zip archive, so that the whole Zip becomes the RO-Crate Root"
    },
    {
      "@id": "#comply-ComputationalWorkflow",
      "@type": "Recommendation",
      "name": "Comply with ComputationalWorkflow profile",
      "category": "SHOULD",
      "itemReviewed": {
        "@id": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE"
      },
      "reviewBody": "The ComputationalWorkflow description of the Main Workflow SHOULD comply with Bioschemas ComputationalWorkflow profile version 1.0 or later.\n\nConformance with the Bioschemas profile SHOULD be indicated with a \"conformsTo\" on the Main Workflow entity."
    },
    {
      "@id": "#include-ComputationalWorkflow",
      "@type": "Recommendation",
      "category": "MUST",
      "name": "Include Main Workflow",
      "reviewBody": "The Crate MUST contain a data entity of type [\"File\", \"SoftwareSourceCode\", \"ComputationalWorkflow\"] as the Main Workflow.\n\nThe Crate MUST refer to the Main Workflow via \"mainEntity\".\n\nThe Main Workflow MUST refer to its type via \"programmingLanguage\".",
      "itemReviewed": {
        "@id": "https://bioschemas.org/ComputationalWorkflow"
      }
    },
    {
      "@id": "#include-HowTo",
      "@type": "Recommendation",
      "name": "Include Main Workflow CWL description",
      "category": "COULD",
      "itemReviewed": {
        "@id": "http://schema.org/HowTo"
      },
      "reviewBody": "The Crate COULD contain a data entity of type [\"File\", \"SoftwareSourceCode\", \"HowTo\"] as the Main Workflow CWL Description.\n\nIf present the Main Workflow MUST refer to the Main Workflow CWL Description via \"subjectOf\"."
    },
    {
      "@id": "#include-ImageObject",
      "@type": "Recommendation",
      "name": "Include Main Workflow Diagram",
      "category": "COULD",
      "itemReviewed": {
        "@id": "http://schema.org/ImageObject"
      },
      "reviewBody": "The Crate COULD contain a Main Workflow Diagram. If Main Workflow Diagram is present, the Main Workflow MUST refer to it via \"image\"."
    },
    {
      "@id": "example/",
      "@type": "Dataset",
      "name": "Example RO-Crate following this profile",
      "license": {
        "@id": "http://spdx.org/licenses/CC0-1.0"
      },
      "subjectOf": [
        {
          "@id": "example/ro-crate-metadata.json"
        },
        {
          "@id": "example/ro-crate-preview.html"
        }
      ]
    },
    {
      "@id": "example/ro-crate-preview.html",
      "@type": "CreativeWork",
      "name": "Preview of example RO-Crate",
      "encodingFormat": "text/html"
    },
    {
      "@id": "ro-crate-preview.html",
      "@type": "CreativeWork",
      "name": "Preview of Workflow RO-Crate",
      "encodingFormat": "text/html",
      "about": "./"
    },
    {
      "@id": "https://www.researchobject.org/ro-crate/1.2-DRAFT/profiles",
      "@type": "Guide",
      "name": "Profile Crate",
      "version": "1.2-DRAFT"
    },
    {
      "@id": "example/ro-crate-metadata.json",
      "@type": "CreativeWork",
      "conformsTo": [
        {"@id": "https://w3id.org/ro/crate/1.1"}, 
        {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}
      ],
      "encodingFormat": "application/json",
      "license": {
        "@id": "http://spdx.org/licenses/CC0-1.0"
      }
    },
    {
      "@id": "index.html",
      "@type": "File",
      "mainEntity": {
        "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
      },
      "author": [
        {
          "@id": "https://orcid.org/0000-0002-0048-3300"
        },
        {
          "@id": "https://orcid.org/0000-0003-3156-2105"
        },
        {
          "@id": "https://orcid.org/0000-0003-2130-0865"
        },
        {
          "@id": "https://orcid.org/0000-0001-9842-9718"
        }        
      ],
      "dateModified": "2024-03-13T10:43:00.000Z",
      "name": "Workflow RO-Crate profile description"
    },
    {
      "@id": "languages/",
      "@type": "Dataset",
      "category": "SHOULD",
      "description": "WorkflowHub currently supports CWL, Galaxy, KNIME and Nextflow workflow types. \n\n To ensure compatibility, please include one of the following in the RO-Crate metadata, and refer to it from the Main Workflow's programmingLanguage property",
      "hasPart": [
        {
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl"
        },
        {
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy"
        },
        {
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate#knime"
        },
        {
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
        },
        {
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate#snakemake"
        }
      ],
      "name": "languages"
    },
    {
      "@id": "licenses/",
      "@type": "Dataset",
      "description": "Although the Crate's license field should be a URL, WorkflowHub currently accepts a string from the \"identifier\" field of one of the following licenses:",
      "hasPart": [
        {
          "@id": "http://spdx.org/licenses/AFL-3.0"
        },
        {
          "@id": "http://spdx.org/licenses/APL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/Apache-1.1"
        },
        {
          "@id": "http://spdx.org/licenses/Apache-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/APSL-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/Artistic-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/AAL"
        },
        {
          "@id": "http://spdx.org/licenses/BSD-2-Clause"
        },
        {
          "@id": "http://spdx.org/licenses/BSD-3-Clause"
        },
        {
          "@id": "http://spdx.org/licenses/BitTorrent-1.1"
        },
        {
          "@id": "http://spdx.org/licenses/BSL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/CC0-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/CNRI-Python"
        },
        {
          "@id": "http://spdx.org/licenses/CUA-OPL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/CECILL-2.1"
        },
        {
          "@id": "http://spdx.org/licenses/CDDL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/CPAL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/CATOSL-1.1"
        },
        {
          "@id": "http://spdx.org/licenses/EUDatagrid"
        },
        {
          "@id": "http://spdx.org/licenses/EPL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/ECL-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/EFL-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/Entessa"
        },
        {
          "@id": "http://spdx.org/licenses/EUPL-1.1"
        },
        {
          "@id": "http://spdx.org/licenses/Fair"
        },
        {
          "@id": "http://spdx.org/licenses/Frameworx-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/AGPL-3.0"
        },
        {
          "@id": "http://spdx.org/licenses/GPL-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/GPL-3.0"
        },
        {
          "@id": "http://spdx.org/licenses/LGPL-2.1"
        },
        {
          "@id": "http://spdx.org/licenses/LGPL-3.0"
        },
        {
          "@id": "http://spdx.org/licenses/HPND"
        },
        {
          "@id": "http://spdx.org/licenses/IPL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/IPA"
        },
        {
          "@id": "http://spdx.org/licenses/ISC"
        },
        {
          "@id": "http://spdx.org/licenses/Intel"
        },
        {
          "@id": "http://spdx.org/licenses/LPPL-1.3c"
        },
        {
          "@id": "http://spdx.org/licenses/LPL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/LPL-1.02"
        },
        {
          "@id": "http://spdx.org/licenses/MIT"
        },
        {
          "@id": "http://spdx.org/licenses/mitre"
        },
        {
          "@id": "http://spdx.org/licenses/MS-PL"
        },
        {
          "@id": "http://spdx.org/licenses/MS-RL"
        },
        {
          "@id": "http://spdx.org/licenses/MirOS"
        },
        {
          "@id": "http://spdx.org/licenses/Motosoto"
        },
        {
          "@id": "http://spdx.org/licenses/MPL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/MPL-1.1"
        },
        {
          "@id": "http://spdx.org/licenses/MPL-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/Multics"
        },
        {
          "@id": "http://spdx.org/licenses/NASA-1.3"
        },
        {
          "@id": "http://spdx.org/licenses/NTP"
        },
        {
          "@id": "http://spdx.org/licenses/Naumen"
        },
        {
          "@id": "http://spdx.org/licenses/NGPL"
        },
        {
          "@id": "http://spdx.org/licenses/Nokia"
        },
        {
          "@id": "http://spdx.org/licenses/NPOSL-3.0"
        },
        {
          "@id": "http://spdx.org/licenses/OCLC-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/OFL-1.1"
        },
        {
          "@id": "http://spdx.org/licenses/OGL-UK-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/OGL-UK-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/OGL-UK-3.0"
        },
        {
          "@id": "http://spdx.org/licenses/OGTSL"
        },
        {
          "@id": "http://spdx.org/licenses/OSL-3.0"
        },
        {
          "@id": "http://spdx.org/licenses/PHP-3.0"
        },
        {
          "@id": "http://spdx.org/licenses/PostgreSQL"
        },
        {
          "@id": "http://spdx.org/licenses/Python-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/QPL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/RPSL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/RPL-1.5"
        },
        {
          "@id": "http://spdx.org/licenses/RSCPL"
        },
        {
          "@id": "http://spdx.org/licenses/SimPL-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/Sleepycat"
        },
        {
          "@id": "http://spdx.org/licenses/SISSL"
        },
        {
          "@id": "http://spdx.org/licenses/SPL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/Watcom-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/NCSA"
        },
        {
          "@id": "http://spdx.org/licenses/Unlicense"
        },
        {
          "@id": "http://spdx.org/licenses/VSL-1.0"
        },
        {
          "@id": "http://spdx.org/licenses/W3C"
        },
        {
          "@id": "http://spdx.org/licenses/Xnet"
        },
        {
          "@id": "http://spdx.org/licenses/ZPL-2.0"
        },
        {
          "@id": "http://spdx.org/licenses/WXwindows"
        },
        {
          "@id": "http://spdx.org/licenses/Zlib"
        },
        {
          "@id": "http://spdx.org/licenses/notspecified"
        }
      ],
      "name": "licenses"
    },
    {
      "@id": "https://orcid.org/0000-0001-9842-9718",
      "@type": "Person",
      "name": "Stian Soiland-Reyes"
    },
    {
      "@id": "https://orcid.org/0000-0002-0048-3300",
      "@type": "Person",
      "name": "Finn Bacall"
    },
    {
      "@id": "https://orcid.org/0000-0003-2130-0865",
      "@type": "Person",
      "name": "Stuart Owen"
    },
    {
      "@id": "https://orcid.org/0000-0003-3156-2105",
      "@type": "Person",
      "name": "Alan R Williams"
    },
    {
      "@id": "https://pypi.org/project/rocrate/",
      "@type": "SoftwareApplication",
      "description": "Python library to create/parse RO-Crate (Research Object Crate) metadata.",
      "identifier": "https://doi.org/10.5281/zenodo.5653266",
      "name": "ro-crate-py",
      "url": "https://pypi.org/project/rocrate/",
      "version": "0.5.0"
    },
    {
      "@id": "https://spdx.org/licenses/BSD-3-Clause",
      "@type": "CreativeWork",
      "description": "BSD 3-Clause License\n\nCopyright (c) 2019-2020, The University of Manchester, HITS gGmbH and workflowhub.eu contributors\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n1. Redistributions of source code must retain the above copyright notice, this\n   list of conditions and the following disclaimer.\n\n2. Redistributions in binary form must reproduce the above copyright notice,\n   this list of conditions and the following disclaimer in the documentation\n   and/or other materials provided with the distribution.\n\n3. Neither the name of the copyright holder nor the names of its\n   contributors may be used to endorse or promote products derived from\n   this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n",
      "identifier": "BSD-3-Clause",
      "name": "BSD 3-Clause \"New\" or \"Revised\" License"
    },
    {
      "@id": "https://w3id.org/ro/crate/1.1",
      "@type": "Guide",
      "name": "RO-Crate specification",
      "version": "1.1.1"
    },
    {
      "@id": "https://w3id.org/ro/crate/1.1/context",
      "@type": "CreativeWork",
      "encodingFormat": [
        "application/ld+json",
        {
          "@id": "http://www.w3.org/ns/json-ld#Context"
        }
      ],
      "name": "RO-Crate JSON-LD Context",
      "version": "1.1.1"
    },
    {
      "@id": "https://workflowhub.eu/",
      "@type": "RepositoryCollection",
      "description": "WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows.",
      "name": "WorkflowHub",
      "publisher": {
        "@id": "https://w3id.org/workflowhub/"
      },
      "title": "WorkflowHub"
    },
    {
      "@id": "https://www.nationalarchives.gov.uk/PRONOM/x-fmt/263",
      "@type": "DefinedTerm",
      "name": "ZIP Format"
    },
    {
      "@id": "http://schema.org/HowTo",
      "@type": "DefinedTerm",
      "description": "Instructions that explain how to achieve a result by performing a sequence of steps.",
      "name": "HowTo",
      "termCode": "HowTo"
    },
    {
      "@id": "http://schema.org/ImageObject",
      "@type": "DefinedTerm",
      "description": "An image file",
      "name": "ImageObject",
      "termCode": "ImageObject"
    },
    {
      "@id": "http://spdx.org/licenses/AAL", 
      "@type": "DefinedTerm",
      "termCode": "AAL",
      "identifier": "AAL",
      "name": "Attribution Assurance Licenses",
      "url": "https://opensource.org/licenses/AAL"
    },
    {
      "@id": "http://spdx.org/licenses/AFL-3.0", 
      "@type": "DefinedTerm",
      "termCode": "AFL-3.0", 
      "identifier": "AFL-3.0",
      "name": "Academic Free License 3.0",
      "url": "https://opensource.org/licenses/AFL-3.0"
    },
    {
      "@id": "http://spdx.org/licenses/AGPL-3.0", 
      "@type": "DefinedTerm",
      "termCode": "AGPL-3.0",
      "identifier": "AGPL-3.0",
      "name": "GNU Affero General Public License v3",
      "url": "https://opensource.org/licenses/AGPL-3.0"
    },
    {
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}