{

    "@context": [

        "https://w3id.org/ro/crate/1.1/context",

        {

            "GithubService": "https://w3id.org/ro/terms/test#GithubService",

            "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",

            "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",

            "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",

            "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",

            "TestService": "https://w3id.org/ro/terms/test#TestService",

            "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",

            "TravisService": "https://w3id.org/ro/terms/test#TravisService",

            "definition": "https://w3id.org/ro/terms/test#definition",

            "engineVersion": "https://w3id.org/ro/terms/test#engineVersion",

            "instance": "https://w3id.org/ro/terms/test#instance",

            "resource": "https://w3id.org/ro/terms/test#resource",

            "runsOn": "https://w3id.org/ro/terms/test#runsOn"

        }

    ],

    "@graph": [

        {

            "@id": "./",

            "@type": "Dataset",

            "creativeWorkStatus": "InProgress",

            "datePublished": "2025-01-27T14:45:57+00:00",

            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-deepmodeloptim_logo_dark.png\">\n    <img alt=\"nf-core/deepmodeloptim\" src=\"docs/images/nf-core-deepmodeloptim_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/deepmodeloptim/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/deepmodeloptim/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/deepmodeloptim/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/deepmodeloptim/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/deepmodeloptim/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/deepmodeloptim)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23deepmodeloptim-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/deepmodeloptim)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/deepmodeloptim** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/deepmodeloptim \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/deepmodeloptim/usage) and the [parameter documentation](https://nf-co.re/deepmodeloptim/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/deepmodeloptim/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/deepmodeloptim/output).\n\n## Credits\n\nnf-core/deepmodeloptim was originally written by Mathys Grapotte.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#deepmodeloptim` channel](https://nfcore.slack.com/channels/deepmodeloptim) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/deepmodeloptim for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",

            "hasPart": [

                {

                    "@id": "main.nf"

                },

                {

                    "@id": "assets/"

                },

                {

                    "@id": "conf/"

                },

                {

                    "@id": "docs/"

                },

                {

                    "@id": "docs/images/"

                },

                {

                    "@id": "workflows/"

                },

                {

                    "@id": "subworkflows/"

                },

                {

                    "@id": "nextflow.config"

                },

                {

                    "@id": "README.md"

                },

                {

                    "@id": "nextflow_schema.json"

                },

                {

                    "@id": "CHANGELOG.md"

                },

                {

                    "@id": "LICENSE"

                },

                {

                    "@id": "CODE_OF_CONDUCT.md"

                },

                {

                    "@id": "CITATIONS.md"

                },

                {

                    "@id": "modules.json"

                },

                {

                    "@id": "docs/usage.md"

                },

                {

                    "@id": "docs/output.md"

                },

                {

                    "@id": ".nf-core.yml"

                },

                {

                    "@id": ".pre-commit-config.yaml"

                },

                {

                    "@id": ".prettierignore"

                }

            ],

            "isBasedOn": "https://github.com/nf-core/deepmodeloptim",

            "license": "MIT",

            "mainEntity": {

                "@id": "main.nf"

            },

            "mentions": [

                {

                    "@id": "#9409a0dc-6aae-4911-8324-cd8f483edf4a"

                }

            ],

            "name": "nf-core/deepmodeloptim"

        },

        {

            "@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": "main.nf",

            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],

            "dateCreated": "",

            "dateModified": "2025-01-27T14:45:57Z",

            "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",

            "keywords": [

                "nf-core",

                "nextflow",

                "artificial-intelligence",

                "dataprocessing",

                "deeplearning",

                "genomics",

                "large-scale",

                "optimization",

                "prototyping-tool"

            ],

            "license": ["MIT"],

            "name": ["nf-core/deepmodeloptim"],

            "programmingLanguage": {

                "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"

            },

            "sdPublisher": {

                "@id": "https://nf-co.re/"

            },

            "url": ["https://github.com/nf-core/deepmodeloptim", "https://nf-co.re/deepmodeloptim/dev/"],

            "version": ["1.0.0dev"]

        },

        {

            "@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/"

            },

            "version": "!>=24.04.2"

        },

        {

            "@id": "#9409a0dc-6aae-4911-8324-cd8f483edf4a",

            "@type": "TestSuite",

            "instance": [

                {

                    "@id": "#1a6db2be-77de-4bd1-a2e0-b38728d1b764"

                }

            ],

            "mainEntity": {

                "@id": "main.nf"

            },

            "name": "Test suite for nf-core/deepmodeloptim"

        },

        {

            "@id": "#1a6db2be-77de-4bd1-a2e0-b38728d1b764",

            "@type": "TestInstance",

            "name": "GitHub Actions workflow for testing nf-core/deepmodeloptim",

            "resource": "repos/nf-core/deepmodeloptim/actions/workflows/ci.yml",

            "runsOn": {

                "@id": "https://w3id.org/ro/terms/test#GithubService"

            },

            "url": "https://api.github.com"

        },

        {

            "@id": "https://w3id.org/ro/terms/test#GithubService",

            "@type": "TestService",

            "name": "Github Actions",

            "url": {

                "@id": "https://github.com"

            }

        },

        {

            "@id": "assets/",

            "@type": "Dataset",

            "description": "Additional files"

        },

        {

            "@id": "conf/",

            "@type": "Dataset",

            "description": "Configuration files"

        },

        {

            "@id": "docs/",

            "@type": "Dataset",

            "description": "Markdown files for documenting the pipeline"

        },

        {

            "@id": "docs/images/",

            "@type": "Dataset",

            "description": "Images for the documentation files"

        },

        {

            "@id": "workflows/",

            "@type": "Dataset",

            "description": "Main pipeline workflows to be executed in main.nf"

        },

        {

            "@id": "subworkflows/",

            "@type": "Dataset",

            "description": "Smaller subworkflows"

        },

        {

            "@id": "nextflow.config",

            "@type": "File",

            "description": "Main Nextflow configuration file"

        },

        {

            "@id": "README.md",

            "@type": "File",

            "description": "Basic pipeline usage information"

        },

        {

            "@id": "nextflow_schema.json",

            "@type": "File",

            "description": "JSON schema for pipeline parameter specification"

        },

        {

            "@id": "CHANGELOG.md",

            "@type": "File",

            "description": "Information on changes made to the pipeline"

        },

        {

            "@id": "LICENSE",

            "@type": "File",

            "description": "The license - should be MIT"

        },

        {

            "@id": "CODE_OF_CONDUCT.md",

            "@type": "File",

            "description": "The nf-core code of conduct"

        },

        {

            "@id": "CITATIONS.md",

            "@type": "File",

            "description": "Citations needed when using the pipeline"

        },

        {

            "@id": "modules.json",

            "@type": "File",

            "description": "Version information for modules from nf-core/modules"

        },

        {

            "@id": "docs/usage.md",

            "@type": "File",

            "description": "Usage documentation"

        },

        {

            "@id": "docs/output.md",

            "@type": "File",

            "description": "Output documentation"

        },

        {

            "@id": ".nf-core.yml",

            "@type": "File",

            "description": "nf-core configuration file, configuring template features and linting rules"

        },

        {

            "@id": ".pre-commit-config.yaml",

            "@type": "File",

            "description": "Configuration file for pre-commit hooks"

        },

        {

            "@id": ".prettierignore",

            "@type": "File",

            "description": "Ignore file for prettier"

        },

        {

            "@id": "https://nf-co.re/",

            "@type": "Organization",

            "name": "nf-core",

            "url": "https://nf-co.re/"

        }

    ]

}