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ro-crate-metadata.json
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{
"@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@id": "./",
"@type": "Dataset",
"creativeWorkStatus": "Stable",
"datePublished": "2025-02-12T05:24:37+00:00",
"description": "# CDCgov/aquascope\n\n## Introduction\n\n**CDCgov/aquascope** 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. \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 CDCgov/aquascope \\\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\n## Credits\n\nCDCgov/aquascope was originally written by S. Sevilla.\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\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 CDCgov/aquascope 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\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\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": "workflows/"
},
{
"@id": "subworkflows/"
},
{
"@id": "nextflow.config"
},
{
"@id": "README.md"
},
{
"@id": "nextflow_schema.json"
},
{
"@id": "CHANGELOG.md"
},
{
"@id": "CITATIONS.md"
},
{
"@id": "modules.json"
},
{
"@id": ".nf-core.yml"
},
{
"@id": ".pre-commit-config.yaml"
},
{
"@id": ".prettierignore"
}
],
"isBasedOn": "https://github.com/CDCgov/aquascope",
"mainEntity": {
"@id": "main.nf"
},
"name": "CDCgov/aquascope"
},
{
"@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": "2025-02-12T00:24:37Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"keywords": [
"nf-core",
"nextflow"
],
"license": [
null
],
"name": [
"CDCgov/aquascope"
],
"programmingLanguage": {
"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
},
"sdPublisher": {
"@id": "https://nf-co.re/"
},
"url": [
"https://github.com/CDCgov/aquascope",
"https://nf-co.re/CDCgov/aquascope/4.0.0/"
],
"version": [
"4.0.0"
]
},
{
"@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": "assets/",
"@type": "Dataset",
"description": "Additional files"
},
{
"@id": "conf/",
"@type": "Dataset",
"description": "Configuration 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": "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": ".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/"
}
]
}