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ro-crate-metadata.json
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{
"@context": [
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{
"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"
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"datePublished": "2024-12-20T13:12:56+00:00",
"description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialvi_logo_dark.png\">\n <img alt=\"nf-core/spatialvi\" src=\"docs/images/nf-core-spatialvi_logo_light.png\">\n </picture>\n</h1>[](https://github.com/nf-core/spatialvi/actions/workflows/ci.yml)\n[](https://github.com/nf-core/spatialvi/actions/workflows/linting.yml)[](https://nf-co.re/spatialvi/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/spatialvi)\n\n[](https://nfcore.slack.com/channels/spatialvi)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/spatialvi** 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 -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\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/spatialvi \\\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/spatialvi/usage) and the [parameter documentation](https://nf-co.re/spatialvi/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/spatialvi/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/spatialvi/output).\n\n## Credits\n\nnf-core/spatialvi was originally written by Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj Srivastava.\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 `#spatialvi` channel](https://nfcore.slack.com/channels/spatialvi) (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/spatialvi for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --><!-- 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",
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"name": "nf-core/spatialvi"
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"dateCreated": "",
"dateModified": "2024-12-20T13:12:56Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
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"resource": "repos/nf-core/spatialvi/actions/workflows/ci.yml",
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"url": {
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{
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"@type": "Dataset",
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"@type": "Dataset",
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{
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"description": "Smaller subworkflows"
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{
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"description": "Main Nextflow configuration file"
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{
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"@type": "File",
"description": "Basic pipeline usage information"
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{
"@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"
},
{
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"description": "Ignore file for prettier"
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{
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"@type": "Organization",
"name": "nf-core",
"url": "https://nf-co.re/"
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"@type": "Person",
"email": "[email protected]",
"name": "Sergii Domanskyi"
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"@type": "Person",
"email": "[email protected]",
"name": "Erik Fasterius"
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