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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": "2024-12-17T13:10:09+00:00",
"description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-demo_logo_dark.png\">\n <img alt=\"nf-core/demo\" src=\"docs/images/nf-core-demo_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/nf-core/demo/actions/workflows/ci.yml)\n[](https://github.com/nf-core/demo/actions/workflows/linting.yml)[](https://nf-co.re/demo/results)[](https://doi.org/10.5281/zenodo.12192442)\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/demo)\n\n[](https://nfcore.slack.com/channels/demo)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/demo** is a simple nf-core style bioinformatics pipeline for workshops and demonstrations. It was created using the nf-core template and is designed to run quickly using small test data files.\n\n\n\n1. Read QC ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter and quality trimming ([`SEQTK_TRIM`](https://github.com/lh3/seqtk))\n3. 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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nSAMPLE1_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz\nSAMPLE2_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,\nSAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/demo \\\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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Chris Hakkaart ([@christopher-hakkaart](https://github.com/christopher-hakkaart)).\n\n<!-- We thank the following people for their extensive assistance in the development of this pipeline: -->\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/demo for your analysis, please cite it using the following doi: [10.5281/zenodo.12192442](https://doi.org/10.5281/zenodo.12192442)\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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"isBasedOn": "https://github.com/nf-core/demo",
"license": "MIT",
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"name": "nf-core/demo"
},
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"about": {
"@id": "./"
},
"conformsTo": [
{
"@id": "https://w3id.org/ro/crate/1.1"
},
{
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}
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},
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"@id": "main.nf",
"@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
"creator": [
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"@id": "https://orcid.org/0000-0002-5599-5565"
}
],
"dateCreated": "",
"dateModified": "2024-12-17T14:10:09Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"keywords": ["nf-core", "nextflow", "demo", "minimal-example", "training", "tutorial"],
"license": ["MIT"],
"name": ["nf-core/demo"],
"programmingLanguage": {
"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
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"sdPublisher": {
"@id": "https://nf-co.re/"
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"url": ["https://github.com/nf-core/demo", "https://nf-co.re/demo/dev/"],
"version": ["1.1.0dev"]
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"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
"@type": "ComputerLanguage",
"identifier": {
"@id": "https://www.nextflow.io/"
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"name": "Nextflow",
"url": {
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"version": "!>=24.04.2"
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"name": "Test suite for nf-core/demo"
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"resource": "repos/nf-core/demo/actions/workflows/ci.yml",
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"url": {
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{
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"@type": "Dataset",
"description": "Additional files"
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"description": "Configuration files"
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"@type": "Dataset",
"description": "Markdown files for documenting the pipeline"
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{
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"@type": "Dataset",
"description": "Images for the documentation files"
},
{
"@id": "modules/",
"@type": "Dataset",
"description": "Modules used by the pipeline"
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"@type": "Dataset",
"description": "nf-core modules"
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{
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"@type": "Dataset",
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"@type": "File",
"description": "Information on changes made to the pipeline"
},
{
"@id": "LICENSE",
"@type": "File",
"description": "The license - should be MIT"
},
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"@type": "File",
"description": "The nf-core code of conduct"
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"@type": "File",
"description": "nf-core configuration file, configuring template features and linting rules"
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"name": "nf-core",
"url": "https://nf-co.re/"
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{
"@id": "https://orcid.org/0000-0002-5599-5565",
"@type": "Person",
"email": "[email protected]",
"name": "Matthias H\u00f6rtenhuber"
}
]
}