"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://github.com/nf-core/tools/releases/tag/3.3.1)\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://bsky.app/profile/nf-co.re)[](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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