{"id":48624388,"url":"https://github.com/becavin-lab/nf-core-checkatlas","last_synced_at":"2026-04-09T04:13:18.705Z","repository":{"id":179466578,"uuid":"663503590","full_name":"becavin-lab/nf-core-checkatlas","owner":"becavin-lab","description":"One liner tool to check the quality of your single-cell 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![nf-core/checkatlas](docs/images/nf-core-checkatlas_logo_light.png#gh-light-mode-only) ![nf-core/checkatlas](docs/images/nf-core-checkatlas_logo_dark.png#gh-dark-mode-only)\n\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000\u0026logo=Amazon%20AWS)](https://nf-co.re/checkatlas/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\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000\u0026logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000\u0026logo=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 Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/checkatlas)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23checkatlas-4A154B?labelColor=000000\u0026logo=slack)](https://nfcore.slack.com/channels/checkatlas)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000\u0026logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF\u0026logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000\u0026logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/checkatlas** is a bioinformatics pipeline that ...\n\n\u003c!-- 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--\u003e\n\n\u003c!-- 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.   --\u003e\n\u003c!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline --\u003e\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n\u003e **Note**\n\u003e If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how\n\u003e to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)\n\u003e with `-profile test` before running the workflow on actual data.\n\n\u003c!-- 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--\u003e\n\nNow, you can run the pipeline using:\n\n\u003c!-- TODO nf-core: update the following command to include all required parameters for a minimal example --\u003e\n\n```bash\nnextflow run nf-core/checkatlas \\\n   -profile \u003cdocker/singularity/.../institute\u003e \\\n   --input samplesheet.csv \\\n   --outdir \u003cOUTDIR\u003e\n```\n\n\u003e **Warning:**\n\u003e Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those\n\u003e provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;\n\u003e see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/checkatlas/usage) and the [parameter documentation](https://nf-co.re/checkatlas/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/checkatlas/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/checkatlas/output).\n\n## Credits\n\nnf-core/checkatlas was originally written by Christophe Bécavin.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\u003c!-- TODO nf-core: If applicable, make list of people who have also contributed --\u003e\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 `#checkatlas` channel](https://nfcore.slack.com/channels/checkatlas) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\u003c!-- 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. --\u003e\n\u003c!-- If you use  nf-core/checkatlas for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --\u003e\n\n\u003c!-- TODO nf-core: Add bibliography of tools and data used in your pipeline --\u003e\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\u003e **The nf-core framework for community-curated bioinformatics pipelines.**\n\u003e\n\u003e Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso \u0026 Sven Nahnsen.\n\u003e\n\u003e _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecavin-lab%2Fnf-core-checkatlas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecavin-lab%2Fnf-core-checkatlas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecavin-lab%2Fnf-core-checkatlas/lists"}