https://github.com/becavin-lab/nf-core-checkatlas

One liner tool to check the quality of your single-cell atlases.
https://github.com/becavin-lab/nf-core-checkatlas

Last synced: about 2 months ago
JSON representation

One liner tool to check the quality of your single-cell atlases.

• Host: GitHub
• URL: https://github.com/becavin-lab/nf-core-checkatlas
• Owner: becavin-lab
• License: mit
• Created: 2023-07-07T12:53:08.000Z (almost 3 years ago)
• Default Branch: TEMPLATE
• Last Pushed: 2025-07-07T14:51:30.000Z (11 months ago)
• Last Synced: 2025-09-05T07:51:52.557Z (9 months ago)
• Language: Nextflow
• Size: 2.3 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md
  • Citation: CITATIONS.md

Awesome Lists containing this project

README

          
# ![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)

[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=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)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)

[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)

[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

[![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)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23checkatlas-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/checkatlas)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)

## Introduction

**nf-core/checkatlas** is a bioinformatics pipeline that ...

1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))

2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))

## Usage

> **Note**

> 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.

Now, you can run the pipeline using:

```bash

nextflow run nf-core/checkatlas \

   -profile  \

   --input samplesheet.csv \

   --outdir 

```

> **Warning:**

> 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/usage/configuration#custom-configuration-files).

For 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).

## Pipeline output

To 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.

For more details about the output files and reports, please refer to the

[output documentation](https://nf-co.re/checkatlas/output).

## Credits

nf-core/checkatlas was originally written by Christophe Bécavin.

We thank the following people for their extensive assistance in the development of this pipeline:

## Contributions and Support

If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).

For 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)).

## Citations

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

You can cite the `nf-core` publication as follows:

> **The nf-core framework for community-curated bioinformatics pipelines.**

>

> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

>

> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).