https://github.com/mskcc/bravo

https://github.com/mskcc/bravo

Last synced: about 1 month ago
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• Host: GitHub
• URL: https://github.com/mskcc/bravo
• Owner: mskcc
• License: mit
• Created: 2023-12-14T20:54:23.000Z (about 1 year ago)
• Default Branch: dev
• Last Pushed: 2023-12-19T16:13:55.000Z (about 1 year ago)
• Last Synced: 2023-12-20T08:39:52.263Z (about 1 year ago)
• Language: Nextflow
• Size: 2.02 MB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Citation: CITATIONS.md

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README

        
## Introduction

**mskcc/bravo** is a bioinformatics pipeline that ...

## 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 mskcc/bravo \

   -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).

## Credits

mskcc/bravo was originally written by C. Allan Bolipata.

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).

## Citations

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

This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).

> **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).