smallvariants

KO | EN

gitlite — search

#javascript #python #hacktoberfest #react #ai #typescript #llm #go #golang #android #machine-learning #rust #deep-learning #linux

(★ 13)

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

smallvariants Latest Version Download

Download Latest Version (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# nf-cmgg/smallvariants

[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-cmgg/smallvariants)
[![GitHub Actions CI Status](https://github.com/nf-cmgg/smallvariants/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-cmgg/smallvariants/actions/workflows/nf-test.yml)
[![GitHub Actions Linting Status](https://github.com/nf-cmgg/smallvariants/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/smallvariants/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
[![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 Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-cmgg/smallvariants)

## Introduction

**nf-cmgg/smallvariants** is a nextflow pipeline for calling and annotating small variants from short DNA reads for WES and WGS data.

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

Please have a look at the [documentation](https://nf-cmgg.github.io/smallvariants/latest/) on how to run the pipeline.

## Development environment

A [pixi](https://pixi.prefix.dev/latest/) development environment is available for this pipeline. Run the following command to install the environment:

```
pixi install
```

Then run `pixi shell` to enter the environment and start developing.

smallvariants

smallvariants Latest Version Download

Today's picks

Was this content helpful?

Recent Feedback

smallvariants

smallvariants Latest Version Download

Today's picks

Was this content helpful?

Recent Feedback

Download README