https://github.com/mskcc/tempo

CCS research pipeline to process WES and WGS TN pairs
https://github.com/mskcc/tempo

Last synced: about 1 month ago
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CCS research pipeline to process WES and WGS TN pairs

• Host: GitHub
• URL: https://github.com/mskcc/tempo
• Owner: mskcc
• Created: 2019-01-18T22:18:51.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-11-07T16:13:27.000Z (about 1 month ago)
• Last Synced: 2024-11-07T17:26:13.888Z (about 1 month ago)
• Language: Groovy
• Homepage: https://cmotempo.netlify.app/
• Size: 30.5 MB
• Stars: 12
• Watchers: 19
• Forks: 5
• Open Issues: 56
• Metadata Files:
  • Readme: README.md
  • Contributing: docs/contributing-to-tempo.md

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README

        
[![Build Status](https://travis-ci.com/mskcc/tempo.svg?token=DokCkCiDp43sqzeuXUHD&branch=master)](https://travis-ci.com/mskcc/tempo)

#  TEMPO

Tempo is a CMO Computational Sciences (CCS) research pipeline processing WES & WGS tumor-normal pairs using the [Nextflow framework](https://www.nextflow.io/). Currently the pipeline is composed of alignment and QC, and detection of both somatic alterations and germline variants. Users can begin with inputs of either paired-end FASTQs or BAMs, and process these via the command line. 

For further details of how to begin processing data with Tempo, please view our [documentation](https://cmotempo.netlify.com/). For contributing to this project, please make a pull request as detailed [here](https://cmotempo.netlify.com/contributing-to-tempo.html).

The inspiration for this project derives from [Sarek](https://github.com/SciLifeLab/Sarek), developed at [SciLifeLab](https://github.com/SciLifeLab).

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