https://github.com/griffithlab/bioinformatic-workflows
CWL workflows for bioinformatic analysis
https://github.com/griffithlab/bioinformatic-workflows
Last synced: 5 months ago
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CWL workflows for bioinformatic analysis
- Host: GitHub
- URL: https://github.com/griffithlab/bioinformatic-workflows
- Owner: griffithlab
- Created: 2018-09-05T21:58:21.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2019-08-16T21:19:30.000Z (almost 7 years ago)
- Last Synced: 2025-08-22T13:42:19.783Z (10 months ago)
- Language: Common Workflow Language
- Size: 70.3 KB
- Stars: 1
- Watchers: 16
- Forks: 3
- Open Issues: 1
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Metadata Files:
- Readme: README.md
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README
# Description
This repository holds various bioinformatic workflows. Each workflow is broken down as a main or sub workflow and has an associated .yaml file specifying inputs and are named to correspond with the workflow they are associated with. A list of each available workflow is provided below, for a more complete description of a specific workflow see the [github wiki](https://github.com/griffithlab/bioinformatic-workflows/wiki).
# Main Worfklows
1. kallisto - Run kallisto from a bam file
2. hla_typing - Run optitype and xHLA from a bam file
2. hla_somatic_variants - Call somatic variants within the HLA region
# Sub Workflows
1. bam2fastq - Convert a paired end bam file to fastq files.