In Clara Parabricks each pipeline is a collection of several individual tools that are commonly used together, all wrapped up as a single tool. For example, the deepvariant_germline takes FASTA and FASTQ files as input and produces a VCF and BAM file as output. Internally, it runs BWA mem alignment, performs coordinate sorting, marks duplicates, and then runs DeepVariant.
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Clara Parabricks contains the following pipelines. Click on the name of a pipeline for tool-specific options.
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Tool |
Details |
Run the germline pipeline from FASTQ to VCF using a deep neural network analysis |
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Run the germline pipeline from FASTQ to VCF |
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Run the somatic pipeline from FASTQ to VCF |
While the user cannot alter or create their own Clara Parabricks pipeline, Parabricks containers are compatible with WDL and NextFlow for building customized workflows, intertwining GPU- and CPU-powered tasks with different compute requirements, and deploying at scale.
These enable workflows to be deployed on cloud batch services as well as local clusters (e.g. SLURM) in a well managed process, pulling from a combination of Clara Parabricks and third-party containers and running these on pre-defined nodes.
For further information on running these workflows, and to see the open-source reference workflows, which can be easily forked/edited, visit the Clara Parabricks Workflows repository. This repository includes recommended instance configurations for deploying the GPU-based tools on cloud and can be easily forked/edited for your own purposes.