KIDS25-Team20

Clara Parabricks v 4.5.1 with WDL 1.2

Introduction

This repository contains WDL workflows sing Nvidia Clara Parabricks

Available workflows adapted from (https://github.com/clara-parabricks-workflows/parabricks-wdl) Clara parabricks workflow

• fq2bam : Align reads with Clara Parabricks' accelerated version of BWA mem.
• bam2fq2bam: Extract FASTQ files from a BAM file and realign them to produce a new BAM file on a different reference.
• germline_calling: Run accelerated GATK HaplotypeCaller and/or accelerated DeepVariant to produce germline VCF or gVCF files for a single sample.
• somatic_calling: Run accelerated Mutect2 on a matched tumor-normal sample pair to generate a somatic VCF.
• deepvariant-retraining: Retrain the DeepVariant model on a custom dataset generated from a .bam

Getting Started

All pipelines in this repository have been validated using Sprocket 0.17.1.

Setting up your runtime environment

Insert sprocket github link

Download test data or bring your own

We recommend test data provided by Google Brain's Public Sequencing project. The HG002 FASTQ files can be downloaded with the following commands:

Run your first workflow

There are example JSON input slugs in the example_inputs directory. To run your first workflow, you can edit the minimal inputs file (fq2bam.minimalInputs.json). If you want more advanced control over inputs or need additional ones you can modify the full inputs file (fq2bam.fullInputs.json).