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docs/index.md

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3. Orchestrate individual jobs into analysis workflows using native AWS services like [AWS Step Functions](https://aws.amazon.com/step-functions) and 3rd party workflow engines
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If you're impatient and want to get something up and running immediately, head
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straight to the [TL;DR](tldr) section. Otherwise, continue on for the full details.
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straight to the [Quick Start](quick-start) section. Otherwise, continue on for the full details.
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## Prerequisites
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docs/orchestration/cromwell/cromwell-overview.md

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system for scientific workflows developed by the [Broad Institute](https://broadinstitute.org/)
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and supports job execution using [AWS Batch](https://aws.amazon.com/batch/).
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## Full Stack Deployment (TL;DR)
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## Full Stack Deployment
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If you need a Cromwell server backed by AWS **now** and will worry about the
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details later, use the CloudFormation template below.

docs/orchestration/nextflow/nextflow-overview.md

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Nextflow can be run either locally or on a dedicated EC2 instance. The latter is preferred if you have long running workflows - with the caveat that you are responsible for stopping the instance when your workflow is complete. The architecture presented in this guide demonstrates how you can run Nextflow using AWS Batch in a managed and cost effective fashion.
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## Full Stack Deployment (TL;DR)
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## Full Stack Deployment
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The following CloudFormation template will launch an EC2 instance pre-configured for using Nextflow.
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docs/orchestration/step-functions/step-functions-overview.md

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In the context of genomics workflows, the combination of AWS Step Functions with Batch and Lambda constitutes a robust, scalable, and serverless task orchestration solution.
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## Full Stack Deployment (TL;DR)
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## Full Stack Deployment
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If you need something up and running in a hurry, the follwoing CloudFormation template will create everything you need to run an example genomics workflow using `bwa-mem`, `samtools`, and `bcftools`.
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docs/tldr.md renamed to docs/quick-start.md

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# TL;DR - For rapid deployment
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# Quick Start - For rapid deployment
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## Step 0: Amazon VPC
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mkdocs.yml

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nav:
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- Overview: index.md
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- Disclaimer: disclaimer.md
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- TL;DR: tldr.md
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- Quick Start: quick-start.md
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- Getting Started:
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- Introduction: core-env/introduction.md
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- Data Storage: core-env/create-s3-bucket.md

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