Add Toil engine documentation

Author: adamnovak

site/content/en/docs/Concepts/engines.md

@@ -21,6 +21,7 @@ Currently, Amazon Genomics CLI's officially supported engines can be used to run
 | [Nextflow](https://www.nextflow.io)                       | [Nextflow DSL](https://www.nextflow.io/docs/latest/script.html)                            | Standard and DSL 2                                                                                                      | Head Process |
 | [miniwdl](https://miniwdl.readthedocs.io/en/latest/)      | [WDL](https://openwdl.org)                                                                 | [documented here](https://miniwdl.readthedocs.io/en/latest/runner_reference.html?highlight=errata#wdl-interoperability) | Head Process |
 | [Snakemake](https://snakemake.readthedocs.io/en/stable/)  | [Snakemake](https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html) | All versions                                                                                                            | Head Process |
+| [Toil](http://toil.ucsc-cgl.org/)                | [CWL](https://www.commonwl.org/)                                                                    | All versions up to 1.2                                                                                                  | Server       |
 
 Overtime we plan to add additional engine and language support and provide the ability for third party developers to 
 develop engine plugins.

site/content/en/docs/Workflow engines/toil.md

@@ -0,0 +1,63 @@
+---
+title: "Toil"
+date: 2022-04-26T15:34:00-04:00
+draft: false
+weight: 20
+description: >
+    Details on the Toil engine deployed by Amazon Genomics CLI
+---
+
+## Description
+
+[Toil](http://toil.ucsc-cgl.org/) is a workflow engine developed by the
+[Computational Genomics Lab](https://cglgenomics.ucsc.edu/) at the
+[UC Santa Cruz Genomics Institute](https://genomics.ucsc.edu/). In Amazon Genomics
+CLI, Toil is an engine that can be deployed in a
+[context]( {{< relref "../Concepts/contexts" >}} ) as an
+[engine]( {{< relref "../Concepts/engines">}} ) to run workflows based on the
+[CWL](https://www.commonwl.org/) specification.
+
+Toil is an open source project distributed by UC Santa Cruz under the [Apache 2
+license](https://github.com/DataBiosphere/toil/blob/master/LICENSE) and
+available on
+[GitHub](https://github.com/DataBiosphere/toil).
+
+## Architecture
+
+There are two components of a Toil engine as deployed in an Amazon Genomics
+CLI context:
+
+### Engine Service
+
+The Toil engine is run in "server mode" as a container service in ECS. The
+engine can run multiple workflows asynchronously. Workflow tasks are run in an
+elastic [compute environment]( #compute-environment ) and monitored by Toil.
+Amazon Genomics CLI communicates with the Toil engine via a GA4GH
+[WES](https://github.com/ga4gh/workflow-execution-service-schemas) REST service
+which the server offers, available via API Gateway.
+
+### Compute Environment
+
+Workflow tasks are submitted by Toil to an AWS Batch queue and run in
+Toil-provided containers using an AWS Compute Environment. Tasks which use the
+[CWL `DockerRequirement`](https://www.commonwl.org/user_guide/07-containers/index.html)
+will additionally be run under
+[Singularity](https://github.com/sylabs/singularity#readme). AWS Batch
+coordinates the elastic provisioning of EC2 instances (container hosts) based
+on the available work in the queue. Batch will place containers on container
+hosts as space allows.
+
+#### Disk Expansion
+
+Container hosts in the Batch compute environment use EBS volumes as local
+scratch space. As an EBS volume approaches a capacity threshold, new EBS
+volumes will be attached and merged into the file system. These volumes are
+destroyed when AWS Batch terminates the container host. CWL disk space
+requirements are ignored by Toil when running against AWS Batch.
+
+This setup means that workflows that succeed on AGC may fail on other CWL
+runners (because they do not request enough disk space) and workflows that
+succeed on other CWL runners may fail on AGC (because they allocate disk space
+faster than the expansion process can react).
+
+