# Ready2Run workflows in HealthOmics
Ready2Run workflows

Ready2Run workflows are preconfigured workflows published by third-party publishers. Some publishers, such as Sentieon Inc, offer subscription-based workflows. Other Ready2Run workflows don't require a subscription, and some workflows are open source, such as the NF-Core workflows.

Ready2Run workflows are well-suited to the following scenarios:
+ You want to focus on the analysis of pipeline output and generating results, without the need to set up the underlying infrastructure.
+ You want to replicate your results using established workflows.
+ As a software developer, you want to integrate your application directly with the HealthOmics SDK.

HealthOmics supports versioning for Ready2Run workflows. For a Ready2Run workflow that offers versions, you can specify the version name when you start a run.

All Ready2Run workflows provide logs, including CloudWatch logs, that you can use for troubleshooting.

**Note**  
Sentieon Ready2Run workflows are subscription-based. When you run a Sentieon Ready2Run workflow for the first time in an account, Sentieon automatically creates a two-week evaluation license for your AWS account. The license is valid for all Sentieon Ready2Run workflows. After the evaluation period ends, you can request a permanent license or request an extension to the evaluation license. See **Subscribing to Sentieon Ready2Run workflows** for details. 

**Topics**
+ [

# Available Ready2Run workflows in HealthOmics
](workflows-r2r-table.md)
+ [

# Subscribing to Sentieon Ready2Run workflows
](Ready2Run-workflows-subscribe.md)
+ [

# Starting HealthOmics Ready2Run workflows using the console
](Ready2Run-workflows-console.md)
+ [

# Starting HealthOmics Ready2Run workflows using the API
](Ready2Run-workflows-API.md)

# Available Ready2Run workflows in HealthOmics
Available workflows

The following table lists the Ready2Run workflows that are available in HealthOmics. 

You can log in to the [HealthOmics console](https://console.aws.amazon.com/omics/home#/ready2run) to view detailed information about these workflows, including input parameters and workflow diagrams. For pricing information about Ready2Run workflows, see [HealthOmics Pricing](https://aws.amazon.com/healthomics/pricing/).

**Note**  
Each Ready2Run workflow has a maximum input file size. These maximum file sizes aren't adjustable.


| Workflow name | Publisher | Subscription required? | Maximum input file size (GiB) | Estimated run time (HH:MM) | 
| --- | --- | --- | --- | --- | 
| AlphaFold for 601-1200 residues | Google DeepMind | No | 1 | 11:15 | 
| AlphaFold for up to 600 residues  | Google DeepMind | No | 1 | 7:30 | 
| Bases2Fastq for 2x150  | Element Biosciences | No | 1000 | 1:45 | 
| Bases2Fastq for 2x300  | Element Biosciences | No | 1000 | 1:30 | 
| Bases2Fastq for 2x75  | Element Biosciences | No | 500 | 0:45 | 
| ESMFold for up to 800 residues  | Meta Research | No | 1 | 0:15 | 
| GATK-BP fq2bam  | Broad Institute | No | 64 | 10:10 | 
| GATK-BP Germline bam2vcf for 30x genome  | Broad Institute | No | 39 | 2:45 | 
| GATK-BP Germline fq2vcf for 30x genome  | Broad Institute | No | 64 | 12:30 | 
| GATK-BP Somatic WES bam2vcf  | Broad Institute | No | 86 | 1:30 | 
| NVIDIA Parabricks BAM2FQ2BAM WGS for up to 30X  | NVIDIA Corporation | No | 80 | 1:39 | 
| NVIDIA Parabricks BAM2FQ2BAM WGS for up to 50X  | NVIDIA Corporation | No | 120 | 2:45 | 
| NVIDIA Parabricks BAM2FQ2BAM WGS for up to 5X  | NVIDIA Corporation | No | 20 | 0:18 | 
| NVIDIA Parabricks FQ2BAM WGS for up to 30X  | NVIDIA Corporation | No | 71 | 1:00 | 
| NVIDIA Parabricks FQ2BAM WGS for up to 50X  | NVIDIA Corporation | No | 137 | 1:45 | 
| NVIDIA Parabricks FQ2BAM WGS for up to 5X  | NVIDIA Corporation | No | 13 | 0:15 | 
| NVIDIA Parabricks Germline DeepVariant WGS for up to 30X  | NVIDIA Corporation | No | 71 | 2:00 | 
| NVIDIA Parabricks Germline DeepVariant WGS for up to 50X  | NVIDIA Corporation | No | 137 | 3:30 | 
| NVIDIA Parabricks Germline DeepVariant WGS for up to 5X  | NVIDIA Corporation | No | 12 | 0:30 | 
| NVIDIA Parabricks Germline HaplotypeCaller WGS for up to 30X  | NVIDIA Corporation | No | 71 | 1:15 | 
| NVIDIA Parabricks Germline HaplotypeCaller WGS for up to 50X  | NVIDIA Corporation | No | 137 | 2:00 | 
| NVIDIA Parabricks Germline HaplotypeCaller WGS for up to 5X  | NVIDIA Corporation | No | 13 | 0:15 | 
| NVIDIA Parabricks Somatic Mutect2 WGS for up to 50X  | NVIDIA Corporation | No | 196 | 0:45 | 
| scRNAseq with KallistoBUStools  | NF-Core | No | 119 | 1:30 | 
| scRNAseq with Salmon Alevin-fry  | NF-Core | No | 119 | 2:30 | 
| scRNAseq with STARsolo  | NF-Core | No | 119 | 2:30 | 
| Sentieon Germline BAM WES for up to 300x  | Sentieon, Inc. | Yes | 9 | 1:00 | 
| Sentieon Germline BAM WGS for up to 32x  | Sentieon, Inc. | Yes | 18 | 1:30 | 
| Sentieon Germline FASTQ WES for up to 100x  | Sentieon, Inc. | Yes | 5 | 0:45 | 
| Sentieon Germline FASTQ WES for up to 300x  | Sentieon, Inc. | Yes | 26 | 2:00 | 
| Sentieon Germline FASTQ WGS for up to 32x  | Sentieon, Inc. | Yes | 51 | 3:30 | 
| Sentieon LongRead for ONT  | Sentieon, Inc. | Yes | 25 | 1:30 | 
| Sentieon LongRead for PacBio HiFi  | Sentieon, Inc. | Yes | 58 | 4:00 | 
| Sentieon Somatic WES  | Sentieon, Inc. | Yes | 50 | 2:30 | 
| Sentieon Somatic WGS  | Sentieon, Inc. | Yes | 113 | 4:30 | 
| Ultima Genomics DeepVariant for up to 40x  | Ultima Genomics | No | 91 | 1:55 | 

When you use a Ready2Run workflow, your workflow is preconfigured and can't be edited. In contrast to private workflows, Ready2Run workflows don't support the following:
+ Increasing the maximum input file size
+ Changing the compute resources or run storage 
+ Changing the workflow definition or containers
+ Adding runs to a run group
+ Sharing the workflow

If the publisher has shared the Ready2Run workflow on GitHub, you can make your own private workflow based on the Ready2Run workflow. The following table provides links to GitHub workflows for each publisher.


| Publisher | Workflows on GitHub | 
| --- | --- | 
| Google DeepMind, Meta Research | [Protein folding workflows](https://github.com/aws-samples/amazon-omics-tutorials/tree/main/example-workflows/protein-folding/workflows) | 
| Element Biosciences | For information, contact Element Biosciences | 
| Broad Institute | [GATK workflows](https://github.com/aws-samples/amazon-omics-tutorials/tree/main/example-workflows/gatk-best-practices/workflows) | 
| NVIDIA Corporation | [Parabricks workflows](https://github.com/clara-parabricks-workflows/parabricks-omics-private-workflows) | 
| nf-core | [NF-Core workflows](https://github.com/aws-samples/amazon-omics-tutorials/tree/main/example-workflows/nf-core/workflows/scrnaseq) | 
| Sentieon | [Sentieon workflows](https://github.com/Sentieon/sentieon-amazon-omics) | 
| Ultima Genomics | [Ultima Genomics workflows](https://github.com/Ultimagen/healthomics-workflows) | 

# Subscribing to Sentieon Ready2Run workflows
Subscribing to Sentieon workflows

Sentieon Ready2Run workflows are subscription-based. When you run a Sentieon Ready2Run workflow for the first time in an account, Sentieon automatically creates a two-week evaluation license for your AWS account. The license is valid for all Sentieon Ready2Run workflows. After the evaluation period ends, you can request a permanent license or request an extension to the evaluation license.

Follow these steps to subscribe to the Sentieon Ready2Run workflows:
+ Find your AWS Canonical User ID by following [ these instructions](https://docs.aws.amazon.com/AmazonS3/latest/userguide/finding-canonical-user-id.html).
+ Send an email to the Sentieon support group (support@sentieon.com) to request a software license. Provide your AWS Canonical User ID in the email.

# Starting HealthOmics Ready2Run workflows using the console
Starting Ready2Run workflows (console)

Using Ready2Run workflows in the console is similar to using a private workflow. One key difference is that the workflow publisher provides sample data, so that you can try out the workflow without creating your own data.

**To use a Ready2Run workflow in the console**

1. Open the [HealthOmics console](https://console.aws.amazon.com/omics/).

1.  If required, open the left navigation pane (≡). Choose **Ready2Run workflows**.

1. On the **Ready2Run workflows** page, choose the workflow that you want to use. The console opens the details page for that workflow.

1. The details tab lists information such as the name, list price per run, description, workflow language type, run storage capacity, status, creation date, and parameters with descriptions. The details tab also tells you whether the workflow requires a subscription. 

1. To use the workflow, choose **Create run**

1. In the **Specify run details** page, enter a run name. Optionally, you can specify the workflow version. You can also add run priority to the run.

1. Enter or select an Amazon S3 location for the run output. 

1. For **Run metadata retention mode**, choose whether to retain or remove run metadata. 

1. In the **Service role** panel, choose whether to use an existing service role or create a new one.

1. (Optional) Add tags to help identify and manage your run.

1. Choose **Next**.

1. From the **Add parameters** page, choose one of the options to add the run parameter values:
   + Select a parameter file (in JSON format) from an Amazon S3 location.
   + Select a parameter file (in JSON format) from your local drive.
   + Manually enter the parameter values.
   + Run workflow with Ready2Run sample data provided by the workflow publisher.

1.  If you upload a JSON file, the console parses the file and performs inline validation. You can then manually update the values of your parameters as needed. 

1. Choose **Next**.

1. Review your inputs, then choose **Start run**.

# Starting HealthOmics Ready2Run workflows using the API
Starting Ready2Run workflows (API)

Most of the API operations behave in a similar fashion for Ready2Run workflows and private workflows.

To return a list of available Ready2Run workflows, use **list-workflows** with the `type` parameter set to READY2RUN. 

```
aws omics list-workflows --type READY2RUN                            
```

After you identify the workflow to run from the **list-workflows** response, you can use **get-workflow** with the `--id` parameter to get more details.

```
aws omics get-workflow --type READY2RUN --id workflow id    
```

To run a Ready2Run workflow, you can use **start-run** API operation with the workflow-type parameter set to `READY2RUN`, as shown in the following example

```
aws-omics start-run \
  --workflow-type READY2RUN \
  --workflow-id workflow id \
  --output-uri &example-s3-bucket; \
  --role-arn arn:aws:iam::1234567892012:role/service-role/OmicsWorkflow-20221004T164236 \
  --parameters file:///path/to/parameters.json
```

To specify a workflow version, use the **workflow-version** parameter, as shown in this example.

```
aws-omics start-run \
  --workflow-type READY2RUN \ 
  ...
  --version-name '3.0.0'
```

To monitor your run, you can use the **get-run** API operation, as shown.

```
aws-omics get-run \
  --id run id
```