# CWL

ICA supports running pipelines defined using [Common Workflow Language (CWL)](https://www.commonwl.org/).

## Compute Type

To specify a compute type for a CWL CommandLineTool, either define the **ram and number of cores** **or** use the **resource type and size**. The ICA Compute Type will automatically be determined based on [CWL ResourceRequirement](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement) coresMin/coresMax (CPU) and ramMin/ramMax (Memory) values using a "best fit" strategy to meet the minimum specified requirements (See the [Compute Types](https://help.ica.illumina.com/project/p-flow/f-pipelines/..#compute-types) table to see to what the resources are mapped).

For example, take the following `ResourceRequirements`:

```yaml
requirements:
    ResourceRequirement:
      ramMin: 10240
      coresMin: 6
```

This will result in a best fit of `standard-large` ICA Compute Type request for the task.

{% hint style="info" %}
If the specified requirements can not be met by any of the presets, the task will be rejected and failed.
{% endhint %}

See the example below to use the `ResourceRequirement` in the cwl workflow with the Predefined [Compute Types](https://help.ica.illumina.com/project/p-flow/f-pipelines/..#compute-types)

```yaml
requirements:
    ResourceRequirement:
        https://platform.illumina.com/rdf/ica/resources:type: fpga2
        https://platform.illumina.com/rdf/ica/resources:size: medium 
        https://platform.illumina.com/rdf/ica/resources:tier: standard
```

{% hint style="info" %}

* FPGA requirements can not be set by means of CWL ResourceRequirements.
* The Machine Profile Resource in the graphical editor will override whatever is set for requirements in the ResourceRequirement.
  {% endhint %}

### Standard vs Economy

For each compute type, you can choose between the

* Standard - [**AWS on-demand**](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/ec2-on-demand-instances.html) (Default) or
* Economy - [**AWS spot instance**](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-spot-instances.html) tiers.

You can set economy mode with the "tier" parameter

```yaml
requirements:
    ResourceRequirement:
        https://platform.illumina.com/rdf/ica/resources:type: himem
        https://platform.illumina.com/rdf/ica/resources:size: small 
        https://platform.illumina.com/rdf/ica/resources:tier: economy
```

## Considerations

> If no Docker image is specified, Ubuntu will be used as default. Both : and / can be used as separator.

## CWL Overrides

ICA supports overriding workflow requirements at load time using Command Line Interface (CLI) with JSON input. Please refer to [CWL documentation](https://github.com/common-workflow-language/cwltool/tree/3.0.20201203173111#overriding-workflow-requirements-at-load-time) for more details on the CWL overrides feature.

In ICA you can provide the "override" recipes as a part of the input JSON. The following example uses CWL overrides to change the environment variable requirement at load time.

```bash
icav2 projectpipelines start cwl cli-tutorial --data-id fil.a725a68301ee4e6ad28908da12510c25 --input-json '{
  "ipFQ": {
    "class": "File",
    "path": "test.fastq"
  },
  "cwltool:overrides": {
  "tool-fqTOfa.cwl": {
    "requirements": {
      "EnvVarRequirement": {
        "envDef": {
          "MESSAGE": "override_value"
          }
        }                                       
       }
      }
    }
}' --type-input JSON --user-reference overrides-example
```