CWL

ICA supports running pipelines defined using Common Workflow Language (CWL).
Compute Type
To specify a compute type for a CWL CommandLineTool, use the ResourceRequirement with a custom namespace.
requirements:
    ResourceRequirement:
        https://platform.illumina.com/rdf/ica/resources:type: fpga
        https://platform.illumina.com/rdf/ica/resources:size: small 
        https://platform.illumina.com/rdf/ica/resources:tier: standard
Reference Compute Types for available compute type and sizes.
Considerations
If no Docker image is specified, Ubuntu will be used as default.
CWL Overrides
ICA supports overriding workflow requirements at load time using Command Line Interface (CLI) with JSON input. Please refer to CWL documentation 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.
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

Pipelines

Nextflow

Last modified 1mo ago