CWL
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
If no Docker image is specified, Ubuntu will be used as default.
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
Last modified 1mo ago