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dxapp.json
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dxapp.json
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{
"name": "bcbio-run-workflow",
"title": "Create and run BCBIO Workflow",
"summary": "Creates and runs a BCBIO Workflow on DNAnexus using a YAML template and a sample specification",
"dxapi": "1.0.0",
"version": "0.0.2",
"inputSpec": [
{
"name": "yaml_template",
"label": "YAML template (without input files)",
"class": "file",
"optional": false,
"patterns": [
"*"
],
"help": ""
},
{
"name": "sample_spec",
"label": "CSV Sample Specification (description of input files and batch)",
"class": "file",
"optional": false,
"patterns": [
"*"
],
"help": ""
},
{
"name": "system_configuration",
"label": "YAML System Configuration",
"class": "file",
"optional": false,
"patterns": [
"*"
],
"help": ""
},
{
"name": "output_folder",
"default": "/dx-cwl-run",
"label": "Output folder for workflows and data",
"class": "string",
"optional": false,
"patterns": [
"*"
],
"help": ""
},
{
"name": "reuse_workflow",
"label": "Workflow ID or path within project of existing DNAnexus workflow (as opposed to compiling a new one)",
"class": "string",
"optional": true,
"patterns": [
"*"
],
"help": ""
},
{
"name": "pull_from_docker_registry",
"label": "Pull the bcbio image from the Docker registry as opposed to using a cached asset",
"class": "string",
"optional": true,
"patterns": [
"*"
],
"help": ""
}
],
"outputSpec": [
{
"name": "generated_cwl",
"label": "tar-gz of the generated CWL for this run",
"class": "file",
"optional": false
}
],
"runSpec": {
"assetDepends": [{"name": "bcbio-vm-asset.tar.gz", "id": "record-FK36958017k13PbPKky9j1g8"},
{"name": "quay.io/bcbio/bcbio-vc.tar.gz", "id": "record-FK36jvQ0f5v9fv5J2F9Qb0xy"}],
"timeoutPolicy": {
"*": {
"hours": 72
}
},
"interpreter": "bash",
"release": "14.04",
"distribution": "Ubuntu",
"file": "src/bcbio-run-workflow.sh"
},
"access": {
"project": "CONTRIBUTE",
"allProjects": "VIEW",
"network": [
"*"
]
},
"regionalOptions": {
"aws:us-east-1": {
"systemRequirements": {
"*": {
"instanceType": "mem1_ssd1_x8"
}
}
}
}
}