CWL 1.3 - Convert SBGSECRETS to standard secrets #170
Description
Example of a Seven Bridges CWL that uses secrets.
{
"class": "CommandLineTool",
"cwlVersion": "v1.2",
"$namespaces": {
"sbg": "https://sevenbridges.com"
},
"baseCommand": [
"birdshot"
],
"inputs": [
{
"sbg:secretAlias": "SBGSECRET_USER",
"id": "username",
"type": "string",
"label": "Carta Username"
},
{
"sbg:secretAlias": "SBGSECRET_PASS",
"id": "password",
"type": "string",
"label": "Carta Password"
},
{
"id": "use_development_env",
"type": "boolean?",
"label": "Development Environment",
"doc": "Turn on if the Carta credentials are for the development environment. Default: off (False).",
"default": false
},
{
"id": "no_auth",
"type": "boolean?",
"label": "Disable Authentication",
"doc": "If enabled, this flag prevents authentication. This is useful when no data needs to be retrieved from the BIRDSHOT Google Drive; i.e., all files are local.",
"default": null
},
{
"id": "unpack",
"type": "boolean?",
"label": "Unpack Metadata",
"doc": "If True (default), load metadata into the appropriate node in the graph.",
"default": true
}
],
"outputs": [
{
"id": "output",
"type": "File?",
"outputBinding": {
"glob": "birdshot*.pkl"
}
}
],
"label": "birdshot-graph-download",
"arguments": [
{
"prefix": "--username",
"shellQuote": false,
"position": 0,
"valueFrom": "$SBGSECRET_USER"
},
{
"prefix": "--password",
"shellQuote": false,
"position": 0,
"valueFrom": "$SBGSECRET_PASS"
},
{
"prefix": "--url",
"shellQuote": false,
"position": 0,
"valueFrom": "${\n if(inputs.use_development_env) {\n return \"https://api.sandbox.carta.contextualize.us.com\"\n } else {\n return \"https://api.carta.contextualize.us.com\"\n }\n}"
},
{
"prefix": "",
"shellQuote": false,
"position": 0,
"valueFrom": "${\n if(inputs.no_auth) {\n return \"--no-auth\"\n } else {\n return \"\"\n }\n}"
},
{
"prefix": "",
"shellQuote": false,
"position": 1,
"valueFrom": "graph"
},
{
"prefix": "",
"shellQuote": false,
"position": 2,
"valueFrom": "${\n if(inputs.unpack) {\n return \"push --pass nodes node-filter -n '.*.json' unpack drop pop\"\n } else {\n return \"\"\n }\n}"
},
{
"prefix": "dump",
"shellQuote": false,
"position": 3,
"valueFrom": "${\n var date = new Date();\n return \"birdshot-\" + date.toISOString().split(\"T\")[0] + \".pkl\"\n}"
}
],
"requirements": [
{
"class": "ShellCommandRequirement"
},
{
"class": "DockerRequirement",
"dockerPull": "images.sbgenomics.com/htmdec/birdshot:0.1.8"
},
{
"class": "EnvVarRequirement",
"envDef": [
{
"envName": "SBGSECRET_USER",
"envValue": "$(inputs.username)"
},
{
"envName": "SBGSECRET_PASS",
"envValue": "$(inputs.password)"
},
{
"envName": "DEBUG",
"envValue": "1"
}
]
},
{
"class": "InlineJavascriptRequirement"
}
],
"sbg:projectName": "demo",
"sbg:revisionsInfo": [
{
"sbg:revision": 0,
"sbg:modifiedBy": "htmdec/bkappes",
"sbg:modifiedOn": 1703194967,
"sbg:revisionNotes": null
},
{
"sbg:revision": 1,
"sbg:modifiedBy": "htmdec/bkappes",
"sbg:modifiedOn": 1703196795,
"sbg:revisionNotes": "Initial commit."
},
{
"sbg:revision": 2,
"sbg:modifiedBy": "htmdec/bkappes",
"sbg:modifiedOn": 1703197220,
"sbg:revisionNotes": "Forgot output port."
},
{
"sbg:revision": 3,
"sbg:modifiedBy": "htmdec/bkappes",
"sbg:modifiedOn": 1703197675,
"sbg:revisionNotes": "Forgot to pop the graph back into the queue."
},
{
"sbg:revision": 4,
"sbg:modifiedBy": "htmdec/bkappes",
"sbg:modifiedOn": 1703218588,
"sbg:revisionNotes": "Tracking bug in output file."
},
{
"sbg:revision": 5,
"sbg:modifiedBy": "htmdec/bkappes",
"sbg:modifiedOn": 1703219346,
"sbg:revisionNotes": "Enabled debugging."
},
{
"sbg:revision": 6,
"sbg:modifiedBy": "htmdec/bkappes",
"sbg:modifiedOn": 1703256215,
"sbg:revisionNotes": "Forgot '-n' flag to node-filter."
}
],
"sbg:image_url": null,
"sbg:appVersion": [
"v1.2"
],
"id": "https://api.sbgenomics.com/v2/apps/htmdec/demo/birdshot-graph-download/6/raw/",
"sbg:id": "htmdec/demo/birdshot-graph-download/6",
"sbg:revision": 6,
"sbg:revisionNotes": "Forgot '-n' flag to node-filter.",
"sbg:modifiedOn": 1703256215,
"sbg:modifiedBy": "htmdec/bkappes",
"sbg:createdOn": 1703194967,
"sbg:createdBy": "htmdec/bkappes",
"sbg:project": "htmdec/demo",
"sbg:sbgMaintained": false,
"sbg:validationErrors": [],
"sbg:contributors": [
"htmdec/bkappes"
],
"sbg:latestRevision": 6,
"sbg:publisher": "sbg",
"sbg:content_hash": "a2c1eb446345b451a0ca15e663bfc43fec3cc6bd750fedfa3a03fed4e5894d3f4",
"sbg:workflowLanguage": "CWL"
}