CWL 1.3 - Convert SBGSECRETS to standard secrets

[bkappes]

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"
}

[tetron]

        {
            "sensitive": true,
            "default": {
               "class": "Secret",
               "secretKey": "SBGSECRET_USER"
            },
            "id": "username",
            "type": "string",
            "label": "Carta Username"
        },