{
    "softwareDescription": {
        "version": "0.7.1"
    },
    "documentAuthor": ["boysha", "peter.amstutz@curoverse.com"],
    "schema":"https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/draft-1/schemas/tool.json",
    "requirements": {
        "environment": {
            "container": {
                "type": "docker",
                "uri": "images.sbgenomics.com/rabix/bwa:9d3b9b0359cf",
                "imageId": "9d3b9b0359cf"
            }
        },
        "resources": {
            "cpu": 0,
            "mem": 5000,
            "network": false
        }
    },
    "inputs": {
        "type": "object",
        "required": [
            "reference",
            "reads"
        ],
        "properties": {
            "reference": {
                "type": "file",
                "required": "Yes",
                "adapter": {
                    "order": 2,
                    "secondaryFiles": [
                        "*.amb",
                        "*.ann",
                        "*.bwt",
                        "*.pac",
                        "*.sa"
                    ]
                }
            },
            "reads": {
                "type": "array",
                "required": "Yes",
                "minItems": 1,
                "maxItems": 2,
                "items": {
                    "type": "file"
                },
                "adapter": {
                    "streamable": true
                }
            },
            "minimum_seed_length": {
                "type": "integer",
                "adapter": {
                    "order": 1,
                    "prefix": "-m"
                }
            },
            "min_std_max_min": {
                "type": "array",
                "minItems": 1,
                "maxItems": 4,
                "items": {
                    "type": "number"
                },
                "adapter": {
                    "order": 1,
                    "prefix": "-I",
                    "itemSeparator": ","
                }
            }
        }
    },
    "outputs": {
        "type": "object",
        "required": [
            "sam"
        ],
        "properties": {
            "sam": {
                "type": "file",
                "adapter": {
                    "stdout": "Yes",
                    "glob": "output.sam",
                    "streamable": "Yes"
                }
            }
        }
    },
    "adapter": {
        "baseCmd": [
            "bwa",
            "mem"
        ],
        "stdout": "output.sam",
        "args": [
            {
                "order": 1,
                "prefix": "-t",
                "separator": "",
                "value": {
                    "$expr": "$job.allocatedResources.cpu"
                }
            }
        ]
    }
}