"bwa-mem": {
    "script": "run-command",
    "script_version": "master",
    "repository": "arvados",
    "script_parameters": {
        "command": [
            "bwa",
            "mem",
            "-t",
            "$(node.cores)",
            "$(glob $(dir $(reference_collection))/*.fasta)",
            "$(glob $(dir $(sample))/*_1.fastq)",
            "$(glob $(dir $(sample))/*_2.fastq)"
        ],
        "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
        "reference_collection": {
            "required": true,
            "dataclass": "Collection"
        },
        "samples": {
            "required": true,
            "dataclass": "Collection"
        },
    }
}