{
    "name":"run-command example pipeline",
    "components":{
        "bwa-mem": {
            "script": "run-command",
            "script_version": "master",
            "repository": "arvados",
            "script_parameters": {
                "command": [
                    "bwa",
                    "mem",
                    "-t",
                    "$(node.cores)",
                    "$(glob $(dir $(reference_collection))/*.fasta)",
                    {
                        "foreach": "read_pair",
                        "command": "$(read_pair)"
                    },
                    "$(glob $(dir $(sample))/*_1.fastq)",
                    "$(glob $(dir $(sample))/*_2.fastq)"
                ],
                "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
                "task.foreach": ["sample_subdir", "read_pair"],
                "reference_collection": "2463fa9efeb75e099685528b3b9071e0+438",
                "samples": "df45f4be79668b6d3d974e24f78e766f+149",
                "sample_subdir": "$(dir $(samples))",
                "read_pair": {
                    "group": "sample_subdir",
                    "regex": "(.*)_[12]\\.fastq(\\.gz)?$"
                }
            }
        }
    }
}


                "reference_collection": {
                    "required": true,
                    "dataclass": "Collection"
                },
                "sample": {
                    "required": true,
                    "dataclass": "Collection"
                }