{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.

SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}

{
    "name":"run-command example pipeline",
    "components":{
         "bwa-mem": {
            "script": "run-command",
            "script_version": "master",
            "repository": "arvados",
            "script_parameters": {
                "command": [
                    "$(dir $(bwa_collection))/bwa",
                    "mem",
                    "-t",
                    "$(node.cores)",
                    "-R",
                    "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
                    "$(glob $(dir $(reference_collection))/*.fasta)",
                    "$(glob $(dir $(sample))/*_1.fastq)",
                    "$(glob $(dir $(sample))/*_2.fastq)"
                ],
                "reference_collection": {
                    "required": true,
                    "dataclass": "Collection"
                },
                "bwa_collection": {
                    "required": true,
                    "dataclass": "Collection",
                    "default": "39c6f22d40001074f4200a72559ae7eb+5745"
                },
                "sample": {
                    "required": true,
                    "dataclass": "Collection"
                },
                "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
            }
        }
    }
}