{
    "name": "Tutorial align using bwa mem and SortSam",
    "components": {
        "bwa-mem": {
            "script": "run-command",
            "script_version": "master",
            "repository": "arvados",
            "script_parameters": {
                "command": [
                    "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 $(sample))/*_2.fastq)"
                ],
                "reference_collection": {
                    "required": true,
                    "dataclass": "Collection"
                },
                "sample": {
                    "required": true,
                    "dataclass": "Collection"
                },
                "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
            },
            "runtime_constraints": {
                "docker_image": "arvados/jobs-java-bwa-samtools"
            }
        },
        "SortSam": {
            "script": "run-command",
            "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
            "repository": "arvados",
            "script_parameters": {
                "command": [
                    "java",
                    "-Xmx4g",
                    "-Djava.io.tmpdir=$(tmpdir)",
                    "-jar",
                    "$(dir $(picard))/SortSam.jar",
                    "CREATE_INDEX=True",
                    "SORT_ORDER=coordinate",
                    "VALIDATION_STRINGENCY=LENIENT",
                    "INPUT=$(glob $(dir $(input))/*.sam)",
                    "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
                ],
                "input": {
                    "output_of": "bwa-mem"
                },
                "picard": {
                    "required": true,
                    "dataclass": "Collection",
                    "default": "88447c464574ad7f79e551070043f9a9+1970"
                }
            },
            "runtime_constraints": {
                "docker_image": "arvados/jobs-java-bwa-samtools"
            }
        }
    }
}