"repository": "arvados",
"script_parameters": {
"command": [
- "bwa",
+ "$(dir $(bwa_collection))/bwa",
"mem",
"-t",
"$(node.cores)",
"required": true,
"dataclass": "Collection"
},
+ "bwa_collection": {
+ "required": true,
+ "dataclass": "Collection",
+ "default": "39c6f22d40001074f4200a72559ae7eb+5745"
+ },
"sample": {
"required": true,
"dataclass": "Collection"
},
- "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
+ "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
},
"runtime_constraints": {
- "docker_image": "arvados/jobs-java-bwa-samtools"
+ "docker_image": "bcosc/arv-base-java",
+ "arvados_sdk_version": "master"
}
},
"SortSam": {
}
},
"runtime_constraints": {
- "docker_image": "arvados/jobs-java-bwa-samtools"
+ "docker_image": "bcosc/arv-base-java",
+ "arvados_sdk_version": "master"
}
}
}