doc/_includes/_run_command_foreach_example.liquid

   1 "bwa-mem": {
   2     "script": "run-command",
   3     "script_version": "master",
   4     "repository": "arvados",
   5     "script_parameters": {
   6         "command": [
   7             "bwa",
   8             "mem",
   9             "-t",
  10             "$(node.cores)",
  11             "$(glob $(dir $(reference_collection))/*.fasta)",
  12             "$(glob $(dir $(sample))/*_1.fastq)",
  13             "$(glob $(dir $(sample))/*_2.fastq)"
  14         ],
  15         "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
  16         "reference_collection": {
  17             "required": true,
  18             "dataclass": "Collection"
  19         },
  20         "samples": {
  21             "required": true,
  22             "dataclass": "Collection"
  23         },
  24     }
  25 }