doc/_includes/_run_command_simple_example.liquid

   1 {
   2     "name":"run-command example pipeline",
   3     "components":{
   4         "bwa-mem": {
   5             "script": "run-command",
   6             "script_version": "master",
   7             "repository": "arvados",
   8             "script_parameters": {
   9                 "command": [
  10                     "bwa",
  11                     "mem",
  12                     "-t",
  13                     "$(node.cores)",
  14                     "$(glob $(dir $(reference_collection))/*.fasta)",
  15                     "$(glob $(dir $(sample))/*_1.fastq)",
  16                     "$(glob $(dir $(sample))/*_2.fastq)"
  17                 ],
  18                 "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
  19                 "reference_collection": {
  20                     "required": true,
  21                     "dataclass": "Collection"
  22                 },
  23                 "sample": {
  24                     "required": true,
  25                     "dataclass": "Collection"
  26                 }
  27             }
  28         }
  29     }
  30 }