doc/_includes/_run_command_foreach_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 $(reference_collection))/*.fasta)",
  15                     {
  16                         "foreach": "read_pair",
  17                         "command": "$(read_pair)"
  18                     }
  19                 ],
  20                 "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
  21                 "task.foreach": ["sample_subdir", "read_pair"],
  22                 "reference_collection": {
  23                     "required": true,
  24                     "dataclass": "Collection"
  25                 },
  26                 "sample": {
  27                     "required": true,
  28                     "dataclass": "Collection"
  29                 },
  30                 "sample_subdir": "$(dir $(sample))",
  31                 "read_pair": {
  32                     "value": {
  33                         "group": "sample_subdir",
  34                         "regex": "(.*)_[12]\\.fastq(\\.gz)?$"
  35                     }
  36                 }
  37             }
  38         }
  39     }
  40 }