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                     "$(dir $(bwa_collection))/bwa",
  11                     "mem",
  12                     "-t",
  13                     "$(node.cores)",
  14                     "-R",
  15                     "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
  16                     "$(glob $(dir $(reference_collection))/*.fasta)",
  17                     "$(glob $(dir $(sample))/*_1.fastq)",
  18                     "$(glob $(dir $(sample))/*_2.fastq)"
  19                 ],
  20                 "reference_collection": {
  21                     "required": true,
  22                     "dataclass": "Collection"
  23                 },
  24                 "bwa_collection": {
  25                     "required": true,
  26                     "dataclass": "Collection",
  27                     "default": "39c6f22d40001074f4200a72559ae7eb+5745"
  28                 },
  29                 "sample": {
  30                     "required": true,
  31                     "dataclass": "Collection"
  32                 },
  33                 "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
  34             }
  35         }
  36     }
  37 }