doc/_includes/_run_command_foreach_example.liquid

   1 {% comment %}
   2 Copyright (C) The Arvados Authors. All rights reserved.
   3
   4 SPDX-License-Identifier: CC-BY-SA-3.0
   5 {% endcomment %}
   6
   7 {
   8     "name":"run-command example pipeline",
   9     "components":{
  10         "bwa-mem": {
  11             "script": "run-command",
  12             "script_version": "master",
  13             "repository": "arvados",
  14             "script_parameters": {
  15                 "command": [
  16                     "bwa",
  17                     "mem",
  18                     "-t",
  19                     "$(node.cores)",
  20                     "$(glob $(dir $(reference_collection))/*.fasta)",
  21                     {
  22                         "foreach": "read_pair",
  23                         "command": "$(read_pair)"
  24                     }
  25                 ],
  26                 "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
  27                 "task.foreach": ["sample_subdir", "read_pair"],
  28                 "reference_collection": {
  29                     "required": true,
  30                     "dataclass": "Collection"
  31                 },
  32                 "sample": {
  33                     "required": true,
  34                     "dataclass": "Collection"
  35                 },
  36                 "sample_subdir": "$(dir $(sample))",
  37                 "read_pair": {
  38                     "value": {
  39                         "group": "sample_subdir",
  40                         "regex": "(.*)_[12]\\.fastq(\\.gz)?$"
  41                     }
  42                 }
  43             }
  44         }
  45     }
  46 }