doc/_includes/_run_command_simple_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                     "$(dir $(bwa_collection))/bwa",
  17                     "mem",
  18                     "-t",
  19                     "$(node.cores)",
  20                     "-R",
  21                     "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
  22                     "$(glob $(dir $(reference_collection))/*.fasta)",
  23                     "$(glob $(dir $(sample))/*_1.fastq)",
  24                     "$(glob $(dir $(sample))/*_2.fastq)"
  25                 ],
  26                 "reference_collection": {
  27                     "required": true,
  28                     "dataclass": "Collection"
  29                 },
  30                 "bwa_collection": {
  31                     "required": true,
  32                     "dataclass": "Collection",
  33                     "default": "39c6f22d40001074f4200a72559ae7eb+5745"
  34                 },
  35                 "sample": {
  36                     "required": true,
  37                     "dataclass": "Collection"
  38                 },
  39                 "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
  40             }
  41         }
  42     }
  43 }