doc/_includes/_tutorial_bwa_sortsam_pipeline.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": "Tutorial align using bwa mem and SortSam",
   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 $(sample))/*_1.fastq)).sam"
  40             },
  41             "runtime_constraints": {
  42                 "docker_image": "bcosc/arv-base-java",
  43                 "arvados_sdk_version": "master"
  44             }
  45         },
  46         "SortSam": {
  47             "script": "run-command",
  48             "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
  49             "repository": "arvados",
  50             "script_parameters": {
  51                 "command": [
  52                     "java",
  53                     "-Xmx4g",
  54                     "-Djava.io.tmpdir=$(tmpdir)",
  55                     "-jar",
  56                     "$(dir $(picard))/SortSam.jar",
  57                     "CREATE_INDEX=True",
  58                     "SORT_ORDER=coordinate",
  59                     "VALIDATION_STRINGENCY=LENIENT",
  60                     "INPUT=$(glob $(dir $(input))/*.sam)",
  61                     "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
  62                 ],
  63                 "input": {
  64                     "output_of": "bwa-mem"
  65                 },
  66                 "picard": {
  67                     "required": true,
  68                     "dataclass": "Collection",
  69                     "default": "88447c464574ad7f79e551070043f9a9+1970"
  70                 }
  71             },
  72             "runtime_constraints": {
  73                 "docker_image": "bcosc/arv-base-java",
  74                 "arvados_sdk_version": "master"
  75             }
  76         }
  77     }
  78 }