doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid

   1 {
   2     "name": "Tutorial align using bwa mem and SortSam",
   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 $(sample))/*_1.fastq)).sam"
  34             },
  35             "runtime_constraints": {
  36                 "docker_image": "bcosc/arv-base-java",
  37                 "arvados_sdk_version": "master"
  38             }
  39         },
  40         "SortSam": {
  41             "script": "run-command",
  42             "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
  43             "repository": "arvados",
  44             "script_parameters": {
  45                 "command": [
  46                     "java",
  47                     "-Xmx4g",
  48                     "-Djava.io.tmpdir=$(tmpdir)",
  49                     "-jar",
  50                     "$(dir $(picard))/SortSam.jar",
  51                     "CREATE_INDEX=True",
  52                     "SORT_ORDER=coordinate",
  53                     "VALIDATION_STRINGENCY=LENIENT",
  54                     "INPUT=$(glob $(dir $(input))/*.sam)",
  55                     "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
  56                 ],
  57                 "input": {
  58                     "output_of": "bwa-mem"
  59                 },
  60                 "picard": {
  61                     "required": true,
  62                     "dataclass": "Collection",
  63                     "default": "88447c464574ad7f79e551070043f9a9+1970"
  64                 }
  65             },
  66             "runtime_constraints": {
  67                 "docker_image": "bcosc/arv-base-java",
  68                 "arvados_sdk_version": "master"
  69             }
  70         }
  71     }
  72 }