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                     "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 $(sample))/*_2.fastq)"
  19                 ],
  20                 "reference_collection": {
  21                     "required": true,
  22                     "dataclass": "Collection"
  23                 },
  24                 "sample": {
  25                     "required": true,
  26                     "dataclass": "Collection"
  27                 },
  28                 "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
  29             },
  30             "runtime_constraints": {
  31                 "docker_image": "arvados/jobs-java-bwa-samtools"
  32             }
  33         },
  34         "SortSam": {
  35             "script": "run-command",
  36             "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
  37             "repository": "arvados",
  38             "script_parameters": {
  39                 "command": [
  40                     "java",
  41                     "-Xmx4g",
  42                     "-Djava.io.tmpdir=$(tmpdir)",
  43                     "-jar",
  44                     "$(dir $(picard))/SortSam.jar",
  45                     "CREATE_INDEX=True",
  46                     "SORT_ORDER=coordinate",
  47                     "VALIDATION_STRINGENCY=LENIENT",
  48                     "INPUT=$(glob $(dir $(input))/*.sam)",
  49                     "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
  50                 ],
  51                 "input": {
  52                     "output_of": "bwa-mem"
  53                 },
  54                 "picard": {
  55                     "required": true,
  56                     "dataclass": "Collection",
  57                     "default": "88447c464574ad7f79e551070043f9a9+1970"
  58                 }
  59             },
  60             "runtime_constraints": {
  61                 "docker_image": "arvados/jobs-java-bwa-samtools"
  62             }
  63         }
  64     }
  65 }