haplotypecaller_example.json

{
  "taskName":"HaplotypeCaller",
  "description":"",
  "version":"",
  "maxRetries":0,
  "continueOnReturnCode":"",
  "failOnStderr":false,
  "backends":"SGE",
  "parameter":{
    "mem":{
      "type":"Int",
      "defaultValue":8,
      "required":false,
      "description":"memory(G)"
    },
    "cpu":{
      "type":"Int",
      "defaultValue":1,
      "required":false,
      "description":"thread number"
    },
    "queue":{
      "type":"String",
      "defaultValue":"",
      "required":false,
      "description":"thread number"
    },
    "gatk":{
      "type":"String",
      "required":true,
      "description":"Set it when call this task in workflow"
    },
    "input_bam":{
      "type":"String",
      "required":true,
      "description":"Set it when call this task in workflow"
    },
    "ref_fasta":{
      "type":"String",
      "required":true,
      "description":"Set it when call this task in workflow"
    },
    "interval_list":{
      "type":"String",
      "required":true,
      "description":"Set it when call this task in workflow"
    },
    "gvcf_basename":{
      "type":"String",
      "defaultValue":"part",
      "required":false,
      "description":""
    },
      "interval_padding": {
        "type":"String",
        "required":true,
        "description":"Set it when call this task in workflow"
      }
  },
  "command":"${gatk} --java-options \"-Xms8g -XX:GCHeapFreeLimit=10 -XX:ParallelGCThreads=2\" HaplotypeCaller -R ${ref_fasta} -O ${gvcf_basename}.g.vcf.gz -I ${input_bam} -L ${interval_list} ${\"-ip \" + interval_padding} -ERC GVCF",

  "output":{
    "output_gvcf":{
      "type":"String",
      "expression":"${gvcf_basename}.g.vcf.gz",
      "description":""
    },
    "output_gvcf_index":{
    "type":"String",
    "expression":"${gvcf_basename}.g.vcf.gz.tbi",
    "description":""
    }
  }
}