platypus.json

{
  "sbg:contributors": [
    "Tiffany Delhomme"
  ],
  "sbg:createdBy": "Tiffany Delhomme",
  "description": "platypus variant calling for whole-exome sequencing data",
  "id": "platypus",
  "class": "CommandLineTool",
  "hints": [
    {
      "class": "DockerRequirement",
      "dockerPull": "iarcbioinfo/platypus-nf"
    },
    {
      "class": "sbg:MemRequirement",
      "value": 30000
    },
    {
      "class": "sbg:AWSInstanceType",
      "value": "c4.4xlarge"
    },
    {
      "class": "sbg:CPURequirement",
      "value": 16
    }
  ],
  "requirements": [
    {
      "id": "#cwl-js-engine",
      "requirements": [
        {
          "class": "DockerRequirement",
          "dockerPull": "rabix/js-engine"
        }
      ],
      "class": "ExpressionEngineRequirement"
    }
  ],
  "baseCommand": "/Platypus/bin/Platypus.py callVariants --badReadsThreshold=0 --qdThreshold=0 --rmsmqThreshold=20 --hapScoreThreshold=10 --scThreshold=0.99 --nCPU=16",
  "arguments": [],
  "label": "CWL platypus for exome data",
  "inputs":[
    {
      "sbg:category": "Basic",
      "type": [
        "File"
      ],
      "description": "BAM file to be called with platypus.",
      "label": "input BAM file",
      "id": "#bamfile",
      "sbg:fileTypes": "BAM",
      "required" : true,
      "inputBinding": {
        "separate": false,
        "sbg:cmdInclude": true,
        "position": 0,
        "prefix" : "--bamFiles=",
        "secondaryFiles" : "^.bai"
      }
    },
    {
      "sbg:category": "Basic",
      "type": [
        "File"
      ],
      "description": "Genome reference in FASTA format",
      "label": "reference FASTA file",
      "id": "#ref",
      "sbg:fileTypes": "FASTA",
      "required" : true,
      "inputBinding": {
        "separate": false,
        "sbg:cmdInclude": true,
        "position": 1,
        "prefix" : "--refFile=",
        "secondaryFiles" : ".fai"
      }
    },
    {
      "sbg:category": "Basic",
      "type": [
        "string"
      ],
      "description": "Name of the variant calling output file.",
      "label": "output VCF file name",
      "id": "#output_vcf_name",
      "required" : false,
      "inputBinding": {
        "separate": false,
        "sbg:cmdInclude": true,
        "position": 2,
        "prefix" : "--output=",
        "valueFrom" : {
          "class": "Expression",
          "script": "x=$job.inputs.bamfile.name; x.split('.bam')[0] + '_platypus.vcf' ",
          "engine": "#cwl-js-engine"
        }
      }
    }
  ],
  "outputs":[
    {
      "id": "#output_vcf",
      "type": [
        "File"
      ],
      "description" : "Output variant calling file from platypus.",
      "sbg:fileTypes": "vcf",
      "outputBinding": {
        "glob": {
          "class": "Expression",
          "script": "x = $job.inputs.bamfile.name; x.split('.bam')[0] + '_platypus.vcf'",
          "engine": "#cwl-js-engine"
        }
      }
    }
  ]
}