pipeline-builder-demo/src/data/tool-groups.json

Pipeline Builder

[
  {
    "groupName":"BWA",
    "tools":[
      {
        "name":"mem",
        "wdl":"task mem {\n  File fasta\n  File fastq_1\n  File fastq_2\n  command {\n    java -jar bwa_wrapper-1.0.jar\\\n    mem\\ \n    '${fasta}' \\\n    '${fastq_1}' \\\n    '${fastq_2}' \n  }\n}"
      },
      {
        "name":"aln",
        "wdl":"task aln {\n  File fasta\n  command {\n    java -jar bwa_wrapper-1.0.jar\\\n    aln\\ \n    '${fasta}'\n    'default.sai'}\n  output { \nFile sai = \"default.sai\"\n}\n}"
      },
      {
        "name":"samse",
        "wdl":"task samse {\n  File fasta\n  File in_sai\n  command {\n    java -jar bwa_wrapper-1.0.jar\\\n    samse\\ \n    '${fasta}' \\\n    '${in_sai}' \n  }\n}"
      }
    ]
  },
  {
    "groupName":"PICARD",
    "tools":[
      {
        "name":"MergeSamFiles",
        "wdl":"task MergeSamFiles {\n  File INPUT1\n  File INPUT2\n  command {\n    java -jar picard.jar\\\n    MergeSamFiles\\ \n    INPUT1='${INPUT1}' \\\n    INPUT2='${INPUT2}' \n  }\n}"
      },
      {
        "name":"EstimateLibraryComplexity",
        "wdl":"task EstimateLibraryComplexity {\n  File INPUT\n  command {\n    java -jar picard.jar\\\n    EstimateLibraryComplexity\\ \n    INPUT='${INPUT}' \n  }\n}"
      },
      {
        "name":"NiceTool",
        "wdl":"task NiceTool {\n  File INPUT\n  command {\n    java -jar picard.jar\\\n    NiceTool\\ \n    INPUT='${INPUT}' \n  }\n}"
      },
      {
        "name":"MarkDuplicates",
        "wdl":"task MarkDuplicates {\n  File bam\n  command {\n    java -jar picard.jar\\\n    MarkDuplicates\\ \n    INPUT='${bam}' \n    OUTPUT='default.bam'\n    METRICS_FILE='default.txt'\n   }\n      output {        File bam_out = \"default.bam\"\n     File txt = \"default.txt\" }\n}"
      },
      {
        "name":"CollectWgsMetrics",
        "wdl":"task CollectWgsMetrics {\n  File INPUT\n  File REFERENCE_SEQUENCE\n  command {\n    java -jar picard.jar\\\n    CollectWgsMetrics\\ \n    INPUT='${INPUT}' \\\n    REFERENCE_SEQUENCE='${REFERENCE_SEQUENCE}' \n  }\n}"
      },
      {
        "name":"BuildBamIndex",
        "wdl":"task BuildBamIndex {\n  File INPUT\n  command {\n    java -jar picard.jar\\\n    BuildBamIndex\\ \n    INPUT='${INPUT}' \n  }\n}"
      }
    ]
  }
]