encga.opencga-test.2.8.2.1.source-code.configuration.yml Maven / Gradle / Ivy

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#There are some variables that we can include in both the caller and aligner instructions. These variables are:
# ${PARAMS} It must be put in the place that the instruction requires the parameters
# ${INDEX} Its value is the one that exists in the index field of the reference
# ${OUTPUT} It is the output directory
# ${BAM} It is the path of the sorted bam file
# ${REFERENCE.PATH} Its value is the one that exists in the path field of the reference
# ${FASTQNAME} Is the name of one of the input fastq files, with no extension
# ${FASTQ1} Is the name of the first of the input fastq files of the pair
# ${FASTQ2} Is the name of the second of the input fastq files of the pair

execution:
  id: "k8s Jobs"
  queue: "queue1"
  azureCredentials: ""
  options:
    - "option1"
envs:
  - id: "corpasome-1"
    description: "generate son's vcf for corpasome-grch38"
    dataset:
      path: "/home/juanfe/trainning/"
      paired: true
    data:
      path: "/home/juanfe/trainning/data/"
    reference:
      path: "/home/juanfe/trainning/index/Falbicolis.chr5.fa"
      index: "/home/juanfe/trainning/index/"
    aligner:
      #skip: true
      name: "BWA v0.7.17-r1188"
      image: "opencb/opencga-ext-tools"
      command: "bwa mem ${PARAMS} ${INDEX}Falbicolis.chr5.fa ${FASTQ1} ${FASTQ2} > ${OUTPUT}"
      params:
        - "-t 4"
        - "-R '@RG\\tID:${FASTQNAME}\\tSM:${FASTQNAME}'"
    callers:
      - name: "GATK v4.2.6.1"
        #skip: true
        image: "broadinstitute/gatk:4.2.6.1"
        command: "gatk HaplotypeCaller ${PARAMS} >/dev/null 2>&1"
        params:
          - "--input ${BAM}"
          - "--output ${OUTPUT}"
          - "--reference ${REFERENCE.PATH}"
logger:
  logLevel: "off"