upload:
  dir: upload
details:
  - analysis: variant2
    algorithm:
      aligner: bwa
      #aligner: novoalign
      variantcaller: [samtools, gatk-haplotype, freebayes]
      #variantcaller: gatk-haplotype
      #variantcaller: freebayes
      #variantcaller: cortex
      #sv_detection: hydra
      recalibrate: false
      realign: false
      ensemble:
        numpass: 2
      quality_format: Standard
      tools_off: [gemini]
      trim_reads: true
      align_split_size: 9000
      variant_regions: ../data/automated/variant_regions-variantcall.bed
      coverage: ../data/automated/variant_regions-variantcall.bed
      validate: ../data/reference_material/7_100326_FC6107FAAXX-grade.vcf
    description: Test1
    metadata:
      batch: TestBatch1
    genome_build: hg19
    files: [../data/100326_FC6107FAAXX/7_100326_FC6107FAAXX_1_fastq.txt, ../data/100326_FC6107FAAXX/7_100326_FC6107FAAXX_2_fastq.txt]
    lane: 7

upload:
  dir: upload
details:
  - analysis: variant2
    algorithm:
      aligner: bwa
      #aligner: novoalign
      variantcaller: [samtools, gatk-haplotype, freebayes]
      #variantcaller: gatk-haplotype
      #variantcaller: freebayes
      #variantcaller: cortex
      #sv_detection: hydra
      recalibrate: false
      realign: false
      ensemble:
        numpass: 2
      quality_format: Standard
      tools_off: [gemini]
      trim_reads: true
      align_split_size: 9000
      variant_regions: ../data/automated/variant_regions-variantcall.bed
      coverage: ../data/automated/variant_regions-variantcall.bed
      validate: ../data/reference_material/7_100326_FC6107FAAXX-grade.vcf
      priority_regions: ../data/automated/variant_regions-variantcall.bed
    description: Test1
    metadata:
      batch: TestBatch1
    genome_build: hg19
    files: [../data/100326_FC6107FAAXX/7_100326_FC6107FAAXX_1_fastq.txt, ../data/100326_FC6107FAAXX/7_100326_FC6107FAAXX_2_fastq.txt]
    lane: 7

Add priority gene coverage to integraton tests.
Add priority gene coverage to integraton tests.
