# Configuration comparing alignment methods, preparation approaches
# and variant callers for a CEPH NA12878 whole genome trio, using Illumina platinum
# genome inputs and Genome in a Bottle reference calls.
#
# See the bcbio-nextgen documentation for full instructions to
# run this analysis:
# https://bcbio-nextgen.readthedocs.org/en/latest/contents/testing.html#example-pipelines
---
upload:
  dir: ../final
details:
  - files: [../input/NA12878_1.fastq.gz, ../input/NA12878_2.fastq.gz]
    description: NA12878
    metadata:
      batch: ceph
      sex: female
    analysis: variant2
    genome_build: hg38
    algorithm:
      aligner: bwa
      exclude_regions: [lcr]
      mark_duplicates: true
      recalibrate: false
      realign: false
      variantcaller: gatk-haplotype
      validate: giab-NA12878/truth_small_variants.vcf.gz
      validate_regions: giab-NA12878/truth_regions.bed
  - files: [../input/NA12891_1.fastq.gz, ../input/NA12891_2.fastq.gz]
    description: NA12891
    metadata:
      batch: ceph
      sex: male
    analysis: variant2
    genome_build: hg38
    algorithm:
      aligner: bwa
      mark_duplicates: true
      recalibrate: false
      realign: false
      variantcaller: gatk-haplotype
  - files: [../input/NA12892_1.fastq.gz, ../input/NA12892_2.fastq.gz]
    description: NA12892
    metadata:
      batch: ceph
      sex: female
    analysis: variant2
    genome_build: hg38
    algorithm:
      aligner: bwa
      mark_duplicates: true
      recalibrate: false
      realign: false
      variantcaller: gatk-haplotype