# Example configuration for running a whole genome variant calling
# pipeline on public NA12878 data from Illumina's Platinum Genome project
# http://www.illumina.com/platinumgenomes/
#
# For a quick-start guide to running this analysis, see the example
# pipeline section of the documentation:
# https://bcbio-nextgen.readthedocs.org/en/latest/contents/testing.html#example-pipelines
---
upload:
  dir: ../final
fc_date: '130327'
fc_name: iplat
details:
  - algorithm:
      aligner: bwa
      variantcaller: gatk-haplotype
      validate: giab-NA12878/truth_small_variants.vcf.gz
      validate_regions: giab-NA12878/truth_regions.bed
    analysis: variant2
    description: NA12878
    genome_build: GRCh37
    metadata:
      sex: female
    files: [../input/ERR091571_1.fastq.gz, ../input/ERR091571_2.fastq.gz]