gatk-base_recalibration_print_reads.yml

# -R takes also .fai and .dict
reference_genome:
  class: File
  path: /mnt/input/hs37d5.fa

# -I from ir step realigned BAM
# also .bai
input:
  class: File
  path: /mnt/input/abc1.sorted.md.realigned.bam
# -o
# output_filename: recalibrated.bam

dict:
  class: File
  path: /mnt/input/hs37d5.dict

# -BQSR   array of files?
br_model:
  class: File
  path: /mnt/input/abc1.sorted.md.realigned.br_model