bwa.yaml

# Full hg38/GRCh38 reference genome distributed by 1000 genomes
# Derived from NCBI set with HLA and decoy alternative alleles
# http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/
# Pre-build bwa indices
---
attributes:
  name: bwa
  version: 1000g-20150219 
recipe:
  full:
    recipe_type: bash
    recipe_cmds:
      - |
        url=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome
        base=GRCh38_full_analysis_set_plus_decoy_hla.fa
        new=hg38.fa
        mkdir -p bwa
        for suffix in .bwt .amb .ann .pac .sa .alt
        do
          [[ -f bwa/$new$suffix ]] || wget -c -O bwa/$new$suffix $url/$base$suffix
        done
    recipe_outfiles:
      - bwa