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@chapmanb @naumenko-sa @matthdsm
# 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