# Panels of normals (PONs) for variant calling
# germline_het_pon -- Locations of likely germline heterogygote sites
---
attributes:
  name: varpon
  version: 20181105
recipe:
  full:
    recipe_type: bash
    recipe_cmds:
      - |
        ref=../seq/hg38.fa
        mkdir -p variation
        wget --no-check-certificate -O - 'https://nc.hartwigmedicalfoundation.nl/index.php/s/a8lgLsUrZI5gndd/download?path=%2FHMF-Pipeline-Resources&files=GermlineHetPon.hg38.bed.gz' | gunzip -c | python -c 'import sys; want=tuple(["chr%s" % x for x in list(range(1, 23)) + ["X", "Y"]]); [sys.stdout.write(l) for l in sys.stdin if l.startswith(want)]' | gsort -m 3000 /dev/stdin $ref.fai | bgzip -c > variation/germline_het_pon.bed.gz
        tabix -f -p bed variation/germline_het_pon.bed.gz
    recipe_outfiles:
      - variation/germline_het_pon.bed.gz
      - variation/germline_het_pon.bed.gz.tbi

# Panels of normals (PONs) for variant calling
# germline_het_pon -- Locations of likely germline heterogygote sites
---
attributes:
  name: varpon
  version: 20181105
recipe:
  full:
    recipe_type: bash
    recipe_cmds:
      - |
        ref=../seq/hg38.fa
        mkdir -p variation
        wget --no-check-certificate -O - 'https://s3.amazonaws.com/biodata/collections/hg38/variation/germline_het_pon.bed.gz' > variation/germline_het_pon.bed.gz
        wget --no-check-certificate -O - 'https://s3.amazonaws.com/biodata/collections/hg38/variation/germline_het_pon.bed.gz.tbi' > variation/germline_het_pon.bed.gz.tbi
    recipe_outfiles:
      - variation/germline_het_pon.bed.gz
      - variation/germline_het_pon.bed.gz.tbi

Use biodata bucket for download instead of hartwig
Use biodata bucket for download instead of hartwig

I think the hartwig download site is down or moved, so grab these files from
our bucket instead.

Fixes bcbio/bcbio-nextgen#2923. Thanks to @LimWChing for bringing up the issue.
