<commit_before># Annotation files for vcfanno variant annotation
# Feeds into vcf2db GEMINI database creation and other annotation tasks
---
attributes:
  name: vcfanno
  version: 20170522
recipe:
  full:
    recipe_type: bash
    recipe_cmds:
      - |
        vcfanno_githash=5fcce8db2aeee016ab927c8ca36a715c02f982f9
        bcbio_githash=5bcfde79c083d5c34f13f81fe578b4606a7cc80c
        mkdir -p config/vcfanno
        cd config/vcfanno
        gemini_baseurl=https://github.com/brentp/vcfanno/raw/$vcfanno_githash/example
        wget --no-check-certificate -O gemini.lua -c $gemini_baseurl/custom.lua
        wget --no-check-certificate -O gemini.conf -c $gemini_baseurl/gem.conf
        bcbio_baseurl=https://github.com/chapmanb/bcbio-nextgen/raw/$bcbio_githash/config/vcfanno
        wget --no-check-certificate -O rnaedit.conf -c $bcbio_baseurl/GRCh37-rnaedit.conf
        wget --no-check-certificate -O rnaedit.lua -c $bcbio_baseurl/GRCh37-rnaedit.lua
        wget --no-check-certificate -O dbnsfp.conf -c $bcbio_baseurl/GRCh37-dbnsfp.conf
        wget --no-check-certificate -O dbscsnv.conf -c $bcbio_baseurl/GRCh37-dbscsnv.conf

    recipe_outfiles:
      - config/vcfanno/gemini.lua
      - config/vcfanno/gemini.conf
      - config/vcfanno/rnaedit.lua
      - config/vcfanno/rnaedit.conf
      - config/vcfanno/dbnsfp.conf
      - config/vcfanno/dbscsnv.conf<commit_msg>hg19: Fixed configuration for GEMINI clinvar<commit_after># Annotation files for vcfanno variant annotation
# Feeds into vcf2db GEMINI database creation and other annotation tasks
---
attributes:
  name: vcfanno
  version: 20170611
recipe:
  full:
    recipe_type: bash
    recipe_cmds:
      - |
        vcfanno_githash=10f067337d1a4651882aded670b283593f94700f
        bcbio_githash=5bcfde79c083d5c34f13f81fe578b4606a7cc80c
        mkdir -p config/vcfanno
        cd config/vcfanno
        gemini_baseurl=https://github.com/brentp/vcfanno/raw/$vcfanno_githash/example
        wget --no-check-certificate -O gemini.lua -c $gemini_baseurl/custom.lua
        wget --no-check-certificate -O gemini.conf -c $gemini_baseurl/gem.conf
        bcbio_baseurl=https://github.com/chapmanb/bcbio-nextgen/raw/$bcbio_githash/config/vcfanno
        wget --no-check-certificate -O rnaedit.conf -c $bcbio_baseurl/GRCh37-rnaedit.conf
        wget --no-check-certificate -O rnaedit.lua -c $bcbio_baseurl/GRCh37-rnaedit.lua
        wget --no-check-certificate -O dbnsfp.conf -c $bcbio_baseurl/GRCh37-dbnsfp.conf
        wget --no-check-certificate -O dbscsnv.conf -c $bcbio_baseurl/GRCh37-dbscsnv.conf

    recipe_outfiles:
      - config/vcfanno/gemini.lua
      - config/vcfanno/gemini.conf
      - config/vcfanno/rnaedit.lua
      - config/vcfanno/rnaedit.conf
      - config/vcfanno/dbnsfp.conf
      - config/vcfanno/dbscsnv.conf
{'fraction_non_alphanumeric': 0.09688952449052557, 'fraction_numerical': 0.047550947443689665, 'mean_word_length': 2.9408450704225353, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2112429', 'n_tokens_mistral': 1172, 'n_tokens_neox': 1098, 'n_words': 162}