<commit_before># coding: utf-8
#
# Cookbook Name:: variant-call
# Recipe:: data
#
# Copyright (c) 2015 <NAME>, All Rights Reserved.

kgenomes_url_base = "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG02025/sequence_read/SRR"
kgenomes_dir = "#{node["dir"]["data"]}/#{node.kgenomes.dirname}"
annodb_hg38_dir = "#{node["dir"]["data"]}/annodb_hg38"
annodb_hg38_idlist = ["refGene.txt", "refGeneMrna.fa", "refGeneVersion.txt"]

include_recipe "chef-bioinf-worker::hg38"

# create directories
directory node["dir"]["data"]
directory kgenomes_dir
directory node["dir"]["data"]<commit_msg>Warnings also removed for data recipe.<commit_after># coding: utf-8
#
# Cookbook Name:: variant-call
# Recipe:: data
#
# Copyright (c) 2015 <NAME>, All Rights Reserved.

kgenomes_url_base = "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG02025/sequence_read/SRR"
kgenomes_dir = "#{node["dir"]["data"]}/#{node["kgenomes"]["dirname"]}"
annodb_hg38_dir = "#{node["dir"]["data"]}/annodb_hg38"
annodb_hg38_idlist = ["refGene.txt", "refGeneMrna.fa", "refGeneVersion.txt"]

include_recipe "chef-bioinf-worker::hg38"

# create directories
directory node["dir"]["data"]
directory kgenomes_dir
directory node["dir"]["data"]
{'fraction_non_alphanumeric': 0.18909991742361684, 'fraction_numerical': 0.03963666391412056, 'mean_word_length': 7.134228187919463, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, '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': '1725195', 'n_tokens_mistral': 505, 'n_tokens_neox': 467, 'n_words': 74}