<commit_before>urls="http://" "" "" "" "" "" "" "" "" "" "" "";
samples=getReads(urls:urls);
samplesfq=convert2fastq(samples);

deftask getReads(sample(File):url) in bash *{
  sample=wget($urls)
}*

deftask convert2fastq(fqfile(File):srafile(File)) in bash *{
  fqfile=srafile
}*<commit_msg>added genome download and struct to create decoys.<commit_after>urls="http://" "" "" "" "" "" "" "" "" "" "" "";
samples=download(urls:urls);
samplesfq=convert2fastq(samples);
expectedContaminatingGenomeURLs="" "" "" "" "";
expectedContaminationgGenomes(File)=download(sample:expectedContaminatingGenomeURLs);
targetGenomeURLs="";
targetGenomeFiles=download(sample:targetGenomeURLs);
decoyGenomeFiles=shuffle(input:targetGenomeFiles);

deftask shuffle(decoy(File):input(File)) in bash *{
  decoy=input
}*

deftask download(sample(File):url) in bash *{
  sample=wget($urls)
}*

deftask convert2fastq(fqfile(File):srafile(File)) in bash *{
  fqfile=srafile
}*
{'fraction_non_alphanumeric': 0.1877637130801688, 'fraction_numerical': 0.004219409282700422, 'mean_word_length': 8.683673469387756, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 5, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3129547', 'n_tokens_mistral': 352, 'n_tokens_neox': 351, 'n_words': 43}