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Add --threads to bowtie-index command #16

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Add --threads to bowtie-index command #16

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4 changes: 4 additions & 0 deletions humann2/search/nucleotide.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,10 @@ def index(custom_database):

args=["-f",custom_database,index_name]

#add threads
if config.threads > 1:
args+=["--threads",config.threads]

outfiles=[index_name + ext for ext in config.bowtie2_index_ext_list]

# if custom_database is large (>4G) then use the --large-index flag
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