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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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add possibility for "sequence" rank when filtering KU output #144

Open LeandroRitter opened 10 months ago

LeandroRitter commented 10 months ago

We need to replace this line:

kraken_output_df = kraken_output_df[kraken_output_df["rank"] == "species"]

by this line:

kraken_output_df = kraken_output_df[(kraken_output_df["rank"] == "species") | (kraken_output_df["rank"] == "sequence")]

In the aMeta/workflow/scripts/filter_krakenuniq.py