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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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Make sure pathogens are detected for mapdamage to run #1

Closed percyfal closed 2 years ago

percyfal commented 2 years ago

Currently no pathogens are detected, which has to do with test data setup. Make sure there is output data for mapdamage to work on. One could possibly also rewrite the rule such that mapdamage will write empty output files and warn that no pathogens were found.

LeandroRitter commented 2 years ago

maoDamage seems to work fine when the pathogensFound.tab file is made tab-delimited. The issue seems to have been not due to absence of pathogens (there is in fact Y.pestis) but the pathogensFound.tab file that could not be properly read (because of spaces in the file) and intersected with the filtered output from KrakenUniq

percyfal commented 2 years ago

Fixed by #8.