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ellisrichardj / BovTB-nf

Nextflow script for processing WGS data
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Reliably detect M.bovis when it's at low prevalence in the sample #17

Open ellisrichardj opened 4 years ago

ellisrichardj commented 4 years ago

Need to filter kraken/bracken output so that presence of M.bovis in the sample is recognised and flagged. This should be added to the output csv file

ellisrichardj commented 4 years ago

M. bovis is classified as 'S1' level in kraken output (M. tuberculosis var. bovis) so bracken needs to filter on this level

ellisrichardj commented 4 years ago

Use grep to parse bracken output for M.bovis presence. However, if not present grep gives and exit code and process fails.

ellisrichardj commented 4 years ago

Need to look though existing data and determine threshold / cut-off abundance for positive/negative