Check samples with a low (< 1%) snpit Percentage

BCCDC-PHL / tbprofiler-nf

Nextflow Wrapper for TBProfiler

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Check samples with a low (< 1%) snpit Percentage #26

Closed dfornika closed 5 months ago

dfornika commented 5 months ago

Fixes #22

If a sample has a Percentage below 1.0 in its snpit output, then we check its tbprofiler report for main_lin = lineage4 and pct_reads_mapped > 98%. If both of those are true then the Species is changed to M. tuberculosis. The Name and Percentage are changed to N/A