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ellisrichardj / BovTB-nf

Nextflow script for processing WGS data
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Add explanations to output for failure to assign WGS Cluster #11

Closed ellisrichardj closed 4 years ago

ellisrichardj commented 5 years ago

Currently if WGS cluster is not assigned, either bTB or LowCoverage is output. By using the data captured on %mapped and number of reads, it should be possible to determine if the sample should be repeated.

ellisrichardj commented 5 years ago

Flags are now included in the final output file: "Pass", "Contaminated" or "Insufficient data", calculated from depth of coverage and % mapped

ellisrichardj commented 4 years ago

Now closed - happy that flags indicate reasons for inability to assign WGS cluster