surveillance report generation doesn't work as expected if Index column not defined as a surveillance column

stenglein-lab / tick_surveillance

Bioinformatics pipeline for analysis of amplicon sequencing of tick-associated microbes

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surveillance report generation doesn't work as expected if Index column not defined as a surveillance column #61

Closed stenglein-lab closed 1 year ago

stenglein-lab commented 1 year ago

This is because assign_observed_sequences_to_ref_seqs.R refers to the Index column in a hardcoded way and if it's not present the report doesn't properly populate with values.