Table options (report options 1 and 2)

How to customise tables in the civet report.

There are two sets of configurable tables in the civet report. Each argument takes a comma separated string of column names found in the background or input metadata files.

Query table content (report option 1)

Table summarising various aspects of the queries.

Default:
--background_id_column,--background_date_column,source,lineage,country,catchment

See Background column configuration for more information on these arguments.

Usage:
--query-table-content {$LIST}

Catchment table content (report option 2)

Table summarising various aspects of the sequences found in the catchment around each query.

Default:
count,country,lineage

Usage:
--catchment-table-content {$LIST}