Each element of the civet report is associated with a number:
Provide combinations of these letters as a comma separated string to define the elements present in the report.
You can also use presets report configuration using -rp/--report-preset:
Default:
the usual (1,2,3,4,5)
Usage:
--report-content {$LIST} or -rc {$LIST}
--report-preset {$PRESET} or -rp {$PRESET}
Title to show at the top of the report.
Default:
civet report
Usage:
--report-title {$TITLE} or -rt {$TITLE}
Report theme colour, specifiy a HEX colour code to colour the panels and highlighting in the report.
Default:
#7178bc
Usage:
-ct/--colour-theme {$HEX_CODE}
Comma separated string of HEX codes or HTML-support names to colour factors in different figures in the report by.
Default:
civet logo colours
Usage:
--colour-map/-cmap {$LIST}
Provides anonymised IDs to replace sequence names for display in the report.
Alternatively, you may provide a column in the metadata to refer to queries by using -rcol/--report-column. See Input column configuration
Default:
False
Usage:
--anonymise