Created script for formatting Cecret results for clinical measles samples for easily updating WGS Tracking Google Sheet.

[robbysainsbury]

No description provided.

[erinyoung]

This is great!

Can you put together a few sentences about this script in the main readme?

mev_cecret_to_sheets.py

This script merges sequencing output (from the "Cecret" pipeline) with a sample sheet based on a run name provided as a command-line argument. It creates a standardized tracking file by selecting specific columns, adding placeholders for manual entry, and validating that the detected organism is Measles (Morbillivirus hominis), flagging the row if it is not.

Example

python3 /General_LW_scripts/mev_cecret_to_sheets.py <run name>

[erinyoung]

Thanks!