Generate detailed UK report

Generates UK report for weekly COG-UK data

Inputs required:

• metadata csv

• In individual folders for each global lineage (if you want tree rendering):

  • subtrees cut up into newick files

Caveats:

• The lineage subfolders must all be in one directory with nothing else in it
• The date format in the metadata must be yyyy-mm-dd if there are months/days

Adding figures and text

Scripts for data management and figure generation are in /utils.

The report is made using UK_report_templatev2.pmd. This is where the calls to these scripts are made, and text added. Therefore if you want to add a new figure or text, you must put a callable python script in /utils and add the function call to the template.

Report generation

This template is then parsed to make the pmd file with inputs, and weaved to create an md file using Pweave (http://mpastell.com/pweave/). This MD file is then converted to a PDF using pandoc.

To generate the report:

1. Clone this repo
2. cd Reports
3. pip install .
4. If you haven't run it before, make the environment by running conda env create -f UK_full_report/environment.yml
5. Activate the environment by running conda activate report
6. Run the command: generate_report --m path/to/metadata --w relevant_week --s file_name_stem --od path/to/output

For filtering reports:

• --sc sequencing_centre which lets you filter the metadata by sequencing centre, for example: --sc NORW
• --adm adm1_country produces UK country specific reports

This will produce a MD file, a PDF and the figures as PNGs. Depending on your output file path, the markdown may not contain the figures, but the PDF will.

Acknowledgements

Tree visualisations are undertaken using baltic (https://github.com/evogytis/baltic)

Shape files for mapping for England, Wales and Scotland were taken from the Global Administrative Database (https://gadm.org/)

Shape files for mapping Northern Ireland were taken from Open Data NI (https://www.opendatani.gov.uk/dataset?tags=Counties)

Shape files for mapping the channel islands were taken from https://gist.github.com/markmarkoh