add section on CIVET reports

[tavareshugo]

• See these materials for inspiration
• I think the data can be downloaded from COG-UK website (see the links at the very bottom of the page)
• The data it needs are detailed in the CIVET docs (alignment.fasta, metadata.csv, phylogeny.nexus)

[tavareshugo]

I need to put these things down in scripts, but for now just documenting it here:

• Default installation of civet failed, due to an error from snakemake. In the environment.yml they set <=6.8.0, but updating it to 7.16.0 fixed the problem.
• Downloaded background data from GISAID following these instructions: https://cov-lineages.org/resources/civet/walkthrough.html#background_dataset
• Ran: civet -bd align_curate -bd-seqs hcov_asia/hcov_asia.fasta -bd-metadata hcov_asia/hcov_asia.tsv --sequence-id-column strain
• Then the analysis: civet -i report/metadata.csv -f report/consensus.fa -icol sample -idate date -d resources/civet_data -o results/civet -bicol modified_strain