This is using the Nextclade "coverage" as "genome_coverage" and the Nextclade "failedCdses"
to check if E_coverage is present or not.

fixup: use 1 instead of true

This can be one gene or a set of genes, can then be used to calculate gene_coverage columns.

Move intermediate files to the "data" folder

… acid FASTA file

Adds the following rules for gene coverage

* calculate_gene_coverage: calls a python script which takes a Nextclade CDS translation FASTA and calculates (valid AA)/(total length). The percentage is rounded to 3 significant figures.
* aggregate_gene_coverage_by_gene: combines the gene_coverage files by gene (e.g. ["E", "NS1"] ) across all serotypes (e.g. denv1-4)
* appends_gene_coverage_columns: Add each gene_coverage column (e.g. "E_coverage", "NS1_coverage") to the the final metadata

Co-authored-by: Jover Lee <joverlee521@gmail.com>

#36 (comment)

Since we are not using the E_indicator column, drop it.
We have separate steps to calculate the E_coverage column.

…g params so they don't get out of sync between rules

Encode serotype and gene as part of the directory structure where possible.

As suggested by #36 (comment)
Merge ID should be the first item in the map