Add HGVS names to GVFs and mutation index

cidgoh / nf-ncov-voc

A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.

MIT License

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Add HGVS names to GVFs and mutation index #149

Closed miseminger closed 7 months ago

miseminger commented 7 months ago

Main changes:

get rid of 'alias_Pokay_annotation' column since it's no longer needed (functional annotations are added to GVFs based on both Name and Alias already)
add HGVS names to mutation index
if no starting mutation index is provided, make a new one using the files in args.gvf_files

miseminger commented 7 months ago

Adds HGVS names to GVFs and mutation index. All main types are covered except for nucleotide-level delins, because I need to look into why some mutations that are "delins" at the protein level aren't also "delins" at the nucleotide level (see comment to Issue 151). Any mutation name patterns that aren't recognized by this code are denoted "n/a" for troubleshooting.