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.
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get sample_size from any row in sample_stats for user-uploaded fasta #164
User-uploaded fastas result in single-line sample_stats files, so take sample_size from the first row, just like for wastewater. This will eliminate pattern-matching errors with different file name formats.
User-uploaded fastas result in single-line sample_stats files, so take sample_size from the first row, just like for wastewater. This will eliminate pattern-matching errors with different file name formats.