compile_viralrecon: Compile Results from nf-core/viralrecon for inclusion in...

In CUGBF/deidentifiedDB: Utility to Manage Clemson University COVID-19 Surveillance Data

Compile Results from nf-core/viralrecon for inclusion in deidentifiedDB database

Description

Compile Results from nf-core/viralrecon for inclusion in deidentifiedDB database

Usage

compile_viralrecon(
  filepath,
  run_date,
  viralrecon_version,
  primer_set_version,
  primer_set = "artic",
  variant_caller = "ivar",
  sequencing_platform = "illumina"
)

Arguments

filepath	Path to the multiqc summary csv for the viralrecon run
run_date	Start Date of the viralrecon run (for example, 2021-08-01 for August 1, 2021)
viralrecon_version	Version of viralrecon used for this run
primer_set_version	Primer set version (eg. 3, 4, 4.1)
primer_set	Name of the primer set used (eg. 'artic' , 'midnight')
variant_caller	Was 'iVar' or 'BCFTools' used for variant calling ?
sequencing_platform	Sequencing Technology Used (eg. 'illumina', 'nanopore')

Value

Tibble containing results from nf-core/viralrecon for inclusion to deidentifiedDB database

CUGBF/deidentifiedDB documentation built on Sept. 13, 2023, 6:28 a.m.