R/gather_run_info.R

In johnmcculloch/JAMS_BW: Just A Microbiology System

#' gather_run_info
#'
#' JAMSalpha function
#' @export

gather_run_info <- function(opt = NULL){

    flog.info("Gathering information on JAMS analysis run.")
    stunde <- round(as.numeric((opt$endtime - opt$starttime), units = "hours"), 2)

    Run_info = c("JAMS_version", "JAMS_Kdb_Version", "JAMS_Kdb_Confidence", "Sample_name", "Run_start", "Run_end", "Duration_hours", "CPUs_used")
    Run_value = c(opt$verstr, opt$JAMS_Kdb_Version, as.character(opt$krakenconfidencescore), opt$prefix, as.character(opt$starttime), as.character(opt$endtime), stunde, opt$threads)
    projinfo <- data.frame(Run_info = Run_info, Run_value = Run_value)

    if ("readsdir" %in% names(opt)){
        process <- "Assemble_from_reads"
        Run_info <- c("Run_type", "Process", "Sequencing_chemistry", "Library_strategy", "Contig_assembler", "Contig_assembler_version", "Host_species")
        Run_value <- c(opt$analysis, process, opt$seqtype, opt$libstructure, opt$assembler, opt$assemblerversion, opt$host)

    } else {
        process <- "Contigs_supplied"
        Run_info <- c("Run_type", "Process")
        Run_value <- c(opt$analysis, process)
    }

    projinfosup <- data.frame(Run_info = Run_info, Run_value = Run_value)

    opt$projinfo <- rbind(projinfo, projinfosup)

    return(opt)
}