R/cwlSearch.R

In RcwlPipelines: Bioinformatics pipelines based on Rcwl

#' cwlSearch
#'
#' Function to search Rcwl tools and pipelines.
#' @param keyword A (vector of) character string as keywords to search
#'     for tools or pipelines. Will be used to match patterns against
#'     `rname`, `rpath`, `fpath`, `Command` and `Container` column in
#'     the `bfc` object.
#' @param bfc The `BiocFileCache` object for the recipes returned from
#'     `cwlUpdate`. The default is NULL which automatically detect the
#'     "Rcwl" cache directory.
#' @param ... More options from the internal `bfcquery` function.
#' @return A BiocFileCache tibble.
#' @export
#' @examples
#' \dontrun{
#' tls <- cwlSearch(c("bwa", "mem"))
#' data.frame(tls)
#' }

cwlSearch <- function(keyword, bfc = NULL, ...){
    if(is.null(bfc)){
        cachePath <- user_cache_dir("Rcwl")
        bfc <- BiocFileCache(cachePath, ask = FALSE)
    }
    bfcquery(bfc, query = keyword,
             field = c("rname", "rpath", "fpath", "Command", "Container"),
             ...)
}