Adding param file

Replace or adding a input configuration setting at "YML" param file

config.param(input_file = NULL, param, file = "default", silent = FALSE)

Arguments

input_file

a list of parameters, param file path, or SYSargs2 object.

param

object of class list, expressing the values and names to be added or replace at the command-line definition or the configuration files.

file

name and path of the new file. If set to default, the name of the write file will have the pattern: <Date-Time>_<OriginalName>.yml. If set to append, the param information it will be append on the same file.

silent

if set to TRUE, all messages returned by the function will be suppressed.

Author

Daniela Cassol

Examples

if (FALSE) {
input_file <- system.file("extdata", "cwl/hisat2/hisat2-mapping-se.yml", package="systemPipeR")
param <- list(thread=10, fq=list(class="File", path="./results2"))
input <- config.param(input_file=input_file, param, file="default")
 }