Arguments
indirs
A character vector of directory paths containing NGS pipeline output
outdir
A character string pointing to a non-existing output directory
prepend_str
A character string, containing a prefix going to be appended on all output result files
num_cores
Number of cores available for parallel processing (for the merge bam step)
config_update
List of name value pairs that will update the config parameters
preMergeChecks.do
A logical, indicating whether to perform pre merge checks
ignoreConfigParameters
A character vector containing the configuration parameters that are not required to be identical