% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/clean_all_folders.R
\name{clean_all_folders}
\alias{clean_all_folders}
\title{Delete the internal folder hierarchy}
\usage{
clean_all_folders(foldernames)
}
\arguments{
\item{foldernames}{a character vector storing the folder names that shall be deleted.}
}
\value{
This is a void function.
}
\description{
This function deletes all internal folders that have been created
during pipeline processing. Internally this function uses \code{\link{unlink}}
to delete all folders created by the pipline.
}
\details{
This function takes a vector storing the names of the folders
that shall be deleted, e.g.: \code{clean_all_folders( c("_alignment", "_blast_db", "_calculation") )}.

Since \pkg{orthologr} is a package for pipeline processing based on interface functions,
many partial results need to be written to a hard drive to allow subsequent programs
to access the output of previous computations. The R core conventions do not favour this
behaviour of functions. This would indicate that the \code{clean_folders} argument had to be \code{TRUE}
by default in all functions. Nevertheless, this would distract some pipeline functions and therefore
\code{clean_folders} = \code{FALSE} by default leaving you with a folder environment that needs
to be cleaned by hand, meaning that when using a specific function or pipeline function
you must specify \code{clean_folders} = \code{TRUE} in case you want to remove all internal folders
after pipeline processing.
}
\seealso{
\code{\link{divergence_stratigraphy}}, \code{\link{blast}}, \code{\link{blast_best}}, 
\code{\link{blast_rec}}, \code{\link{dNdS}}
}
\author{
Hajk-Georg Drost
}
