This function deletes all internal folders that have been created
during pipeline processing. Internally this function uses unlink
to delete all folders created by the pipline.
clean_all_folders(foldernames)a character vector storing the folder names that shall be deleted.
This is a void function.
This function takes a vector storing the names of the folders
that shall be deleted, e.g.: clean_all_folders( c("_alignment", "_blast_db", "_calculation") ).
Since 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 clean_folders argument had to be TRUE
by default in all functions. Nevertheless, this would distract some pipeline functions and therefore
clean_folders = 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 clean_folders = TRUE in case you want to remove all internal folders
after pipeline processing.