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.




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.


Hajk-Georg Drost