The cleanup command
bpipe cleanup [-y] [<file1>] [<file2>]...
Deletes intermediate files from outputs of a pipeline. The primary purpose of this command is to save space in storing unnecessary intermediate files that are not needed after a pipeline is finished running.
Intermediate files are files that are not final outputs ie. that are used as inputs in the pipeline for creating other outputs, and which have not been explicitly marked by the user as 'preserved' using the preserve command or annotation. Since these files are often not needed once the final result has been computed and are merely computational results that can be recreated from the inputs, it often makes sense to remove them. The cleanup command computes which files are intermediates and removes them for you automatically, while also marking that they were removed by cleanup in the file meta data so that the removal is logged, and dependency calculations can understand that it is not necessary to recreate these files when running the pipeline again unless it is explicitly required.
-y option, the cleanup command will not ask the user for confirmation. Otherwise it will list the files to be deleted and give the user the option to proceed by deleting, moving to "trash" or cancelling.
Cleanup all intermediate files without prompting
bpipe cleanup -y
*Cleanup all Intermediate BAM files
bpipe cleanup *.bam