The cleanup statement

Synopsis

  cleanup <file pattern>, <file pattern>, ...

Availability

  0.9.8.7+

Behavior

The cleanup statement causes Bpipe to remove the files matching the given patterns in such a way that they are not recreated if Bpipe is re-executed, unless they are required to produce an output that is out of date. This behavior is identical to passing the same files to the bpipe cleanup command.

Examples

Clean up intermediate BAM files produced

   cleanup_bams = {
        cleanup "*.dedupe.bam", "*.realign.bam"
   }