WISH: Add `--cleanup` to each script / step (was 5.cleanup.R)

[HenrikBengtsson]

Add a cleanup step (5.cleanup.R) after:

• Rscript 1.mpileup.R
  • write to folder seqzData/<dataset>,mpileup/
• Rscript 2.sequenza.R
  • reads from folder seqzData/<dataset>,mpileup/
  • write to folder seqzData/<dataset>,seqz/
  • when complete, the above input folder is no longer needed.
• Rscript 3.pscbs.R
  • reads from folder seqzData/<dataset>,seqz/
  • writes to folder pscbsData/<dataset>,seqz,<binsize>,tcn=2/
  • when complete, the above input folder is no longer needed.
• Rscript 4.reports.R
  • reads from folder pscbsData/<dataset>,seqz,<binsize>,tcn=2/

[HenrikBengtsson]

@SRHilz, I'm looking into adding the "cleanup" feature to the PSCN-Seq pipeline. See my original post of this issue for what folders can be deleted and when.

As an alternative to adding a separate 5.cleanup.R script at the very end, would it make sense to add an optional --cleanup command-line options to each step instead? That would delete the input files if (and only if) the script completes successfully. This would delete the files sooner with the increased risk of making it hard to troubleshoot. For instance, running

$ Rscript 2.sequenza.R --cleanup

Comments - what do you think?

[SRHilz]

I think this is even better, as it will ensure things are cleaned up as they run. If troubleshooting does need to be done, the scripts can then be re-run individually without --cleanup, and clean up can then be done manually. Thanks, Henrik!

[HenrikBengtsson]

That makes sense - useful feedback. Adding --cleanup is a decision