Nextflow clean -f -but <mnemonic> behavior unclear

[Matteo Schiavinato]

Hi,

In my work I often use nextflow developing workflows as I go, figuring out the next step (i.e. the next process to add to the workflow) once the previous one has completed.

This makes my workflows grow a lot, so every now and then I run a nextflow clean -f -but <last_mnemonic>  so to remove all the files in the work directory from previous runs.

The way I understood it, that command would sort of "raster" the analysis to the last run, cleaning up the work directory a bit.

In one of my latest workflows I am working with 204 samples, and when I do this cleaning command I systematically lose the cached files of a dozen samples. When I run the workflow with -resume, these dozen restart from the beginning while the others are cached.

I hope my doubt is clear: is nextflow clean expected to leave all cached files that were used in the run that is kept with -but, or when removing previous runs it removes also cached files generated in those?

Thanks in advance for the clarification,

Matteo