Remove skeleton data

[mbhall88]

I know there is an option to force override existing skeleton files, but I feel like that should be more of an opt-in feature rather than opt-out? I have never used these files and I doubt many others have.

I propose removing them by default and adding a flag to keep them.

[martinghunt]

The skeleton files are used by default if they are then on disk, and created if they are not found. It means if you run on >1 sample, then cortex build gets run on the first sample, then doesn't need to get run for all the subsequent ones. I expect lots of users use the skeleton files all the time.

There is a related issue though, that if you fire off >1 job at the same time and the skeleton files don't exist, then it will crash.

[mbhall88]

I see. I didn't realise they were sample-independent.

I've experienced the race condition behaviour with the skeleton files before, but I generally run mykrobe in a shadow directory using snakemake so it doesn't bother me too much.

I'm happy to leave it as is.