Add a scipipe cleantemp command to clean temporary folders

[samuell]

It is really annoying when runs are stopped because of existing temp folders, and one need to craft an rm command to delete them (which is also a bit dangerous).

A subcommand cleantemp in the scipipe command could take care of this.

[ziscky]

Hey, I would like to work on this.

[samuell]

@ziscky That's great to hear! You can find the code for the scipipe command, it's flag parsing code et.c. in this file. Feel free to send a PR whenever you have some code, and I've happy to have a look.

[ziscky]

@samuell Is there a specific workflow that generates the temp files ? Or should I check here for how they are cleaned up in the examples: https://github.com/scipipe/scipipe/blob/master/examples/clean.sh

[samuell]

@ziscky The temporary folder paths are created here, with the prefix specified on the first of these lines, so it should be possible to do the analog of rm -rf _scipipe_tmp*, but I think there needs to be an Are you sure? Y/n] prompt, to ensure these are not deleted accidentally e.g. by bringing up the cleancommand from history.

[samuell]

@ziscky Had a chance to have a look at this? :) I hope to get this included in a new release somewhat soon.

(Btw, I'm quite sure there will be more such good first issues to do later also, in case you find you need more time).

[samuell]

Also, I think the command should probably be just scipipe clean. One can later add flags like -t etc, if there turns out to be multiple sets of files that can be cleaned separately.