Behaviour and location of workdir, and removing hippunfold/ toplevel folder #338
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- WIP - sets workdir to a temp directory by default - the files won't be deleted by the workflow, but we could make use of temp() to do so..
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Previously, each hippunfold output directory would contain hippunfold and work sub-directories. This moves the work folder to a temporary location (e.g. a folder in /tmp), and then removes the extra top-level hippunfold folder. That extra folder level isn't really needed removing it makes hippunfold more bids-derivatives compliant.
There is no automatic archiving of the work directory anymore as well, so the --keep-work option is removed. We also have a new CLI option for setting the location of the workdir. By default, the files in work are not deleted by snakemake, so the user could keep them by setting --workdir appropriately, or point it to e.g. $SLURM_TMPDIR.
We can also make use of the temp() directive in the workflow to have snakemake delete the files after they are no longer needed, which can be disabled with --notemp. I don't think its really critical to do that though, since the workdir can be put in a place where the system will delete them later..