Tested single channel tif with LOCI bioformats

Automatic reading of calibration from .tif files

Varying z-slices should be possible now, loads them automatically
But not tested yet

At the moment only one z-stack size possible
compress not supported anymore

Update to new master

Tempfiles and .czi calibration, thanks!

Merge branch 'master' of https://github.com/mpicbg-scicomp/snakemake-workflows into mpicbg-scicomp-master

Conflicts:
	spim_registration/timelapse/Snakefile
	spim_registration/timelapse/single_test.yaml

Now recongnizes only first .czi file and fixes first job bug

This reverts commit fe74d067.

Conflicts:

	spim_registration/timelapse/Snakefile

Testtools

Added sysconfcpus option. it's very flexible now. ready to go ...

Merge pull request #7 from schmiedc/threadbug

But needs to be rewritten and merged onto a single Fiji

Rule registration depends on the output of hdf5_xml and resave_hdf5
Protects it against too early deletion.

This approach assumes that the processing itself runs without error.
When Fiji fails in on process then the whole workflow needs to restart.
Because the dummy files are now gone.

Threadbug, cleaning up is good

Threadbug

Now uses sysconfcpus and cluster.jason is adjusted for these parameters

Fixed first job bug and added Email