BUG: "Single Channel" is not a valid choice for "Process_channel"
When choosing Single channel in reg_process_channel then
this is not a valid input for the macro.
Now reg_process_channel is set to All Channel for Single
Channel processing

External transformation has a bug it breaks the .xml file
External tranformation is disabled for now.

Added new cluster settings for resave_hdf5_output in cluster.json

BUG in export_output.bsh: took subsampling and chunk sizes from
resave hdf5. But these were not good.
Added new chunck size and subsampling option

Started to update fusion

Added dual channel processing for these parts
updated .bsh file

Added channel selection

Merge branch 'yaml-support' of https://github.com/psteinb/snakemake-workflows into psteinb-yaml-support

Conflicts:
	spim_registration/timelapse/Snakefile

more bugfixes related to removing superfluous information for .tif files

used a regexp replace to look for the correct input files in define_xml_tif (just looking for *.tif might not do it as the deconvolution might produce .tif as well)

fixed permissions to be non-executable

Merge branch 'adding_resave' of https://github.com/psteinb/snakemake-workflows into psteinb-adding_resave

Conflicts:
	spim_registration/timelapse/tomancak_czi.json

various changes: removed dummy files between registration->xml_merge; spotted problem in timepoint number for registration; refactored padding

Merge branch 'adding_resave' of https://github.com/psteinb/snakemake-workflows into psteinb-adding_resave

Conflicts:
	spim_registration/timelapse/Snakefile

Takes now the fusion - deconvolution switch into account.