Added dual channel processing for these parts
updated .bsh file

Added channel selection

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)

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

Takes now the fusion - deconvolution switch into account.

calculation of job number is performed in export.bsh script

Padding and calcluation of job_number for resave_hdf5

adapted snakemake file to new requirements (comply with tif/czi filled directories, config file needs to state number of timepoints)

Build in a switch to decide witch fusion method should be used.
Tested workflow and works.

* updated Snakefile accordingly