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

Merge pull request #7 from schmiedc/threadbug

Threadbug, cleaning up is good

Threadbug

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

Fixed first job bug and added Email

* added new function that replaces occurrences of a defined set of parameters
  (required to handle brackets inside filenames)
* using glob_and_escape in Snakefile now

Update to documentation

Documentation

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

New improved workflow

Improved workflow, am working on the 1st job bug.

Pipeline tested and works with single channel data

the output rule now references to the correct xml filename

Log files are ordered

hdf5_xml_output rule does again touch the output
Tested and works

Update to newest master