Rewrite

[bkohrn]

Rewrite script to accomplish the following:

• Add modules and templates
• Restrict each process to only accessing its own working directory
• Add options to cellprofiler to fix temp directory and set relative input directory
• Simplify processes
• Create fixed .cppipe files, instead of customizing them for each run (since realistically, the only reason to do that was to be able to specify paths outside the working directory).
• Simplify metadata generation by only inputting a list of file names to create metadata from, as the metadata creation doesn't need to access the input files themselves
• Simplify group creation by pulling the data for that from the metadata file, rather than creating a separate file for the groups
• Simplify R pipeline calling, since anything in bin is automatically on PATH within the process.
• Clean up nextflow.config a little, so it is less single-cluster based (if you need to specify other options, the pipeline nextflow.config can be overridden by either a nextflow.config file in the current directory, or by a config file provided on the command line with -c my_config).

This may address issues #6 and #3, and may help with fixing issue #2 (with extra modifications to the listFiles.sh template)