Extract data processing custom tools to own repos

[grosscol]

Rationale

• Facilitate a la carte installation of custom tools use in nextflow workflow.
• Make it easier to install applications to common location on slurm cluster.
• Reduce readme scope.
• Separation of concerns and dependencies

Actions

• Split out tolls that need to be compiled (tools/cpp_tools) and python processing tools (tools/base_coverage and tools/py_tools) into their own repositories. Use a clone and remove contents strategy to preserve commit history and attribution.

• Include tool projects in data prep as submodules. Update installation instructions to shallow clone submodules.