Create separate modules for pre_analysis, analysis and post_analysis

[dfornika]

For each pipeline there are three phases:

1. Pre-analysis: Anything needed to set up the pipeline analysis (making symlinks, samplesheets, directories, etc.)
2. Analysis: Running the pipeline
3. Post-analysis: Anything needed to be done after the pipeline completes (check the outputs of the pipeline analysis, create samplesheets for downstream pipelines, cleanup temp files, etc.)

On some of our other automation systems (like auto-cpo for example) we've created separate modules for pre_analysis, analysis and post_analysis. We should set up a similar codebase structure here.