Fix kable table rendering
Fix positioning in PipelineErrorFigure
Add cache folder
Incorporate error effect simulation
Correct capitalizaton in PipelineErrorFigureB
Clean up code formatting in code for figures
Export nseqs before and after basic filtering
Put sequence counts into ReasonsLost table
Add remaining outline and punchlist to finish paper
Add note that Table 1 needs attention
Finalize table numbering
Renumber figures and tables
Modify pdf situation in gitignore
Add figures folder with png and pdf files