Re-organize outputs by 'analysis stage'

[dfornika]

The overall analysis includes several stages:

• Read normalization
• Assembly
• Scaffolding
• Read mapping
• Variant calling
• Consensus sequence generation
• Reporting & Summary

It would be helpful for troubleshooting and data management if each stage wrote its outputs into a separate sub-directory.

Create an analysis_by_stage sub-directory under the --outdir

Create sub-directories under that, named like:

analysis_by_stage/00_read_normalization
analysis_by_stage/01_assembly
analysis_by_stage/02_scaffolding

...etc. Below that, create an 'inputs' and an 'outputs' sub-directory.

Write bash script(s) into the analysis stage directories to document & aid with troubleshooting.

'Publish' final outputs under outdir.