Updated documentation (#150)

- Updated Pipeline doc
    - added missing output files for assembly based processing
    - added links between steps for file references
    - fixed step references
- Created examples/runsheet folder for CSV examples files
	- Added runsheet documentation
- Updated ChangeLog
   - added ChangeLog documentation
   - reformatted references to pipeline and previous snakemake workflow
   - added closed issue references
   - added other workflow specific updates vs previous snakemake
     workflow (checkm implementation)
- Updated Workflow README
   - add docker references since both Docker and Singularity are
     supported
   - regularize capitalization of Nextflow and Singularity to match
     the tools' documentation
   - reorganize post-processing output definition to match other assays
   - clarify installation instructions for conda in workflow document
- Added missing assay suffix to "Failed" assembly file name
- Rename NF_MGIllumina-A to NF_MGIllumina
- Checked and updated all broken links

Author: bnovak32