Update

[WQ-CHENG]

1. updated the output directory structure;
2. added new rules to enable the NovaScope to create SGE in FICTURE-compatible format and hexagon-based SGE in 10x genome format;
3. update the job configuration file structure
4. update the way to assign resources for alignment with option filesize
5. update how to process the job configuration file in the main snakemake file
6. docs were updated to accommodate the above changes and added some extension of mkdocs for visualization.