Merge request

Please fill in the checklist below and comment as needed.

• Was code modified? Briefly describe. Yes, see below
• Was documentation modified? Briefly describe. Yes, see below
• Is this a bug-fix? Briefly describe. No
• Is this a feature addition? Briefly describe. Yes, see below
• Did you modify QuaC-Watch config file? If so, did you modify multiqc template configs/multiqc_config_template.jinja2 and script src/quac_watch/create_mutliqc_configs.py as necessary? No, config file unmodified
• Did you perform system-level testing manually as described in master readme doc? Did it pass completely? If not why? Yes
• Updated Changelog.md file with change logs in recommended format?

Anything else reviewer should know?

As part of making QuaC publicly available, following updates were made to make it more generic to the environment and user friendly:

• Removes prerun QC from small variant caller pipeline as requirement to QuaC (closes #45 (closed))
• Explicitly defines conda environments (closes #49 (closed))
• Uses container solution for covviz installation instead of conda to avoid pip based installation (closes #52 (closed))
• Removes git submodules and instead saves their local copy to repo (closes #53 (closed))
• Loads singularity module loading prior to executing the runner script
• Uses minimal snakemake instead of full-featured snakemake (closes #56 (closed))