QuaC - First major review

QuaC pipeline has been modified to make it user-friendly and share interface similar to other pipelines at CGDS.

Note that one major deviation compared to our other pipeline is that QuaC uses recent snakemake version (6.0.5), and they are made available via conda environment. That is, we don't use snakemake module from cheaha.

The following may need review at some level. Note: This list is not exhaustive.

• Snakemake pipeline
• Documentation. I kept it simple; let me know if it needs more info.

README.md

@@ -15,8 +15,8 @@
 
 ## Who am I?
 
-QuaC is a pipeline developed using snakemake, which runs a set of selected QC tools on NGS samples. Here are the tool I
-can quack:
+QuaC is a pipeline developed using snakemake, which runs a set of selected QC tools on NGS samples. Here are the tools it
+can currently quack on:
 
 | Tool                                                              | Use                                                        |
 | ----------------------------------------------------------------- | ---------------------------------------------------------- |
@@ -105,7 +105,7 @@ conda env update --file configs/env/quac.yaml
 
 In the activate conda environment, QuaC is run using script `src/quac.py`. Here are all the options available:
 
-```
+```sh
 $ ./src/run_quac.py -h
 usage: run_quac.py [-h] [--project_name] [--projects_path] [--pedigree]
                    [--outdir] [-m] [--exome] [--cluster_config] [--log_dir]
@@ -118,7 +118,7 @@ optional arguments:
 
 QuaC workflow options:
   --project_name      Project name (default: None)
-  --projects_path     Path where all projects are hosted. Don't include
+  --projects_path     Path where all projects are hosted. Dont include
                       project name here. (default:
                       /data/project/worthey_lab/projects/)
   --pedigree          Pedigree filepath. Must correspond to the project