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.

src/run_quac.py

@@ -9,8 +9,11 @@ along with their required modules, and submits them as slurm job.
 Run the script with --help flag to see its available options.
 
 Example usage:
-python src/run_quac.py --project_name CF_CFF_PFarrell --pedigree data/raw/ped/CF_CFF_PFarrell.ped -l -n
-
+# First create environment as described in documentation
+python src/run_quac.py --project_name CF_CFF_PFarrell --pedigree data/raw/ped/CF_CFF_PFarrell.ped
+python src/run_quac.py --project_name HCC --pedigree data/raw/ped/HCC.ped --exome
+python src/run_quac.py --project_name UnusualCancers_CMGalluzi --projects_path /data/project/sloss/cgds_path_cmgalluzzi/ \
+        --pedigree data/raw/ped/UnusualCancers_CMGalluzi.ped --exome
 """
 
 import argparse
@@ -57,6 +60,8 @@ def create_snakemake_command(args):
         "--cluster 'sbatch --ntasks {cluster.ntasks} --partition {cluster.partition}"
         " --cpus-per-task {cluster.cpus-per-task} --mem {cluster.mem}"
         " --output {cluster.output} --parsable'",
+        "--wms-monitor http://10.111.161.152/panoptes",
+        f"--wms-monitor-arg name=22 id=4365",
     ]
 
     # add any user provided extra args for snakemake