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

@@ -86,3 +86,76 @@ conda activate quac
 conda env update --file configs/env/quac.yaml
 ```
 
+## How to run QuaC
+
+In the activate conda environment, QuaC is run using script `src/quac.py`. Here are all the options available:
+
+```
+$ ./src/run_quac.py -h
+usage: run_quac.py [-h] [--project_name] [--projects_path] [--pedigree]
+                   [--outdir] [-m] [--exome] [--cluster_config] [--log_dir]
+                   [-e] [-n] [-l] [--rerun_failed]
+
+Wrapper tool for QuaC pipeline.
+
+optional arguments:
+  -h, --help          show this help message and exit
+
+QuaC workflow options:
+  --project_name      Project name (default: None)
+  --projects_path     Path where all projects are hosted. Don't include
+                      project name here. (default:
+                      /data/project/worthey_lab/projects/)
+  --pedigree          Pedigree filepath. Must correspond to the project
+                      supplied via --project_name (default: None)
+  --outdir            Out directory path (default:
+                      $USER_SCRATCH/tmp/quac/results)
+  -m , --modules      Runs only these user-specified modules(s). If >1, use
+                      comma as delimiter. See QuaC snakemake script for
+                      available options. Useful for development. (default:
+                      all)
+  --exome             Flag to run in exome mode (default: False)
+
+QuaC wrapper options:
+  --cluster_config    Cluster config json file. Needed for snakemake to run
+                      jobs in cluster. (default: /data/project/worthey_lab/pro
+                      jects/experimental_pipelines/mana/quac/configs/cluster_c
+                      onfig.json)
+  --log_dir           Directory path where logs (both workflow's and
+                      wrapper's) will be stored (default:
+                      $USER_SCRATCH/tmp/quac/results/../logs)
+  -e , --extra_args   Pass additional custom args to snakemake. Equal symbol
+                      is needed for assignment as in this example: -e='--
+                      forceall' (default: None)
+  -n, --dryrun        Flag to dry-run snakemake. Does not execute anything,
+                      and just display what would be done. Equivalent to '--
+                      extra_args "-n"' (default: False)
+  -l, --run_locally   Flag to run the snakemake locally and not as a Slurm
+                      job. Useful for testing purposes. (default: False)
+  --rerun_failed      Number of times snakemake restarts failed jobs. This may
+                      be set to >0 to avoid pipeline failing due to job fails
+                      due to random SLURM issues (default: 0)
+```
+
+
+### Example usage
+
+`project_name` and `pedigree` are required options to run the tool.
+
+```sh
+# for a WGS project
+python src/run_quac.py --project_name CF_CFF_PFarrell --pedigree data/raw/ped/CF_CFF_PFarrell.ped
+
+# for an exome project
+python src/run_quac.py --project_name HCC --pedigree data/raw/ped/HCC.ped --exome
+
+# run for an exome project which is not in the default CGDS projects_path
+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
+
+# for a WGS project, run specific modules/tools
+python src/run_quac.py --project_name CF_CFF_PFarrell --pedigree data/raw/ped/CF_CFF_PFarrell.ped --modules somalier
+
+```