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_pipeline.py

@@ -7,8 +7,7 @@ along with their required modules, and submits them as slurm job.
 Run the script with --help flag to see its available options.
 
 Example usage:
-IO_CONFIG=".test/configs/user_io_config.yaml"
-src/run_pipeline.py --io_config $IO_CONFIG
+python src/run_pipeline.py --project_name CF_CFF_PFarrell --pedigree data/raw/ped/CF_CFF_PFarrell.ped -l -n
 
 """
 
@@ -36,8 +35,8 @@ def create_snakemake_command(args):
     # snakemake command to run
     cmd = [
         "snakemake",
-        f"--snakefile {snakefile_path}",
-        f"--config modules='{args.modules}' project_name={args.project_name} ped={args.pedigree} out_dir={args.outdir} log_dir={args.log_dir}",
+        f"--snakefile '{snakefile_path}'",
+        f"--config modules='{args.modules}' project_name='{args.project_name}' ped='{args.pedigree}' out_dir='{args.outdir}' log_dir='{args.log_dir}'",
         f"--restart-times {args.rerun_failed}",
         "--use-conda",
         f"--profile '{snakemake_profile_dir}'",
@@ -64,28 +63,20 @@ def main(args):
     snakemake_cmd = create_snakemake_command(args)
 
     # put together pipeline command to be run
-    anaconda_module = "Anaconda3/2020.02"
-    snakemake_module = "snakemake/5.9.1-foss-2018b-Python-3.6.6"
     pipeline_cmd = "\n".join(
         [
-            f"module reset",
-            f"module load {anaconda_module}  {snakemake_module}",
             " \\\n\t".join(snakemake_cmd),
         ]
     )
 
     print(
         f'{"#" * 40}\n'
-        # f"Input-output configs provided by user: '{args.io_config}'\n"
-        f"Cluster configs                      : '{args.cluster_config}'\n\n"
         "Command to run the pipeline:\n"
         "\x1B[31;95m" + pipeline_cmd + "\x1B[0m\n"
         f'{"#" * 40}\n'
     )
 
     # submit snakemake command as a slurm job
-    # Choose resources depending on if manta_execute rule will be run
-    # as localrule in snakemake or not.
     slurm_resources = {
         "partition": "short",  # express(max 2 hrs), short(max 12 hrs), medium(max 50 hrs), long(max 150 hrs)
         "ntasks": "1",
@@ -122,7 +113,7 @@ def is_valid_dir(p, arg):
 
 if __name__ == "__main__":
     PARSER = argparse.ArgumentParser(
-        description="A wrapper for QuaC pipeline.",
+        description="Wrapper tool for QuaC pipeline.",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
 
@@ -136,7 +127,7 @@ if __name__ == "__main__":
     )
     WORKFLOW.add_argument(
         "--pedigree",
-        help="Pedigree filepath. Must be specific for the project supplied via --project_name",
+        help="Pedigree filepath. Must correspond to the project supplied via --project_name",
         type=lambda x: is_valid_file(PARSER, x),
         metavar="",
     )
@@ -152,7 +143,7 @@ if __name__ == "__main__":
         "-m",
         "--modules",
         help="Runs only these user-specified modules(s). If >1, use comma as delimiter. \
-            Useful for development.",
+            See QuaC snakemake script for available options. Useful for development.",
         default="all",
         metavar="",
     )
@@ -172,7 +163,7 @@ if __name__ == "__main__":
     LOGS_DIR_DEFAULT = f"{QUAC_OUTDIR_DEFAULT}/../logs"
     WRAPPER.add_argument(
         "--log_dir",
-        help="Directory path where logs (both workflow and wrapper) will be stored",
+        help="Directory path where logs (both workflow's and wrapper's) will be stored",
         default=LOGS_DIR_DEFAULT,
         type=lambda x: is_valid_dir(PARSER, x),
         metavar="",