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

@@ -19,13 +19,6 @@ import yaml
 from utility_cgds.cgds.pipeline.src.submit_slurm_job import submit_slurm_job
 
 
-def is_valid_file(p, arg):
-    if not Path(arg).is_file():
-        p.error("The file '%s' does not exist!" % arg)
-    else:
-        return arg
-
-
 def make_dir(d):
     """
     Ensure directory exists
@@ -149,25 +142,69 @@ def main(args):
     return None
 
 
+def is_valid_file(p, arg):
+    if not Path(arg).is_file():
+        p.error("The file '%s' does not exist!" % arg)
+    else:
+        return arg
+
+
+def is_valid_dir(p, arg):
+    if not Path(os.path.expandvars(arg)).is_dir():
+        p.error("The directory '%s' does not exist!" % arg)
+    else:
+        return os.path.expandvars(arg)
+
+
 if __name__ == "__main__":
     PARSER = argparse.ArgumentParser(
         description="A wrapper for QuaC pipeline.",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
 
+    ############ Args for QuaC workflow  ############
+    WORKFLOW = PARSER.add_argument_group("QuaC workflow options")
+
+    WORKFLOW.add_argument(
+        "--project_name",
+        help="Project name",
+        metavar="",
+    )
+    WORKFLOW.add_argument(
+        "--pedigree",
+        help="Pedigree filepath. Must be specific for the project supplied via --project_name",
+        type=lambda x: is_valid_file(PARSER, x),
+        metavar="",
+    )
+    QUAC_OUTDIR_DEFAULT = "$USER_SCRATCH/tmp/quac/results"
+    WORKFLOW.add_argument(
+        "--outdir",
+        help="Out directory path",
+        default=QUAC_OUTDIR_DEFAULT,
+        type=lambda x: is_valid_dir(PARSER, x),
+        metavar="",
+    )
+    WORKFLOW.add_argument(
+        "-m",
+        "--select_modules",
+        help="Runs only these user-specified modules(s). If >1, use comma as delimiter. \
+            Useful for development.",
+        default="all",
+        metavar="",
+    )
+
     ############ Args for QuaC wrapper tool  ############
     WRAPPER = PARSER.add_argument_group("QuaC wrapper options")
 
-    cluster_config_fname_default = (
-        Path(__file__).absolute().parents[1] / "configs/cluster_config.json"
-    )
+    CLUSTER_CONFIG_DEFAULT = Path(__file__).absolute().parents[1] / "configs/cluster_config.json"
     WRAPPER.add_argument(
         "--cluster_config",
         help="Cluster config json file. Needed for snakemake to run jobs in cluster.",
-        default=cluster_config_fname_default,
+        default=CLUSTER_CONFIG_DEFAULT,
         type=lambda x: is_valid_file(PARSER, x),
         metavar="",
     )
+
     WRAPPER.add_argument(
         "-e",
         "--extra_args",
@@ -198,45 +235,6 @@ if __name__ == "__main__":
         metavar="",
     )
 
-    # REQUIRED_ARGS = PARSER.add_argument_group("required named arguments")
-    # REQUIRED_ARGS.add_argument(
-    #     "--io_config",
-    #     help="Input-output config yaml file provided by user",
-    #     required=True,
-    #     type=lambda x: is_valid_file(PARSER, x),
-    #     metavar="",
-    # )
-
-    ############ Args for QuaC workflow  ############
-    WORKFLOW = PARSER.add_argument_group("QuaC workflow options")
-
-    WORKFLOW.add_argument(
-        "--project_name",
-        help="Project name",
-        metavar="",
-    )
-
-    WORKFLOW.add_argument(
-        "--pedigree",
-        help="Pedigree filepath. Must be specific for the project supplied via --project_name",
-        metavar="",
-    )
-
-    WORKFLOW.add_argument(
-        "--outdir",
-        help="Out directory path",
-        metavar="",
-    )
-
-    WORKFLOW.add_argument(
-        "-m",
-        "--select_modules",
-        help="Runs only these user-specified modules(s). If >1, use comma as delimiter. \
-            Useful for development.",
-        default="all",
-        metavar="",
-    )
-
     ARGS = PARSER.parse_args()
 
     main(ARGS)