add non-slurm cores command

grubaughlab · Apr 2, 2024 · cfb74de · cfb74de
1 parent 003cbac
commit cfb74de
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Showing 2 changed files with 7 additions and 0 deletions.
diff --git a/denv_pipeline/command.py b/denv_pipeline/command.py
@@ -40,6 +40,7 @@ def main(sysargs = sys.argv[1:]):
 
     parser.add_argument("--slurm", help="flag for if running on HPC with slurm", action="store_true")
     parser.add_argument("--slurm-cores", help="number of slurm cores to assign. Default is 10", dest="slurm_cores", type=int)
+    parser.add_argument("--cores", help="number of non-slurm cores to assign. Default is 1", type=int)
     parser.add_argument("--verbose", "-v", dest="verbose", action="store_true")
     parser.add_argument("--help", "-h", action="store_true", dest="help")
     parser.add_argument("--overwrite", help="overwrite current results", action="store_true")
@@ -111,6 +112,10 @@ def main(sysargs = sys.argv[1:]):
             status = snakemake.snakemake(snakefile, printshellcmds=False, forceall=True, force_incomplete=True,
                                     workdir=cwd,config=config,lock=False, slurm=True, cores=config["slurm_cores"]
                                     )
+        elif config["cores"]:
+            status = snakemake.snakemake(snakefile, printshellcmds=False, forceall=True, force_incomplete=True,
+                                    workdir=cwd,config=config,lock=False, cores=config["cores"]
+            )
         else:
             status = snakemake.snakemake(snakefile, printshellcmds=False, forceall=True, force_incomplete=True,
                                     workdir=cwd,config=config,lock=False

diff --git a/denv_pipeline/utils/set_up_scripts.py b/denv_pipeline/utils/set_up_scripts.py
@@ -23,6 +23,7 @@ def get_defaults(config):
     config["verbose"] = False
     config["slurm"] = False
     config["slurm_cores"] = 10
+    config["cores"] = False
     config["download"] = False
     config["temp"] = False
     config["overwrite"] = False
@@ -210,6 +211,7 @@ def get_valid_keys():
     valid_keys.append("download")
     valid_keys.append("slurm")
     valid_keys.append("slurm_cores")
+    valid_keys.append("cores")
     valid_keys.append("verbose")
     valid_keys.append("config")
     valid_keys.append("dry_run")