Merge pull request #48 from sterrettJD/work_dir

Add alternative working directory functionality

README.md

@@ -31,6 +31,9 @@ If running HoMi on a cluster with SLURM, please setup a [Snakemake SLURM profile
 ### Conda environment building
 If conda environments have already been built, and you'd like snakemake to not build them, pass the argument `--conda_prebuilt`. This is particularly useful if running HoMi on a system with ARM architecture, like a Mac with M1/M2 chip. 
 
+### Working directory
+The working directory for HoMi can be set using the `--workdir` flag. This will set the "home base" for any relative filepaths within HoMi or your config, but it will not affect the filepath of the config or profile provided to HoMi.
+
 ### Running with example dataset
 ```
 # Create the mock community (too big for github)

src/HoMi.py

@@ -6,21 +6,31 @@
 
 def get_args():
     parser = argparse.ArgumentParser()
-    parser.add_argument("config", help="path config file for pipeline (yaml)")
+    parser.add_argument("config", 
+                        help="path to YAML-formatted config file for pipeline")
     parser.add_argument("-p", "--profile", 
-                        help="path to a snakemake profile, such as a profile to submit jobs to SLURM",
+                        help="Path to a snakemake profile, such as a profile to submit jobs to SLURM",
+                        default=None)
+    parser.add_argument("-c", "--cores", 
+                        help="Number of cores for snakemake to use",
+                        type=int, 
                         default=None)
-    parser.add_argument("-c", "--cores", help="Number of cores for snakemake to use",
-                        type=int, default=None)
     parser.add_argument("--conda_prebuilt", 
                         action="store_true",
-                        help="All conda environments have been prebuilt, snakemake should not build them")
-    parser.add_argument("--unlock", action="store_true",
+                        help="Pass this if all conda environments have been prebuilt, \
+                              and snakemake should not build them")
+    parser.add_argument("--unlock", 
+                        action="store_true",
                         help="Pass this to unlock a snakemake directory before running the pipeline.\
                               This is useful if the pipeline failed and you need to rerun it.")
+    parser.add_argument("--workdir",
+                        help="Directory in which the work should be performed. \
+                              Any relative filepaths used in HoMi will start here.",
+                        default=None)
     parser.add_argument("--snakemake_extra",
                         help="Extra parameters to pass snakemake",
                         default=None)
+
     return parser.parse_args()
 
 
@@ -77,12 +87,29 @@ def construct_snakemake_command(snakepath, args):
         command.append("--cores")
         command.append(str(args.cores))
 
+    if args.workdir is not None:
+        command.append("--directory")
+        command.append(args.workdir)
+
     if args.snakemake_extra is not None:
         command.extend(args.snakemake_extra.split())
 
     return command
 
 
+def unlock_snakemake_directory(snakepath, args):
+    command = ["snakemake", 
+                "-s", snakepath,
+                "--configfile", args.config,
+                "--unlock"]
+
+    if args.workdir is not None:
+        command.append("--directory")
+        command.append(args.workdir)
+
+    return subprocess.run(command)
+
+
 def main():
     args = get_args()
 
@@ -92,10 +119,7 @@ def main():
         snakepath = make_prebuilt_conda_snakefile(snakepath)
 
     if args.unlock == True:
-        subprocess.run(["snakemake", 
-                        "-s", snakepath,
-                        "--configfile", args.config,
-                        "--unlock"])
+        completed_unlock = unlock_snakemake_directory(snakepath, args)
 
     command = construct_snakemake_command(snakepath, args)
     completed_process = subprocess.run(command)