updates

hippunfold/config/snakebids.yml

@@ -264,11 +264,6 @@ parse_args:
     nargs: '+'
     help: 'Run hipp (CA + subiculum) alone or include dentate (default: %(default)s)'
 
-  --workdir:
-    help: 'Folder for storing working files, if not specified, will make a temporary folder with tempfile.mkdtemp() (default: %(default)s)'
-    default: None
-    type: Path
-
   --force_nnunet_model:
     help: 'Force nnunet model to use (expert option). (default: %(default)s)'
     default: False
@@ -294,6 +289,14 @@ parse_args:
     action: "store_false"
     default: True
 
+  --workdir:
+    help: |
+      Folder for storing working files. If not specified, a temporary folder
+      will be made in your system's temp directory (e.g. /tmp). You can also
+      use environment variables when setting the workdir, e.g. --workdir '$SLURM_TMPDIR'.
+    default: null
+    type: str
+
 
   --version:
     help: 'Print the version of HippUnfold'

hippunfold/workflow/Snakefile

@@ -4,6 +4,7 @@ import snakebids
 from snakebids import bids, set_bids_spec
 from tempfile import mkdtemp
 
+
 configfile: "config/snakebids.yml"
 
 
@@ -94,13 +95,11 @@ wildcard_constraints:
     template="[a-zA-Z0-9]+",
 
 
-#root = os.path.normpath(os.path.join(config["root"], "hippunfold"))
-#work = os.path.normpath(os.path.join(config["root"], "work"))
-
-root = os.path.expandvars(config["root"])
 if config["workdir"] == None:
     config["workdir"] = mkdtemp()
 work = os.path.expandvars(config["workdir"])
+root = os.path.expandvars(config["root"])
+
 
 include: "rules/common.smk"
 include: "rules/download.smk"

hippunfold/workflow/rules/common.smk

@@ -376,7 +376,6 @@ if "corobl" in ref_spaces:
             "cp {input} {output}"
 
 
-
 def get_download_dir():
     if "HIPPUNFOLD_CACHE_DIR" in os.environ.keys():
         download_dir = os.environ["HIPPUNFOLD_CACHE_DIR"]
@@ -385,5 +384,3 @@ def get_download_dir():
         dirs = AppDirs("hippunfold", "khanlab")
         download_dir = dirs.user_cache_dir
     return download_dir
-
-