Handle scratch_directory as None as expected

LCR-BCCRC · Jun 25, 2020 · 2c251b5 · 2c251b5
1 parent 8931548
commit 2c251b5
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/oncopipe/oncopipe/__init__.py b/oncopipe/oncopipe/__init__.py
@@ -1610,7 +1610,7 @@ def setup_subdirs(module_config, subdirectories, scratch_subdirs=()):
         )
 
     # If `scratch_directory` is None, then don't worry about `scratch_subdirs`
-    scratch_directory = module_config.get("scratch_directory", "")
+    scratch_directory = module_config.get("scratch_directory")
     if scratch_directory is None:
         scratch_subdirs = ()
 
@@ -1626,11 +1626,11 @@ def setup_subdirs(module_config, subdirectories, scratch_subdirs=()):
     name = module_config["name"]
     version = module_config["version"]
     parent_dir = module_config["dirs"]["_parent"]
-    scratch_parent_dir = os.path.join(scratch_directory, f"{name}-{version}")
     for num, subdir in zip(numbers, subdirectories):
         subdir_full = os.path.join(parent_dir, f"{num}-{subdir}/")
         module_config["dirs"][subdir] = subdir_full
         if subdir in scratch_subdirs:
+            scratch_parent_dir = os.path.join(scratch_directory, f"{name}-{version}")
             scratch_subdir_full = os.path.join(scratch_parent_dir, f"{num}-{subdir}/")
             os.makedirs(scratch_subdir_full, exist_ok=True)
             relative_symlink(scratch_subdir_full, subdir_full, overwrite=False)

diff --git a/oncopipe/oncopipe/__version__.py b/oncopipe/oncopipe/__version__.py
@@ -6,7 +6,7 @@
 
 __title__ = "oncopipe"
 __description__ = "Functions for running Snakemake modules"
-__version__ = "1.0.4"
+__version__ = "1.0.5"
 __author__ = "Bruno Grande"
 __author_email__ = "[email protected]"
 __license__ = "MIT"