Merge branch 'dev-v2.0.0' into speeed

khanlab · Jan 22, 2025 · ba89e1d · ba89e1d
2 parents 2807f5c + ccf2b76
commit ba89e1d
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Showing 5 changed files with 9 additions and 9 deletions.
diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -273,10 +273,10 @@ parse_args:
 
   --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 '$SLURM_TMPDIR'.
-    default: null
+      Folder for storing working files. If not specified, will be in "work/" subfolder 
+      in the output folder. You can also use environment variables when setting the 
+      workdir, e.g. --workdir '$SLURM_TMPDIR'.
+    default: work
     type: str
 
 

diff --git a/hippunfold/workflow/Snakefile b/hippunfold/workflow/Snakefile
@@ -91,8 +91,6 @@ wildcard_constraints:
     template="[a-zA-Z0-9]+",
 
 
-if config["workdir"] == None:
-    config["workdir"] = mkdtemp()
 work = os.path.expandvars(config["workdir"])
 root = os.path.expandvars(config["root"])
 

diff --git a/hippunfold/workflow/rules/common.smk b/hippunfold/workflow/rules/common.smk
@@ -219,6 +219,8 @@ def get_final_output():
 
 if "corobl" in ref_spaces:
 
+    ruleorder: equivolume_coords > laplace_coords_hipp > laplace_coords_dentate > copy_coords_to_results
+
     rule copy_coords_to_results:
         input:
             os.path.join(work, "{pre}_space-corobl_{post}{suffix}.{ext}"),
@@ -231,7 +233,7 @@ if "corobl" in ref_spaces:
 
     rule copy_xfm_to_results:
         input:
-            os.path.join(work, "{pre}_{fromto,from|to}-corobl_{post}{suffix}.{ext}"),
+            os.path.join(work, "{pre}_{fromto}-corobl_{post}{suffix}.{ext}"),
         output:
             os.path.join(
                 root, "{pre,[^/].+}_{fromto,from|to}-corobl_{post}{suffix,xfm}.{ext}"

diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
@@ -187,7 +187,7 @@ rule affine_gii_to_native:
             datatype="surf",
             den="{density}",
             suffix="{surfname}.surf.gii",
-            space="{native_modality}",
+            space="{native_modality,T1w|T2w}",
             hemi="{hemi}",
             label="{autotop,hipp|dentate}",
             **inputs.subj_wildcards

diff --git a/hippunfold/workflow/rules/native_surf.smk b/hippunfold/workflow/rules/native_surf.smk
@@ -738,7 +738,7 @@ rule affine_gii_corobl_to_modality:
             root=root,
             datatype="surf",
             suffix="{surfname}.surf.gii",
-            space="{native_modality}",
+            space="{native_modality,T1w|T2w}",
             hemi="{hemi}",
             label="{autotop,hipp|dentate}",
             **inputs.subj_wildcards