From 48694bc5b558987328372ab037bc1d58dc7fb1bf Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Sun, 29 Dec 2024 20:12:15 -0500
Subject: [PATCH] remove redundant rule, linting

---
 hippunfold/workflow/rules/common.smk      |  1 +
 hippunfold/workflow/rules/gifti.smk       | 32 -----------------------
 hippunfold/workflow/rules/native_surf.smk |  4 ---
 3 files changed, 1 insertion(+), 36 deletions(-)

diff --git a/hippunfold/workflow/rules/common.smk b/hippunfold/workflow/rules/common.smk
index 322e7286..a2816633 100644
--- a/hippunfold/workflow/rules/common.smk
+++ b/hippunfold/workflow/rules/common.smk
@@ -280,6 +280,7 @@ def get_final_output():
     subj_output.extend(get_final_qc())
     return subj_output
 
+
 if "corobl" in ref_spaces:
 
     rule copy_coords_to_results:
diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
index 56321960..8d3637e4 100644
--- a/hippunfold/workflow/rules/gifti.smk
+++ b/hippunfold/workflow/rules/gifti.smk
@@ -142,38 +142,6 @@ rule constrain_surf_to_bbox:
         "../scripts/constrain_surf_to_bbox.py"
 
 
-# needed for if native_modality is corobl
-rule cp_corobl_root:
-    input:
-        gii=bids(
-            root=work,
-            datatype="surf",
-            den="{density}",
-            suffix="{surfname}.surf.gii",
-            space="corobl",
-            hemi="{hemi}",
-            label="{autotop}",
-            **inputs.subj_wildcards
-        ),
-    output:
-        gii=bids(
-            root=root,
-            datatype="surf",
-            den="{density}",
-            suffix="{surfname}.surf.gii",
-            space="corobl",
-            hemi="{hemi}",
-            label="{autotop}",
-            **inputs.subj_wildcards
-        ),
-    group:
-        "subj"
-    container:
-        config["singularity"]["autotop"]
-    shell:
-        "cp {input} {output}"
-
-
 # warp from corobl to native
 rule affine_gii_to_native:
     input:
diff --git a/hippunfold/workflow/rules/native_surf.smk b/hippunfold/workflow/rules/native_surf.smk
index acc69d35..3d81d591 100644
--- a/hippunfold/workflow/rules/native_surf.smk
+++ b/hippunfold/workflow/rules/native_surf.smk
@@ -1448,7 +1448,3 @@ rule atlas_label_to_unfold_nii:
     shell:
         "wb_command -label-to-volume-mapping {params.label_gii} {params.midthickness_surf} {input.ref_nii} {output.label_nii} "
         " -nearest-vertex 1000"
-        #use really large distance to ensure all voxels labelled
-
-
-#        " -ribbon-constrained {params.inner_surf} {params.outer_surf}"