add labelmerge container

khanlab · Nov 30, 2022 · 707904c · 707904c
1 parent b5ab130
commit 707904c
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/dbsc/config/snakebids.yml b/dbsc/config/snakebids.yml
@@ -175,5 +175,6 @@ singularity:
   freesurfer: "docker://pwighton/freesurfer:7.2.0"
   neuroglia-core: "docker://khanlab/neuroglia-core:latest"
   mrtrix: "docker://brainlife/mrtrix:3.0.3"
+  labelmerge: "docker://kaitj/labelmerge:v0.1.0"
 
 fs_license: /path/to/fs/license
diff --git a/dbsc/workflow/rules/zona_bb_subcortex.smk b/dbsc/workflow/rules/zona_bb_subcortex.smk
@@ -150,6 +150,7 @@ rule labelmerge:
         zona_desc="ZonaBBSubcor",
         fs_desc="FreesurferThal",
         labelmerge_dir=directory(labelmerge_dir),
+        labelmerge_container=config["singularity"]["labelmerge"],
     output:
         seg=expand(
             bids_labelmerge(
@@ -169,10 +170,8 @@ rule labelmerge:
             ),
             subject=config["input_lists"]["dwi"]["subject"],
         ),
-    # ADD CONTAINER
     shell:
-        # TO BE UPDATED WITH APPROPRIATE COMMAND
-        "run.py {params.zona_dir} {params.labelmerge_dir} --overlay_bids_dir {params.fs_dir} --overlay_desc {params.fs_desc} --base_desc {params.zona_desc}"
+        "singularity run {params.labelmerge_container} {params.zona_dir} {params.labelmerge_dir} --base_desc {params.zona_desc} --overlay_bids_dir {params.fs_dir} --overlay_desc {params.fs_desc}"
 
 
 rule binarize: