Update apply_mumford option with

remove_reg_standard flag.

clpipe/cli.py

@@ -395,25 +395,30 @@ def glm_l2_preparefsf_cli(glm_config_file, l2_name, debug):
               help='Your GLM configuration file.')
 @click.option('-l1_feat_folders_path', type=CLICK_DIR_TYPE_EXISTS,
               default=None, required=False,
-              help='Location of your L1 FEAT folders.')
-@click.option('-debug', is_flag=True,
+              help='Directory containing your L1 FEAT folders.')
+@click.option('-remove_reg_standard', is_flag=True, default=False,
+              help='Remove reg_standard folders (generated by L2) in addition to reg.')
+@click.option('-debug', is_flag=True, default=False,
               help='Flag to enable detailed error messages and traceback')
 def glm_apply_mumford_workaround_cli(glm_config_file, l1_feat_folders_path,
-                                     debug):
+                                     remove_reg_standard, debug):
     """
     Apply the Mumford registration workaround to L1 FEAT folders. 
     
     Applied by default in glm-l2-preparefsf. This command is useful for applying
     the Mumford workaround to single-run subjects who skip L2, allowing you to still
     combine them with multiple-run subjects at L3.
+
+    Must provide GLM config file OR a path to your L1 FEAT folders.
     """
     from .glm_l2 import glm_apply_mumford_workaround
     if not (glm_config_file or l1_feat_folders_path):
         click.echo(("Error: At least one of either option '-glm_config_file' "
                     "or '-l1_feat_folders_path' required."))
     glm_apply_mumford_workaround(
         glm_config_file=glm_config_file,
-        l1_feat_folders_path=l1_feat_folders_path, debug=debug
+        l1_feat_folders_path=l1_feat_folders_path, debug=debug,
+        remove_reg_standard=remove_reg_standard
     )