FIX: File sinking

Author: effigies

scripts/generate_reference_mask.py

@@ -1,15 +1,16 @@
 #!/usr/bin/env python
 import sys
-import os
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
-from nipype.utils.filemanip import fname_presuffix, copyfile
 from fmriprep.workflows.bold.util import init_bold_reference_wf
 
 
 def sink_ref_file(in_file, orig_file, out_dir):
+    import os
+    from nipype.utils.filemanip import fname_presuffix, copyfile
+    os.makedirs(out_dir, exist_ok=True)
     out_file = fname_presuffix(orig_file, suffix='_ref', newpath=out_dir)
-    copyfile(in_file, out_file)
+    copyfile(in_file, out_file, copy=True, use_hardlink=True)
     return out_file
 
 
@@ -20,9 +21,10 @@ def init_main_wf(bold_file, out_dir, base_dir=None, name='main_wf'):
     wf.base_dir = base_dir
     wf.inputs.inputnode.bold_file = bold_file
 
-    sink = pe.Node(niu.Function(function=sink_ref_file, out_dir=out_dir,
-                            orig_file=bold_file),
+    sink = pe.Node(niu.Function(function=sink_ref_file),
                    name='sink')
+    sink.inputs.out_dir = out_dir
+    sink.inputs.orig_file = bold_file
     wf.connect([
         (wf.get_node('outputnode'), sink, [('bold_mask', 'in_file')]),
         ])