convert out_files for AFNI 3dZeropad to absolute paths in list_outputs

Author: Zach Lindsey

nipype/interfaces/afni/tests/test_extra_Zeropad.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+from nipype import Node
 from nipype.interfaces.afni import Zeropad
 from nipype.testing.fixtures import create_files_in_directory
 
@@ -23,3 +24,16 @@ def test_zeropad_handles_outfile_specified_nii_gz(create_files_in_directory):
 
     assert (Path(outdir) / "padded.nii.gz").exists()
     assert Path(result.outputs.out_file).name == "padded.nii.gz"
+
+
+def test_zeropad_keeps_file_after_node_run(create_files_in_directory):
+    filelist, outdir = create_files_in_directory
+
+    zp = Node(
+        Zeropad(I=1, out_file="padded.nii.gz"), name="test_zeropad", base_dir=outdir
+    )
+    zp.inputs.in_files = Path(outdir) / filelist[0]
+
+    result = zp.run()
+    assert (Path(zp.output_dir()) / "padded.nii.gz").exists()
+    assert Path(result.outputs.out_file).name == "padded.nii.gz"

nipype/interfaces/afni/utils.py

@@ -3502,5 +3502,4 @@ def _list_outputs(self):
 
         if not isdefined(out_file):
             out_file = "zeropad+tlrc.BRIK"
-
-        return {"out_file": out_file}
+        return {"out_file": op.abspath(out_file)}