An interface that gathers all of the files you pass it into a single directory using hard links.

gistfile1.py

import os
from nipype.interfaces.base import BaseInterface, InputMultiPath,\
    OutputMultiPath, BaseInterfaceInputSpec, traits, File, TraitedSpec

class CCPGatherFilesInputSpec(BaseInterfaceInputSpec):
    files = InputMultiPath(
            traits.Either(traits.List(File(exists=True)),File(exists=True)),
            mandatory=True,
            desc='a list of files you would like to gather into one directory with symlinks',
            copyfile=False)

class CCPGatherFilesOutputSpec(TraitedSpec):
    links = OutputMultiPath(
            traits.List(File(exists=True)),
            desc='a list of files, all in the same directory.')

class CCPGatherFiles(BaseInterface):
    input_spec = CCPGatherFilesInputSpec
    output_spec = CCPGatherFilesOutputSpec
    d_files = []
    def _run_interface(self, runtime):
        import os
        files = self.inputs.files
        new_dir = os.path.abspath('link_dir')
        os.mkdir(new_dir)
        for f in files:
            fname = os.path.split(f)[-1]
            os.link(f, os.path.join(new_dir, fname))
        return runtime

    def _list_outputs(self):
        from glob import glob
        import os
        outputs = self._outputs().get()
        outputs['links'] = glob(os.path.join(os.path.abspath('.'), 'link_dir','*'))
        return outputs