RF: Resume external nipype dependency

[effigies]

Purges niworkflows.nipype in favor of nipype.

Pins nipreps/niworkflows#241.

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Original text:

This is just to validate nipreps/niworkflows#238. Should be a functionally inert refactor, so can wait for the next niworkflows release to actually update the pin.

[effigies]

@oesteban There's another ICA-AROMA bug popping up. I think you've been paying closer attention to these than I have... Could you take a quick look to see if it's an old problem reemerging or something I'm introducing?

[oesteban]

The symptoms indicate a regression of AROMA writing in /opt/ICA-AROMA/:

Step 1) MELODIC
  - The existing/specified MELODIC directory will be used.
Standard error:
Traceback (most recent call last):
  File "/opt/ICA-AROMA/ICA_AROMA.py", line 193, in <module>
    aromafunc.runICA(fslDir, inFile, outDir, melDir, mask, dim, TR)
  File "/opt/ICA-AROMA/ICA_AROMA_functions.py", line 55, in runICA
    os.symlink(melDirIn, melDir)
FileExistsError: [Errno 17] File exists: '/scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_01_wf/ica_aroma_wf/melodic' -> 'out/melodic.ica'
Return code: 1

I bet that out/melodic.ica is being linked under /opt/ICA-AROMA. Maybe the new report capable interfaces are not taking in the rewrite of the input?

EDIT: the previous error not finding an input would be caused by Nipype looking for the output under the node's folder, while they are under /opt/ICA-AROMA.

[oesteban]

Oh yeah, look at the command line, the output arg is just -o out.

[effigies]

Gotcha. Merging nipype/master in. Didn't realize I hadn't.