🐛 KeyError: 'in_file' in _configure_exec_node

[shnizzedy]

Describe the bug

210920-19:51:13,496 nipype.workflow INFO:
	 Workflow cpac_sub-0010001_ses-1 settings: ['check', 'execution', 'logging', 'monitoring']
210920-19:52:26,514 nipype.workflow WARNING:
	 Report generation failed for /output/log/pipeline_cpac-default-pipeline/sub-0010001_ses-1/callback.log
NoneType: None
210920-19:52:26,515 nipype.workflow INFO:
	 

Error of subject workflow cpac_sub-0010001_ses-1

CPAC run error:

    Pipeline configuration: cpac-default-pipeline
    Subject workflow: cpac_sub-0010001_ses-1
    Elapsed run time (minutes): 10.007248385747273
    Timing information saved in /output/log/cpac_individual_timing_cpac-default-pipeline.csv
    System time of start:      2021-09-20 19:49:50


Traceback (most recent call last):
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 488, in run_workflow
    workflow.run(plugin=plugin, plugin_args=plugin_args)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 629, in run
    self._configure_exec_nodes(execgraph)
  File "/code/CPAC/pipeline/nipype_pipeline_engine/engine.py", line 247, in _configure_exec_nodes
    ).inputs['in_file']
KeyError: 'in_file'

To reproduce

docker run --security-opt=apparmor:unconfined -v /home/tgeorge/Documents/C-PAC:/code -v /home/tgeorge/Documents/C-PAC/dev/docker_data/run.py:/code/run.py -v /home/tgeorge/Documents/C-PAC/dev/docker_data/run-with-freesurfer.sh:/code/run-with-freesurfer.sh -v /home/tgeorge/Documents/C-PAC/CPAC/pipeline/schema.py:/code/schema.py -v /home/tgeorge/Documents/C-PAC/dev/docker_data/bids_utils.py:/code/bids_utils.py -v /home/tgeorge/Documents/C-PAC/dev/docker_data/default_pipeline.yml:/cpac_resources/default_pipeline.yml -v /home/tgeorge/Documents/C-PAC/config_N4_volume.yml:/config_N4_volume.yml -v /data3/cnl/tgeorge/issue_runs/n4-volume_fix:/output fcpindi/c-pac:nightly s3://fcp-indi/data/Projects/ADHD200/RawDataBIDS/NYU /output participant --save_working_dir --skip_bids_validator --n_cpus 1 --mem_gb 15 --participant_label sub-0010001 --pipeline_file /config_N4_volume.yml

Expected behavior

Runs without crashing or provides a crashfile

Acceptance criteria

• config_N4_volume.yml runs without error
  OR
• The crash generates a crash file

Screenshots

No response

C-PAC version

v1.8.2-develop @ 4c70815

Container platform

Docker

Docker and/or Singularity version(s)

version 18.06.1-ce, build e68fc7a

Additional context

my output director[y] was the same as my last run before the merging, so the only crash files are from the last run.

[shnizzedy]

Fixed in #1574