Rename modules

[tsalo]

cis.py and cis_proc.py should be renamed.

Each module has both a main workflow function and associated CLI. A brief summary of each workflow:

• cis_proc.py:
  1. Copy raw data tarfile to scratch
  2. Copy necessary Singularity images to scratch
  3. Run BIDSifier Singularity image on tarfile.
  4. Merge mini BIDS dataset in /scratch into main BIDS dataset in /data.
  5. Run MRIQC Singularity image on new mini-BIDS dataset.
  6. Merge MRIQC derivatives in /scratch into main derivatives folder in /data.
  7. Clean up working directory in /scratch.
• cis.py:
  1. Copy XNAT downloader Singularity image to scratch.
  2. Download tarfile using XNAT downloader.
  3. Run protocol check on downloaded data.
  4. Email project-related personnel warnings about missing data based on protocol check.
  5. Submit cis_proc workflow as a job.
  6. Email project-related personnel update about downloaded/converted data.

NOTE: Neither workflow uses mriqc.mriqc_group() at the moment.

Based on what each workflow does, what do you think we should rename them to?

[akimbler]

@tsalo maybe cis_proc -> build_bids and cis -> pull_dicoms

[tsalo]

I like pull_dicoms, but instead of build_bids what about conversion_workflow? I think including workflow in the filenames will make it easier for people to distinguish between what they should run and what it called internally.