Batch Queuing

heudiconv.queue.clean_args(hargs: list[str], iterarg: str, iteridx: int) → list[str]

Filters arguments for batch submission.

Parameters:

  • hargs (list) – Command-line arguments

  • iterarg (str) – Multi-argument to index (subjects OR files)

  • iteridx (int) – iterarg index to submit

Returns:

cmdargs – Filtered arguments for batch submission

Return type:

list

Example

>>> from heudiconv.queue import clean_args
>>> cmd = ['heudiconv', '-d', '/some/{subject}/path',
...                     '-q', 'SLURM',
...                     '-s', 'sub-1', 'sub-2', 'sub-3', 'sub-4']
>>> clean_args(cmd, 'subjects', 0)
['heudiconv', '-d', '/some/{subject}/path', '-s', 'sub-1']
heudiconv.queue.queue_conversion(queue: str, iterarg: str, iterables: int, queue_args: str | None = None) → None

Write out conversion arguments to file and submit to a job scheduler. Parses sys.argv for heudiconv arguments.

Parameters:

  • queue (string) – Batch scheduler to use

  • iterarg (str) – Multi-argument to index (subjects OR files)

  • iterables (int) – Number of iterarg arguments

  • queue_args (string (optional)) – Additional queue arguments for job submission