Batch Queuing

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

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: Optional[str] = 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