===========
prodigal.py
===========

.. code-block:: bash

	usage: prodigal.py

	Calls ORFs with provided input assembly

	optional arguments:
	  -h, --help            show this help message and exit
	  --assembly filepath   Path to metagenome assembly (default: None)
	  --output-nucls filepath
	                        Path to output nucleotide ORFs (default: None)
	  --output-prots filepath
	                        Path to output amino-acid ORFs (default: None)
	  --cpus int            Number of processors to use. (If more than one this
	                        will parallelize prodigal using GNU parallel)
	                        (default: 1)
	  --force               Overwrite existing output ORF filepaths (default:
	                        False)