support an explicit output argument

[george-githinji]

Support for a -o or --output_dir argument for the output folder. Currently attempting to run IVA as part of an automated pipeline and getting an error

iva --threads $T --verbose 2 -f $forwards -r $reverse $output_dir

$output_dir is a path to the output directory

I get an error
iva: error: unrecognized argurments assembly/samplename

How can this be resolved?

[martinghunt]

The --verbose option doesn't take any values. Use it more times for more verbosity. This works for me:

iva --threads $T --verbose --verbose -f $forwards -r $reverse $output_dir

or less typing to do:

iva --threads $T -v -v -f $forwards -r $reverse $output_dir

[george-githinji]

OK. It was not clear from the documentation that the -v option does not take arguments. Thank you for the clarification!