autobin command doesn't include output parameter

[enes-ak]

Hi,
I just want to add an suggestion.

I am creating pipeline via snakemake. While I integrating CNVkit into pipeline, autobin step give "output" error because of there is no parmeter as -o/--output

I would be very glad if the output parameter is added to this command. Thank you!

[tskir]

Hi! Fair point. I've submitted a PR to enable this.

For maximum flexibility, these are going to be two parameters: --target-output-bed and --antitarget-output-bed. This should make it easier to plug into any workflow system.