Copy-Number Enhancements - Ascat penality

[seedgeorge]

Description of feature

Hi there. I think Sarek is in a good place with the current ASCAT implementation, but I'd like to point towards two things that I think would be helpful for the community.

• The function ascat.aspcf() (found in the ascat module) accepts a parameter penalty which controls the sensitivity of the tool to potential segment breakpoints. The default is 70 which is usually fine, but for individuals using panel/wes data being able to change this value might be helpful - any chance of exposing this as a param?

Kind regards, George

EDIT by @maxulysse - created https://github.com/nf-core/sarek/issues/1512

[maxulysse]

The function ascat.aspcf() (found in the ascat module) accepts a parameter penalty which controls the sensitivity of the tool to potential segment breakpoints. The default is 70 which is usually fine, but for individuals using panel/wes data being able to change this value might be helpful - any chance of exposing this as a param?

This seems easy enough, I'm fairly sure we can add that for 3.5.0

I split your initial issue in 2 different feature requests