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cancerit / cgpCaVEManWrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis
http://cancerit.github.io/cgpCaVEManWrapper/
GNU Affero General Public License v3.0
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--debug option #29

Closed ramaniak closed 7 years ago

ramaniak commented 7 years ago

Hello, I was wondering how to invoke the debug parameter when executing the caveman-wrapper? Specifically, I am trying to get estep to run with the debug option look at every position considered. 

-s  --debug     Adds an extra output to a debug file. Every base analysed has an output

The '-s' flag is confused by the caveman wrapper as species and therefore throws an error.

thanks Arun

keiranmraine commented 7 years ago

Resolved by #30

ramaniak commented 7 years ago

Hi Keiran, I was wondering what the solution to my issue is?

thanks Arun

keiranmraine commented 7 years ago

Have you viewed the issue on GitHub (for full history)? We have exposed the value to the wrapper code and are in the process of testing the release.

ramaniak commented 7 years ago

Apologies, I did not. Thanks for taking care of this.

Arun