Background: The possibility to check for LD between variants and the gwascatalog associations around them is partially (but not completely/correctly) implemented into the compare script. However, this has not been a partially high priority task and therefore the feature is not finished.
It was also implemented to the wdl, but since it does not work as it's supposed, it's not really something that should be there. Also the parameter names are misleading.
This PR removes the parameters related to that feature from the WDL pipeline and its configuration files, so that they are less misleading.
In case the LD checking feature gets completed at some point (https://github.com/FINNGEN/autoreporting/issues/26), these parameters can be added into the WDL, with better names so they are less misleading.
Background: The possibility to check for LD between variants and the gwascatalog associations around them is partially (but not completely/correctly) implemented into the compare script. However, this has not been a partially high priority task and therefore the feature is not finished.
It was also implemented to the wdl, but since it does not work as it's supposed, it's not really something that should be there. Also the parameter names are misleading.
This PR removes the parameters related to that feature from the WDL pipeline and its configuration files, so that they are less misleading.
In case the LD checking feature gets completed at some point (https://github.com/FINNGEN/autoreporting/issues/26), these parameters can be added into the WDL, with better names so they are less misleading.