Enable configurable paths for inputs, intermediate files and outputs in Docker image

[vladimirkovacevic]

parliament.py and parliament.sh contain many hardcoded absolute paths for input, intermediate, log and output files inside Docker image. Some environments require positioning of them in some specific locations and on these environments Parliament2 cannot be executed. Perfect solution would be to be able to set as Parliament2 parameter all mentioned locations.

[gevro]

Hi, Is this being addressed? This causes pretty major issues when trying to use parliament2 in wdl/cromwell cloud pipelines.