absence of command line options overrides provided pipeline.yml

[alexlicohen]

the pipeline file is loaded before the command line options are parsed, leading to the fact that absence of a command line option --report for instance, overriding the settings in a specified pipeline file.

One solution would be a disclaimer to use either the command line options OR provide a pipeline file.

Another would be to add a line re-loading the pipeline_file if not equal to /qap_resources/default.yml