Update PairAligner_conf.pm

Moved 'remove_inconsistencies_after_net' ahead of 'create_filter_duplicates_net_jobs' in the workflow. Seems it was unconsistent before with 'remove_inconsistencies_after_net' waiting for 'filter_duplicates_net' and 'create_filter_duplicates_net_jobs' waiting for 'remove_inconsistencies_after_net'!