Fixed wrong command in web_name_patches config
EG's PairAligner inherits from Ensembl's version

Only one file contains the pipeline structure. Both files define their
own parameters / memory requirements.
Print the debug in debug mode only
Various fixes
New reasource classes and updated hmm_library_basedir directory.
Added topup clustering_mode. Updated insert mode for dnafrags.
Updated resource class for using gpfs.
Added control to check if its an updated pipeline run. Allowing us to fetch the genetree and alignment from different clusterset_ids.
Minimize gene tree to avoid disavowed members.
Merge remote branch 'github/master' into feature/update_pipeline