Set defaults for boolean values

Co-authored-by: Davy Cats <davycats.dc@gmail.com>

Update CPAT to version 3.0.4

Task issue 281

Try to adjust localization.

fix some runtime settings

BIOWDL-531: Update tool versions.

Move pacbio-merge image to quay.io

Docker hub has started to remove unused images from free accounts, which
means that it might remove images used by this pipeline without notice.
Therefore the pipeline now exclusively uses images from quay.io or
official repositories from docker hub, which do not have this
limitation.

Fix memory values.