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For reasons that I don't quite understand, HGFA currently needs to be set in the
eval/config.groovyin the installation directory (or by setting XIMMER_REF env variable, which then writes toeval/config.groovy).This is undesirable for a few reasons (see for instance mention in #25, and #29 is related since a singularity container would run as non-root in the container, and not be able to write to
eval/config.groovyin the installation directory.This patch may not be the best approach (I actually think that cfg.HGFA should override pipelineCfg.HGFA, using the principle that the most-user-specified should override the installation default, but leave that up to the maintainer(s) to decide.