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In a few places (READMEs, readthedocs, configs), note the deprecation of Broad_LSF and Broad_UGER execution modes. Delete the standalone
ref_assisted
Snakemake workflow that hasn't been used since Jan 2015 (and whose features still exist inpipes/rules/interhost.rules
). Start some documentation stubs for WDL pipelines in readthedocs. Update some of the GCP/dsub/docker documentation.