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As per conversation on IRIDA Gitter, IRIDA does not seem to have a good way to display compound datatypes. HTML support was added recently in phac-nml/irida#849.
As noted in this issue phac-nml/irida#1057, the problem comes when Galaxy turns the HTML into a ZIP at download time. If, as the last stage in the workflow, you change the Datatype to txt, then this conversion does not happen. This might be a solution to making the MultiQC output work.
MultiQC HTML visualisation not correct as it is in zip format. Liase with IRIDA core team.
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