I tried again with the updated bed tools but I still get the same outcome. I can’t attach screenshots because the galaxy emails don’t allow it but I don’t mind you checking my run under current history (RUN12_Minion) if it will help?
Hi @Kathleen_Subramoney - I’ve checked and something seems to have gone wrong with the latest update of the bedtools intersect tool on usegalaxy.eu. Somehow the tool interface got updated without an accompanying version bump. We’re investigating how that is possible.
usegalaxy.org is unaffected AFAIK if that helps you in any way.
Summary for now: the workflow is ok, but it’s a .eu server issue, which we are trying to fix.
Thanks for the update. I will run the workflow on .org in the meantime. Would the output generated from Illumina COVID-19 workflow using the same beds fine since there were no errors from it?