dockstore workflow download --entry github.com/cancerit/workflow-seq-import/chksum_seqval_wf_interleaved_fq:0.4.0
works to download the correct directory structure which is probably related to why it works that way (and might be a workaround depending on what you're working on). Right now I'm thinking that its not the indexing, but an issue with how we translate the paths for display/TRS, so it may be the case that after we fix it, it might just work. Will update in the ticket when we have more