Coverage/Program/Platform not output into flatfiles despite being mandatory #76
Description
In February, I noticed that the following required manifest fields are not output into the ENA assemblies/flatfiles: Coverage, Program, Platform
I raised this with ENA as [EXTERN] [broker #792221] AutoReply: [ena-brokers] Potential processing bug: Manifest metadata goes missing from assemblies
Key details of the answer:
You are correct that we currently do not expose this information. The
information provided in the manifest file is stored in the analysis object/
XML (i.e ERZ25039233 for your assembly), which, for non-covid data is only
accessible from a submitter's private environment in the Webin Submissions
Portal. (For the purposes of data sharing in the pandemic, we had exposed
COVID ERZ### accessions to present such information in the browser).
I agree with you that we should be displaying these manifest file fields,
particularly as they are mandatory for submission. This has been raised
previously and is on our roadmap, but I will raise the priority of this.
Interestingly, the information is shared with NCBI and is available on the GCA page (which Pathoplexus doesn't link to yet but maybe should as it's a nice summary of everything): https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_965120225.1/