Current genbank.wdl is still very pre-Terra-centric in use pattern (it takes in multiple input samples from the same species/taxon and preps a bulk submission zip file for the batch).
Current multi-pathogen projects in Terra would benefit if we had a workflow that:
prepared genbank submissions in a pathogen agnostic manner
ran on one assembly at a time
relied instead on something like Theiagen's ZipColumnContent wdl to make the final submission zip file from many rows in the Terra table instead of us making the zip ourselves
And... while we're at it (wish list):
update to table2asn as tbl2asn is now deprecated
utilize VADR for applicable taxa to 1) create the tbl files (do the annotation transfers) and 2) pre-screen passing/failing submissions (fall back to our custom tbl transfer single for taxa unsupported by VADR)
dpark01
commented
5 months ago
Current genbank.wdl is still very pre-Terra-centric in use pattern (it takes in multiple input samples from the same species/taxon and preps a bulk submission zip file for the batch).
Current multi-pathogen projects in Terra would benefit if we had a workflow that:
And... while we're at it (wish list):
table2asnastbl2asnis now deprecated