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update / make new Terra-friendly genbank prep workflow #531

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dpark01 opened this issue Apr 2, 2024 · 1 comment
Open

update / make new Terra-friendly genbank prep workflow #531

dpark01 opened this issue Apr 2, 2024 · 1 comment

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@dpark01
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dpark01 commented Apr 2, 2024

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
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dpark01 commented Apr 5, 2024

depends on #532

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