Nextclade Flu NA outputs not populated to Terra data table

[kapsakcj]

🐛

📝 Describe the Issue

The TheiaCoV_Illumina_PE_PHB workflow runs Nextclade on the NA segment, which provides a clade for this segment, but this output is not populated back to the Terra data table unfortunately. You will have to look into the output files on the step that is specific to running nextclade on the NA segment.

It seems the other outputs are also missing, like the nextclade_tsv File, nextclade_json File, nextclade_qc String, maybe more?

It looks like the aa substitutions and deletions are concatenated with those from the HA segment, so no need to output those separately

🔁 How to Reproduce

• Was this run on the Terra platform?
  • Terra on GCP or Azure? GCP
• Or were the workflows run locally using miniwdl or cromwell?
  • What was the exact command was used to launch the workflow?
• If possible, we may ask you to share your Terra workspace with us. Usually READER access is sufficient, but we may ask for WRITER access if we need to make changes to the workspace to reproduce the issue.

Example sample F14049 from the 1-3-0 validation: https://app.terra.bio/#workspaces/theiagen-validations/PHB_Validation_v1-3-0/job_history/9e255e81-77ca-4353-9ce3-9191d3bde5a1

🎣 Expected Behavior

Output the Nextclade results and files from running nextclade on the NA segment to the Terra data table.

💾 Version Information

v1.3.0 as well as the current state of main branch

1.3.0: https://app.terra.bio/#workspaces/theiagen-validations/PHB_Validation_v1-3-0/job_history/9e255e81-77ca-4353-9ce3-9191d3bde5a1

main: https://app.terra.bio/#workspaces/theiagen-validations/PHB_Validation_nextcladeV3testing/job_history/44abfcc6-90d5-4c91-a4b3-98dff1e0a50e

Look at sample F14049 for example

ℹ️ Additional Information