[Mercury] potential issue with mercury_prep_n_batch with clearlabs data

[kapsakcj]

:bug:

:pencil: Describe the Issue

A user notified us that after running the Mercury_prep_n_batch workflow on a set of SC2 genomes sequenced on a clearlabs platform, the SRA metdata sheet and GISAID metadata sheet disagreed in two columns.

For the SRA metadata, the column raw_sequence_data_processing_method was populated with TheiaCoV (PHB v1.2.1): Medaka via artic 1.3.0

For the GISAID metadata, the column covv_assembly_method was populated with Clear Dx SARS-CoV-2 WGS v3.0

:repeat: How to Reproduce

• Was this run on the Terra platform? yes
  • Terra on GCP or Azure? GCP
• Or were the workflows run locally using miniwdl or cromwell? No
  • 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.

I can provide the terra workspace, workflow, & affected set privately.

:fishing_pole_and_fish: Expected Behavior

The user expected both columns to state Clear Dx SARS-CoV-2 WGS v3.0 since they were submitting CL-generated FASTA files, not FASTA files generated via TheiaCov workflows.

:floppy_disk: Version Information

Mercury_prep_n_batch v1.2.1

:information_source: Additional Information

I'm not intimately familiar with this workflow, so I don't have a recommended solution, but wanted to document this issue so that we can work on a solution (whether that involves a code change or another solution)

[kapsakcj]

Closing as this issue was resolved by editing metadata TSV files prior to submission to GISAID & SRA. User has not communicated about this issue in >1 year