Add Influenza submission

[nbx0]

• [x] GISAID using their CLI API
• [x] NCBI - BioSample
• [x] NCBI - Genbank
• [x] NCBI - SRA
• [x] NCBI - Table2asn

cc: @leebrian @rchau88 @kristinelacek

[dthoward96]

Currently doing bug fixes/testing. Have a meeting on Wednesday to discuss Docker changes. Then I'll update the instructions for the new functionality. Will have a fork to share for testing at end of week/early next week

[ammaraziz]

As an end user of SeqSender, along time uploader of influenza data to gisaid and as someone who is pushing for upload to NCBI/genbank, please let me know if there's any space for assisting in integrating influenza submission into seqsender.

Happy to beta test anything!

[nbx0]

@ammaraziz thanks for the support Ammar!

[dthoward96]

It's taken me a little longer to work out the bugs and do more testing. I have it working and tested for BioSample and SRA. I have GISAID via CLI working and doing further testing to ensure there is no issues. Currently working through a bug with Genbank for when uploading influenza via FTP instead of emailing via table2asn. Once I've got it ironed out and finalized the updates for the documentation I'll push the updates for testing. @nbx0

[nbx0]

Thanks D.

We are really counting on having flu-genbank ready in the coming weeks so that we can incorporate into MIRA for our early August training.

Cc: @rchau88

From: Dakota Howard @.> Sent: Tuesday, June 20, 2023 8:38 AM To: CDCgov/seqsender @.> Cc: Rambo Martin, Benjamin (CDC/DDID/NCIRD/ID) @.>; Mention @.> Subject: Re: [CDCgov/seqsender] Add Influenza submission (Issue #4)

It's taken me a little longer to work out the bugs and do more testing. I have it working and tested for BioSample and SRA. I have GISAID via CLI working and doing further testing to ensure there is no issues. Currently working through a bug with Genbank for when uploading influenza via FTP instead of emailing via table2asn. Once I've got it ironed out and finalized the updates for the documentation I'll push the updates for testing. @nbx0https://github.com/nbx0

— Reply to this email directly, view it on GitHubhttps://github.com/CDCgov/seqsender/issues/4#issuecomment-1598691738, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AJPHCXTPPVIOYGYF274B4I3XMGKRPANCNFSM6AAAAAAYDYP5JY. You are receiving this because you were mentioned.Message ID: @.**@.>>

[dthoward96]

@nbx0 Reina and I have setup multiple meetings next week for testing/bug fixing for each database to hopefully finalize everything

[dthoward96]

Successful submissions to each database, I updated original issue to include table2asn which is also supported. Working on doing final bug checks/fixes and updating the readme and test sets.

[dthoward96]

influenza submission currently working in "merged" branch