Terra.bio seqsender submission workflows

[erikwolfsohn]

Hey Dakota,

The v1.2.1 release looks great, I'm really excited to start using it!

I wanted to quickly mention a couple of submission workflows I've been developing in case they're useful for you or other seqsender users.

You might already be familiar with Terra.bio - it's a bioinformatics workflow platform similar to Nextflow Tower/GalaxyTrakr. My lab and other labs I work closely with use Terra for sequence analysis and submission prep, so one of my goals has been enabling submission directly from Terra workspaces without needing to download or run anything locally.

There are two workflows here along with some documentation:

seqsender_submission_prep ingests a terra table + the contents of two configuration files and outputs a seqsender-compatible metadata csv.
seqsender_submit performs a submission or checks the status of an existing submission

Currently these workflows support BioSample and SRA submission with any BioSample package and GISAID SARS-CoV-2 submissions. I've tested them thoroughly with SARS-CoV-2 submissions to all three repositories and OneHealth Enteric submissions to BioSample and SRA. The next release will support the full range of GISAID pathogens + GenBank.

If this ends up being of interest for you or any other seqsenders users, definitely let me know! I'm happy to offer assistance with setup and take any feedback.

Thanks again for all your work on seqsender and for getting out the v1.2.1 release so quickly!