Related Issues (18)
- Automate interactions with metadata for release workflow HOT 2
- Halt flagging of changes in non-coding regions
- Automate upload to GISAID, Github, Google Drive, SD County HOT 3
- config.json is hardcoded in run for alab_release
- Automate combining *_white.fa and *_inspect_fa, aligned -> unaligned conversion, and multifasta to individual_fasta HOT 1
- Create NCBI Upload Pipe HOT 1
- Add semi-automated sequence filters during release workflow
- Merge genbank, SRA, and biosample IDs to HCoV-19-Genomics Metadata HOT 3
- Change samples column in output so files are alphabetical and ", " separated
- Simplify env.yaml HOT 1
- Update and formalize generating list of files that need to be uploaded to ncbi
- Automate NCBI upload workflow kickoff HOT 1
- Reduce folder output to minimum required
- Select for n-stretch in samples as further filtering metric
- Create rejected fasta folder for biolab_genomics
- Use mutations.py from bjorn proper and remove instance in this repo
- Update readme to reflect new workflow
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