Issues

• GISAID build fails due to new "country" Lugansk missing from weights

  bug
  nextstrain/ncov-ingest#514 · Filter by author corneliusroemer opened on Dec 11, 2025
  3

• format_date does not mask incomplete dates

  nextstrain/ncov-ingest#499 · Filter by author joverlee521 opened on Apr 14, 2025
  1

• Properly handle CSV-like TSVs

  nextstrain/ncov-ingest#482 · Filter by author joverlee521 opened on Dec 6, 2024

• GitHub actions log is >2hr behind actual AWS run

  bug
  nextstrain/ncov-ingest#474 · Filter by author corneliusroemer opened on Aug 22, 2024
  8

• Benchmark in every rule is annoying - extra 2 lines that should not be necessary

  nextstrain/ncov-ingest#472 · Filter by author corneliusroemer opened on Aug 22, 2024
  2

• Do we need uncompress_cog_uk_metadata and compress_cog_uk_metadata?

  nextstrain/ncov-ingest#450 · Filter by author joverlee521 opened on Jun 17, 2024
  1

• Rename master to main

  blockedenhancement
  nextstrain/ncov-ingest#449 · Filter by author genehack opened on Jun 13, 2024
  1

• Explore parallelizing transform-gisaid

  nextstrain/ncov-ingest#448 · Filter by author joverlee521 opened on Jun 13, 2024

• GISAID workflow hitting max_session_duration

  nextstrain/ncov-ingest#446 · Filter by author joverlee521 opened on Jun 11, 2024
  11

  

• Lock dependencies using pip-compile

  enhancement
  nextstrain/ncov-ingest#438 · Filter by author victorlin opened on Feb 21, 2024

• Ingest VirusSeq data

  enhancement
  nextstrain/ncov-ingest#421 · Filter by author chaoran-chen opened on Dec 7, 2023
  3

• Make use of genbank's purpose_of_sampling field

  enhancement
  nextstrain/ncov-ingest#415 · Filter by author corneliusroemer opened on Aug 10, 2023

• Most RKI sequences lack submission date

  nextstrain/ncov-ingest#410 · Filter by author corneliusroemer opened on Jul 11, 2023
  1

  

• Send error logs to Slack

  enhancement
  nextstrain/ncov-ingest#408 · Filter by author joverlee521 opened on Jun 28, 2023

• Add reasonable default for clade_legacy so that new clade doesn't require changes in ingest's clade-legacy-mapping.yml

  enhancement
  nextstrain/ncov-ingest#406 · Filter by author corneliusroemer opened on Jun 21, 2023
  

• Add Genbase sequences to open data

  enhancement
  nextstrain/ncov-ingest#402 · Filter by author corneliusroemer opened on May 5, 2023
  3

• ENH: Use benchmark: to find memory intensive rules

  enhancement
  nextstrain/ncov-ingest#378 · Filter by author corneliusroemer opened on Dec 14, 2022

• ENH: Produce "small" metadata.tsv with only essential columns

  enhancement
  nextstrain/ncov-ingest#376 · Filter by author corneliusroemer opened on Dec 13, 2022

• Nextclade refactor grab list

  enhancement
  nextstrain/ncov-ingest#375 · Filter by author corneliusroemer opened on Dec 13, 2022

• Pull data directly from COG-UK Data

  enhancement
  nextstrain/ncov-ingest#329 · Filter by author joverlee521 opened on Jul 25, 2022
  2

• Allow ncov-ingest to upload to non-AWS remote file paths

  enhancement
  nextstrain/ncov-ingest#308 · Filter by author huddlej opened on May 13, 2022

• Allow ncov-ingest to download from non-AWS remote file paths

  enhancement
  nextstrain/ncov-ingest#307 · Filter by author huddlej opened on May 13, 2022
  2

• Include quick clade count after every ingest in logs

  enhancement
  nextstrain/ncov-ingest#251 · Filter by author corneliusroemer opened on Dec 10, 2021

• check-locations: Columns have mixed types

  bug
  nextstrain/ncov-ingest#249 · Filter by author ivan-aksamentov opened on Dec 10, 2021

• Revisit fetch from GISAID

  enhancement
  nextstrain/ncov-ingest#242 · Filter by author joverlee521 opened on Dec 3, 2021
  2