Issues

• AWS Batch job stuck as RUNNABLE

  bug
  nextstrain/cli#546 · Filter by author victorlin opened on Oct 7, 2026
  3

  

• view: use Auspice v3 CLI args

  nextstrain/cli#545 · Filter by author joverlee521 opened on Sep 4, 2026
  2

• nextstrain run: Analysis directory configuration

  enhancement
  nextstrain/cli#544 · Filter by author victorlin opened on Aug 12, 2026
  9

  

• Standalone bundle ships botocore 1.43.0 without botocore[crt], breaking login for users with local AWS config

  bug
  nextstrain/cli#533 · Filter by author trvrb opened on Jun 2, 2026
  4

  

• New command to list pathogen repos

  enhancement
  nextstrain/cli#510 · Filter by author victorlin opened on Feb 19, 2026
  1

• Add docs for nextstrain-pathogen.yaml file

  documentation
  nextstrain/cli#505 · Filter by author joverlee521 opened on Feb 4, 2026
  1

• Pathogen repo usage flow

  nextstrain/cli#504 · Filter by author victorlin opened on Feb 3, 2026
  

• nextstrain run: third-party pathogen repo support

  nextstrain/cli#449 · Filter by author victorlin opened on Jul 1, 2025
  1

• Bundle runtimes with pathogen repos

  enhancement
  nextstrain/cli#448 · Filter by author victorlin opened on Jul 1, 2025
  3

• [aws-batch] refresh AWS SSO session tokens

  enhancement
  nextstrain/cli#443 · Filter by author joverlee521 opened on Jun 16, 2025
  7

• nextstrain update conda fails when runtime has not been set up

  bug
  nextstrain/cli#440 · Filter by author corneliusroemer opened on Jun 4, 2025
  3

• nextstrain view automatic opening of browser does not work on Windows

  bugsource: office hours
  nextstrain/cli#435 · Filter by author victorlin opened on May 1, 2025
  7

• Bump micromamba to support new nextstrain/conda-base package

  enhancement
  nextstrain/cli#429 · Filter by author joverlee521 opened on Apr 17, 2025
  3

• [aws batch] Structured output of AWS Batch job id for programmatic use

  nextstrain/cli#426 · Filter by author tsibley opened on Mar 28, 2025
  2

• [aws batch] Overlays (e.g. --augur) in uploaded workdir ZIP include too much

  nextstrain/cli#421 · Filter by author tsibley opened on Mar 18, 2025
  6

• Communicate why an upload action was not allowed

  enhancement
  nextstrain/cli#395 · Filter by author jameshadfield opened on Aug 29, 2024
  1

• Update "build directory" terminology in help and docs

  documentation
  nextstrain/cli#371 · Filter by author tsibley opened on May 29, 2024
  5

• shell: Command hangs when --conda is used and the runtime has not been set up

  bug
  nextstrain/cli#363 · Filter by author victorlin opened on Mar 19, 2024
  13

• Pass AWS credentials from standard file to Docker

  enhancement
  nextstrain/cli#342 · Filter by author huddlej opened on Dec 27, 2023
  1

• Unhandled exception when renewing login from a different Cognito user pool

  bug
  nextstrain/cli#339 · Filter by author victorlin opened on Dec 15, 2023
  1

• CLI-ception: Some commands do not work in managed runtime shells

  bug
  nextstrain/cli#336 · Filter by author victorlin opened on Dec 7, 2023
  4

• remote/s3 should instantiate its own MimeTypes instance

  nextstrain/cli#331 · Filter by author joverlee521 opened on Nov 16, 2023

• Consider UI/UX for AWS Batch runtime without Docker runtime

  nextstrain/cli#328 · Filter by author joverlee521 opened on Nov 8, 2023
  3

• nextstrain view can't connect to host on a Mac inside a Conda environment

  bug
  nextstrain/cli#317 · Filter by author huddlej opened on Sep 22, 2023
  8

• Test compatibility with SingularityCE 4.x series

  nextstrain/cli#315 · Filter by author tsibley opened on Sep 19, 2023