Adds community pipeline support [WIP] by johnchase · Pull Request #21 · cymis/adagio-cli

Commits on Nov 13, 2025

Fixes docker and pyproject.

John Chase
authored and
John Chase
committed

Commits on Feb 1, 2026

Merge pull request #3 from cymis/feature/acl
johnchase
authored

Commits on Feb 17, 2026

Adds pipeline parsing

John Chase
authored and
John Chase
committed
Adds pipeline parsing

John Chase
authored and
John Chase
committed

Commits on Feb 22, 2026

Fixes merge conflict in pyproject.toml

John Chase
authored and
John Chase
committed
Fixes merge conflict

John Chase
authored and
John Chase
committed
Adds pipeline cli interface

John Chase
authored and
John Chase
committed
Adds arguments

John Chase
authored and
John Chase
committed
removes example

John Chase
authored and
John Chase
committed

Commits on Feb 24, 2026

Adds dummy progress

John Chase
authored and
John Chase
committed
Adds dummy progress

John Chase
authored and
John Chase
committed
Small refactor

John Chase
authored and
John Chase
committed
fix merge conflict

John Chase
authored and
John Chase
committed

Commits on Feb 25, 2026

Adjusts progress bars

John Chase
authored and
John Chase
committed
Adds param grouping

John Chase
authored and
John Chase
committed

Commits on Feb 26, 2026

Fixes runtime

John Chase
authored and
John Chase
committed

Commits on Feb 28, 2026

Adds serial qiime runner with docker

John Chase
authored and
John Chase
committed

Commits on Mar 4, 2026

Fizes output name issue

John Chase
authored and
John Chase
committed

Commits on Mar 25, 2026

Temporary move imports to be lazy

John Chase
authored and
John Chase
committed
Adds apptainer support

John Chase
authored and
John Chase
committed

Commits on Mar 26, 2026

Fizes bug where host packages were injected into container

John Chase
authored and
John Chase
committed

Commits on Mar 27, 2026

Adds param descriptions to help

John Chase
authored and
John Chase
committed
Adds pipeline summary commmand

John Chase
authored and
John Chase
committed
Writes files to disk as they are created

John Chase
authored and
John Chase
committed

Commits on Mar 31, 2026

Adds collection support

John Chase
authored and
John Chase
committed

Commits on Apr 3, 2026

fix flicker

John Chase
authored and
John Chase
committed
Second attempt at fixing flicker

John Chase
authored and
John Chase
committed
Next attempt at render

John Chase
authored and
John Chase
committed

Commits on Apr 8, 2026

Fix flickering tty

John Chase
authored and
John Chase
committed
Merge pull request #13 from cymis/codex/adagio-cli-cache-reuse
johnchase
authored
Merge pull request #15 from cymis/config-toml
johnchase
authored
Merge pull request #16 from cymis/add-param-description
johnchase
authored
Merge pull request #17 from cymis/show-pipeline
johnchase
authored
Merge pull request #18 from cymis/collections
johnchase
authored
Merge pull request #19 from cymis/apptainer
johnchase
authored
Adds qapi token submission

John Chase
authored and
John Chase
committed
Merge pull request #20 from cymis/qapi-token
johnchase
authored

Commits on Apr 14, 2026

Adds community pipeline support

John Chase
authored and
John Chase
committed

Commits on May 5, 2026

Removes user configuration

John Chase
authored and
John Chase
committed
Fixed merge conflicts

John Chase
authored and
John Chase
committed
remove formatting

John Chase
authored and
John Chase
committed

Commits

Commits on Nov 13, 2025

Commits on Feb 1, 2026

Commits on Feb 17, 2026

Commits on Feb 22, 2026

Commits on Feb 24, 2026

Commits on Feb 25, 2026

Commits on Feb 26, 2026

Commits on Feb 28, 2026

Commits on Mar 4, 2026

Commits on Mar 6, 2026

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Commits on Mar 10, 2026

Commits on Mar 13, 2026

Commits on Mar 20, 2026

Commits on Mar 24, 2026

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Commits on Mar 26, 2026

Commits on Mar 27, 2026

Commits on Mar 31, 2026

Commits on Apr 3, 2026

Commits on Apr 8, 2026

Commits on Apr 14, 2026

Commits on May 5, 2026