This release is a pre-release and may not be stable for production use.
Adagio CLI
adagio-cli is the Python command-line interface for Adagio pipeline execution.
For user-facing documentation and product guides, please reference the docs:
The adagio frontend is used to build pipelines that can be run with this package on the command line It can be found here:
Development
Set up the project and run the test suite with:
uv sync --group dev
uv run pytest
Runtime environments
By default, adagio run resolves plugin actions to Docker images. A runtime
config passed with --config can override that per default, plugin, or task.
Conda environments are supported with kind = "conda":
version = 1
[defaults]
kind = "conda"
environment = "qiime2-2026.1"
[plugins]
dada2 = { kind = "conda", prefix = "/opt/conda/envs/q2-dada2" }
The environment must already exist and contain QIIME 2 plus the plugins needed
by the pipeline. Adagio enters it with conda run; it does not create or manage
the environment.
Catalog pipelines
Run a pipeline from the Adagio pipeline catalog:
adagio pipeline show @adagio/microbial-diversity
adagio run @adagio/microbial-diversity --cache-dir /path/to/cache --arguments run-arguments.json
@adagio/<slug> first resolves against a nearby local adagio-pipelines
checkout when one is available. If no local catalog is found, Adagio fetches
pipeline.adg from cymis/adagio-pipelines on GitHub, checking official
before community.
During adagio run, remote catalog pipelines are downloaded under the selected
--cache-dir and reused by source name and slug on later runs. adagio pipeline show uses a temporary download when it fetches from GitHub because it does not
take a cache directory.
Private GitHub access is explicit: set GITHUB_TOKEN or GH_TOKEN to a token
that can read cymis/adagio-pipelines; with a token, the CLI fetches through
the GitHub contents API. The CLI does not read browser, git, or gh credentials
automatically.
1 maintainer
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