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CLI Reference

Syntax, arguments, and options for the codaris command-line interface. The CLI Commands page walks through each subcommand with examples; this page is the compact reference.

Command Syntax

codaris [--json] <verb> [ARGS] [OPTIONS]

Three invocation forms share the same entry point.

Invocation Behaviour
codaris Launches the interactive REPL
codaris <text that is not a verb> Launches the REPL with the text as the opening prompt
codaris <verb> ... Runs the named subcommand headlessly

Global Options

Option Description
--json Print one machine-readable JSON object instead of text. Accepted before or after the verb.
-h, --help Show the help message for the CLI or for a subcommand.
-v, --verbose When given alone, launch the REPL with verbose tracing.

Exit Codes

Code Meaning
0 Success
1 The command ran and reported a failure
2 A required capability is unavailable, or a build has open blocking questions
130 Interrupted with Ctrl+C

Subcommands

codaris doctor (alias status)

codaris doctor [--json]
Checks Nextflow, nf-core, Docker, seqtk, the toolchain container, and the stores.

codaris stores

codaris stores check|fetch [--force] [--base-url URL]
Verifies or downloads the versioned store artifacts. CODARIS_STORES_BASE_URL overrides the release base URL.

codaris plan

codaris plan <prompt> [--out PATH] [--model NAME] [--playbooks-dir PATH] [--interactive] [--answers FILE]
Turns a prompt into a BuildPlan JSON (default build_plan.json) and either asks the reference and test-data questions on the terminal, answers them from a file, or writes <plan>.questions.json with defaults.

codaris build

codaris build <plan.json> [--output-dir PATH] [--model NAME] [--self-review] [--confirm-nonstandard] [--use-defaults]
Compiles a pipeline directory from the plan and runs nf_validate and nf-core pipelines lint. Exits 2 on open blocking questions unless --use-defaults is given.

codaris test

codaris test <pipeline_dir> [--profile NAME] [--timeout SECONDS] [--fix-budget N] [--skip-readiness] [--llm-repair] [--llm-repair-budget N] [--llm-repair-model NAME]
Runs the test profile (default test_codaris,docker) with readiness checks, the resource fixer, and an optional LLM repair escalation logged to .codaris/repair_log.json.

codaris review (alias audit)

codaris review <pipeline_dir> [--profile core|full] [--provider openai|anthropic] [--model NAME] [--quick] [--quiet]
Read-only compliance audit with scorecard and report artifacts.

codaris remediate

codaris remediate <pipeline_dir> [--profile core|full] [--provider openai|anthropic] [--model NAME] [--quick] [--quiet] [--allow-destructive] [--max-iterations N]
Applies rollback-safe compliance fixes with backups in .codaris_fix_backups/.

codaris lint

codaris lint <pipeline_dir> [--timeout SECONDS]
Runs nf-core pipelines lint and classifies the result.

codaris judge

codaris judge <pipeline_dir | plan.json> [--criteria LIST] [--no-verify] [--quiet]
Evaluates a built pipeline or a plan against the six semantic criteria.

codaris nf-test

codaris nf-test <pipeline_dir> [--force]
Writes the nf-test harness and CI job.

codaris publish

codaris publish <pipeline_dir> [destination] [--project NAME] [--pipeline NAME]
Copies a built pipeline and its record to a destination (default $CODARIS_PUBLISH_DIR/<name>).

codaris bench

codaris bench [--playbooks-dir PATH] [--out PATH] [--only KEY ...] [--work-dir PATH] [--reuse-work-dir] [--skip-plan] [--skip-build] [--skip-test] [--skip-review] [--model NAME]
Benchmarks playbooks through plan, build, test, and review, and writes a scorecard.

codaris chat

codaris chat [prompt] [--model NAME] [--workspace PATH] [--mode build|plan|review] [--verbose]
Starts the interactive agent. See the Interactive REPL page.

codaris web (aliases ui, serve)

codaris web [--host ADDRESS] [--port PORT] [--reload]
Launches the web studio and API service (default 127.0.0.1:8000).