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Codaris

Architecture compiler for Nextflow DSL2 and nf-core pipelines
Describe the analysis in plain language. Codaris plans the module chain, scaffolds an nf-core pipeline, compiles the workflow, checks that it parses and lints, and scores it against a 249-rule nf-core ruleset.


Run the web studio GitHub repository

What Codaris is made of

  • Two engines

    A local decision model (Primeomicx/nf-pilot) classifies intent, triages failures, and picks among candidate tools in milliseconds. A cloud or local language model writes and repairs the code.

    → Dual-engine architecture

  • A bounded tool surface

    Each turn binds a fixed set of file, build, data, and run tools, plus the tools a slash command or a research turn asks for. A policy gate decides at dispatch time what a tool may do.

    → Tool surface

  • One container

    The web studio, the API, Nextflow 25.10.4, nf-core 4.1.0, nf-test 0.9.5, Java 17, and Python 3.11 ship in one image for linux/amd64 and linux/arm64.

    → Container quickstart

  • Compliance scoring

    A versioned ruleset of 249 rules derived from the nf-core specifications scores a pipeline, and a remediation pass applies rollback-safe fixes. The score describes nf-core conformance; it is not a regulatory certification.

    → Compliance scoring

  • A terminal client

    codaris opens a REPL that streams the same turns as the web studio, and the headless verbs (doctor, plan, build, test, review, remediate) run in scripts and CI.

    → Interactive REPL

  • Assay playbooks

    Starting points for bulk RNA-seq, germline and somatic WGS, ChIP-seq, ATAC-seq, single-cell, metagenomics, and amplicon analyses.

    → Domain playbooks

Quick start

Run the web studio from the published image. HOME is passed through so the container keeps chats, settings, and keys in your ~/.codaris:

docker run -d --name codaris \
  -p 127.0.0.1:3000:3000 -p 127.0.0.1:8000:8000 \
  -e HOME="${HOME}" \
  -v "${HOME}/.codaris:${HOME}/.codaris" \
  -v "${HOME}/projects:${HOME}/projects" \
  -v /var/run/docker.sock:/var/run/docker.sock \
  ghcr.io/primeomicx/codaris:latest

Open http://localhost:3000, add a model API key under Customizations, and describe the pipeline you want. The container quickstart covers the Docker socket, Compose, and the command line inside the image.

To run the command line from a source checkout:

git clone https://github.com/PrimeOmicX/codaris.git
cd codaris/backend
python3.11 -m venv .venv && source .venv/bin/activate
pip install torch --index-url https://download.pytorch.org/whl/cpu
pip install -r requirements.txt
cd .. && ./bin/codaris doctor

Capabilities at a glance

Pillar Capability What it delivers
Planning Intent elicitation and staged questions A BuildPlan with the assay, the module chain, the reference assets, the sample sheet layout, and the parameter defaults, each confirmed with you before anything is written.
Synthesis nf-core scaffold plus a compiled workflow nf-core pipelines create lays down the template; the compiler installs the nf-core modules, writes workflows/<name>.nf, conf/modules.config, the test profile, and a sample sheet.
Verification Compile gate, symbol repair, and lint nextflow run . -preview resolves every include and call, a positive check confirms the entry point and the planned steps are present, and nf-core pipelines lint runs before the report.
Conversion Legacy workflow ingestion Nextflow DSL1, CWL, WDL, and Snakemake sources are converted to nf-core-shaped DSL2 through the same scaffold and verification path.
Portability nf-core profiles The generated pipeline carries the template's docker, singularity, apptainer, and conda profiles, the institutional configs from nf-core/configs, and resourceLimits-based resource labels.
Containers Version-tagged biocontainers Every process declares a quay.io/biocontainers image with an explicit version tag; a latest tag is reported as a violation, and the registry lookup confirms the tag exists.