Workflow package contract

RAFT workflow configuration repositories can provide more than the execution .config file. A complete workflow package can define how RAFT creates a project, guides manifest creation, builds reports, and checks project status.

Recommended files

For a workflow package such as lens-human-fastqs, use these filenames:

lens.human.fastqs.config
lens.human.fastqs.json
lens.human.fastqs.manifest-ui.json
lens.human.fastqs.report-ui.json
lens.human.fastqs.status.json
README.md

Execution config

<workflow>.<species>.<input>.config contains default Nextflow parameters and container settings copied into generated projects.

<workflow>.<species>.<input>.json tells RAFT which modules, workflow steps, references, post-processing commands, and text replacements are needed to build the project.

Manifest UI config

<workflow>.<species>.<input>.manifest-ui.json customizes the manifest generator. It should define:

• required and optional columns

• allowed values

• sample type conventions

• workflow-specific requirements

For LENS, this is where columns such as Group and Alleles should be explained for users.

Report UI config

<workflow>.<species>.<input>.report-ui.json customizes the report viewer and report bundle. It should define:

• report sections

• file patterns to include

• renderers

• table columns

• QC sections

Use narrow file patterns so report bundles include final review files instead of large intermediate tables.

Status config

<workflow>.<species>.<input>.status.json customizes raft project-status. It can define:

• expected output paths

• globbed output families with minimum counts

• final report patterns

• required report columns

• value-count summaries

• all-blank column warnings

The command remains read-only. Status configs should warn about suspicious or missing outputs; they should not repair or modify project files.

Project README

RAFT writes a generated README.md into each project directory. Workflow packages can still include their own repository README.md to document workflow-specific inputs, outputs, and interpretation.

Maintenance checklist

When updating a workflow package:

• keep execution config and metadata JSON in sync

• update manifest UI columns when workflow inputs change

• update report UI patterns when output filenames change

• update status checks when final reports or required columns change

• run raft available-workflows --workflow <workflow> --species <species> --input <input> to inspect what RAFT sees

• run raft project-status on a completed example project