annopi-ts

TypeScript bioinformatics pipeline workflow engine — YAML to shell to DAG execution.

What is annopi-ts?

annopi-ts is the TypeScript rewrite of annopi — a bioinformatics pipeline orchestration engine. It reads pipeline.yml and project.yml, expands parameters per sample, generates shell/*.sh scripts and tasks.yml, then executes tasks with checkpoint/resume via .sign files.

V1 Scope

V1 delivers:

Command	Purpose
`annopi conf`	Validate configs, generate scripts and `tasks.yml`
`annopi run`	Execute pending tasks from `tasks.yml`
`annopi install`	Install or update task modules

V1 does not include annopi report. Report design targets ../rst — see the report design doc.

Packages

@seqyuan/annopi-core    Pure models, parsers, validators, param resolver, DAG
@seqyuan/annopi-node    File I/O, module loading, generators, runtime
@seqyuan/annopi     Command-line interface
@seqyuan/annopi-extension   TypeScript API for annovibe / OpenVibe
@seqyuan/annopi-report      Report helpers (depends on rst)

Report rendering uses the published rst packages:

@seqyuan/rst-renderer   Template + RST → HTML / Markdown / React
@seqyuan/rst-cli        rst-render CLI for report pipeline tasks

Execution Model

annopi-ts generates runcmd strings in tasks.yml for two executor modes:

Mode	runcmd shape	Runner
local	`{runner} -i script -l N -t M`	`ata` or `annotask` (no `local` subcommand)
qsubsge	`{annotask} qsubsge -i script ...`	`annotask` with cluster options

Global runner paths are configured via pipeline deps:

deps:
  ata: /path/to/ata
  annotask: /path/to/annotask

See Runners for details.

Compatibility

annopi-ts aims for two kinds of compatibility with Python annopi:

Config compatibility — both engines read the same pipeline.yml / project.yml
Execution compatibility — both can run tasks.yml generated by the other

Architecture

pipeline.yml + project.yml
        │
        ▼
  annopi-core   (parse → validate → ParamResolver → DAG)
        │
        ▼
  annopi-node   (ScriptGenerator → TasksYmlGenerator → runPipeline)
        │
        ▼
  annopi CLI    (conf / run / install)

Get Started

Quick Start — clone, build, and run the example pipeline
Usage — conf and run workflow
Runners — ata / annotask path configuration
Configuration — pipeline.yml and project.yml reference