Usage

Overview

annopi-ts follows a two-step workflow:

1. conf — parse configs, validate references, expand parameters, generate shell/*.sh and tasks.yml
2. run — execute pending tasks from tasks.yml, respecting dependencies and .sign checkpoints

pipeline.yml + project.yml
        │ conf
        ▼
  shell/*.sh + tasks.yml
        │ run
        ▼
  .sign files + task outputs

annopi conf

annopi conf \
  -p <pipeline.yml> \
  -c <project.yml> \
  -o <outdir>

What conf does

1. Loads and merges pipeline.yml with imported task modules
2. Validates deps, config, and sample references
3. Expands parameters (single / sample / cmp modes)
4. Builds the task DAG and topological order
5. Writes one shell script per numbered task to <outdir>/shell/
6. Writes <outdir>/tasks.yml with runcmd, depends, and status: pending

Example output

[CHECK] task 'cellranger' ... OK
[CHECK] task 'qc' ... OK
Generated 2 task scripts in /tmp/annopi-out/shell
Generated tasks.yml in /tmp/annopi-out

Shell script format

Each shell/N-M-taskname.sh file contains one command per line — the format expected by ata and annotask -i input files.

annopi run

annopi run -o <outdir>

What run does

1. Reads <outdir>/tasks.yml
2. Refreshes task status from .sign files in shell/
3. Schedules ready tasks (dependencies satisfied, status pending)
4. Executes runcmd for each ready task
5. Writes .sign on success

Resume behavior

If all tasks are already done:

All tasks already done.

To force re-run, delete the corresponding .sign files in shell/.

annopi install

annopi install <source>
annopi install <source> --update

Installs or updates a task module from a local path or git URL. Module tasks can be referenced via imports in pipeline.yml.

Python ↔ TypeScript Interop

annopi-ts is designed so that:

• Python annopi conf output can be run by annopi-ts run
• annopi-ts conf output can be run by Python annopi run

Both engines should produce compatible tasks.yml semantics. Exact YAML formatting may differ.

Fixtures

Test fixtures live under tests/fixtures/annopi/:

See Configuration for YAML field reference.