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How Spectio works

Spectio sits between you and your workflow engine. It does not replace Nextflow or Snakemake: it launches them on your cluster, follows them through their own events, explains failures, and relaunches them. Most pipelines simply run from start to end. Gates, stops between stages for a quality check, are optional.

Five words

Word What it means
Run One execution of a pipeline, with its parameters, samples and outputs.
Stage A group of steps in a pipeline: for example qc, then align, then quantify.
Gate Optional. A stop between two stages. The run waits there until someone decides.
Decision Approve, exclude samples, change a parameter and rerun the stage, or stop. A person, an AI agent or a robot can decide.
Runner The small program next to the compute (a SLURM login node, a Kubernetes cluster, a laptop) that starts the engine and reports back.

A run without gates

  1. Launch from the web form, the CLI or the API, on the environment you choose.
  2. Watch its stages, tasks, samples and logs, and what the scheduler does with its jobs.
  3. When something fails, Spectio tells you why (out of memory, out of time, a tool error, a node lost) and proposes a change. Relaunch: finished work comes back from the cache.
  4. When it finishes, outputs, reports and logs stay attached to the run, and can be handed to depictio.

A run with a gate (optional)

Stop at the QC gate, drop a sample, resume Stop at the QC gate, drop a sample, resume

  1. Launch. You pick a pipeline and its parameters, and say "stop after qc".
  2. Stop at the gate. Spectio uses the engine's own way of stopping, so the run ends cleanly after qc.
  3. Decide. The gate shows the QC evidence. Here, sample S03 has 40 reads instead of 400, so the reviewer excludes it and approves.
  4. Resume. Spectio starts the engine again with the new samplesheet. Everything already computed comes back from the cache.

This has been tested on a small test pipeline with both engines: after the QC gate, 25 of the 65 tasks come back from the cache. The cluster, the runner and the phone in the figure are the planned flow; they are not built yet.

What it looks like in a terminal

The same stop and resume, with Snakemake, recorded from a real run:

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