workflow

cli.workflow

tvbo workflow — emit Slurm / Snakemake / Nextflow artefacts from a Study.

Attributes

Name	Description
app

Functions

Name	Description
backends	List execution backends and their ontology-derived capabilities (continuous/spiking/jit/etc.).
nextflow	Emit a self-contained Nextflow kit (main.nf + scripts + frozen spec).
plan_cmd	Show the resolved workflow plan for spec without emitting any artefacts.
slurm	Emit a self-contained sbatch kit (run.sbatch + scripts + frozen spec).
snakemake	Emit a self-contained Snakemake kit (Snakefile + scripts + frozen spec).

backends

cli.workflow.backends(json=typer.Option(False, '--json'))

List execution backends and their ontology-derived capabilities (continuous/spiking/jit/etc.).

nextflow

cli.workflow.nextflow(
    spec=typer.Argument(...),
    backend=typer.Option('tvboptim', '--backend', '-b'),
    experiment=typer.Option(None, '--experiment'),
    output=typer.Option(None, '-o', '--output', help='Output directory.'),
    override=typer.Option([], '--set'),
    stdout=typer.Option(False, '--stdout', help='Print artefact only; do not write a kit.'),
)

Emit a self-contained Nextflow kit (main.nf + scripts + frozen spec).

plan_cmd

cli.workflow.plan_cmd(
    spec=typer.Argument(..., help='Path, CURIE, or DB name (Study or Experiment).'),
    backend=typer.Option('tvboptim', '--backend', '-b'),
    engine=typer.Option('local', '--engine', '-e'),
    experiment=typer.Option(None, '--experiment'),
    override=typer.Option([], '--set', help='Override a workflow spec key, e.g. ``--set slurm.account=foo`` (repeatable).'),
    json=typer.Option(False, '--json'),
)

Show the resolved workflow plan for spec without emitting any artefacts.

Reports the chosen study/experiment, backend, engine, vectorized vs workflow-fanned axes, total cell count, chunking, and applied overrides.

slurm

cli.workflow.slurm(
    spec=typer.Argument(...),
    backend=typer.Option('tvboptim', '--backend', '-b'),
    experiment=typer.Option(None, '--experiment'),
    output=typer.Option(None, '-o', '--output', help='Output directory.'),
    override=typer.Option([], '--set'),
    stdout=typer.Option(False, '--stdout', help='Print artefact only; do not write a kit.'),
)

Emit a self-contained sbatch kit (run.sbatch + scripts + frozen spec).

snakemake

cli.workflow.snakemake(
    spec=typer.Argument(...),
    backend=typer.Option('tvboptim', '--backend', '-b'),
    experiment=typer.Option(None, '--experiment'),
    output=typer.Option(None, '-o', '--output', help='Output directory.'),
    override=typer.Option([], '--set'),
    stdout=typer.Option(False, '--stdout', help='Print artefact only; do not write a kit.'),
)

Emit a self-contained Snakemake kit (Snakefile + scripts + frozen spec).