Nextflow

Run Nextflow pipelines on Flyte.

The Nextflow head runs inside a Flyte task, and the nf-flyte Nextflow plugin turns every Nextflow task into a child action of that task, so a whole pipeline is a single Flyte run.

        
    
import flyte
from flyteplugins.nextflow import nextflow_image, run_nextflow

env = flyte.TaskEnvironment(name="nextflow", image=nextflow_image())

@env.task
async def demo() -> flyte.io.Dir:
    return await run_nextflow("nf-core/demo", revision="1.2.0", profile="test", outdir="results")

Exception	Description
`NextflowError`	Raised when `nextflow run` exits with a non-zero status.

Method	Description
`nextflow_image()`	Image for the task that runs the Nextflow head: a JRE, Nextflow, the nf-flyte plugin and this package.
`run_nextflow()`	Run a Nextflow pipeline from inside a Flyte task.

Property	Type	Description
`DEFAULT_NEXTFLOW_VERSION`	`str`
`DEFAULT_NF_FLYTE_VERSION`	`str`

Methods

nextflow_image()

        
    
def nextflow_image(
    nextflow_version: str = '25.10.6',
    nf_flyte: str | Path = '0.1.0',
    base: flyte.Image | None = None,
    name: str = 'nextflow',
) -> flyte.Image

Image for the task that runs the Nextflow head: a JRE, Nextflow, the nf-flyte plugin and this package.

Pipeline processes don’t run in this image; each one runs in its own container.

Parameter	Type	Description
`nextflow_version`	`str`	Nextflow release to install.
`nf_flyte`	`str \| Path`	nf-flyte plugin to install, either a version from the Nextflow plugin registry or the path to a locally built plugin zip (`nf-flyte-<version>.zip`).
`base`	`flyte.Image \| None`	Image to add Nextflow to (default: the Flyte debian base image).
`name`	`str`	Image name.

run_nextflow()

        
    
def run_nextflow(
    pipeline: str,
    revision: str | None = None,
    profile: str | None = None,
    params: Mapping[str, Any] | None = None,
    outdir: str | None = None,
    work_dir: str | None = None,
    config: str | Path | None = None,
    resume: bool = False,
    report: bool = False,
    extra_args: Sequence[str] = (),
) -> Dir | None

Run a Nextflow pipeline from inside a Flyte task. On a Flyte cluster, every Nextflow task runs as a child action of the calling task, through the nf-flyte executor; the calling task must use nextflow_image(). In a local run, Nextflow uses its own executors instead (local unless config or profile selects another, e.g. docker).

Parameter	Type	Description
`pipeline`	`str`	Pipeline to run: a repository (e.g. `nf-core/rnaseq`), URL or local path.
`revision`	`str \| None`	Pipeline revision (git tag, branch or commit).
`profile`	`str \| None`	Comma separated Nextflow config profiles, e.g. `test`.
`params`	`Mapping[str, Any] \| None`	Pipeline parameters, passed through a params file.
`outdir`	`str \| None`	Output directory, passed as `--outdir`. A relative path is placed under this task’s raw data prefix. The directory is returned as a `Dir`.
`work_dir`	`str \| None`	Work directory; on a cluster, an object store location Flyte can read. Defaults to a `nextflow-work` prefix under this task’s raw data prefix, which is shared by all attempts of the task, so a retried task resumes where the failed attempt stopped. Set a fixed location to resume across runs.
`config`	`str \| Path \| None`	Extra Nextflow config: a path to a config file, or config text.
`resume`	`bool`	Resume a previous run that used the same `work_dir`. Always on when the task is being retried.
`report`	`bool`	Render Nextflow’s execution report, timeline and DAG into the task’s Flyte report. The task must be declared with `report=True`.
`extra_args`	`Sequence[str]`	Extra arguments for `nextflow run`.

Returns: The outdir as a Dir, or None when no outdir is given.

Nextflow

Directory

Errors

Methods

Variables

Methods

nextflow_image()

run_nextflow()