# {py:mod}`ovo.core.scheduler.nextflow_scheduler`

```{py:module} ovo.core.scheduler.nextflow_scheduler
```

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler
:allowtitles:
```

## Module Contents

### Classes

````{list-table}
:class: autosummary longtable
:align: left

* - {py:obj}`NextflowScheduler <ovo.core.scheduler.nextflow_scheduler.NextflowScheduler>`
  -
````

### API

`````{py:class} NextflowScheduler(name: str, workdir: str, reference_files_dir: str, allow_submit: bool = True, submission_args: dict = None)
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler

Bases: {py:obj}`ovo.core.scheduler.base_scheduler.Scheduler`, {py:obj}`ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin`

````{py:method} submit(pipeline_name: str, params: dict = None, submission_args: dict = None) -> str
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.submit

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.submit
```

````

````{py:method} _run_subprocess(command: list[str], job_id: str, sync: bool = False)
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._run_subprocess

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._run_subprocess
```

````

````{py:method} queue_run_task(job_id: str, task: typing.Any)
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.queue_run_task

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.queue_run_task
```

````

````{py:method} run(pipeline_name: str, output_dir: str = None, params: dict = None, submission_args: dict = None, link=False) -> str
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.run

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.run
```

````

````{py:method} _create_run_command(pipeline_name: str, params: dict = None, sync: bool = False, submission_args: dict = None) -> list[str]
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._create_run_command

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._create_run_command
```

````

````{py:method} _get_module_path(module_name) -> str
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_module_path

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_module_path
```

````

````{py:method} _get_default_config_path()
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_default_config_path

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_default_config_path
```

````

````{py:method} _get_pipeline_dir(pipeline_name: str) -> str
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_pipeline_dir

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_pipeline_dir
```

````

````{py:method} get_trace_table(job_id: str) -> pandas.DataFrame | None
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_trace_table

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_trace_table
```

````

````{py:method} get_status_label(job_id: str) -> str
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_status_label

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_status_label
```

````

````{py:method} get_result(job_id: str) -> bool | None
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_result

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_result
```

````

````{py:method} get_log(job_id: str) -> str | None
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_log

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_log
```

````

````{py:method} cancel(job_id)
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.cancel

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.cancel
```

````

````{py:method} get_output_dir(job_id: str)
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_output_dir

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_output_dir
```

````

````{py:method} _get_exec_dir(job_id: str)
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_exec_dir

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_exec_dir
```

````

````{py:method} _get_pid(job_id) -> int
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_pid

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_pid
```

````

````{py:method} get_job_start_time(job_id: str) -> datetime.datetime | None
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_job_start_time

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_job_start_time
```

````

````{py:method} get_job_stop_time(job_id: str) -> datetime.datetime | None
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_job_stop_time

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_job_stop_time
```

````

````{py:method} _get_shared_module_paths()
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_shared_module_paths

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_shared_module_paths
```

````

````{py:method} _get_shared_modules_string() -> str
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_shared_modules_string

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler._get_shared_modules_string
```

````

````{py:method} get_pipeline_names() -> list[str]
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_pipeline_names

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_pipeline_names
```

````

````{py:method} get_param_schema(pipeline_name: str) -> dict | None
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_param_schema

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_param_schema
```

````

````{py:method} get_failed_message(job_id)
:canonical: ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_failed_message

```{autodoc2-docstring} ovo.core.scheduler.nextflow_scheduler.NextflowScheduler.get_failed_message
```

````

`````