Overview

What is the expectmine-pipeline?

The Expectmine-Pipeline aims to create a simple interface for researchers to build processing pipelines for their workflows. It is built with reducing the interface overhead from the start which tries to the process of integrating new steps or adding library support as easy as possible.

In action

Creating a pipeline to execute in python directly is super easy, just import the get_quickstart_config method and initialize a pipeline directly from it.

from pathlib import Path

from expectmine.pipeline.pipeline import Pipeline
from expectmine.pipeline.utils import get_quickstart_config

pipeline = Pipeline(*get_quickstart_config(output_path=Path("pipeline_output")))

You can make it more specialized if you want. But the following code snippet shows the simplest pipeline in its entirety.

from pathlib import Path

from expectmine.pipeline.pipeline import Pipeline
from expectmine.pipeline.utils import get_quickstart_config
from expectmine.steps.steps import SiriusFingerprint
from expectmine.steps.steps.mzmine3.mzmine3 import MZmine3

pipeline = Pipeline(*get_quickstart_config(output_path=Path("pipeline_output")))

pipeline.set_input([Path("file1.mzml"), Path("file2.mzml")])

pipeline.add_step(
    MZmine3,
    {
        "mzmine3_path": Path(
            "/Applications/MZmine.app/Contents/MacOS/MZmine", absolute=True
        ),
        "batchfile": Path("batchfile.xml"),
    }
)

pipeline.add_step(
    SiriusFingerprint,
    {
        "sirius_path": Path(
            "/Applications/sirius.app/Contents/MacOS/sirius", absolute=True
        ),
        "set_max_mz": False,
        "instrument": "orbitrap",
    }
)

pipeline.run()