Your first pipeline

Initializing a simple pipeline

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")))

Adding input files

To add input files to the pipeline, just give it an array of paths to the individual files. The files you provide will serve as input to the first step.

pipeline.set_input([Path('file1.mzml')])

Adding steps

To add a step, just provide the type of step you want to add and an io object, which is used to configure the step.

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

Run the pipeline

After calling run the pipeline will then run and output files for each step in the directory you provided as output_path.

pipeline.run()

Summary

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()