modal_nextflow_example.py

from subprocess import run

from modal import App, Image

nextflow_script = '''#!/usr/bin/env nextflow
process sayHello {
    output:
        stdout
    """
    echo 'Hello World!'
    """
}

workflow {
    sayHello()
}
'''

image = (
    Image.debian_slim()
    .apt_install("git", "wget", "curl", "unzip", "zip", "procps")
    .pip_install("polars")
    #
    # Install nextflow
    #
    # no idea why sdkman is so difficult to install but it was a pain
    .run_commands(["rm /bin/sh && ln -s /bin/bash /bin/sh"])
    .run_commands('curl -s "https://get.sdkman.io" | bash')
    .env({"BASH_ENV": "/root/.sdkman/bin/sdkman-init.sh"})
    .run_commands("/bin/bash -c 'sdk install java 17.0.10-tem'")
    .run_commands("curl -s https://get.nextflow.io | bash")
    #
    # Install conda (taken from modal slack, not all steps necessary)
    #
    .run_commands(
        "wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && "
        "chmod +x Miniconda3-latest-Linux-x86_64.sh && "
        "./Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3 && "
        'export PATH="$HOME/miniconda3/bin:$PATH" && '
        'echo "export PATH=$HOME/miniconda3/bin:$PATH" >> /etc/environment && '
        "source $HOME/miniconda3/etc/profile.d/conda.sh && "
        "conda init && "
        "source ~/.bashrc"
    )
)


app = App("nextflow_example", image=image)


@app.function()
def run_nextflow():
    with open("hello-world.nf", "w") as out:
        out.write(nextflow_script)

    cmd = "/nextflow run hello-world.nf"
    run(cmd, shell=True, check=True)


@app.local_entrypoint()
def main():
    run_nextflow.remote()