dry-pipe 0.0.8

A Python DSL for bioinformatics pipelines

DryPipe

A Python DSL for bioinformatics pipelines

Getting Started

1 Install dry-pipe in your virtualenv

    pyton3.8 -m venv your_venv 
    source your_venv/bin/activate
    pip install dry-pipe

2 Write your pipeline

    from dry_pipe import DryPipe
    
    def my_pipeline_task_generator(dsl):
        yield dsl.task(key="task1") 
            .consumes(x=dsl.val(123)) 
            .produces(result=dsl.file("f.txt"))
            .calls("""
                #!/usr/bin/env bash                
                echo $x > $result
            """)
        
    def my_pipeline():
        return DryPipe.create_pipeline(my_pipeline_task_generator)

3 Run it

(assuming the above code is in module my_module.py)

    drypipe run --pipeline='my_module:my_pipeline'