A Python DSL for bioinformatics pipelines
Project description
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'
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