protocol_mappings.yaml maps protocols to pipelines
pipeline_interface.yaml resources vary by input file size
Project API Single-input runs
All you need is love project_config.yaml
Flexible compute Job status-aware
Looper only submits jobs for samples not already flagged as running, completed, or failed.
Lets you define multiple projects in a single file
Collate input files
Combine for a complete pipelining system
How is this better than _____ ?
low barrier to entry (ie, language)
decoupled single-sample (pypiper) from deploy (looper)
Parallel by sample
Parallel by process
Parallel by dependence
Read the docs!
Using a pipeline
Create a sample_annotation.csv
Create a project_config.yaml
Templates exist for both, follow tutorials for Looper.
Building a pipeline
Follow tutorials for Pypiper .
Write a Pypiper pipeline to handle a single sample.
Connect to looper with protocol mapping and pipeline interface.