This repository contains examples of PEPs (Portable Encapsulated Projects). Visit the PEP2.0.0 specification webiste to learn more about the PEP standard and features. Explore the examples interactively with Python or R:
Here is a list of PEPs included in this repository. All PEPs must adhere to the PEP2.0.0 spec (validate against PEP2.0.0 schema)
These PEPs demonstrate the features described in the PEP2.0.0 framework and implemented in peppy and pepr
- example_basic: the simplest PEP, not using any
sample_modifiersorproject_modifiers - example_append: demonstrates
sample_modifiers.appendfeature - example_remove: demonstrates
sample_modifiers.removefeature - example_duplicate: demonstrates
sample_modifiers.duplicatefeature - example_derive: demonstrates
sample_modifiers.derivefeature - example_imply: demonstrates
sample_modifiers.implyfeature - example_derive_imply: demonstrates the combination of
sample_modifiers.implyandsample_modifiers.derivefeatures - example_imports: demonstrates the
importsfeature - example_imports2: shows how to use
importswith derived attributes - example_amendments: demonstrates
project_modifiers.amendfeature - example_subtable: demonstrates
sample_subtablefeature
These PEPs extend the PEP2.0.0 framework and may include additional fields used by other tools that build on peppy or pepr
- example_piface: defines
pipeline_interfaceproperty for each sample, which is used bylooper- a pipeline submission engine - example_BiocProject: defines a
bioconductorsection that is used byBiocProjectto link PEPs with Bioconductor
Your basic python workflow uses the peppy package and starts out like this:
import peppy
proj1 = peppy.Project("example_basic/project_config.yaml")More detailed Python vignettes are available as part of the documentation for the peppy package.
Your basic R workflow uses the pepr package and starts like this:
library('pepr')
p = pepr::Project("example_basic/project_config.yaml")More detailed R vignettes are available as part of the documentation for the pepr package.