pepkit / example_peps

Some simple examples of PEP-compatible projects

Example PEPs

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:

Index

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)

General

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_modifiers or project_modifiers
• example_append: demonstrates sample_modifiers.append feature
• example_remove: demonstrates sample_modifiers.remove feature
• example_duplicate: demonstrates sample_modifiers.duplicate feature
• example_derive: demonstrates sample_modifiers.derive feature
• example_imply: demonstrates sample_modifiers.imply feature
• example_derive_imply: demonstrates the combination of sample_modifiers.imply and sample_modifiers.derive features
• example_imports: demonstrates the imports feature
• example_imports2: shows how to use imports with derived attributes
• example_amendments: demonstrates project_modifiers.amend feature
  • example_amendments1
  • example_amendments2
• example_subtable: demonstrates sample_subtable feature
  • example_subtable1
  • example_subtable2
  • example_subtable3
  • example_subtable4
  • example_subtable5
  • example_subtables

Specialized

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_interface property for each sample, which is used by looper - a pipeline submission engine
• example_BiocProject: defines a bioconductor section that is used by BiocProject to link PEPs with Bioconductor
  • example_BiocProject
  • example_BiocProject_exceptions
  • example_BiocProject_remote

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Read PEPs in Python

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.

Read PEPs in R

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.