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
sample_modifiers
or project_modifiers
sample_modifiers.append
featuresample_modifiers.remove
featuresample_modifiers.duplicate
featuresample_modifiers.derive
featuresample_modifiers.imply
featuresample_modifiers.imply
and sample_modifiers.derive
featuresimports
featureimports
with derived attributesproject_modifiers.amend
featuresample_subtable
featureThese PEPs extend the PEP2.0.0 framework and may include additional fields used by other tools that build on peppy
or pepr
pipeline_interface
property for each sample, which is used by looper
- a pipeline submission enginebioconductor
section that is used by BiocProject
to link PEPs with BioconductorYour 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.
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