Portable Encapsulated Projects

looper

A job submitter for Portable Encapsulated Projects

hello_looper

A Hello World! example repository for looper

pipestat

Pipeline results reporting package

pepspec

Documentation for PEP specification and all PEPkit software

pephub

A web API and database for biological sample metadata

peppy

Project metadata manager for PEPs in Python

geopephub

Automatic uploader of GEO metadata to PEPhub.

attmap

Key-value mapping that supports nested attribute-style access

pephubclient

A tool to provide Python and CLI interface and Python API for PEPhub.

ubiquerg

Tools for work (erg) everywhere (ubique)

eido

Validator for PEP objects

pepdbagent

Database for storing sample metadata

geofetch

Builds a PEP from SRA or GEO accessions

pepembed

pep-pipelines

Examples of how to use PEP to run pipelines with different workflow systems

pep-snakemake

Example simple and bioinformatic pipelines using PEPs and snakemake.

pep-cwl

pep-nextflow

pepr

Project metadata manager for PEPs in R

example_peps

Some simple examples of PEP-compatible projects

BiocProject

BiocProject provides a PEP-compatible R package for autoloading biological data

pephub.databio.org

Data stores for pephub PEPs

divvy

Standardized computing resource configuration

example-pephub-spa

example-pephub-cli

pephub-ui

pepingester

divcfg

DIvvy computing configuration files.

pipestat_reader

web API generator for pipeline results

pifaces

A collection of looper pipeline interfaces for common tasks