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bigbio/pride-molecules-indexer

PRIDE Archive nextflow molecules indexer pipeline for complete submission submissions.

install with conda

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Quick Start

  1. Install nextflow (>=20.04.0)

  2. Te tool works with Conda

  3. Start running your own analysis!

     nextflow run main.nf -c nextflow.config -profile ebitools --project_accession PXD004016

See usage docs for all the available options when running the pipeline. Or configure the pipeline via nf-core launch from the web or the command line.

Pipeline Summary

By default, the pipeline currently performs the following:

  • Get the result files from a Complete Submission
  • Get the releated (spectra) files for each result files
  • Generate Json files for Spectra, PSM and Proteins

Documentation

Credits

bigbio/pride-molecules-indexer was originally written by Yasset Perez-Riverol.

Contributions and Support

Discussions & Chat & QA