PRIDE Archive nextflow molecules indexer pipeline for complete submission submissions.
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.
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Install
nextflow(>=20.04.0) -
Te tool works with Conda
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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.
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
bigbio/pride-molecules-indexer was originally written by Yasset Perez-Riverol.