00mjk / nf-workflows

Repository of Nextflow+BioContainers workflows

Proteomics and Multi-omics workflows

This repository store different workflows to analysis proteomics and multi-omics data using BioContainers and Nextflow. Each workflow resolve one specific proteomics experiment and should be seen as a tutorial to proteomics, biocontainers and nextflow. We are reciving Issues and PR from contributors. It is important to notice that all pipelines will be run using local setup for nextflow, but this can be easily addapted to other architectures or executors

• Mass spectrometry Search : This example perform a protein database search unsing an ms2 (mass spectra file) and protein database (fasata database).

• Converting the raw data from RAW to mzML : This example allow you to dowload the raw data from PRIDE ftp and convert the files to mzML and get the json file with the metadata.

• Run QC before identification using quameter : This workflow download some data from PRIDE and perform QC using the quameter with ID free option.

• Using spectral-clustering to infer additional PSMs: This workflow uses spectral-clustering to infer additional PSMs which can subsequently be used to improve label-free quanitation. The workflow searches the passed MGF files uses X!Tandem and MSGF+ and processes both results in parallel for benchmark reasons.