ELIXIR Implementation Study "Comparison, benchmarking and dissemination of proteomics data analysis pipelines"

See also https://elixir-europe.org/about-us/commissioned-services/proteomics-pipelines

IMPORTANT NOTE:

__We now moved to https://github.com/orgs/wombat-p/ __

The aim of this study is to create different pipelines for the analysis of label-free proteomics data and systematically compare their results. If possible, the workflows are implemented in NextFlow to allow reproducible results and scalable execution on different computer architectures.

File structure of repository

For examples and simple templates containing e.g. a workflow for file conversion (Thermo raw -> mgf), see Examples_and_templates

Each of the different workflows is represented by a folder containing the subfolders "Nextflow" and "Results"

Content of Nextflow folder

To allow fully reproducible results, each workflow should be executable using the "docker" option in Nextflow

• Nextflow script Full set of routines to run the workflow
• Nextflow configuration file Default options and basic profiles to run the workflow
• environment.yml Conda packages all software available via (bio)conda
• Dockerfile Installations instructions for all tools with automatic inclusion of conda packages
• data Folder with simple example data set to test the workflow
• conf Folder with configuration files for testing and execution
• README.md Detailed description of parameter files and how to run the workflow on our data set. Include details about source of data and database. Please also include other options (e.g. command line options/flags) necessary to run the workflow

Content of Result folder

• Result files from each lab for identified and quantified peptides and proteins, preferably in the form of a table. Please change the name of the files to WorkflowName_Lab_originalfilename
• Parameter files for running the workflow on the data set
• Performance report (TODO: details) E.g. execution time on defined architecture, ...