Update

This project and workflow has been merged into the WOMBAT pipelines.

Please go to https://github.com/wombat-p/WOMBAT-Pipelines

Workflow to analyze label-free data with the compomics pipeline

This workflow is based on a docker image which is available at the docker hub (https://hub.docker.com/repository/docker/veitveit/compomicsworkflow) and is downloaded automatically. If you want to build your own docker image, be aware that it needs to be named veitveit/compomicsworkflow:dev or change the name in the configuration file.

Content

Nextflow folder: Implementation of workflow

data folder: additional data to run the UPS data set (NOT including the RAW files)

Results folder: Results from the running the UPS data set

Getting started

Here is a little script that can be used to test the workflow execution. This script assumes that Docker is available on your system and is targeting Debian/Ubuntu linux distributions.

# Install Java
sudo apt-get install openjdk-8-jdk

# Fix docker permission issue (https://stackoverflow.com/questions/48957195/how-to-fix-docker-got-permission-denied-issue)
# Note: this allows to run docker as non-root user
sudo usermod -aG docker $USER
newgrp docker

# Fetch scripts and data
git clone https://github.com/veitveit/IS_Benchmarking.git
cd ./Compomics-Workflow/Nextflow/data

# Nextflow
cd ..
curl -s https://get.nextflow.io | bash

# Worfklow
./nextflow run main.nf -profile docker,test

Run benchmarking data set

You should have successfully tested the workflow using the procedure above.

Download the raw files from PRIDE: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001819

Run the workflow with the following command and parameters after changing RAWFOLDER to the folder where the raw files are located. You will also need to place the files yeast_UPS.fasta and pxd001819.txt into in the current folder. These files is given in the Results folder: https://github.com/veitveit/IS_Benchmarking/tree/master/Compomics/Results

Also adjust the parameter values max_cpus and max_memory to the computing power you have available.

nextflow run main.nf --raws 'RAWFOLDER/*.raw' --fasta '../data/yeast_UPS.fasta' --miscleavages 2 \
  --fragment_mass_tolerance 0.8 --precursor_mass_tolerance 5 --enzyme 'Trypsin (no P rule)' \
  --variable_mods 'Oxidation of M,Acetylation of protein N-term' \
  --experiment_design '../data/pxd001819.txt' \
  --max_cpus 8 --max_memory 8GB \
  -profile docker -with-report -with-trace -with-timeline