This project and workflow has been merged into the WOMBAT pipelines.
Please go to https://github.com/wombat-p/WOMBAT-Pipelines
Nextflow folder: Implementation of workflow
Results folder: Output from running the UPS data set
The provided workflow is based on the docker image wombatp/proline-pipeline that is automatically downloaded.
You can also create the image by the following command:
# main.nf workflow image creation from the Nextflow folder
docker build -t "wombat/proline-pipeline:dev" .
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/wombat-p/Proline-Workflow.git
cd ./Proline-Workflow/Nextflow/data
wget ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R1.raw
# Nextflow
cd ..
curl -s https://get.nextflow.io | bash
# Worfklow
./nextflow run main.nf -profile docker,test
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 adjust the paths to pxd001819.txt, yeast_UPS.fasta and lfq_param_file.txt. These files are given in the data folder of this workflow: https://github.com/wombat-p/Proline-Workflow/tree/dev/data
Also adjust the parameter values max_cpus and max_memory to the computing power you have available. When running all files, Proline will need at least 16GB.
nextflow run main.nf --raws 'RAWFOLDER/*.raw' --fasta '../data/yeast_UPS.fasta' --precursor_mass_tolerance 5 \
--fragment_mass_tolerance 0.8 --miscleavages 2 --variable_mods 'Oxidation of M, Acetylation of protein N-term' \
--experiment_design '../data/pxd001819.txt' --lfq_param '../data/lfq_param_file.txt' \
--max_cpus 8 --max_memory 16GB -profile docker -with-report -with-trace -with-timeline
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