nf-SearchEngine

nf-SearchEngine is a Nextflow pipeline that execute the MSFragger search engine for the peptide identification.

nf-SearchEngine was developed by the Cardiovascular Proteomics Lab/Proteomic Unit at The National Centre for Cardiovascular Research (CNIC, https://www.cnic.es).

This application is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) License. For further details, read the https://creativecommons.org/licenses/by-nd/4.0/.

Installation

Prerequisites

Before you begin, ensure you have met the following requirements:

• A Linux operating system is needed on your machine.

Linux operating system on Windows

If you are using a Windows operating system, refer to the section Install WSL on Windows to set up a Linux operating system on your Windows machine.

Install Singularity

For more information, read the How to install Singularity section.

Install Nextflow

For more information, read the How to install Nextflow section.

Install Git

For more information, read the How to install Git section.

Download the pipeline with the latest release

Export an environment variable to define the version:

export PIPELINE_VERSION=0.1.4

Note: The list of releases is located on the releases page.

You can clone the latest release directly using git with the following command:

git clone https://github.com/CNIC-Proteomics/nf-SearchEngine.git --branch ${PIPELINE_VERSION} --recursive

With the --recursive parameter, the submodules repositories are cloned as well.

Download Singularity images

Export an environment variable to define the version of singularity image:

export IMAGE_VERSION=0.1.4

Note: The list of releases is located on the singularity repository page.

Navigate to the backends folder:

cd nf-SearchEngine/backends

You need to download the Singularity image for the pipeline, ensuring version compatibility with the Nextflow pipeline. See the above versions section:

singularity pull --arch amd64 library://proteomicscnic/next-launcher/search_engine:${IMAGE_VERSION}

You might see warning messages like the following. You can discard or ignore them:

WARNING: failed to get key material: 404 Not Found: entity not found
WARNING: integrity: signature object 5 not valid: openpgp: signature made by unknown entity
WARNING: Skipping container verification

Create a symbolic link

ln -s search_engine_${IMAGE_VERSION}.sif search_engine.sif

Usage

Execute the pipeline with samples

1. Download sample files

cd samples && \
wget https://zenodo.org/records/14446572/files/nf-SearchEngine_Heteroplasmic_Muscle.zip?download=1 -O nf-SearchEngine_Heteroplasmic_Muscle.zip && \
unzip nf-SearchEngine_Heteroplasmic_Muscle.zip && \
cd ..

2. Execute the pipeline:

nextflow \
    -log "/tmp/nextflow/log/nf-searchengine.log" \
    run main.nf   \
        -profile singularity \
        --create_mzml false \
        --add_decoys true \
        --raw_files "samples/heteroplasmic_muscle/inputs/mzMLs/*.mzML" \
        --database "samples/heteroplasmic_muscle/inputs/database.fasta" \
        --decoy_prefix "DECOY_"\
        --msf_params_file "samples/heteroplasmic_muscle/inputs/msf_params_file.params" \
        --reporter_ion_isotopic "samples/heteroplasmic_muscle/inputs/reporter_ion_isotopic.tsv" \
        --outdir  "samples/heteroplasmic_muscle/results" \
        -resume

Image Version History

For more information about the program version included within the Singularity version, refer to the changelog for the current version.