Skip to content

Installation

Requirements

Install Nextflow

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

# Move to a directory in your PATH
mv nextflow ~/bin/

# Verify
nextflow -version

Run the Test Profile

The fastest way to verify your setup:

# With Docker
nextflow run bigbio/quantms -profile test,docker --outdir test_results/

# With Singularity
nextflow run bigbio/quantms -profile test,singularity --outdir test_results/

# With Conda
nextflow run bigbio/quantms -profile test,conda --outdir test_results/

This downloads a small test dataset and runs the full pipeline. Should complete in ~10 minutes.

Container Profiles

Profile Command Notes
docker -profile docker Recommended for local development
singularity -profile singularity Recommended for HPC clusters
conda -profile conda Slower setup, useful when containers unavailable

Cloud Execution

quantms runs on any cloud platform supported by Nextflow:

AWS Batch

nextflow run bigbio/quantms \
    -profile docker \
    --input s3://bucket/samplesheet.csv \
    --database s3://bucket/uniprot.fasta \
    --outdir s3://bucket/results/ \
    -work-dir s3://bucket/work/

Google Cloud Life Sciences

nextflow run bigbio/quantms \
    -profile docker \
    --input gs://bucket/samplesheet.csv \
    --outdir gs://bucket/results/ \
    -work-dir gs://bucket/work/

Azure Batch

nextflow run bigbio/quantms \
    -profile docker \
    --input az://container/samplesheet.csv \
    --outdir az://container/results/ \
    -work-dir az://container/work/

HPC (SLURM)

nextflow run bigbio/quantms \
    -profile singularity \
    --input samplesheet.csv \
    --outdir results/ \
    -queue your_partition

Specific Versions

# Run a specific release
nextflow run bigbio/quantms -r v1.2.0 -profile docker --outdir results/

# Pull the latest version
nextflow pull bigbio/quantms

Offline Mode

For environments without internet access:

# On a machine with internet: pull pipeline and containers
nextflow pull bigbio/quantms
nextflow run bigbio/quantms -profile singularity --outdir /dev/null

# Transfer the Nextflow cache and Singularity images to your offline machine