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Installation

Requirements

Install Nextflow

curl -s https://get.nextflow.io | bash
mv nextflow ~/bin/
nextflow -version

Container Profiles

# Docker (local/cloud)
nextflow run bigbio/quantmsdiann -profile docker

# Singularity (HPC)
nextflow run bigbio/quantmsdiann -profile singularity

Cloud Execution

# AWS Batch
nextflow run bigbio/quantmsdiann -profile docker \
    --input s3://bucket/samplesheet.csv \
    --outdir s3://bucket/results/

# Google Cloud
nextflow run bigbio/quantmsdiann -profile docker \
    --input gs://bucket/samplesheet.csv \
    --outdir gs://bucket/results/

Test Run

# Quick test (~10 min)
nextflow run bigbio/quantmsdiann -profile test,docker --outdir test_results/

# Test with DIA-NN 2.2.0
nextflow run bigbio/quantmsdiann \
    -profile test,docker \
    -c conf/diann_versions/v2_2_0.config \
    --outdir test_results/

DIA-NN Versions

quantmsdiann supports multiple DIA-NN versions:

DIA-NN Version Config Notes
1.8.1 conf/diann_versions/v1_8_1.config Legacy, widely validated
2.1.0 conf/diann_versions/v2_1_0.config Improved algorithms
2.2.0 conf/diann_versions/v2_2_0.config Latest, best performance 
# Specify version
nextflow run bigbio/quantmsdiann \
    -profile docker \
    -c conf/diann_versions/v2_2_0.config \
    --input samplesheet.csv \
    --database uniprot.fasta \
    --outdir results/