Summary

A Nextflow plugin for accessing Synapse (Sage Bionetworks) files using syn:// URIs. The plugin enables transparent reading of Synapse files directly in pipelines and publishing pipeline outputs to Synapse folders using publishDir. It supports versioned files, automatic subfolder creation, secure authentication via Nextflow secrets, and use of Synapse URIs in samplesheets.

Get Started

Installation

Add to your nextflow.config:

plugins {
    id 'nf-synapse@0.1.1'
}

Nextflow will automatically download the plugin from the Nextflow plugin registry.

Configuration

Set your Synapse Personal Access Token as a Nextflow secret:

nextflow secrets set SYNAPSE_AUTH_TOKEN syn_pat_xxxxxxxxxx

You can create a Personal Access Token at: https://www.synapse.org/#!PersonalAccessTokens:

The plugin automatically looks for a secret named SYNAPSE_AUTH_TOKEN. For optional custom endpoint configuration:

synapse {
    endpoint = 'https://repo-prod.prod.sagebase.org'  // default
}

Examples

Direct File Access

// Access a Synapse file (latest version)
synapse_file = file('syn://syn26947830')

// Access a specific version
versioned_file = file('syn://syn26947830.1')

In a Process

process ANALYZE {
    input:
    path input_file

    output:
    path "result.txt"

    script:
    """
    echo "Processing: ${input_file}"
    analyze.sh ${input_file} > result.txt
    """
}

workflow {
    synapse_file = file('syn://syn26947830')
    ANALYZE(synapse_file)
}

With Samplesheets

// samplesheet.csv:
// sample_id,synapse_uri
// sample1,syn://syn26947830
// sample2,syn://syn26947830.1

Channel.fromPath('samplesheet.csv')
    .splitCsv(header: true)
    .map { row -> tuple(row.sample_id, file(row.synapse_uri)) }
    .set { samples_ch }

samples_ch.view { sample_id, f -> "Sample: ${sample_id}, File: ${f.name}" }

Publishing to Synapse

params.outDir = 'syn://syn25858544'  // Synapse folder ID

process ANALYZE {
    publishDir params.outDir, mode: 'copy'

    input:
    path input_file

    output:
    path "results.txt"

    script:
    """
    analyze.sh ${input_file} > results.txt
    """
}

Publishing to Subfolders

process ANALYZE {
    publishDir "${params.outDir}/${sample_id}/results", mode: 'copy'

    input:
    tuple val(sample_id), path(input_file)

    output:
    path "output.txt"

    script:
    """
    analyze.sh ${input_file} > output.txt
    """
}

License

Apache License 2.0