Summary

A Nextflow plugin for accessing Synapse (Sage Bionetworks) files using syn:// URIs. The plugin enables transparent file access in pipelines, supporting both reading Synapse files as process inputs and publishing pipeline outputs directly to Synapse folders. Features include support for versioned files, automatic subfolder creation, secure authentication via Nextflow secrets, and the ability to use Synapse URIs in samplesheets.

Get Started

Installation

Note: This plugin is not yet published to the Nextflow plugin registry. You must build and install locally.

# Clone the repo
git clone https://github.com/Sage-Bionetworks-Workflows/nf-synapse-plugin.git
cd nf-synapse-plugin

# Build and install to ~/.nextflow/plugins
make install

Then add to your nextflow.config:

plugins {
    id 'nf-synapse@0.1.0'
}

synapse {
    authToken = secrets.SYNAPSE_AUTH_TOKEN
}

Authentication

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:

Optional Configuration

synapse {
    authToken = secrets.SYNAPSE_AUTH_TOKEN
    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