0.1.3

What's Changed

• Support decorative file extensions in syn:// entity URIs by @adamjtaylor in #10

Full Changelog: 0.1.2...0.1.3

0.1.2

What's Changed

• Auth token auto-discovery: The plugin now automatically looks up the SYNAPSE_AUTH_TOKEN Nextflow secret by default. No synapse { authToken = ... } block needed in nextflow.config unless you want to use a different secret name.
• Release automation: Releases are now published to the Nextflow plugin registry automatically via GitHub Actions when a new release is created.

Upgrading

If you previously had this in your nextflow.config:

synapse {
    authToken = secrets.SYNAPSE_AUTH_TOKEN
}

You can remove the synapse block entirely — the plugin will find the secret automatically.

0.1.1

Full Changelog: 0.1.0...0.1.1

0.1.0

🎉 nf-synapse plugin is live on the Nextflow plugin registry!
(Thanks to some inspiration from Adam Talbot at Seqera, and a few mornings with Claude Code)

You can now use syn:// URIs natively in Nextflow pipelines — no separate staging workflow needed. This replaces the old nf-syn plugin which has been unmaintained for 4+ years and
 lacked write support.

What it does:

• Read Synapse files directly as process inputs: file('syn://syn1234567')
• Publish outputs to Synapse folders via publishDir
• Works in samplesheets, supports versioned files (eg syn://syn1234567.3), auto-creates
    subfolders on write.

Get started:

Add this to your nextflow config

 plugins {
   id 'nf-synapse@0.1.0'
 }
 synapse {
   authToken = secrets.SYNAPSE_AUTH_TOKEN
 }

2. Ensure your Synapse auth token is set as a nextflow secret

secrets set SYNAPSE_AUTH_TOKEN syn_pat_xxx

Then your syn:// URIs just work.

Full docs + source: https://github.com/Sage-Bionetworks-Workflows/nf-synapse-plugin

Note that there are many cases where the separate nf-synapse workflow is more appropriate. The plugin runs in the head job and so is best suited to when you are reading or writing a relatively small number of files if you need to stage or publish large  batches of files, the nf-synapse workflow is a better fit as it parallelises transfers across worker nodes. But if you are willng to wait and dont want the overhead of orchestrating sequential workflows the plugin should suit you well.

Full Changelog: https://github.com/Sage-Bionetworks-Workflows/nf-synapse-plugin/commits/0.1.0