Changelog
SeqDesk releases frequently on a single stable channel. The authoritative release history is on GitHub, alongside the source:
Which version am I running?
Three ways, in increasing order of detail:
| Where | What it tells you |
|---|---|
GET /api/version on your instance | The running version as JSON, e.g. {"version":"1.1.125"}. No authentication needed |
seqdesk doctor --dir <install-dir> | A health report for the install — the reported Version is the seqdesk launcher’s own version, not the app’s |
Settings → Info (/admin/settings) | Running version, whether an update is available, tool versions, feature flags, and which configuration layer each effective value came from |
The update check calls https://seqdesk.org/api/version with your current
version and the stable channel, and caches the answer. It is also what sends
the optional telemetry heartbeat — see
Operational Telemetry if you would
rather it did not.
What the 1.1.x line contains
The current line is a working sequencing-facility platform. The headline capabilities:
Order and sample management
- Configurable sequencing order form with a field builder, field groups, admin-only facility fields, and Markdown post-submission instructions
- Excel round trip for sample tables (template download, validated upload)
- NCBI taxonomy lookup on the Organism field
- Nine optional modules covering MIxS metadata, funding, billing, ENA sample fields, sequencing technology, dynamic studies, AI validation, account validation and email notifications
- Department-based access sharing
Sequencing data
- File discovery and R1/R2 pairing over a configured storage root
- Direct upload with size and checksum tracking
- Live MinKNOW stream ingest for Oxford Nanopore, matched by barcode
- Read data classes (
cleaned/raw/unknown) with supersession chains - An explicit delivery gate: cleaned reads and customer-facing reports are published to the requesting researcher by hand
Pipelines
Manifest-driven packages executed through Nextflow, locally or on SLURM, with a DAG view, a weblog event feed and parser-driven result write-back. Bundled packages:
| Package | Scope | What it does |
|---|---|---|
| Simulate Reads | Order | Generates dummy FASTQ files for the samples in an order |
| FASTQ Checksum | Order | Computes MD5 checksums for linked FASTQ files |
| FastQC | Order | Per-sample FastQC quality control |
| NanoPlot | Order | Long-read QC for Oxford Nanopore and PacBio |
| Read Cleaning | Order | Screens raw/unknown reads for host and contaminant sequence (nf-core/detaxizer) and stages cleaned reads for admin promotion |
| Quality Overview | Study | Per-sample FASTQ statistics with an HTML summary |
| Study MultiQC | Study | Aggregates prior study QC outputs into one MultiQC report |
| Kraken2 + Bracken | Study | Taxonomic profiling with per-sample Krona charts |
| MAG | Study | Metagenome assembly and binning (nf-core/mag 3.0.0) |
| Study Demo Report | Study | Example outputs, for verifying study-level execution |
| Submit to ENA | Study | Builds and submits an ENA package with submg |
Further packages, MetaxPath among them, are installable from the pipeline registry rather than bundled — see Available Pipelines and Adding Pipelines.
Publication
ENA study and sample registration with a test-server mode on by default, accession write-back onto the SeqDesk records, and a submissions dashboard.
Operations
Self-update with backup and rollback, a /setup diagnostic screen, background
worker controls, and an optional telemetry heartbeat.
Staying up to date
SeqDesk checks for updates itself and can install them in place, keeping the previous release so you can roll back.
Before you design around something described as missing in What SeqDesk doesn’t do (yet), check the releases page — that list moves.