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Seqera Cloud v26.2.0_cycle58

Feature updates and improvements​

Access control​

Compute environments​

  • Added security group name search to AWS drop-downs.

Pipelines​

  • Surfaced launch-time settings, including profiles and syntax parser, in the run config tab.

Bug fixes​

Data explorer​

  • Fixed IGV index file handling by presigning indexURLs independently.

Pipelines​

  • Fixed the Nextflow syntax parser v2 toggle to seed from the saved launch config.
  • Included syntaxParser in the workflow launch API response.
  • Cleared stale main script launch errors.
  • Fixed the launch form to skip the lineage request in user space.

Nextflow 26.04.3

Feature updates and improvements​

Language features​

  • Improved the error message when enabling types with syntax parser v1 by @jorgee in #7173

Plugins​

  • Made plugin metadata prefetch resilient to registry rate limiting by @pditommaso in #7181

Fusion​

  • Added support for fetching local files in FUSION_CONTAINER_CONFIG_URL by @alberto-miranda in #7142

Bug fixes​

S3​

  • Fixed bucket cleanup in S3 test by @bentsherman in #7172

General​

  • Fixed docs CI on Python 3.14 by upgrading Sphinx by @jorgee in #7175

Dependencies​

  • Bumped nf-azure@1.22.5
  • Bumped nf-google@1.27.3
  • Bumped nf-k8s@1.5.4
  • Bumped nf-seqera@0.20.1
  • Bumped nf-tower@1.28.0
  • Bumped nf-wave@1.21.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.3

Seqera Cloud v26.2.0_cycle57

Feature updates and improvements​

Pipelines​

  • Exposed tower.launch.config.maxSize to frontend validators so launch configuration size limits stay aligned with the backend.

Bug fixes​

Pipelines​

  • Added frontend validation of paramsText against its JSON-serialized size to align launch parameter limits with backend submission constraints.
  • Added missing metadata, pipeline versioning, and data lineage fields to the workflow launch form summary.
  • Fixed the workflow launch payload to always send lineage.enabled so the data lineage toggle setting persists correctly.

General​

  • Fixed the workspace switcher to keep the search input focused during arrow-key navigation.
  • Fixed background worker shutdown by draining workers before JedisPool shutdown to prevent dropped jobs.
  • Fixed navigation switcher responsiveness.

Seqera Enterprise v26.1

Seqera Platform Enterprise version 26.1 introduces Co-Scientist for Enterprise, broader cloud credential support (AWS role-based access, Azure Entra service principal, GCP Workload Identity Federation), Nextflow data lineage in pipeline runs and Data Explorer, and a redesigned audit log experience with CSV export.

Highlights​

Seqera Cloud v26.1.0_cycle56

Feature updates and improvements​

Compute environments​

  • Added a configurable boot disk size for Azure Batch pools.
  • Added r8idn, r8idb, m8idn, and m8idb instance families to the NVMe list.

Pipelines​

  • Added the Lineage ID to the Run Info page.

General​

  • Introduced a panel search input and integrated it into the navigation switcher component.
  • Improved workspace switch redirects to preserve the active sidebar section.

Bug fixes​

Compute environments​

  • Deduplicated the compute environment entry in the launch drop-down.

Data Explorer​

  • Made credentials a required field in the Add data repository form.

Pipelines​

  • Refined workflow_updated events that contain no diff.
  • Prevented duplicate GitHub credentials across PAT and GitHub App types.
  • Resolved file paths to the most recent lineage record.

Nextflow 26.04.2

Feature updates and improvements​

Language features​

  • Validated module spec against JSON schema by @pditommaso in #7094
  • Updated guidelines for strict parser by @bentsherman in #7134

General​

  • Honored token field in BitbucketServerRepositoryProvider by @jorgee in #7120
  • Picked up force-pushed branches in multi-revision repo strategy by @jorgee in #7103
  • Tightened CI security and removed dead code in workflows by @ewels in #7139
  • Updated GitHub Actions with security updates by @ewels in #7138

Dependencies​

  • Pinned python to 3.14.5 by @seqeralabs-renovate in #7152
  • Bumped nf-azure@1.22.4 by @pditommaso in 2bcc6e8c
  • Bumped nf-k8s@1.5.3 by @pditommaso in b2ea7492
  • Bumped nf-seqera@0.20.0 by @pditommaso in 4d55e81e

Bug fixes​

Language features​

  • Fixed module run to allow optional path inputs by @bentsherman in #7163
  • Fixed destructured record input in module run by @bentsherman in #7164
  • Fixed function calls in typed process outputs by @bentsherman in #7148
  • Fixed strict parser to include params refs in task hash by @bentsherman in #7165
  • Normalized TaskPath to Path in typed process outputs by @stekaz in #7090

Azure​

  • Fixed Azure rnaseq-nf test by @bentsherman in #7143

General​

  • Released HTTP sockets when reading HTTP attributes to avoid 503 throttling by @jorgee in f2b0284e

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.2

Seqera Cloud v26.1.0_cycle55

Feature updates and improvements​

Compute environments​

  • Added a CloudInfo cloud instance type catalog and chip-selector filters specification.
  • Added a description field to the Compute Environment V2 form.

Datasets​

  • Exposed dataset file size in version API responses.

Pipelines​

Studios​

  • Added the compute environment name to the Studios row card.
  • Added new API endpoints to fetch compatible compute environments for a Studio and update the compute environment on a Studio.
  • Enabled updating the compute environment on a Studio.
  • Resolved the user on SSH Studio connection attempts.

Bug fixes​

Data Explorer​

  • Supported GCS pre-signed URLs with WIF credentials in Data Explorer.

Pipelines​

  • Disabled the lineage launch toggle when lineage settings are not configured or when the compute environment does not support lineage.

Studios​

  • Recovered legacy Studio event names in the usage query.
  • Fell back to baseline Studio capabilities when the manifest is missing or the Studio version is not found in the manifest.

MultiQC v1.35

This release has a very nice shiny new feature for you: the MultiQC Configuration Wizard! 👨🏻‍🎨 🎨

This has an interactive form where you can browse all MultiQC config attributes (there are quite a lot). See them organised with help text and examples. Enter values into the form and have them validated in real time. 📋 ✅

Then see your generated YAML config in a code editor (where you can paste existing configs if you wish). See the config file explained, validated and suggestions for fixes. 📚

The config wizard is a static HTML file that is bundled with the MultiQC repo, but it's easiest to try out online: https://seqera.io/multiqc_config_wizard ✨

CleanShot 2026-05-13 at 02 56 00@2x

New modules​

  • CheckAtlas (#3545)
    • A one-liner tool for quality control of single-cell atlases.
  • Deacon (#3564)
    • Search and depletion of FASTA/FASTQ files and streams using accelerated minimizer matching.
  • FastQE (#3490)
    • Uses emoji to represent FASTQ sequence quality scores.
  • hicstuff (#3541)
    • Hi-C pipeline that generates contact maps from sequencing reads.
  • HiFi-Trimmer (#3513)
    • Filters and trims adapter sequences from HiFi reads using BLAST.
  • Riker (#3540)
    • Fast Rust toolkit that ports key sequencing QC tools from Picard.
  • sincei (#1946)
    • Toolkit for processing and analysing single-cell (epi)genomics data.
  • Trim Galore (#3538)
    • Native v2.x support: quality and adapter trimming for next-generation sequencing data, with special handling for RRBS libraries.

Module updates​

  • Bases2Fastq: Major upgrade to the module, now shows a lot more information (#3460)
  • Falco: Add native recognition for Falco output (#3497)
  • Fastp: Add % surviving bases (#3472)
  • Sequali: Expand general statistics, add normalised plots (#3530)

Module fixes​

  • Bcftools: Fix stats zero-depth plot crash (#3556)
  • Cell Ranger ARC: Fix key collisions between ATAC and GEX metrics (#3480)
  • Dragen: Fix incorrect average GC% in FastQC for all samples except the first in batch (#3505)
  • Haplocheck: Don't overwrite prior results, allow multiple samples (#3512)

Feature updates and improvements​

  • Config: Major new automations using config schema (#3183, #3558, #3561)
    • Automated markdown reference documentation of all config attributes for the docs
    • New interactive tool for building, editing and validating MultiQC config files: https://seqera.io/multiqc_config_wizard
  • AI: Catch unexpected AWS Bedrock response shapes (#3440)
  • custom_plot_config: Fix deprecated camelCase aliases (e.g. yPlotBands) (#3547)
  • custom_plot_config: Per-tab targeting for multi-data_labels plots (#3548)
  • Custom content: Fix crash on data type conflict between files (#3560)
  • Custom images: Support more MIME types, add custom favicon (#3469)
  • Plots: Add section alerts for filtered samples (#3549)
  • Plots: Fix barplot ValueError when all categories are zero (#3563)
  • Report: Add spacing between AI summary and general stats (#3470)
  • Run merging: Fix grouped sample totals and hierarchy being lost during parquet merging (#3559)
  • Tables: Allow defaultsort to include the first column header (#3519)
  • Tests: Fix pytest warning sources (#3551)

Fixes​

  • Config: Fix env var overwrite where booleans/ints/floats were stored as strings (#3557)
  • Core: Fix rich.panel import in module-failure exception handler (#3537)
  • custom_plot_config: Fix parsing of y_bands/x_bands/x_lines/y_lines (#3459)
  • Report: Fix race causing empty zip files when exporting plots (#3555)

Infrastructure and packaging​

  • Claude Code: Update agent instructions (#3552)
  • Frontend: Update npm packages (#3562)
  • Packaging: Bump minimum Python to 3.9 (#3542)
  • Polars: Replace deprecated polars-lts-cpu dependency (#3553)
  • Polars: Use Pyodide-compatible dependency on Emscripten (#3554)

Optimization, refactoring and typing​

  • Linting: Drop Python 2-era idioms (#3546)

New Contributors​

Full Changelog: https://github.com/MultiQC/MultiQC/compare/v1.34...v1.35