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MultiQC v1.33

New modules​

  • Seqkit stats (#3401)
    • A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  • RiboTish (#3384)
    • Ribo-seq quality metrics
  • Sylph (#3370)
    • Sylph is a program that performs metagenomic profiling or containment average nucleotide identity querying for metagenomic shotgun sequencing samples.
  • Bbsplit basic stats (#3394)
    • New submodule for bbtools

Feature updates and improvements​

  • Custom logo: dark mode option, custom width option. (#3400)
  • Update Seqera AI chat URL (#3415)
  • Add sample_groups configuration for visual grouping in bar graphs (#3404)
  • Custom content: strip whitespace around categories for tsv,csv (#3421)
  • General Stats: Add configurable help text (#3341)
  • Custom content: support passing help text (#3338)
  • Add new flag "axis_controlled_by_switches" to pconfig that allow control of which axis to apply logarithmic scale (#3423)

Module updates​

  • fastp: Add support for naming samples after --report_title in Fastp command (#3418)
  • Glimpse: Add more decimal to general table stats (#3423)
  • Refactor BISCUIT module for better consistency with current MultiQC codebase (#3345, #3426)
  • Add version fetching for HiCUP, QoRTs, QualiMap, RNA-SeQC (#3420)

Fixes​

  • Fix MultiQC plotly export bug affecting FastQC heatmaps (#3402)
  • Fix bug with sample filter buttons in new template (#3389)
  • Fix KeyError in bargraph when using reference lines with horizontal orientation (#3385)

Module fixes​

  • Fix validation errors in strict mode for invalid plot config options (#3428)
    • Remove invalid hide_zero_cats from line plot configs (mosdepth, bamdst, samtools/coverage, humid, dragen_fastqc)
    • Fix bar plot category configs using invalid fields (picard/IlluminaBasecallingMetrics, motus)
  • Samtools coverage: Don't crash if incorrect number of columns found (#3419)
  • Lima: split delimiter is a tab, not any whitespace. (#3395)
  • Homer: Fix unique / total count swap in homer/tagdirectory (#3381)

Infrastructure and packaging​

  • Avoid Python 3.14.1 (#3414)
  • Version check: Add installation method to detect installs using uv (#3422)
  • Bump pre commit versions (#3417)

Optimization​

  • Make Parquet merging much, much faster (60% faster) (#3403)

New Contributors​

Full Changelog: https://github.com/MultiQC/MultiQC/compare/v1.32...v1.33

Seqera Cloud v25.3.0_cycle34

Feature updates and improvements​

Studios​

  • Added the ability to configure a custom container repository path for Wave-built Studio images in workspace settings, providing greater control over where container images are stored and distributed.

Bug fixes​

General​

  • Addressed a security vulnerability related to resource allocation, improving overall Platform security.

Resource labels​

  • Fixed an issue with interpolated values in dynamic resource labels (e.g., label-name=${workflowId}). Dynamic resource labels now work correctly when enabling the feature for all workspaces.

Workflows​

  • Fixed an issue with deleted workflows incorrectly counted toward organization quota limits. Active workflow counts now accurately exclude deleted workflows.

Nextflow 25.10.1

Nextflow 25.10 is a stable release

See the Migrating to 25.10 for a comprehensive list of changes since the last stable release.

Feature updates and improvements​

Configuration​

  • Added default value to Apptainer pull timeout config parameter by @jorgee in #6534

Dependencies​

  • Bumped logback 1.5.20 by @pditommaso in 904d968
  • Bumped nf-amazon@3.4.2 by @pditommaso in 2411115
  • Bumped nf-tower@1.17.2 by @pditommaso in 9f13afd

Bug fixes​

Language features​

  • Fixed error with dynamic directives with named arguments by @bentsherman in #6550
  • Fixed issue with optional workflow output by @bentsherman in #6519

S3​

  • Fixed incorrect AWS region when specifying a S3 regional endpoint by @jorgee in #6530
  • Fixed unordered completed parts in AWS multipart upload by @jorgee in #6560

Fusion​

  • Fixed Fusion license JWT token refresh by reusing TowerClient by @jorgee in 561ed6c

Configuration​

  • Fixed false config validation warnings for process selectors by @bentsherman in #6542

Plugins​

  • Reverted Plugins.init() in run command to original location by @jorgee in #6568

General​

  • Fixed asset detection when item is not a sibling of the executed script by @DriesSchaumont in #6605

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.1

Nextflow 25.11.0-edge

Feature updates and improvements​

Google Batch​

  • Added Google Batch LogsPolicy PATH option for logging to GCS by @dglazer in #6431
  • Optimized exit code handling by relying on scheduler status for successful executions by @jorgee in #6484

Kubernetes​

  • Changed log level from warn1 to debug1 for K8s Job Pod Warnings by @BioWilko in #6523

Language features​

  • Removed unnecessary runtime checks with strict syntax by @bentsherman in #6539

Plugins​

  • Allowed pre-existing write-protected plugins directory to be used by @bentsherman in #6594
  • Updated migration timeline for plugin registry by @bentsherman in #6543
  • Added admonition to clarify plugin provider and org by @christopher-hakkaart in #6536

Configuration​

  • Added default value to Apptainer pull timeout config parameter by @jorgee in #6534
  • Added test case for printing config with nested includes by @Lehmann-Fabian in #2498
  • Added external links via config by @ewels in #6563

Fusion​

  • Marked Fusion.tags as supported only for S3 by @fntlnz in #6601

General​

  • Improved error message for invalid accelerator resource by @bentsherman in #6585
  • Improved error message for invalid contribution type in manifest contributors by @bentsherman in #6593
  • Moved task error formatting logic into separate class by @bentsherman in #6551
  • Removed unused BatchHelper class by @pditommaso in #6547
  • Removed wiremock-groovy dependency and updated tests using this dependency by @jorgee in #6611
  • Updated bundled Docker runtime to 19.03.15 by @yarikoptic in #6565
  • Updated trace table columns in Reports page by @JustinBellavance in #6483
  • Upgraded from Apache Commons Lang 2.6 to Commons Lang3 3.18.0 by @pditommaso in #6511
  • Added admonition to inputs and index words by @christopher-hakkaart in #6461
  • Improved task previousTrace documentation by @rnaidu in #6538
  • Updated feature flags page by @christopher-hakkaart in #6504
  • Updated task directives by @christopher-hakkaart in #6506

Dependencies​

  • Bumped Fusion to version 2.5 by @jordeu in #6557
  • Bumped Gradle 9.2.0 by @pditommaso in 2657524
  • Bumped groovy 4.0.29 by @pditommaso in #6510
  • Bumped logback to version 1.5.20 by @pditommaso in 462eec5
  • Bumped org.bouncycastle:bcpkix-jdk18on from 1.78.1 to 1.79 by @dependabot in #6537
  • Bumped nf-amazon@3.5.0 by @pditommaso in 17cc2b0
  • Bumped nf-azure@1.21.0 by @pditommaso in 0b56d2a
  • Bumped nf-google@1.24.0 by @pditommaso in 81a5a05
  • Bumped nf-k8s@1.3.0 by @pditommaso in 7146011
  • Bumped nf-tower@1.18.0 by @pditommaso in 86da3b7
  • Bumped nf-wave@1.17.0 by @pditommaso in de02e8b

Bug fixes​

Kubernetes​

  • Fixed Do not delete K8s jobs when ttlSecondsAfterFinished is set by @bentsherman in #6597
  • Fixed K8sTaskHandlerTest method name typos by @pditommaso in bcf81d9

Fusion​

  • Fixed Fusion license JWT token refresh by reusing TowerClient by @jorgee in 498125d

S3​

  • Fixed incorrect AWS region when specifying a S3 regional endpoint by @jorgee in #6530
  • Fixed unordered completed parts in AWS multipart upload by @jorgee in #6560

Language features​

  • Fixed Invalid type error detection by @pditommaso in 9e3aeed
  • Fixed CSV splitter when skipping empty lines by @bentsherman in #6586
  • Fixed documentation of unique operator by @bentsherman in #6541
  • Fixed error with dynamic directives with named arguments by @bentsherman in #6550
  • Fixed false error with task ext blocks in strict syntax by @bentsherman in #6569
  • Fixed invalid cache write when cacheable split operation fails by @bentsherman in #6588
  • Fixed issue with optional workflow output by @bentsherman in #6519
  • Fixed issues with rsync stage-out mode by @bentsherman in #6587

Configuration​

  • Fixed false config validation warnings for process selectors by @bentsherman in #6542

Plugins​

  • Fixed Plugins.init() in run command to original location by @jorgee in #6568

General​

  • Fixed asset detection when item is not a sibling of the executed script by @DriesSchaumont in #6605
  • Fixed security vulnerabilities in org.json dependency by @pditommaso in c7161c2
  • Fixed TowerJsonGenerator thread-safety issue by @pditommaso in #6619
  • Fixed security vulnerabilities for wiremock by @jorgee in #6607
  • Fixed replace complete plotly bundle with smaller more specific one by @mashehu in #6527
  • Fixed stageFileEnabled flag to control .command.stage file creation by @pditommaso in #6618

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.11.0-edge

Wave v1.30.0

Feature updates and improvements​

Singularity​

  • Added configurable Singularity init container image by @pditommaso in #937

Container building​

  • Used Seqera-hosted buildkit image by @pditommaso in #938

General​

  • Added labels in ConfigSpec by @munishchouhan in #934

Bug fixes​

General​

  • Fixed typos in Wave Kubernetes install by @christopher-hakkaart in #930
  • Fixed scan and mirror enabled flag bug by @munishchouhan in #935
  • Fixed wave.scan.enabled feature flag and YAML indentation by @pditommaso in #936

Full changelog: https://github.com/seqeralabs/wave/compare/v1.29.1...v1.30.0

Seqera Cloud v25.3.0_cycle33

Feature updates and improvements​

Studios​

  • Updated the Add Studio page to a single-step form.

Compute environments​

  • AWS Batch compute environments now use AmazonLinux2023-based AMIs by default, offering improved security (IMDSv2), better performance with gp3 EBS volumes, and a more recent kernel. Existing compute environments continue to function with AmazonLinux2 without changes, though we recommend migrating to newer compute environments before AmazonLinux2 reaches end-of-life in June 2026.

Bug fixes​

Compute environments​

  • Fixed compute environment variables created without specifying a target environment (head or compute), which prevented the system from applying variables during workflow execution. The system now validates that at least one target environment is specified, preventing invalid configurations and providing clear error messages.

Pipelines​

  • Fixed display issues with long helper text in pipeline schema forms. Helper text now wraps properly within form controls, improving readability for parameter descriptions with technical specifications or long value lists.

Seqera Cloud v25.3.0_cycle32

Bug fixes​

Launchpad​

  • Fixed an empty launch form issue when launching shared pipelines from another workspace. The launch form now correctly retrieves and displays all pipeline configuration when launching shared pipelines across workspaces.

General​

  • Fixed OIDC authentication errors with spaces or special characters that caused application crashes instead of displaying proper error messages. Authentication errors during login now display correctly to users, preventing application failures.