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MultiQC v1.34

New modules​

  • Methurator (#3447)
    • A Python package designed to estimate CpGs saturation for DNA methylation sequencing data.
  • riboWaltz (#3465)
    • Computes P-site offsets and performs quality control for ribosome profiling (Ribo-seq) data.

Feature updates and improvements​

  • Add uv as an installation method in docs and README (#3493)
  • Add Claude PostToolUse hook for code formatting (#3461)
  • Bump default AI models for Anthropic (#3430)
  • Remove HTML tags in generated module docs (#3509)
  • Enable code review workflow to post comments on PRs (#3506)
  • better header k/v spacing (#3471)
  • Hide AI summary sections when simple_output is enabled (#3500)
  • export_plots_timeout: Add docs and increase default to 60s (#3433)

Module updates​

  • Clarify RSeQC bam_stat proper pairs column title (#3526)
  • Fix mosdepth coverage in general stats if key is missing (#3432)
  • fastp: Add limits, update color scale of % PF/% Adapter (#3454)
  • fastp: Pick up version number for fasterp runs (#3392)
  • Freyja: Use safe alternative to eval() (#3531)

Fixes​

  • Fix heatmap axis labels not updating when toggling clustering (#3487)
  • Fix bug: Toggling highlighting for AI summary sample names didn't work (#3455)
  • fix table scroll styling with sticky headers (#3437)

Module fixes​

  • Fix sample name cleaning in CheckM and CheckM2 modules (#3464)
  • CrosscheckFingerprints: Fix bug due to overwriting row_number variable (#3458)
  • Porechop: Fix bug with "End Trimmed Percent" denominator (#3456)
  • Fix incorrect plot title in umicollapse module (#3446)
  • SNPsplit: Fix module datetime serialization error (#3444)

Infrastructure and packaging​

  • Switch from pre-commit to prek (#3467)

New Contributors​

Full Changelog: https://github.com/MultiQC/MultiQC/compare/v1.33...v1.34

Nextflow 26.03.3-edge

Feature updates and improvements​

Language features​

  • Added option to disable printing workflow outputs by @bentsherman in #7018
  • Resolved structured process input types by @bentsherman in #7014

S3​

  • Applied socket timeout to S3 CRT connections by @jorgee in #7024
  • Managed AWS SDK exceptions to convert to the appropriate IO exceptions by @jorgee in #6707

Plugins​

  • Updated missing pf4j updates by @jorgee in #7016

Fusion​

  • Added Fusion GPU metrics collection by @pditommaso in #7022
  • Used Fusion trace metrics to replace bash command-trace wrapper by @pditommaso in #7041

General​

  • Added -files-from option to lint command to avoid ARG_MAX limit by @adamrtalbot in #6858
  • Added 26.04 migration docs by @bentsherman in #7000
  • Allowed cloning from local Git repositories when --offline by @MatthiasZepper in #7035
  • Allowed running pipeline from URL and main script path by @jorgee in #6602
  • Filtered autoLabels to selected workflow-metadata fields by @pditommaso in #7049
  • Honored process.resourceLabels in nf-seqera executor by @pditommaso in #7048
  • Renamed module info subcommand to module view by @pditommaso in #7052
  • Simplified demo module README template by @pditommaso in #7051
  • Suppressed lint progress logging with -q flag by @ewels in #6880

Bug fixes​

Language features​

  • Fixed formatting issues with complex expressions by @bentsherman in #7027

S3​

  • Fixed S3FileSystemProvider.newInputStream() draining full object on close by @jorgee in #7046

Plugins​

  • Fixed inconsistent indentation in nf-amazon by @bentsherman in #7047
  • Fixed nextflowVersion for nf-tower and nf-seqera plugins by @pditommaso in cbc0a2d8e

General​

  • Fixed generated process name in module create command by @jorgee in #7008
  • Fixed module info formatting separator by @pditommaso in #7033
  • Fixed resolution of -with-tower with TOWER_API_ENDPOINT by @bentsherman in #7045
  • Fixed saveCacheFiles early return skipping log file uploads by @munishchouhan in #7015

Dependencies​

  • Bumped org.bouncycastle:bcpkix-jdk18on from 1.79 to 1.84 by @dependabot in #7042
  • Bumped nf-amazon@3.8.3
  • Bumped nf-k8s@1.5.2
  • Bumped nf-seqera@0.18.0
  • Bumped nf-tower@1.25.0
  • Bumped nf-wave@1.19.1

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.03.3-edge

Seqera Cloud v26.1.0_cycle51

Feature updates and improvements​

Compute environments​

  • Replaced Azure Batch JobCleanupPolicy with DeleteTasks, DeleteJobs, and TerminateJob boolean options in the API.
  • Added configurable head job CPUs and memory for Azure Batch.
  • Renamed Instance type to Head instance type in AWS Cloud compute environments.

Pipelines​

  • Added resourceAllocation to task data extension.
  • Added bucket events to Actions.

Access control​

  • Disabled collaborators for Cloud Pro SSO.
  • Mapped Auth0 organization claim to user profile.
  • Improved SSO collaborators and members error banners.

Bug fixes​

Pipelines​

  • Fixed forbidden repository schema requests for shared pipelines.
  • Fixed permission check for the browse button in the launch form.
  • Added missing -X POST to the Action curl snippet.

General​

  • Fixed resource labels value search in label suggestions.
  • Added missing InputNormalizeDirective to the workspace form.

Wave v1.33.2

Feature updates and improvements​

Container Building​

  • Added max size validation for container layer location by @pditommaso in #1006

General​

  • Updated wave.build.public-repo reference language by @christopher-hakkaart in #1008
  • Replaced local DurationUtils with shared lib-util-time by @pditommaso in #1010

Dependencies​

  • Updated actions/checkout action to v4.3.1 by @seqeralabs-renovate[bot] in #1013
  • Updated actions/setup-java action to v4.8.0 by @seqeralabs-renovate[bot] in #1014
  • Updated actions/setup-node action to v4.4.0 by @seqeralabs-renovate[bot] in #1015
  • Updated actions/upload-artifact action to v4.6.2 by @seqeralabs-renovate[bot] in #1016
  • Updated aws-actions/amazon-ecr-login action to v1.7.1 by @seqeralabs-renovate[bot] in #1017
  • Updated aws-actions/configure-aws-credentials action to v1.7.0 by @seqeralabs-renovate[bot] in #1018
  • Updated dependency node to v20.20.2 by @seqeralabs-renovate[bot] in #1019
  • Updated docker/login-action action to v3.7.0 by @seqeralabs-renovate[bot] in #1020
  • Updated docker/setup-buildx-action action to v3.12.0 by @seqeralabs-renovate[bot] in #1021
  • Upgraded third-party dependencies to latest stable versions by @cristianrcv in #998
  • Pinned dependencies by @seqeralabs-renovate[bot] in #1012

Bug fixes​

Container Building​

  • Fixed Conda builds for packages requiring __cuda virtual package by @pditommaso in #1027

Singularity​

  • Fixed build error with --build-template conda/micromamba:v2 for Singularity by @munishchouhan in #972

Full changelog: https://github.com/seqeralabs/wave/compare/v1.33.1...v1.33.2

Seqera Cloud v26.1.0_cycle50

Feature updates and improvements​

Compute environments​

  • Added support for separate head and worker pools in Azure Batch compute environments.
  • Added the jobMaxWallClockTime option to Azure Batch compute environments.

Studios​

  • Added the ability to edit a stopped Studio.

Access control​

  • Decoupled the Auth0 Management API audience from the OIDC issuer to support custom Auth0 domains.

General​

  • Introduced secondary tab navigation for organization and workspace pages.

Bug fixes​

Compute environments​

  • Fixed Forge disposal failures being silently swallowed by propagating the underlying exceptions.
  • Fixed job cancellation to be idempotent for already-canceled jobs.
  • Fixed Azure Batch error handling to return an actionable message when the configured pool is missing.
  • Fixed silently swallowed GCP Forge disposal failures by propagating the underlying exceptions.
  • Fixed Azure Batch dual-pool mode to assign only the relevant managed identity to each pool.

Data explorer​

  • Fixed IGV MIME type resolution in Data explorer.

Pipelines​

  • Fixed the placement of the "compute environment not available" message in the pipeline form.

Studios​

  • Fixed route URL mutation in the Studio resolver.

Nextflow 26.03.2-edge

Feature updates and improvements​

Language features​

  • Added typed workflows by @bentsherman in #6881

Modules​

  • Added module create subcommand by @pditommaso in #6992
  • Added module spec command by @jorgee in #6859
  • Added module validate subcommand by @pditommaso in #6993
  • Replaced custom ModuleRegistryClient with npr-client API by @pditommaso in #7012

General​

  • Added compute env ID and provider support to Seqera executor by @pditommaso in #6906
  • Added resourceAllocation field to trace record by @pditommaso in #6973
  • Replaced Auth0 with Platform OIDC PKCE for auth login by @pditommaso in #6953
  • Used inline metadata from trace create response by @pditommaso in #6976

Bug fixes​

General​

  • Fixed NPE in GitLab/Gitea getGitCredentials when password is null but token is set by @robsyme in #7007
  • Fixed missing version for junit-platform-launcher dependency by @pditommaso in #7011

Dependencies​

  • Bumped nf-amazon@3.8.2
  • Bumped nf-seqera@0.17.0
  • Bumped nf-tower@1.24.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.03.2-edge

Seqera Cloud v26.1.0_cycle49

Feature updates and improvements​

Studios​

  • Updated Studios micromamba to conda/micromamba:v2 and Wave to 1.33.0.

Compute environments​

  • Added private VNet and subnet support for Azure Batch compute environments.
  • Added separate Azure managed identities for head and compute jobs.
  • Improved compute environment metering system with observability and retry logic.

Datasets​

  • Added frontend implementation for dataset import from URL.
  • Added preview support for linked datasets.

Data Explorer​

  • Added Fusion symlink support in Data Explorer.
  • Increased maximum data-link name length to 512 characters.

Bug fixes​

Compute environments​

  • Fixed projectId on WIF LoggingOptions for log retrieval.
  • Fixed WIF log retrieval to resolve project number to project name.
  • Fixed WIF organization and workspace context propagation for log retrieval and data links.

Pipelines​

  • Fixed parallel requests to pipeline info in launch form.

Datasets​

  • Fixed dataset name field to apply input normalization.
  • Fixed column order preservation in dataset preview for TSV files.

Access control​

  • Fixed handling of absent Auth0 organization context.

Seqera Cloud v26.1.0_cycle48

Feature updates and improvements​

Studios​

  • Added Wave nameStrategy workspace setting for Studios.

Compute environments​

  • Added Azure service principal credentials support.
  • Added Workload Identity Federation support for Google Batch compute environments.
  • Added Entra credentials for Azure Batch Forge and Fusion v2.
  • Added resource labels as metadata on Azure Batch jobs.
  • Added support for multiple machine types in Google Batch compute environments.

Pipelines​

  • Added Nextflow CLI as a static OIDC client.

Datasets​

  • Added URL redirection logic to dataset file endpoint.

Data Explorer​

  • Added extensible view mode selection for JSON files.
  • Added open in new tab support for all files.

Monitoring​

  • Updated database model to include target resource name.

General​

  • Applied new email design to all email templates.
  • Updated copy in delete workspace confirmation modal.
  • Removed unused Containers page.
  • Upgraded to Angular 21.

Bug fixes​

Studios​

  • Fixed git config file validation when creating a Studio.

Compute environments​

  • Fixed errors not propagated when a job is terminated asynchronously.
  • Removed deprecated seqera.executor.predictionModel configuration.
  • Removed terminateAsync default implementation.

Access control​

  • Fixed Auth0 OAuth2 flow to handle ResponseClosedException.

Monitoring​

  • Fixed credential audit events to include metadata.
  • Fixed task logging to use populated taskId instead of empty id.

General​

  • Fixed page-header actions, documentation links, and spacing.
  • Fixed forbidden page icon size.

Wave v1.33.1

Feature updates and improvements​

Container building​

  • Refactored build vs cache IAM permission structure by @gwright99 in #999

UI/UX​

  • Updated list to cards on tutorials page by @christopher-hakkaart in #993

General​

  • Updated index page by @christopher-hakkaart in #1004
  • Updated copyright to 2026 by @munishchouhan in #1003
  • Updated token cache duration and clarified public repository documentation by @munishchouhan in #1007

Dependencies​

  • Migrated dependencies to Gradle version catalog (libs.versions.toml) by @cristianrcv in #996
  • Bumped Netty to 4.2.10.Final and Micronaut to 4.10.10 by @pditommaso in #1001

Full changelog: https://github.com/seqeralabs/wave/compare/v1.33.0...v1.33.1

Nextflow 26.03.1-edge

Feature updates and improvements​

Language features​

  • Hardened ProcessEntryHandler types and added test for dot-notation conflicts by @pditommaso in #6966
  • Added print workflow outputs on run completion by @bentsherman in #6875
  • Used destructuring syntax for process record/tuple inputs by @pditommaso in #6912

General​

  • Added -project-dir option to lint command by @bentsherman in #6728
  • Added platform-related metadata to WorkflowRun lineage record by @jorgee in #6545
  • Added request timeout to tower client by @jorgee in #6950
  • Added support for Java 26 by @pditommaso in #6969
  • Improved module command: enabled logging for module run, fixed info URL and search output by @pditommaso in #6961
  • Skipped launch metadata fetch for CLI-submitted runs by @pditommaso in #6975
  • Used -d flag for bkill in LSF executor by @cgoina in #6784

Bug fixes​

Language features​

  • Fixed handling of empty publishedValues in PublishOp.onComplete for optional outputs by @jorgee in #6979
  • Fixed incorrect evaluation of secret process directive by @bentsherman in #6934
  • Fixed params block in included module by @bentsherman in #6940

S3​

  • Fixed download of empty files in old MinIO-based S3 transfers by @jorgee in #6944

AWS Batch​

  • Fixed AWS Batch machine type trace for new instance families by @FloWuenne in #6952

Plugins​

  • Fixed jackson-databind dependency in nf-amazon by @pditommaso in #6941

Dependencies​

  • Fixed netty and jackson vulnerabilities by @jorgee in #6955
  • Fixed security vulnerabilities by @jorgee in #6938

General​

  • Fixed AgentLogObserver printing [SUCCESS] on failed runs by @pditommaso in #6962
  • Fixed LogsCheckpoint thread interrupt race condition by @pditommaso in #6939
  • Fixed module run CLI params cast to declared meta.yml input types by @jorgee in #6968
  • Fixed typo in TowerRetryPolicy: maxAttemps → maxAttempts by @robsyme in #6949

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.03.1-edge