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Nextflow 26.04.7

Bug fixes​

Language features​

  • Fixed error checking in workflow emits by @bentsherman in #7058
  • Fixed the formatter dropping the main: label when onComplete: or onError: is present by @ewels in #7346

Configuration​

  • Fixed config rendering of nested closures by @bentsherman in #7375

S3​

  • Fixed S3 directory upload skipping symbolic links by @jorgee in #7515

Dependencies​

  • Bumped vulnerable dependencies to patched releases by @jorgee in #7598
  • Bumped nf-amazon@3.9.3
  • Bumped nf-azure@1.22.7
  • Bumped nf-codecommit@0.5.4
  • Bumped nf-google@1.27.4
  • Bumped nf-k8s@1.5.5
  • Bumped nf-seqera@0.21.2
  • Bumped nf-tower@1.28.3

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.7

Nextflow 26.09.2-edge

Feature updates and improvements​

Language features​

  • Added pipeline composition by @bentsherman in #7213
  • Allowed any return type for a closure with a boolean signature by @bentsherman in #7688
  • Added type checking for the type arguments of call arguments by @bentsherman in #7728
  • Improved lint errors for common gotchas by @bentsherman in #7742
  • Moved v1 process output resolution to TaskOutputResolverV1 by @bentsherman in #7036
  • Published workflow outputs with FilePublisher by @bentsherman in #7745
  • Added recognition of Record::subMap() in the type checker by @bentsherman in #7743
  • Added an error for a closure or function that returns no value by @bentsherman in #7714
  • Added an error for a missing return statement in a closure or function by @bentsherman in #7738
  • Changed invalid script definitions to report the real syntax error by @bentsherman in #7675
  • Added a type error for record field assignment by @bentsherman in #7718
  • Skipped argument checks for plugin functions in typed scripts by @bentsherman in #7726
  • Added support for a map of source-to-target pairs in the output path directive by @bentsherman in #7646
  • Changed unnamed typed process outputs to use the inferred type by @pditommaso in #7757
  • Added runtime validation of record fields for process record inputs by @bentsherman in #7692

Configuration​

  • Added the seqera.executor.machineRequirement.onDemandCostRatio option by @pditommaso in #7710

Wave​

  • Added conda/micromamba:v2-fast and conda/pixi:v1-fast to the wave.build.template docs by @pditommaso in #7727

General​

  • Centralized shared dependency versions in gradle.properties by @pditommaso in #7704
  • Made HashBuilder.isAssetFile public by @jorgee in #7723
  • Changed CSV output to quote values only when required by @xHaMMaDy in #7377
  • Changed lineage to record only tasks that completed by @jorgee in #7664
  • Replaced LockManager with Guava Striped locks by @pditommaso in #7736
  • Changed sched multi-attempt tasks to report the final attempt's start time by @pditommaso in #7755
  • Changed the console log to go to stderr when ANSI logging is disabled by @bentsherman in #7741
  • Added CI validation of agent examples against a staged runner image by @pditommaso in #7761

Bug fixes​

Language features​

  • Fixed formatting of directives with a list argument by @bentsherman in #7679
  • Fixed lineage path references for typed processes by @jorgee in #7713
  • Fixed an NPE when all publish statements in a workflow output are no-ops by @bentsherman in #7674
  • Fixed an NPE when publishing an external file with a publish statement by @bentsherman in #7721
  • Fixed record cast of non-local Path values by @bentsherman in #7684
  • Fixed serialization of dataflow params by @pinin4fjords in #7759
  • Fixed the params block breaking piped operators in the entry workflow by @bentsherman in #7405

Plugins​

  • Fixed plugin functions that return or take a channel by @bentsherman in #7715

General​

  • Fixed a grep broken pipe error when reading the CPU model in the trace script by @bentsherman in #7672
  • Fixed stale ANSI log lines when COLUMNS does not match the terminal width by @pditommaso in #7705
  • Fixed the launcher Java version cache and md5 fallback by @ewels in #7695
  • Fixed LsfExecutor.parseJobId() swallowing submit failures by @Arthur031221 in #7730
  • Fixed the validate.sh image override with a relative results directory and Wave images by @pditommaso in #7763

Dependencies​

  • Bumped Jackson to 2.21.7 and 2.18.11 to fix security advisories by @jorgee in #7732
  • Bumped nf-agent-pi to 0.5.4 with pi-coding-agent 1.0.2 so the catalog includes GPT-6 Luna by @edmundmiller in #7748
  • Bumped pi-coding-agent to 0.86.1 to fix undici advisories by @jorgee in #7733
  • Bumped sched-client to 0.100.0 in nf-seqera by @pditommaso in fe446ce6d
  • Bumped slf4j to 2.0.20 by @pditommaso in #7703
  • Bumped nf-agent@0.1.2
  • Bumped nf-agent-pi@0.5.4
  • Bumped nf-azure@1.24.1
  • Bumped nf-google@1.28.2
  • Bumped nf-seqera@0.26.0
  • Bumped nf-tower@1.31.0
  • Bumped nf-wave@1.22.2

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.09.2-edge

Nextflow 26.09.1-edge

Feature updates and improvements​

Language features​

  • Moved the type checker into nf-lang and brought static typing out of preview by @bentsherman in #7656

Google Batch​

  • Deprecated Google Batch machine type selection via Cloud Info by @bentsherman in #7677

Plugins​

  • Allowed a cache factory to decline a session by @jorgee in #7681

General​

  • Added a hint to nextflow log and nextflow clean errors that the commands do not support the cloud cache by @bentsherman in #7676
  • Removed a stray git push from the release task by @bentsherman in #7678

Bug fixes​

S3​

  • Fixed S3 upload retries by making ByteBufferInputStream resettable by @jorgee in #7577

Google Batch​

  • Fixed Google Batch array-child tasks reporting a null machine type by @pditommaso in #7629

Dependencies​

  • Bumped Bouncy Castle to 1.85 to fix critical CVEs by @pditommaso in #7658
  • Bumped pi-coding-agent to 0.84.4 to fix npm advisories by @pditommaso in #7659
  • Bumped slf4j to 2.0.19 by @pditommaso in #7661
  • Fixed npm advisories in the docs site dependencies by @pditommaso in #7660
  • Bumped nf-agent-pi@0.5.3
  • Bumped nf-amazon@3.11.1
  • Bumped nf-cloudcache@0.6.2
  • Bumped nf-google@1.28.1
  • Bumped nf-k8s@1.6.1

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.09.1-edge

Nextflow 26.09.0-edge

Feature updates and improvements​

Language features​

  • Added direct execution of named workflows by @jorgee in #7379
  • Added workflow modules by @bentsherman in #7342
  • Deprecated the storeDir directive and documented an alternative approach by @bentsherman in #7574
  • Documented multiple architectures in the arch directive by @pditommaso in #7622
  • Made eval output names stable across runs by @bentsherman in #7575
  • Reported a syntax error for an invalid output or emit assignment by @bentsherman in #7547
  • Reported an error for an aliased type include by @bentsherman in #7557
  • Reported invalid escape sequences at the exact position by @bentsherman in #7608

Configuration​

  • Added a directory option to resolve report paths against outputDir by @bentsherman in #7553
  • Added the manifest.diagram config option by @pinin4fjords in #7578

Azure​

  • Added Azure Compute Gallery image and verification options by @LennyBEL in #7338

Google Batch​

  • Sped up submission of Google Batch array jobs by @thalassemia in #6847

Kubernetes​

  • Changed the default k8s compute resource type to Job by @bentsherman in #7524

Plugins​

  • Added extension points for task caching and object-storage access by @jorgee in #7638
  • Removed support for nf-weblog by @bentsherman in #7639

General​

  • Added automatic resource labels for any executor by @pditommaso in #7528
  • Added a codespell CI check and fixed existing typos by @ewels in #7594
  • Added configurable timeouts to SCM API requests by @robsyme in #7536
  • Added deep links to migration notes by @bentsherman in #7624
  • Added retries for request timeouts in the Tower and Wave HTTP clients by @pditommaso in #7604
  • Adopted the shared io.seqera:lib-util-net ProxyConfig for egress proxy handling by @pditommaso in #7587
  • Cleaned local task directories in hybrid runs by @bentsherman in #7611
  • Cleaned up ADR prose and fixed typos by @bentsherman in #7595
  • Cleaned up the 26.08.0-edge changelog by @pditommaso in #7527
  • Deduplicated include URI resolution logic by @bentsherman in #7644
  • Improved resilience to delayed shared file system visibility by @pditommaso in #7489
  • Made NXF_AGENT_MODE an explicit override of agent mode auto-detection by @bentsherman in #7615
  • Renamed SCM HTTP client timeouts to the global NXF_HTTPCLIENT_* namespace by @pditommaso in #7567
  • Stopped Nextflow submitting queued tasks after the session has aborted by @Mohit-Ak in #7482

Dependencies​

  • Aligned the nf-agent test Groovy dependency to 4.0.33 by @pditommaso in #7559
  • Fixed Jackson, Netty, and gRPC CVEs via API-scoped dependency constraints by @jorgee in #7329

Bug fixes​

Language features​

  • Fixed cloning of typed process outputs to also clone topics by @bentsherman in #7556
  • Fixed formatting of legacy type annotations by @bentsherman in #7525

Configuration​

  • Fixed a false warning for executor selectors by @bentsherman in #7555
  • Fixed the description for process config options with method overloads by @bentsherman in #7442
  • Fixed the resume config breaking other CLI commands by @bentsherman in #7581

S3​

  • Fixed S3 directory upload skipping symbolic links by @jorgee in #7515
  • Fixed workflow output publishing to S3 with the default path by @bentsherman in #7518

Azure​

  • Fixed nf-azure plugin tier-1 bugs by @adamrtalbot in #6831

Google Batch​

  • Fixed nextflow clean aborting on GCS pseudo-directories by @bentsherman in #7630
  • Fixed the env config scope not applied with Google Batch by @bentsherman in #7609
  • Fixed Google Batch storing symlinked task outputs as gcsfuse placeholders by @bentsherman in #7612

Plugins​

  • Fixed resolution of non-core plugin dependencies from the registry by @bentsherman in #7613

General​

  • Fixed a typo in the error message for an invalid LID path by @ewels in #7593
  • Fixed the lineage checksum computed in standard mode regardless of label by @bentsherman in #7582
  • Fixed a local executor resource accounting race by @pditommaso in #7652
  • Fixed the multi-revision test failing locally by @bentsherman in #7541
  • Fixed the output index file write to object storage by @bentsherman in #7635
  • Improved NFS lock error handling in DefaultCacheStore by @matthdsm in #6997

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.09.0-edge

Nextflow 26.08.0-edge

Feature updates and improvements​

Language features​

  • Added an agent primitive to run AI agents as first-class Nextflow tasks by @pditommaso in #7477
  • Added syntax error reporting for an unexpected character in a gstring by @bentsherman in #7353
  • Updated the formatter to preserve comments by @ewels in #7346

Configuration​

  • Added the seqera.executor.maxCpusPerUser config option by @jonmarti in #7367
  • Added the singularity.resourceLimits config option by @bentsherman in #7352
  • Split CLI config handling out of ConfigBuilder by @bentsherman in #7373

S3​

  • Dropped transient object tags when publishing files to S3 by @pditommaso in #7344

Kubernetes​

  • Treated a missing k8s config scope as an empty one by @pditommaso in #7452

Plugins​

  • Aligned the Seqera executor maxSpotAttempts and Fusion handling by @pditommaso in #7412
  • Bounded Seqera executor scheduler requests with a request timeout by @pditommaso in #7466
  • Stopped fabricating a memory request for the Seqera executor by @pditommaso in #7488
  • Used the Platform user identity for the Seqera executor userName label by @pditommaso in #7413
  • Used registry config for plugin repos by @jorgee in #7180

General​

  • Accepted the http requesting protocol for HTTPS proxy CONNECT tunnel authentication by @bentsherman in #7369
  • Added --console=plain to Gradle commands in the Makefile by @pditommaso in #7400
  • Added componentName to the module view command output by @pditommaso in #7385
  • Added a note about AI co-authorship to CLAUDE.md by @bentsherman in #7357
  • Added smolvm container engine support by @pditommaso in #7386
  • Added support for authenticated forward HTTP/HTTPS proxies across the client stack by @pditommaso in #7331
  • Aligned the build to the Java 25 toolchain, targeting Java 17 via --release by @pditommaso in #7370
  • Cached the task context for exec tasks by @pditommaso in #7499
  • Documented the exit logic in the task wrapper script by @bentsherman in #7290
  • Honored COLUMNS when determining ANSI output width by @Eldergenix in #7144
  • Pre-pulled the integration tests container by @pditommaso in #7432
  • Refactored HubOptions from a trait into a record by @bentsherman in #7372
  • Removed dead SpuriousDeps.cmdCloud reflection by @bentsherman in #7371
  • Reported the task directives read while the command is rendered by @bentsherman in #7506
  • Separated the CLI from the runtime by @bentsherman in #5971
  • Updated the CI bucket to s3://nextflow-oss-ci by @bentsherman in #7440
  • Used the WireMock self-contained distribution in nf-tower by @pditommaso in #7485
  • Used command -v instead of which in the launcher Java lookup by @pditommaso in #7433

Dependencies​

  • Bumped Groovy 4.0.33 by @pditommaso in #7429
  • Bumped Netty and Apache HttpComponents to patched releases by @pditommaso in #7484
  • Updated the docs site dependencies to patched releases by @pditommaso in #7486

Bug fixes​

Language features​

  • Fixed a function call in a process directive value with the v2 parser by @bentsherman in #7374
  • Fixed lint reporting of excluded paths by @bentsherman in #7354
  • Fixed a parameterized type cast in a process body by @bentsherman in #7382
  • Fixed a variable incorrectly resolved to an included function name by @bentsherman in #7358

Configuration​

  • Fixed config rendering of nested closures by @bentsherman in #7375
  • Fixed plugin blocks incorrectly merged in the v2 config parser by @bentsherman in #7350

Azure​

  • Fixed detection of Azure virtual directories without a trailing slash by @adamrtalbot in #6428

Wave​

  • Fixed a spurious 'Unrecognized config option' warning for wave.build.compression and wave.build.conda by @pditommaso in #7355

General​

  • Fixed cache invalidation for module binaries by @FloWuenne in #6914
  • Fixed independently-verified findings from a security audit by @ewels in #7503
  • Fixed a negative duration error on a short run by @bentsherman in #7351
  • Fixed the PBS Pro server status query by @jscgh in #7366
  • Fixed the publish mode override when re-publishing an existing file by @bentsherman in #7364
  • Fixed a race condition calling workflow onComplete twice by @bentsherman in #7349
  • Fixed tests failing on macOS and on hosts with NXF_REGISTRY_TOKEN by @pditommaso in #7457
  • Fixed workflow metadata when failOnIgnore is true by @ehsanestaji in #7356
  • Guarded the trace log against string formatting errors by @bentsherman in #7347
  • Prevented a world-readable race window when storing local secrets by @aknownuser in #7307
  • Reverted the stream swap after the redirect to .command.out and .command.err by @tcezard in #7300

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.08.0-edge

Nextflow 26.07.0-edge

Feature updates and improvements​

Language features​

  • Added a Semantics reference page to the docs by @bentsherman in #7271

Configuration​

  • Added the docker.cpuLimits config option by @bentsherman in #7289
  • Added the seqera.executor.providerConfig option by @pditommaso in #7335

Google Batch​

  • Added a docs note about IAM roles for google.batch.serviceAccountEmail by @bentsherman in #7291

Plugins​

  • Sent pipeline-secret references to the Seqera Scheduler from nf-seqera by @pditommaso in #7314
  • Skipped nf-tower when superseded by nf-seqera by @jorgee in #7283
  • Reverted "Consolidate nf-tower plugin into nf-seqera (#7252)" by @pditommaso in da5afcfe9
  • Reverted "Skip nf-tower when superseded by nf-seqera (#7283)" by @pditommaso in c5dec3b4e

General​

  • Added a graceful fallback for the array directive with unsupported executors by @bentsherman in #7296
  • Added two Indian scientists to NameGenerator by @deepmind11 in #7079
  • Clarified Bitbucket API token auth requirements in the docs by @pditommaso in #7279
  • Clarified the override behavior of the resourceLabels directive in the docs by @bentsherman in #7287
  • Dropped the dead oss.sonatype.org repository by @pditommaso in #7282
  • Showed the absolute path in the missing main script error by @bentsherman in #7286
  • Used the scheduler API exit code, falling back to the .exitcode file by @jordeu in #7273

Dependencies​

  • Bumped jackson 2.21.1 to 2.21.4 to fix high-severity CVEs by @pditommaso in #7274
  • Bumped jackson-databind to patched versions to fix deserialization CVEs by @jorgee in #7322
  • Replaced the discontinued bcprov-ext with bcprov-jdk18on 1.84 to fix CVE-2025-14813 by @pditommaso in #7284
  • Used the wiremock self-contained distribution to drop vulnerable handlebars by @pditommaso in #7275
  • Pinned Docusaurus dependencies by @seqeralabs-renovate in #7324
  • Updated the actions/checkout action to v6.0.3 by @seqeralabs-renovate in #7325
  • Updated the anthropics/claude-code-action action to v1.0.168 by @seqeralabs-renovate in #7326
  • Updated ch.qos.logback:logback-classic to v1.5.37 by @seqeralabs-renovate in #7327
  • Updated ch.qos.logback:logback-core to v1.5.35 (security) by @seqeralabs-renovate in #7297
  • Updated com.azure:azure-compute-batch to v1.0.0-beta.6 by @seqeralabs-renovate in #7128
  • Bumped nf-amazon@3.10.1
  • Bumped nf-azure@1.23.1
  • Bumped nf-google@1.27.4
  • Bumped nf-k8s@1.5.5
  • Bumped nf-seqera@0.23.0
  • Bumped nf-tower@1.29.1
  • Bumped nf-wave@1.21.1

Bug fixes​

Language features​

  • Fixed error checking in workflow emits by @bentsherman in #7058
  • Fixed path input for exec processes by @bentsherman in #7272

Configuration​

  • Excluded null config environment entries from the task environment by @bentsherman in #7294

AWS Batch​

  • Fixed containerOptions --opt=value parsing for AWS Batch by @bentsherman in #7288
  • Rounded up CPUs to the nearest valid value for AWS Batch Fargate by @bentsherman in #7295

Azure​

  • Tolerated stale or transient resize errors on autoscale Azure Batch pools by @jorgee in #7312

Fusion​

  • Keyed the Fusion license token cache by product and version by @robsyme in #7320

General​

  • Fixed a high-severity form-data CRLF injection in the docs site by @pditommaso in #7276
  • Fixed a Kryo deserialization error with enum types by @bentsherman in #7277
  • Fixed URL percent-encoding lost on resume for HTTP/FTP paths by @bentsherman in #7333
  • Force-created staged input symlinks to allow task re-runs by @bentsherman in #7285

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.07.0-edge

Nextflow 26.04.5

Feature updates and improvements​

General​

  • Added GPU metrics to workflow-level execution summary by @cristianrcv in #7229
  • Propagated Seqera Intelligent Compute scheduler run identifier to Platform by @jorgee in #7228

Bug fixes​

Language features​

  • Fixed flatMap tuple error for dataflow value by @bentsherman in #7254

Dependencies​

  • Bumped nf-seqera@0.22.0
  • Bumped nf-tower@1.29.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.5

Nextflow 26.06.0-edge

Feature updates and improvements​

Language features​

  • Clarified storeDir caveats with env, eval, and stdout outputs by @bentsherman in #7235

Azure​

  • Added docs tip for relocating Docker storage on Azure Batch nodes by @adamrtalbot in #6937

Fusion​

  • Added a clear error when Fusion is enabled without an access token by @jorgee in #7263

Plugins​

  • Consolidated the nf-tower plugin into nf-seqera by @pditommaso in #7252

General​

  • Added Fibonacci and Pareto to the run name generator by @bentsherman in #7255
  • Normalized version callouts in the docs by @bentsherman in #7256
  • Propagated the Seqera Intelligent Compute scheduler run identifier to Platform by @jorgee in #7228
  • Removed uncommitted specs by @bentsherman in #7267

Dependencies​

  • Bumped nf-seqera@1.0.0

Bug fixes​

Language features​

  • Fixed docs example for record operations by @bentsherman in #7250
  • Fixed flatMap tuple error for dataflow value by @bentsherman in #7254

General​

  • Fixed failing unit tests with clean build by @bentsherman in #7264
  • Lowered trace-access.nf memory to fit CI runner capacity by @pditommaso in #7266

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.06.0-edge