Version 26.08.0-edge

• Accept http requesting-protocol for https proxy CONNECT tunnel auth (#7369) [cac2e0d]
• Add --console=plain to gradle commands in Makefile (#7400) [40fc962]
• Add componentName to 'module view' command output (#7385) [0e1bf39]
• Add note about AI co-authorship to CLAUDE.md (#7357) [d11c550]
• Add seqera.executor.maxCpusPerUser option (#7367) [a2ef396]
• Add smolvm container engine support (#7386) [5b23a4e]
• Add singularity.resourceLimits config option (#7352) [98e8573]
• Agent primitive: AI agents as first-class Nextflow tasks (#7477) [b148cfb]
• Align Seqera executor maxSpotAttempts and Fusion handling (#7412) [22214c5]
• Bound Seqera executor scheduler requests with a request timeout (#7466) [ed08167]
• build(java): align to Java 25 toolchain, target Java 17 via --release (#7370) [9fc31ed]
• Bump Groovy 4.0.33 (#7429) [c8800d8]
• Bump netty and Apache HttpComponents to patched releases (#7484) [3aef1da]
• Cache the task context for exec tasks (#7499) [9eb270c]
• Detect Azure virtual directories without a trailing slash (#6428) [b4ab2e1]
• Document exit logic in task wrapper script (#7290) [b61eda2]
• Drop transient object tags when publishing files to S3 (#7344) [f1f1e60]
• Fix cache invalidation for module binaries (#6914) [029e52e]
• Fix config rendering of nested closures (#7375) [f6684a3]
• Fix function call in process directive value with v2 parser (#7374) [91004f7]
• Fix independently-verified findings from a security audit (#7503) [5400da6]
• Fix lint reporting of excluded paths (#7354) [b36bb31]
• Fix negative duration error on short run (#7351) [6471c29]
• Fix parameterized type cast in process body (#7382) [aaffabc]
• Fix PBS Pro server status query (#7366) [c7e02c0]
• Fix plugin blocks incorrectly merged in v2 config parser (#7350) [795d487]
• Fix publish mode override when re-publishing an existing file (#7364) [61243b0]
• Fix race condition calling workflow onComplete twice (#7349) [14d5f26]
• Fix spurious 'Unrecognized config option' warning for wave.build.compression and wave.build.conda (#7355) [37da32c]
• Fix tests failing on macOS and on hosts with NXF_REGISTRY_TOKEN (#7457) [a7a7d53]
• Fix variable incorrectly resolved to included function name (#7358) [e98351e]
• Fix workflow metadata when failOnIgnore is true (#7356) [6860022]
• fix: prevent world-readable race window when storing local secrets (#7307) [f520534]
• Guard trace log against string formatting errors (#7347) [8a0c921]
• Honor COLUMNS when determining ANSI output width (#7144) [3f69dca]
• Pre-pull the integration tests container (#7432) [82f59c7]
• Preserve comments in formatter (#7346) [0fe6ef2]
• Refactor HubOptions from a trait into a record (#7372) [cb22231]
• Remove dead SpuriousDeps.cmdCloud reflection (#7371) [aa9e875]
• Report syntax error for unexpected character in gstring (#7353) [7fae3ff]
• Report the task directives read while the command is rendered (#7506) [1b4e757]
• Revert the stream swap after the redirect to .command.out and .command.err (#7300) [d971319]
• Separate CLI from runtime (#5971) [1dc8cf6]
• Split CLI config handling out of ConfigBuilder (#7373) [34ac1d1]
• Stop fabricating a memory request for the Seqera executor (#7488) [cdf4254]
• Support authenticated forward HTTP/HTTPS proxies across the client stack (#7331) [064a038]
• Treat a missing k8s config scope as an empty one (#7452) [568680f]
• Update CI bucket to s3://nextflow-oss-ci (#7440) [55a6932]
• Update the docs site dependencies to patched releases (#7486) [e5dfe3d]
• Use Platform user identity for the Seqera executor userName label (#7413) [1bb78e2]
• Use registry config for plugin repos (#7180) [2856de8]
• Use the wiremock self-contained distribution in nf-tower (#7485) [3db6edf]
• Use command -v instead of which in the launcher Java lookup (#7433) [cd03dc3]

Version 26.07.0-edge

• Add docker.cpuLimits config option (#7289) [60c7ae9]
• Add graceful fallback for array directive with unsupported executors (#7296) [24ed218]
• Add seqera.executor.providerConfig option (#7335) [5b8ce02]
• Bump jackson 2.21.1 to 2.21.4 to fix high-severity CVEs (#7274) [a6fddfa]
• Bump jackson-databind to patched versions to fix deserialization CVEs (#7322) [8d4423e]
• chore: pin Docusaurus dependencies (#7324) [373a83d]
• chore: update actions/checkout action to v6.0.3 (#7325) [ci fast] [5dc9bbb]
• chore: update anthropics/claude-code-action action to v1.0.168 (#7326) [ci fast] [2cc1428]
• chore: update dependency ch.qos.logback:logback-classic to v1.5.37 (#7327) [15ed1a3]
• chore: update dependency ch.qos.logback:logback-core to v1.5.35 [security] (#7297) [1e53f4a]
• chore: update dependency com.azure:azure-compute-batch to v1.0.0-beta.6 (#7128) [ci fast] [1c98412]
• docs: Add note about IAM roles for google.batch.serviceAccountEmail (#7291) [87943ba]
• docs: add Semantics reference page (#7271) [5a64223]
• docs: clarify Bitbucket API token auth requirements (#7279) [37984dd]
• docs: Clarify override behavior of resourceLabels directive (#7287) [1439ebf]
• Drop dead oss.sonatype.org repository (#7282) [ci fast] [527a314]
• Exclude null config env entries from task environment (#7294) [0ba281e]
• feat(nf-seqera): send pipeline-secret references to the Seqera Scheduler (#7314) [df61a13]
• feat: add two Indian scientists to NameGenerator (#7079) [ci fast] [142ab0e]
• Fix containerOptions --opt=value parsing for AWS Batch (#5190) (#7288) [b1f31a3]
• Fix CVE-2025-14813: replace discontinued bcprov-ext with bcprov-jdk18on 1.84 (#7284) [17ef32d]
• Fix error checking in workflow emits (#7058) [56b574d]
• Fix high-severity form-data CRLF injection in docs site (#7276) [241612b]
• Fix Kryo deserialization error with enum types (#7277) [0167eb6]
• Fix path input for exec processes (#7272) [afab66b]
• Fix URL percent-encoding lost on resume for http/ftp paths (#7333) [79594e7]
• fix: key Fusion license token cache by product and version (#7320) [ci fast] [d95f506]
• Force-create staged input symlinks to allow task re-runs (#7285) [ac7eb26]
• Revert "Consolidate nf-tower plugin into nf-seqera (#7252)" [da5afcf]
• Revert "Skip nf-tower when superseded by nf-seqera (#7283)" [c5dec3b]
• Round up CPUs to nearest valid value for AWS Batch Fargate (#7295) [fd6012b]
• Show absolute path in missing main script error (#7286) [8373569]
• Skip nf-tower when superseded by nf-seqera (#7283) [57a52cf]
• Tolerate stale/transient resize errors on autoscale Azure Batch pools (#7312) [46392e6]
• Use scheduler API exit code, fall back to .exitcode file (#7273) [ci skip] [751effc]
• Use wiremock self-contained distribution to drop vulnerable handlebars (#7275) [27646a7]
• Bump nf-amazon@3.10.1
• Bump nf-azure@1.23.1
• Bump nf-google@1.27.4
• Bump nf-k8s@1.5.5
• Bump nf-seqera@0.23.0
• Bump nf-tower@1.29.1
• Bump nf-wave@1.21.1

Version 25.10.7

• Fix issues with v2 config parser (#7249) [0316e83]
• Add support for latest-generation Google Cloud machine families (#6841) [8714c7c]
• Bump nf-google@1.23.6

Version 26.04.6

• Bump nf-seqera@0.21.1
• Bump nf-tower@1.28.2

Version 26.04.5

• Add GPU metrics to workflow-level execution summary (#7229) [d72c88e]
• Fix flatMap tuple error for dataflow value (#7254) [0df0bfb]
• Propagate Seqera Intelligent Compute scheduler run identifier to Platform (#7228) [6c7547c]
• Bump nf-seqera@0.22.0
• Bump nf-tower@1.29.0

Version 26.06.0-edge

• Add docs tip for relocating Docker storage on Azure Batch nodes (#6937) [d2ecd7a]
• Add Fibonacci and Pareto to the run name generator (#7255) [c9e9cfb]
• Consolidate nf-tower plugin into nf-seqera (#7252) [1cdd0bc]
• docs: Clarify storeDir caveats with env, eval, stdout outputs (#7235) [e97f337]
• docs: Normalize version callouts (#7256) [85b945e]
• Fail with a clear error when Fusion is enabled without an access token (#7263) [83d452a]
• Fix docs example for record operations (#7250) [e30c380]
• Fix failing unit tests with clean build (#7264) [e3a44ba]
• Fix flatMap tuple error for dataflow value (#7254) [e4e9a2c]
• fix: lower trace-access.nf memory to fit CI runner capacity (#7266) [fcf52e5]
• Propagate Seqera Intelligent Compute scheduler run identifier to Platform (#7228) [e2a673f]
• Remove uncommitted specs [ci skip] (#7267) [22894f7]
• Bump nf-seqera@1.0.0

Version 26.05.0-edge

• Add -help as alias for -h in top-level CLI options (#7238) [ea3f2aa]
• Add GPU metrics to workflow-level execution summary (#7229) [43da3f1]
• Add hidden plural/singular aliases for noun subcommands (#7239) [fe3da84]
• Add Nextflow module info to lineage TaskRun entry (#7160) [1be0561]
• Add seqera:// data-links support to nf-tower filesystem (#7070) [7d6f8c4]
• Add shellEnabled option and per-task prediction model to Seqera executor (#7204) [810fd16]
• Add workflow DAG reporting to nf-tower plugin (#7218) [3041af8]
• Add nextflow logfile command (#7177) [c689c25]
• ADR: data lineage (#7187) [ae58c91]
• Allow plugin version to be specified when running a plugin command (#7113) [7eeeb77]
• Change stdout outputs to stderr, to not break piped output (#7121) [dd9c2eb]
• docs: Clarify distinction between modules and script inclusion (#7217) [2294ab1]
• docs: Migrate docs to new build (#7119) [93b2444]
• Fix "No such variable" in typed output block with job arrays (#7221) [064404b]
• Fix cast and instanceof with record types (#7185) [0834c83]
• Fix issue with workflow completion handler being called twice (#7191) [93c2122]
• Fix lineage records for stub-run and eval outputs (#7211) [52d62a7]
• Fix netty CVE-2026-44249 via AWS SDK bump and azure-core-http-netty pin (#7223) [ab6a6e6]
• Fix nxf_date for uutils coreutils (Ubuntu 26.04+) (#7118) [5504f64]
• Fix staging of Path fields of included record types (#7226) [72ab749]
• Improve Azure Batch VM image diagnostics and fix stale 24.04 docs (#7200) [8e5e611]
• Improve Tower telemetry error handling on transient gateway failures (#7190) [b0d7e33]
• Mirror test containers to public.cr.seqera.io to harden CI against quay.io outages (#7195) [539081b]
• Preserve order of plugin declarations in config (#7227) [3fa70ed]
• Promote 'latest' stable channel by version comparison instead of branch name [b5ac62e]
• Refactor changelog.txt -> CHANGELOG.md (#7179) [c19a87e]
• Remove deprecated echo process directive (#7206) [362f6fd]
• Sample nxf_date seconds and nanoseconds atomically (#7207) [6636c8c]
• Support accelerator directive for local executor (#5850) [0285c3b]
• Support record type input with dot-notation CLI params (#7170) [48bf94f]
• Use a stop flag instead of thread interrupt to shut down the logs checkpoint (#7193) [1faf69d]
• nextflow plugins -help: show subcommands (#7197) [429fd8e]
• Bump nf-amazon@3.10.0
• Bump nf-azure@1.23.0
• Bump nf-codecommit@0.6.0
• Bump nf-seqera@0.22.0
• Bump nf-tower@1.29.0

Version 26.04.4

• Add Nextflow module info to lineage TaskRun entry (#7160) [7b7678b]
• Bump default plugin create template to v0.4.0 (#7234) [a12f27f]
• Fix "No such variable" in typed output block with job arrays (#7221) [81c35b4]
• Fix cast and instanceof with record types (#7185) [0dffb8a]
• Fix issue with workflow completion handler being called twice (#7191) [95c0dae]
• Fix nxf_date for uutils coreutils (Ubuntu 26.04+) (#7118) [2e9ea02]
• Fix staging of Path fields of included record types (#7226) [6bc3510]
• Preserve order of plugin declarations in config (#7227) [d33bee4]
• Sample nxf_date seconds and nanoseconds atomically (#7207) [ea81fd0]
• Bump nf-amazon@3.9.2
• Bump nf-azure@1.22.6
• Bump nf-codecommit@0.5.3
• Bump nf-seqera@0.21.0
• Bump nf-tower@1.28.1

Version 25.10.6

• Update default Azure Batch pool image to Ubuntu 24.04 [114d0e4]
• Fix world-readable seqera-auth.config credential file (#7182) [a2813c6]
• Fix S3FileSystemProvider.newInputStream() draining full object on close (#7046) [13cbdd8]
• Fix LogsCheckpoint thread interrupt race condition (#6939) [c455156]
• Pin rnaseq-nf to v2.3 in Azure validation script [8f7e578]
• Bump nf-amazon@3.4.5 [b9074b2]
• Bump nf-tower@1.17.7 [da09f09]
• Bump nf-azure@1.20.3 [1e000af]

Version 26.04.3

• Fix bucket cleanup in S3 test (#7172) [4fcc583]
• Fix docs CI on Python 3.14 by upgrading Sphinx (#7175) [71665de]
• Improve message error when enabling types with syntax parser v1 (#7173) [13282b5]
• Make plugin metadata prefetch resilient to registry rate limiting (#7181) [1c47215]
• Support fetching local files in FUSION_CONTAINER_CONFIG_URL (#7142) [0d1ece8]
• Bump nf-azure@1.22.5
• Bump nf-google@1.27.3
• Bump nf-k8s@1.5.4
• Bump nf-seqera@0.20.1
• Bump nf-tower@1.28.0
• Bump nf-wave@1.21.0