nextflow Files

• Add publish-artifacts step to release process [75d8ebf9b]
• Add type checking utils (#6482) [3e9a2c091]
• Fix no secrets in AWS Batch jobs (#6499) [c76c32582]
• Prioritize Google Batch API exit codes with fallback to .exitcode file (#6498) [6ac2efcba]
• Show workspace roles in 'auth status', tweak error message on 403 (#6497) [0633d90d1]
• Simplify S3 configuration options (#6496) [0b7f18049]
• Track remote input files in lineage (#6490) [b0660caf3]
• Bump nf-amazon@3.4.1 [0d5ced94a]
• Bump nf-google@1.23.3 [e6c765217]
• Bump nf-tower@1.17.1 [2069c9729]

25.09.2-edge - 21 Oct 2025

• Add .command.log redirection in K8s container command (#6455) [e6eed7949]
• Add nextflow auth command for Seqera Platform authentication (#6463) [bedf02a99]
• Add nextflow launch command (#6491) [7c8fa3d9d]
• Bring workflow outputs out of preview (#6487) [c41677b40]
• Fix e2e test infrastructure and add config.schema compatibility aliases (#6495) [d3cee2bab]
• Fix false error for executor.jobName config option (#6375) [81ae62bf2]
• Fix false error with storeDir and val outputs (#6408) [1aa8c4468]
• Fix type casting in PluginSpec for ConfigScope (#6469) [b00644c9b]
• Improve plugin create confirmation prompt (#6473) [215925c47]
• Improve release script validation [3e3a938d6]
• Limit S3 client connections when using virtual threads (#6369) [295c60b5c]
• Migrate SraExplorer to use HxClient for HTTP operations (#6467) [84e3e7873]
• Rename config.schema package to config.spec (#6485) [ef0d2d601]
• Typed processes (#6368) [30f3c3c2a]
• Update buildInfo on releaseInfo [46a8a2b53]

25.09.1-edge - 9 Oct 2025

• Improve build metadata generation and validation [60225374f]
• Fix Missing static type definition [67a532040]
• Add rnaseq-nf tutorial (#6440) [a830125c4]

25.09.0-edge - 8 Oct 2025

• Add listDirectory traversal API to RepositoryProvider abstraction (#6430) [1449fdfec]
• Add step to claim plugin in Gradle plugin migration docs (#6450) [3b709004b]
• Add support for comma-separated file paths in ProcessEntryHandler (#6434) [fe627644d]
• Add support for Java 25 (#6419) [dc8d474d6]
• Add unit test for invalid workflow entry name error handling (#6409) [249eb1aaa]
• Fix cache command to check session cloudCachePath [a88e2cdf2]
• Fix cache command to use SysEnv for cloudcache path check (#6432) [771b8b60e]
• Fix cookie policy for Seqera Platform JWT token refresh (#6411) [c3959cfc3]
• Fix CVE-2025-55163 in nf-google plugin [7d7061797]
• Fix default fields in trace config (#6403) [3eddfad68]
• Fix pod log warning with Fusion enabled (#6449) [8c78b3126]
• Fix SIGTERM forwarding in AWS Batch jobs (#6414) [abbef79b7]
• Fix "Strings must not be null" error message (#6404) [24314b112]
• Fix unstage controls in command.run when using storeDir (#6364) [a5756da3e]
• Generate plugin spec (#6361) [ed6bb6037]
• Get exit code from pod to manage OOM in k8s (#6442) [f258a758e]
• Limit S3 concurrent downloads to fix Java Heap OOM (#6402) [fd71d0e8c]
• Update Gradle build system to version 9.1.0 (#6418) [e2bb2f083]
• Bump Google Cloud libraries to latest versions (#6438) [59a63f1ae]
• Bump nextflow-gradle-plugin version 1.0.0-beta.10 [812ed7f9f]
• Bump nf-amazon@3.3.0 [3561c26e9]
• Bump nf-azure@1.20.1 [fae3c2d58]
• Bump nf-codecommit@0.5.0 [91514a6f6]
• Bump nf-google@1.23.1 [153745a16]
• Bump nf-k8s@1.2.1 [c4f4eca9b]
• Bump nf-tower@1.16.0 [ef9110407]
• Bump nf-wave@1.16.0 [be01d3f96]

25.08.0-edge - 14 Sep 2025

• Add Claude Code GitHub Action integration (#6389) [1073a1da]
• Add Value type for dataflow values (value channels) (#6372) [8de2339e]
• Add descriptions to plugin MANIFEST.MF files (#6348) [d558ee33]
• Add null checks in TowerClient onFlowComplete method (#6384) [de968f03]
• Add plugins redirects (#6385) [3fb8a586]
• Add test for prefetchMetadata call in pullPlugins method (#6396) [a5c19b89]
• Add Type annotations (#6278) [0008707e]
• Fix CLI param override in strict config parser (#6377) [e146b412]
• Fix GString equality checks with String (#6330) [01e18883]
• Fix GitHub Actions commit message parsing to use only first line [5bc91622]
• Fix NPE when contributors omit contribution field in manifest (#6383) [dd2154ca]
• Fix Platorm refresh token handling [ba78ef74]
• Fix duplicate page and redirects in docs (#6386) [efba138f]
• Fix false warning for map config options (#6359) [872d124c]
• Fix groupTuple operator to handle GString vs String keys consistently (#6400) [206cc015]
• Fix incorrect spelling in docs (#6336) [00150f2a]
• Fix null reference error in workflow output (#6374) [d1f43c5d]
• Fix typo in task config eval (#6392) [e60978f4]
• Implement Process Execution with Command-Line Parameter Mapping (#6381) [experimental] [6d5a0bd0]
• Improve secret loading documentation and rename ConfigNullProvider to EmptySecretProvider [9e4c975a]
• Minor TowerClient improment (#6387) [d7436674]
• New executor for Fujitsu Technical Computing Suite (TCS) (#5928) [dd87b2fb]
• Preserve method parameter names in nf-lang JAR (#6355) [83160d66]
• Refactor Wave and Tower client to use lib-httpx library (#6354) [148a8a13]
• Replace custom JWT refresh logic with standardized HxClient (#6398) [c68c1e9e]
• Replace custom retry strategy with HxClient in RepositoryProvider (#6351) [af8ba8c8]
• Simplify plugin download implementation (#6349) [a3db0f88]
• Support standard environment variables for ANSI terminal output (#6362) [ede13441]
• Update core plugins to use Nextflow Gradle plugin (#6379) [a7e4ea86]
• Warn when file() matches a collection of files (#5507) [726bf484]
• Workflow params (#5929) [876d8052]
• Bump netty deps to version 4.1.124.Final [9e8d5969]

25.07.0-edge - 15 Aug 2025

• Add -template option to plugin create command and improve class name normalization (#6334) [c2c879d7]
• Add read permissions to nextflow launcher (#6288) [3614aea1]
• Add support for Bitbucket API tokens instead of access tokens (#6337) [1d73b87f]
• Add token support for BitBucket, Gitea and Gitlab repository providers (#6212) [9d8943e1]
• Add version, kind, and spec to lineage schema (#6075) [63286135]
• Add warning for Azure Batch lowPriority pools (#6261) [a32fd50c]
• Add Workflow onComplete and onError sections (#6275) [4fd97b9e]
• Add custom date time format support with configurable NXF_DATE_FORMAT (#6013) [163cd37b]
• BREAKING: Improve eval output hash with semantic names instead of raw commands (#6346) [d86be1a1]
• Fix Fail if splitFastq receives incomplete record (#6268) [0869a34a]
• Fix AWS transfer manager anonymous fallback (#6296) [ed5c99e1]
• Fix Azure Batch startTask concatenation issue (#6300) (#6305) [81d5c0dc]
• Fix AzureRepositoryProvider readBytes operation (#6286) [f6eb2f71]
• Fix CSV writer with empty list (#6333) [46ae10df]
• Fix ExecutorRetryConfig null pointer exception [ae661026]
• Fix Job arrays exceeding queue size limit (#5920) (#6345) [66abf249]
• Fix NPE in GoogleBatchMachineTypeSelector when spotPrice is null [a797a795]
• Fix Reset terminal color after lint success/failure message (#6323) [17b05bae]
• Fix bug in DefaultObserverFactory (#6259) [bec4bf7a]
• Fix bug with workflow output index file (#6328) [fa972305]
• Fix bugs with workflow output and lineage (#6254) [21a64705]
• Fix explicit it closure parameter (#6276) [99f9edf1]
• Fix formatting of channel factories (#6282) [f73f87b2]
• Fix new plugins registry download when OCI repositories require tokens (#6303) [12fbef34]
• Fix silent failure when downloading a directory with AWS SDK v2 (#6266) [2d76d8f0]
• Fix submitted count when aborting submitted tasks (#6281) [d0d3e100]
• Fix typos (#6291) [18c278b9]
• Fix error_action typo (#6283) [cc5a9c98]
• Fix GitlabRepositoryProvider now handles leading slashes for content URLs (#6284) [b7fa6f4e]
• Fix Invoke workflow complete handler on all workflow errors (#4299) [9d246154]
• Fix Improve Fusion license error message (#6313) [c3f397ea]
• Migration guide for workflow outputs (#6162) [9a4f79d5]
• Move AST transforms to nf-lang (#6247) [824dabbb]
• Register fully-qualified process names at compile-time (#6312) [9a70cdbb]
• Remove warning on missing config [14be407a]
• Rephrase nf-core extension pack description (#6273) [1446e542]
• Unify nf-lang config scopes with runtime classes (#6271) [bfa67ca3]
• Update AWS Java SDK v2 guide [#6269] [4a61e283]
• Update Azure and AWS deps (#6343) [ff00e2de]
• Update Gitea provider to gitea.com as default server (#6285) [cbfa2323]
• Update changelog [e2e prod] [b48c0698]
• Update nf-codecommit to AWS SDK v2 with corrected test (#6293) [1557a91a]
• Update standard types docs (#6329) [a76b7604]
• Update to plugin registry V1 (#6316) [9b1d1b6d]
• Update trace observers to V2 (#6257) [544b8c47]
• Bump groovy 4.0.28 (#6304) [a468f8ef]
• Bump netty-codec-http2:4.1.124.Final [7e690b44]
• Bump nextflow registry as default (#6339) [eaf1048f]
• Bump org.apache.commons:commons-lang3 from 3.12.0 to 3.18.0 (#6272) [b8ccddb5]
• Bump nf-wave@1.14.1 [5ee40f0e]
• Bump nf-tower@1.14.0 [fe399deb]
• Bump nf-k8s@1.1.1 [821f6996]
• Bump nf-google@1.22.2 [9a4e5795]
• Bump nf-codecommit@0.3.0 [3ec9e583]
• Bump nf-azure@1.19.0 [8a7e0507]
• Bump nf-amazon@3.1.0 [2fb0f136]

25.06.0-edge - 6 Jul 2025

• Add Git response max length check (#6190) [098fe84f]
• Add docker.registryOverride option (#6205) [e26abe4f]
• Add namespaces to nf-lang (#6176) [c839799b]
• Add support for Bitbucket API token (#6209) [f711f24e]
• Fix AWS NIO tests [069653dd]
• Fix JWT token refresh to Fusion validation request (#6231) [95dfdafd]
• Fix Apptainer and singularity --no-https option (#6216) [66ead2c6]
• Fix class not found exception Google Life science executor (#6193) [7bfb9358]
• Fix false error on nested closure in config process directive (#6203) [481c773b]
• Fix false error when using stdin/stdout in a tuple (#6219) [5d7f12ce]
• Fix false warning in config schema validator (#6240) [4e55ceeb]
• Fix http response err message [1f05451f]
• Fix mamba env create stalls at prompt [e7c93791]
• Fix null reference error in lint command (#6202) [3e1837e6]
• Fix readBytes for non-GitHub providers (#6243) [fa79c12c]
• Fix replace List.getFirst with List.get(0) for compatibility [83428ee2]
• Fix same Conda env is re-created for same module (#6166) [b46f01f9]
• Fix stack overflow error with workflow metadata (#5988) [9d50c495]
• Fix Maven publish with aws credentials [34d64ab3]
• Implement retry strategy for Git repository provider (#6195) [0f922826]
• Implement unordered directory hash (#6197) [a0eeed8d]
• Minor Azure Batch disk slot calculation demoted to debug (#6234) [c65955ce]
• Remove deprecated GsonHelper class [700faddb]
• Remove deprecated nexus-staging plugin [68b449bb]
• Rename IncludeModuleNode to IncludeEntryNode (#6217) [1f456d9c]
• Replace URLConnection with HttpClient (#6188) [d1e6836e]
• Return null result when repository provider has not auth [9d7fd9fc]
• Unwrap Failsafe exception cause in Wave client [0cb39df5]
• Update Google dependencies (#6229) [8bd42acb]
• Update stalebot (#6228) [27174df3]
• Update Wave retryPolicy default values (#6222) [b8069a58]
• Upgrade AWS instructions to AL2023 (#6183) [ed407095]
• Upgrade to AWS Java SDK v2 (#6165) [fc99b447]
• Upload Google Batch log on task exit (#6226) [78d9f473]
• Bump Google instance type for testing [bde9ef1b]
• Bump Logback version 1.5.18 [e3d5cedd]
• Bump Slf4j version 2.0.17 [93199e09]
• Bump gson version 2.13.1 [ab8e36a2]
• Bump nf-wave@1.14.0 [71ecf264]
• Bump nf-tower@1.13.0 [53d1bfb4]
• Bump nf-google@1.22.1 [cdf56d14]
• Bump nf-azure@1.18.0 [fc514062]
• Bump nf-amazon@3.0.0 [ffe699bd]

25.05.0-edge - 2 Jun 2025

• Add Failsafe retry mechanism in K8s (#6083) [9e675c6a]
• Add Platform info to Fusion license (#6142) [75f1bc52]
• Add support for Azure Managed identities on Azure worker nodes with Fusion (#6118) [37981a5f]
• Add support for container build compression (#5964) [daeefa0c]
• Deprecated condaFile attribute [9e52b2ad]
• Fix bug in generated Groovy code (#6082) [f0620656]
• Fix default imports in included configs (#6096) [8f790615]
• Fix variable checking in v2 config parser (#6097) [c3e9367b]
• Force overwritting to trace file (#6105) [b9dace93]
• Improve documentation of splitCsv operator (#6131) [f09ae8d7]
• Make RepositoryProvider readBytes public (#6138) [9221b112]
• Remove Az Fusion environment variable (#6143) [6c595eac]
• Remove deprecated spack options [4e5d32a3]
• Remove task attempt from hash list and add note (#6123) [9b48df4c]
• Return streams in Lineage search and subkeys methods (#6067) [e4af2308]
• Sort linter errors/warnings by source location (#6098) [7c52fafb]
• Sunset the Google LS executor (#6070) [06e0d426]
• Bump Groovy to version 4.0.27 (#6125) [258e1790]
• Bump jgit:7.1.1.202505221757-r [16b88aca]
• Bump nf-wave@1.13.0 [ab1d2dfe]
• Bump nf-tower@1.12.0 [d4d97dfc]
• Bump nf-k8s@1.1.0 [14eb7892]
• Bump nf-google@1.22.0 [0f6498f1]
• Bump nf-azure@1.17.0 [0b491840]