chore(deps): update dependency nextflow-io/nextflow to v25

[renovate]

WARNING

• I have made sure to update the singularity and conda images

This PR contains the following updates:

Package	Update	Change
nextflow-io/nextflow	major	24.10.2 -> 25.10.0

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Release Notes

nextflow-io/nextflow (nextflow-io/nextflow)

v25.10.0: Version 25.10.0

Compare Source

• Add publish-artifacts step to release process [75d8ebf]
• Add type checking utils (#​6482) [3e9a2c0]
• Fix no secrets in AWS Batch jobs (#​6499) [c76c325]
• Prioritize Google Batch API exit codes with fallback to .exitcode file (#​6498) [6ac2efc]
• Show workspace roles in 'auth status', tweak error message on 403 (#​6497) [0633d90]
• Simplify S3 configuration options (#​6496) [0b7f180]
• Track remote input files in lineage (#​6490) [b0660ca]
• Bump nf-amazon@​3.4.1 [0d5ced9]
• Bump nf-google@​1.23.3 [e6c7652]
• Bump nf-tower@​1.17.1 [2069c97]

25.09.2-edge - 21 Oct 2025

• Add .command.log redirection in K8s container command (#​6455) [e6eed79]
• Add nextflow auth command for Seqera Platform authentication (#​6463) [bedf02a]
• Add nextflow launch command (#​6491) [7c8fa3d]
• Bring workflow outputs out of preview (#​6487) [c41677b]
• Fix e2e test infrastructure and add config.schema compatibility aliases (#​6495) [d3cee2b]
• Fix false error for executor.jobName config option (#​6375) [81ae62b]
• Fix false error with storeDir and val outputs (#​6408) [1aa8c44]
• Fix type casting in PluginSpec for ConfigScope (#​6469) [b00644c]
• Improve plugin create confirmation prompt (#​6473) [215925c]
• Improve release script validation [3e3a938]
• Limit S3 client connections when using virtual threads (#​6369) [295c60b]
• Migrate SraExplorer to use HxClient for HTTP operations (#​6467) [84e3e78]
• Rename config.schema package to config.spec (#​6485) [ef0d2d6]
• Typed processes (#​6368) [30f3c3c]
• Update buildInfo on releaseInfo [46a8a2b]

25.09.1-edge - 9 Oct 2025

• Improve build metadata generation and validation [6022537]
• Fix Missing static type definition [67a5320]
• Add rnaseq-nf tutorial (#​6440) [a830125]

25.09.0-edge - 8 Oct 2025

• Add listDirectory traversal API to RepositoryProvider abstraction (#​6430) [1449fdf]
• Add step to claim plugin in Gradle plugin migration docs (#​6450) [3b70900]
• Add support for comma-separated file paths in ProcessEntryHandler (#​6434) [fe62764]
• Add support for Java 25 (#​6419) [dc8d474]
• Add unit test for invalid workflow entry name error handling (#​6409) [249eb1a]
• Fix cache command to check session cloudCachePath [a88e2cd]
• Fix cache command to use SysEnv for cloudcache path check (#​6432) [771b8b6]
• Fix cookie policy for Seqera Platform JWT token refresh (#​6411) [c3959cf]
• Fix CVE-2025-55163 in nf-google plugin [7d70617]
• Fix default fields in trace config (#​6403) [3eddfad]
• Fix pod log warning with Fusion enabled (#​6449) [8c78b31]
• Fix SIGTERM forwarding in AWS Batch jobs (#​6414) [abbef79]
• Fix "Strings must not be null" error message (#​6404) [24314b1]
• Fix unstage controls in command.run when using storeDir (#​6364) [a5756da]
• Generate plugin spec (#​6361) [ed6bb60]
• Get exit code from pod to manage OOM in k8s (#​6442) [f258a75]
• Limit S3 concurrent downloads to fix Java Heap OOM (#​6402) [fd71d0e]
• Update Gradle build system to version 9.1.0 (#​6418) [e2bb2f0]
• Bump Google Cloud libraries to latest versions (#​6438) [59a63f1]
• Bump nextflow-gradle-plugin version 1.0.0-beta.10 [812ed7f]
• Bump nf-amazon@​3.3.0 [3561c26]
• Bump nf-azure@​1.20.1 [fae3c2d]
• Bump nf-codecommit@​0.5.0 [91514a6]
• Bump nf-google@​1.23.1 [153745a]
• Bump nf-k8s@​1.2.1 [c4f4eca]
• Bump nf-tower@​1.16.0 [ef91104]
• Bump nf-wave@​1.16.0 [be01d3f]

25.08.0-edge - 14 Sep 2025

• Add Claude Code GitHub Action integration (#​6389) [1073a1d]
• Add Value type for dataflow values (value channels) (#​6372) [8de2339]
• Add descriptions to plugin MANIFEST.MF files (#​6348) [d558ee3]
• Add null checks in TowerClient onFlowComplete method (#​6384) [de968f0]
• Add plugins redirects (#​6385) [3fb8a58]
• Add test for prefetchMetadata call in pullPlugins method (#​6396) [a5c19b8]
• Add Type annotations (#​6278) [0008707]
• Fix CLI param override in strict config parser (#​6377) [e146b41]
• Fix GString equality checks with String (#​6330) [01e1888]
• Fix GitHub Actions commit message parsing to use only first line [5bc9162]
• Fix NPE when contributors omit contribution field in manifest (#​6383) [dd2154c]
• Fix Platorm refresh token handling [ba78ef7]
• Fix duplicate page and redirects in docs (#​6386) [efba138]
• Fix false warning for map config options (#​6359) [872d124]
• Fix groupTuple operator to handle GString vs String keys consistently (#​6400) [206cc01]
• Fix incorrect spelling in docs (#​6336) [00150f2]
• Fix null reference error in workflow output (#​6374) [d1f43c5]
• Fix typo in task config eval (#​6392) [e60978f]
• Implement Process Execution with Command-Line Parameter Mapping (#​6381) [experimental] [6d5a0bd]
• Improve secret loading documentation and rename ConfigNullProvider to EmptySecretProvider [9e4c975]
• Minor TowerClient improment (#​6387) [d743667]
• New executor for Fujitsu Technical Computing Suite (TCS) (#​5928) [dd87b2f]
• Preserve method parameter names in nf-lang JAR (#​6355) [83160d6]
• Refactor Wave and Tower client to use lib-httpx library (#​6354) [148a8a1]
• Replace custom JWT refresh logic with standardized HxClient (#​6398) [c68c1e9]
• Replace custom retry strategy with HxClient in RepositoryProvider (#​6351) [af8ba8c]
• Simplify plugin download implementation (#​6349) [a3db0f8]
• Support standard environment variables for ANSI terminal output (#​6362) [ede1344]
• Update core plugins to use Nextflow Gradle plugin (#​6379) [a7e4ea8]
• Warn when file() matches a collection of files (#​5507) [726bf48]
• Workflow params (#​5929) [876d805]
• Bump netty deps to version 4.1.124.Final [9e8d596]

25.07.0-edge - 15 Aug 2025

• Add -template option to plugin create command and improve class name normalization (#​6334) [c2c879d]
• Add read permissions to nextflow launcher (#​6288) [3614aea]
• Add support for Bitbucket API tokens instead of access tokens (#​6337) [1d73b87]
• Add token support for BitBucket, Gitea and Gitlab repository providers (#​6212) [9d8943e]
• Add version, kind, and spec to lineage schema (#​6075) [6328613]
• Add warning for Azure Batch lowPriority pools (#​6261) [a32fd50]
• Add Workflow onComplete and onError sections (#​6275) [4fd97b9]
• Add custom date time format support with configurable NXF_DATE_FORMAT (#​6013) [163cd37]
• BREAKING: Improve eval output hash with semantic names instead of raw commands (#​6346) [d86be1a]
• Fix Fail if splitFastq receives incomplete record (#​6268) [0869a34]
• Fix AWS transfer manager anonymous fallback (#​6296) [ed5c99e]
• Fix Azure Batch startTask concatenation issue (#​6300) (#​6305) [81d5c0d]
• Fix AzureRepositoryProvider readBytes operation (#​6286) [f6eb2f7]
• Fix CSV writer with empty list (#​6333) [46ae10d]
• Fix ExecutorRetryConfig null pointer exception [ae66102]
• Fix Job arrays exceeding queue size limit (#​5920) (#​6345) [66abf24]
• Fix NPE in GoogleBatchMachineTypeSelector when spotPrice is null [a797a79]
• Fix Reset terminal color after lint success/failure message (#​6323) [17b05ba]
• Fix bug in DefaultObserverFactory (#​6259) [bec4bf7]
• Fix bug with workflow output index file (#​6328) [fa97230]
• Fix bugs with workflow output and lineage (#​6254) [21a6470]
• Fix explicit it closure parameter (#​6276) [99f9edf]
• Fix formatting of channel factories (#​6282) [f73f87b]
• Fix new plugins registry download when OCI repositories require tokens (#​6303) [12fbef3]
• Fix silent failure when downloading a directory with AWS SDK v2 (#​6266) [2d76d8f]
• Fix submitted count when aborting submitted tasks (#​6281) [d0d3e10]
• Fix typos (#​6291) [18c278b]
• Fix error_action typo (#​6283) [cc5a9c9]
• Fix GitlabRepositoryProvider now handles leading slashes for content URLs (#​6284) [b7fa6f4]
• Fix Invoke workflow complete handler on all workflow errors (#​4299) [9d24615]
• Fix Improve Fusion license error message (#​6313) [c3f397e]
• Migration guide for workflow outputs (#​6162) [9a4f79d]
• Move AST transforms to nf-lang (#​6247) [824dabb]
• Register fully-qualified process names at compile-time (#​6312) [9a70cdb]
• Remove warning on missing config [14be407]
• Rephrase nf-core extension pack description (#​6273) [1446e54]
• Unify nf-lang config scopes with runtime classes (#​6271) [bfa67ca]
• Update AWS Java SDK v2 guide #​6269 [4a61e28]
• Update Azure and AWS deps (#​6343) [ff00e2d]
• Update Gitea provider to gitea.com as default server (#​6285) [cbfa232]
• Update changelog [e2e prod] [b48c069]
• Update nf-codecommit to AWS SDK v2 with corrected test (#​6293) [1557a91]
• Update standard types docs (#​6329) [a76b760]
• Update to plugin registry V1 (#​6316) [9b1d1b6]
• Update trace observers to V2 (#​6257) [544b8c4]
• Bump groovy 4.0.28 (#​6304) [a468f8e]
• Bump netty-codec-http2:4.1.124.Final [7e690b4]
• Bump nextflow registry as default (#​6339) [eaf1048]
• Bump org.apache.commons:commons-lang3 from 3.12.0 to 3.18.0 (#​6272) [b8ccddb]
• Bump nf-wave@​1.14.1 [5ee40f0]
• Bump nf-tower@​1.14.0 [fe399de]
• Bump nf-k8s@​1.1.1 [821f699]
• Bump nf-google@​1.22.2 [9a4e579]
• Bump nf-codecommit@​0.3.0 [3ec9e58]
• Bump nf-azure@​1.19.0 [8a7e050]
• Bump nf-amazon@​3.1.0 [2fb0f13]

25.06.0-edge - 6 Jul 2025

• Add Git response max length check (#​6190) [098fe84]
• Add docker.registryOverride option (#​6205) [e26abe4]
• Add namespaces to nf-lang (#​6176) [c839799]
• Add support for Bitbucket API token (#​6209) [f711f24]
• Fix AWS NIO tests [069653d]
• Fix JWT token refresh to Fusion validation request (#​6231) [95dfdaf]
• Fix Apptainer and singularity --no-https option (#​6216) [66ead2c]
• Fix class not found exception Google Life science executor (#​6193) [7bfb935]
• Fix false error on nested closure in config process directive (#​6203) [481c773]
• Fix false error when using stdin/stdout in a tuple (#​6219) [5d7f12c]
• Fix false warning in config schema validator (#​6240) [4e55cee]
• Fix http response err message [1f05451]
• Fix mamba env create stalls at prompt [e7c9379]
• Fix null reference error in lint command (#​6202) [3e1837e]
• Fix readBytes for non-GitHub providers (#​6243) [fa79c12]
• Fix replace List.getFirst with List.get(0) for compatibility [83428ee]
• Fix same Conda env is re-created for same module (#​6166) [b46f01f]
• Fix stack overflow error with workflow metadata (#​5988) [9d50c49]
• Fix Maven publish with aws credentials [34d64ab]
• Implement retry strategy for Git repository provider (#​6195) [0f92282]
• Implement unordered directory hash (#​6197) [a0eeed8]
• Minor Azure Batch disk slot calculation demoted to debug (#​6234) [c65955c]
• Remove deprecated GsonHelper class [700fadd]
• Remove deprecated nexus-staging plugin [68b449b]
• Rename IncludeModuleNode to IncludeEntryNode (#​6217) [1f456d9]
• Replace URLConnection with HttpClient (#​6188) [d1e6836]
• Return null result when repository provider has not auth [9d7fd9f]
• Unwrap Failsafe exception cause in Wave client [0cb39df]
• Update Google dependencies (#​6229) [8bd42ac]
• Update stalebot (#​6228) [27174df]
• Update Wave retryPolicy default values (#​6222) [b8069a5]
• Upgrade AWS instructions to AL2023 (#​6183) [ed40709]
• Upgrade to AWS Java SDK v2 (#​6165) [fc99b44]
• Upload Google Batch log on task exit (#​6226) [78d9f47]
• Bump Google instance type for testing [bde9ef1]
• Bump Logback version 1.5.18 [e3d5ced]
• Bump Slf4j version 2.0.17 [93199e0]
• Bump gson version 2.13.1 [ab8e36a]
• Bump nf-wave@​1.14.0 [71ecf26]
• Bump nf-tower@​1.13.0 [53d1bfb]
• Bump nf-google@​1.22.1 [cdf56d1]
• Bump nf-azure@​1.18.0 [fc51406]
• Bump nf-amazon@​3.0.0 [ffe699b]

25.05.0-edge - 2 Jun 2025

• Add Failsafe retry mechanism in K8s (#​6083) [9e675c6]
• Add Platform info to Fusion license (#​6142) [75f1bc5]
• Add support for Azure Managed identities on Azure worker nodes with Fusion (#​6118) [37981a5]
• Add support for container build compression (#​5964) [daeefa0]
• Deprecated condaFile attribute [9e52b2a]
• Fix bug in generated Groovy code (#​6082) [f062065]
• Fix default imports in included configs (#​6096) [8f79061]
• Fix variable checking in v2 config parser (#​6097) [c3e9367]
• Force overwritting to trace file (#​6105) [b9dace9]
• Improve documentation of splitCsv operator (#​6131) [f09ae8d]
• Make RepositoryProvider readBytes public (#​6138) [9221b11]
• Remove Az Fusion environment variable (#​6143) [6c595ea]
• Remove deprecated spack options [4e5d32a]
• Remove task attempt from hash list and add note (#​6123) [9b48df4]
• Return streams in Lineage search and subkeys methods (#​6067) [e4af230]
• Sort linter errors/warnings by source location (#​6098) [7c52faf]
• Sunset the Google LS executor (#​6070) [06e0d42]
• Bump Groovy to version 4.0.27 (#​6125) [258e179]
• Bump jgit:7.1.1.202505221757-r [16b88ac]
• Bump nf-wave@​1.13.0 [ab1d2df]
• Bump nf-tower@​1.12.0 [d4d97df]
• Bump nf-k8s@​1.1.0 [14eb789]
• Bump nf-google@​1.22.0 [0f6498f]
• Bump nf-azure@​1.17.0 [0b49184]

v24.10.9: Version 24.10.9

Compare Source

• Fix JWT token refresh to Fusion validation request (#​6231) [716468d]
• Disable latest upload [35b0c5c]
• Bump nf-tower@​1.9.3-patch2 [4ed4083]

v24.10.8: Version 24.10.8

Compare Source

• Add Fusion license validation [02b4dd7]
• Bump nf-wave@​1.7.5-patch1 [cf6af9c]
• Bump nf-tower@​1.9.3-patch1 [bdef217]

v24.10.6: Version 24.10.6

Compare Source

• Add support for Fusion Snapshots (#​5954) [76a997a]
• Bump nf-wave@​1.7.5 [3ddf16f]
• Bump nf-amazon@​2.9.3 [ccf672f]

v24.10.5: Version 24.10.5

Compare Source

• Improve Google Batch executor stability and error handling (#​5690) [1a9e8bf]
• Fix Mount input file buckets in task arrays for Google Batch (#​5739) [0d98442]
• Fix Google Batch task array causes process to fail (#​5780) [d4c1ba1]
• Fixing bug when execution with stub and no stub defined (#​5473) [ba5ab06]
• Fix Conda directive is not honoured by task array (#​5704) [63124eb]
• Fix Use unbound queue for transfer thread pool (#​5700) [d57a85d]
• Bump nf-google@​1.15.4 [ee9c1fd]

v24.10.4: Version 24.10.4

Compare Source

• Fix CLI params normalization (#​5661) [42a9d8a]
• Fix azure repos when clone URL is used (#​5667) [eb092c9]
• Fix Prevent the use existing work dir (#​5682) [7ed233e]

v24.10.3: Version 24.10.3

Compare Source

• Fix Google Batch hang when internal error during scheduling (#​5567) [79374c5]
• Fixing getRepositoryUrl when project name is not provided (#​5560) [9910cec]
• Bump nf-google@​1.15.3 [e80ded3]

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