Skip to main content

19 posts tagged with "nextflow"

View All Tags

Nextflow 25.11.0-edge

Feature updates and improvements​

Google Batch​

  • Added Google Batch LogsPolicy PATH option for logging to GCS by @dglazer in #6431
  • Optimized exit code handling by relying on scheduler status for successful executions by @jorgee in #6484

Kubernetes​

  • Changed log level from warn1 to debug1 for K8s Job Pod Warnings by @BioWilko in #6523

Language features​

  • Removed unnecessary runtime checks with strict syntax by @bentsherman in #6539

Plugins​

  • Allowed pre-existing write-protected plugins directory to be used by @bentsherman in #6594
  • Updated migration timeline for plugin registry by @bentsherman in #6543
  • Added admonition to clarify plugin provider and org by @christopher-hakkaart in #6536

Configuration​

  • Added default value to Apptainer pull timeout config parameter by @jorgee in #6534
  • Added test case for printing config with nested includes by @Lehmann-Fabian in #2498
  • Added external links via config by @ewels in #6563

Fusion​

  • Marked Fusion.tags as supported only for S3 by @fntlnz in #6601

General​

  • Improved error message for invalid accelerator resource by @bentsherman in #6585
  • Improved error message for invalid contribution type in manifest contributors by @bentsherman in #6593
  • Moved task error formatting logic into separate class by @bentsherman in #6551
  • Removed unused BatchHelper class by @pditommaso in #6547
  • Removed wiremock-groovy dependency and updated tests using this dependency by @jorgee in #6611
  • Updated bundled Docker runtime to 19.03.15 by @yarikoptic in #6565
  • Updated trace table columns in Reports page by @JustinBellavance in #6483
  • Upgraded from Apache Commons Lang 2.6 to Commons Lang3 3.18.0 by @pditommaso in #6511
  • Added admonition to inputs and index words by @christopher-hakkaart in #6461
  • Improved task previousTrace documentation by @rnaidu in #6538
  • Updated feature flags page by @christopher-hakkaart in #6504
  • Updated task directives by @christopher-hakkaart in #6506

Dependencies​

  • Bumped Fusion to version 2.5 by @jordeu in #6557
  • Bumped Gradle 9.2.0 by @pditommaso in 2657524
  • Bumped groovy 4.0.29 by @pditommaso in #6510
  • Bumped logback to version 1.5.20 by @pditommaso in 462eec5
  • Bumped org.bouncycastle:bcpkix-jdk18on from 1.78.1 to 1.79 by @dependabot in #6537
  • Bumped nf-amazon@3.5.0 by @pditommaso in 17cc2b0
  • Bumped nf-azure@1.21.0 by @pditommaso in 0b56d2a
  • Bumped nf-google@1.24.0 by @pditommaso in 81a5a05
  • Bumped nf-k8s@1.3.0 by @pditommaso in 7146011
  • Bumped nf-tower@1.18.0 by @pditommaso in 86da3b7
  • Bumped nf-wave@1.17.0 by @pditommaso in de02e8b

Bug fixes​

Kubernetes​

  • Fixed Do not delete K8s jobs when ttlSecondsAfterFinished is set by @bentsherman in #6597
  • Fixed K8sTaskHandlerTest method name typos by @pditommaso in bcf81d9

Fusion​

  • Fixed Fusion license JWT token refresh by reusing TowerClient by @jorgee in 498125d

S3​

  • Fixed incorrect AWS region when specifying a S3 regional endpoint by @jorgee in #6530
  • Fixed unordered completed parts in AWS multipart upload by @jorgee in #6560

Language features​

  • Fixed Invalid type error detection by @pditommaso in 9e3aeed
  • Fixed CSV splitter when skipping empty lines by @bentsherman in #6586
  • Fixed documentation of unique operator by @bentsherman in #6541
  • Fixed error with dynamic directives with named arguments by @bentsherman in #6550
  • Fixed false error with task ext blocks in strict syntax by @bentsherman in #6569
  • Fixed invalid cache write when cacheable split operation fails by @bentsherman in #6588
  • Fixed issue with optional workflow output by @bentsherman in #6519
  • Fixed issues with rsync stage-out mode by @bentsherman in #6587

Configuration​

  • Fixed false config validation warnings for process selectors by @bentsherman in #6542

Plugins​

  • Fixed Plugins.init() in run command to original location by @jorgee in #6568

General​

  • Fixed asset detection when item is not a sibling of the executed script by @DriesSchaumont in #6605
  • Fixed security vulnerabilities in org.json dependency by @pditommaso in c7161c2
  • Fixed TowerJsonGenerator thread-safety issue by @pditommaso in #6619
  • Fixed security vulnerabilities for wiremock by @jorgee in #6607
  • Fixed replace complete plotly bundle with smaller more specific one by @mashehu in #6527
  • Fixed stageFileEnabled flag to control .command.stage file creation by @pditommaso in #6618

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.11.0-edge

Nextflow 25.10.0

Feature updates and improvements​

Language features​

  • Added type checking utils by @bentsherman in #6482

Google Batch​

  • Prioritized Google Batch API exit codes with fallback to .exitcode file by @jorgee in #6498

S3​

  • Simplified S3 configuration options by @bentsherman in #6496

General​

  • Added publish-artifacts step to release process by @pditommaso in 75d8ebf
  • Showed workspace roles in 'auth status', tweaked error message on 403 by @ewels in #6497
  • Tracked remote input files in lineage by @jorgee in #6490

Dependencies​

  • Bumped nf-amazon@3.4.1 by @pditommaso in 0d5ced9
  • Bumped nf-google@1.23.3 by @pditommaso in e6c7652
  • Bumped nf-tower@1.17.1 by @pditommaso in 2069c97

Bug fixes​

AWS Batch​

  • Fixed no secrets in AWS Batch jobs by @jorgee in #6499

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.0

Nextflow 25.09.2-edge

Feature updates and improvements​

Language features​

  • Brought workflow outputs out of preview by @bentsherman in #6487
  • Typed processes by @bentsherman in #6368

Kubernetes​

  • Added .command.log redirection in K8s container command by @jorgee in #6455

S3​

  • Limited S3 client connections when using virtual threads by @jorgee in #6369

Plugins​

  • Improved plugin create confirmation prompt by @robsyme in #6473

Configuration​

  • Renamed config.schema package to config.spec by @bentsherman in #6485

General​

  • Added nextflow auth command for Seqera Platform authentication by @pditommaso in #6463
  • Added nextflow launch command by @jorgee in #6491
  • Improved release script validation by @pditommaso in 3e3a938
  • Migrated SraExplorer to use HxClient for HTTP operations by @pditommaso in #6467
  • Updated buildInfo on releaseInfo by @pditommaso in 46a8a2b

Bug fixes​

Language features​

  • Fixed false error with storeDir and val outputs by @bentsherman in #6408

Configuration​

  • Fixed e2e test infrastructure and added config.schema compatibility aliases by @pditommaso in #6495
  • Fixed false error for executor.jobName config option by @bentsherman in #6375

Plugins​

  • Fixed type casting in PluginSpec for ConfigScope by @pditommaso in #6469

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.09.2-edge

Nextflow 25.09.0-edge

Feature updates and improvements​

Language features​

  • Added support for comma-separated file paths in ProcessEntryHandler by @pditommaso in #6434
  • Added unit test for invalid workflow entry name error handling by @pditommaso in #6409

Plugins​

  • Added step to claim plugin in Gradle plugin migration docs by @christopher-hakkaart in #6450
  • Generated plugin spec by @bentsherman in #6361

General​

  • Added listDirectory traversal API to RepositoryProvider abstraction by @pditommaso in #6430
  • Added support for Java 25 by @pditommaso in #6419
  • Updated Gradle build system to version 9.1.0 by @pditommaso in #6418

Dependencies​

  • Bumped Google Cloud libraries to latest versions by @pditommaso in #6438
  • Bumped nextflow-gradle-plugin version 1.0.0-beta.10 by @pditommaso in 812ed7f
  • Bumped nf-amazon@3.3.0 by @pditommaso in 3561c26
  • Bumped nf-azure@1.20.1 by @pditommaso in fae3c2d
  • Bumped nf-codecommit@0.5.0 by @pditommaso in 91514a6
  • Bumped nf-google@1.23.1 by @pditommaso in 153745a
  • Bumped nf-k8s@1.2.1 by @pditommaso in c4f4eca
  • Bumped nf-tower@1.16.0 by @pditommaso in ef91104
  • Bumped nf-wave@1.16.0 by @pditommaso in be01d3f

Bug fixes​

AWS Batch​

  • Fixed SIGTERM forwarding in AWS Batch jobs by @jorgee in #6414

S3​

  • Limited S3 concurrent downloads to fix Java Heap OOM by @jorgee in #6402

Kubernetes​

  • Fixed pod log warning with Fusion enabled by @jorgee in #6449
  • Got exit code from pod to manage OOM in k8s by @jorgee in #6442

Google Cloud​

  • Fixed CVE-2025-55163 in nf-google plugin by @pditommaso in 7d70617

Configuration​

  • Fixed default fields in trace config by @bentsherman in #6403

General​

  • Fixed cache command to check session cloudCachePath by @pditommaso in a88e2cd
  • Fixed cache command to use SysEnv for cloudcache path check by @pditommaso in #6432
  • Fixed cookie policy for Seqera Platform JWT token refresh by @pditommaso in #6411
  • Fixed "Strings must not be null" error message by @bentsherman in #6404
  • Fixed unstage controls in command.run when using storeDir by @jorgee in #6364

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.09.0-edge

Nextflow 25.08.0-edge

Feature updates and improvements​

Language features​

  • Added Value type for dataflow values (value channels) by @bentsherman in #6372
  • Added Type annotations by @bentsherman in #6278
  • Implemented Process Execution with Command-Line Parameter Mapping [experimental] by @pditommaso in #6381
  • Workflow params by @bentsherman in #5929
  • Warned when file() matches a collection of files by @bentsherman in #5507

Plugins​

  • Added descriptions to plugin MANIFEST.MF files by @pditommaso in #6348
  • Added test for prefetchMetadata call in pullPlugins method by @pditommaso in #6396
  • Simplified plugin download implementation by @pditommaso in #6349
  • Updated core plugins to use Nextflow Gradle plugin by @bentsherman in #6379

Configuration​

  • Improved secret loading documentation and renamed ConfigNullProvider to EmptySecretProvider by @bentsherman in 9e4c975

General​

  • Added Claude Code GitHub Action integration by @pditommaso in #6389
  • Added null checks in TowerClient onFlowComplete method by @robsyme in #6384
  • Added plugins redirects by @christopher-hakkaart in #6385
  • Minor TowerClient improvement by @pditommaso in #6387
  • New executor for Fujitsu Technical Computing Suite (TCS) by @exthnet in #5928
  • Preserved method parameter names in nf-lang JAR by @bentsherman in #6355
  • Refactored Wave and Tower client to use lib-httpx library by @pditommaso in #6354
  • Replaced custom JWT refresh logic with standardized HxClient by @pditommaso in #6398
  • Replaced custom retry strategy with HxClient in RepositoryProvider by @pditommaso in #6351
  • Supported standard environment variables for ANSI terminal output by @ewels in #6362

Dependencies​

  • Bumped netty deps to version 4.1.124.Final by @pditommaso in 9e8d596

Bug fixes​

Language features​

  • Fixed GString equality checks with String by @bentsherman in #6330
  • Fixed groupTuple operator to handle GString vs String keys consistently by @pditommaso in #6400
  • Fixed null reference error in workflow output by @bentsherman in #6374

Configuration​

  • Fixed CLI param override in strict config parser by @bentsherman in #6377
  • Fixed false warning for map config options by @bentsherman in #6359
  • Fixed typo in task config eval by @bentsherman in #6392

General​

  • Fixed GitHub Actions commit message parsing to use only first line by @pditommaso in 5bc9162
  • Fixed NPE when contributors omit contribution field in manifest by @robsyme in #6383
  • Fixed Platform refresh token handling by @pditommaso in ba78ef7
  • Fixed duplicate page and redirects in docs by @christopher-hakkaart in #6386
  • Fixed incorrect spelling in docs by @christopher-hakkaart in #6336

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.08.0-edge

Nextflow 24.09.0-edge

Fusion​

  • Added Fusion version pinning info to Fusion config scope
  • Fixed Azure Fusion env misses credentials when no key or SAS provided

Wave​

  • Improved Wave build timeout handling

AWS Batch​

  • Added Platform workflow prefix in AWS Batch job names
  • Fixed AWS spot attempts with zero value

Configuration​

  • Fixed Inconsistency with camelCase and kebab-case config param
  • Included additional fields to manifest

General​

  • Added container tip in the task error report
  • Added support for Java 23
  • Fixed CI build taking only the commit msg header
  • Fixed XPath default de-serializer issue
  • Fixed failOnIgnore causes task monitor to stop submitting tasks
  • Fixed large mermaid diagrams
  • Removed mini from Flux submit command
  • Updated container handling with charliecloud
  • Updated Documentation structure
  • Updated nextflow install docs

Dependencies​

  • Bumped groovy 4.0.23 by @pditommaso in #5303
  • Bumped nf-wave@1.6.0 by @pditommaso in 179093d
  • Bumped nf-azure@1.10.0 by @pditommaso in 41d37fa
  • Bumped nf-amazon@2.9.0 by @pditommaso in e38980f

https://github.com/nextflow-io/nextflow/releases/tag/v24.09.0-edge

Nextflow 24.04.4

General​

  • Fixed parsing of shm-size containerOptions

AWS Batch​

  • Fixed aws logs group name

Azure Batch​

  • Updated Azure batch deps

Dependencies​

  • Bumped nf-wave@1.4.2-patch1 by @pditommaso in 19a7272
  • Bumped nf-codecommit@0.2.1 by @pditommaso in f2bcce9
  • Bumped nf-azure@1.6.1 by @pditommaso in 0ea1f10
  • Bumped nf-amazon@2.5.3 by @pditommaso in b13b554
  • Bumped wave-api to 0.11.1 by @pditommaso in 87828af
  • Bumped amazon sdk to version 1.12.766 by @pditommaso in 5ce42b7
  • Bumped pf4j to version 3.12.0 by @pditommaso in 1a8f086
  • Bumped jgit to version 6.10.0 by @pditommaso in cc2ccd8

https://github.com/nextflow-io/nextflow/releases/tag/v24.04.4