16 posts tagged with "nextflow"

Feature updates and improvements​

General​

• Added OSC 8 hyperlinks to task hashes in progress output by @bentsherman in #6799
• Improved documentation of workflow outputs by @bentsherman in #6822

Dependencies​

• Bumped ch.qos.logback@1.5.26 to fix false version mismatch warning in shadow JAR by @pditommaso in 0b97f4a
• Bumped ch.qos.logback@1.5.25 (CVE-2026-1225) by @pditommaso in 97dec3a
• Bumped com.gradleup.shadow@9.3.1 (CVE-2025-68161) by @pditommaso in d31e6ed

Bug fixes​

Language features​

• Fixed listDirectory() to follow symbolic links by @bentsherman in #6821

General​

• Fixed JGit resources not being closed in CLI commands by @pditommaso in #6795

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.01.1-edge

Feature updates and improvements​

Language features​

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

AWS Batch​

• Added isCompleted check in getNumSpotInterruptions by @munishchouhan in #6806

Dependencies​

• Bumped nf-amazon@3.4.4 by @pditommaso
• Bumped nf-google@1.23.5 by @pditommaso
• Bumped nf-tower@1.17.5 by @pditommaso

Bug fixes​

Language features​

• Fixed false error with optional param by @bentsherman in #6811
• Fixed false error with multi-line tuple assignment in v2 parser by @bentsherman in #6786
• Fixed false error in v2 parser when including config file from http url by @bentsherman in #6753

General​

• Fixed LogsCheckpoint thread blocking shutdown for up to 90 seconds by @pditommaso in #6787

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.4

Feature updates and improvements​

Language features​

• Allowed collection-type params to be loaded from files by @bentsherman in #6675
• Enabled v2 syntax parser by default by @bentsherman in #6643
• Improved config syntax errors by @bentsherman in #6721
• Improved error message for invalid config statements by @bentsherman in #6804
• Improved error messages for workflow outputs by @bentsherman in #6785
• Moved task hashing logic to TaskHasher class by @bentsherman in #6572

AWS Batch​

• Added aws.batch.forceGlacierTransfer config option by @munishchouhan in #6700

Google Batch​

• Refactored GoogleBatchTaskHandler.newSubmitRequest for reduced complexity by @pditommaso in #6687

Kubernetes​

• Added time-based caching for K8sConfig.getClient() by @munishchouhan in #6742

Configuration​

• Supported multiple config option types in config spec by @bentsherman in #6720

General​

• Added accelerator request to trace record by @munishchouhan in #6703
• Added CloudCacheConfig to register cloudcache config options by @pditommaso in #6774
• Added markdown output mode to lint command by @ewels in #6715
• Added missing provider credentials when updating the bare repo in multi-revision assets by @jorgee in #6698
• Added warning stats to lint summary output by @ewels in #6714
• Added workflow manifest metadata to execution report by @bentsherman in #6689
• Detected conda explicit files by content instead of extension by @bentsherman in #6713
• Excluded nf-test.config from lint by default by @ewels in #6716
• Used conda-forge and bioconda channels by default by @Midnighter in #5423

Dependencies​

• Bumped Groovy to 4.0.30 by @pditommaso in #6747
• Bumped Spock 2.4 by @pditommaso in #6681

Bug fixes​

Language features​

• Fixed caching of task ext properties with the strict parser by @bentsherman in #6696
• Fixed compiler error in v2 parser with enums by @bentsherman in #6781
• Fixed different task hash with v2 parser by @bentsherman in #6789
• Fixed false error in v2 parser when including config file from http url by @bentsherman in #6753
• Fixed false error with multi-line tuple assignment in v2 parser by @bentsherman in #6786
• Fixed false error with optional param by @bentsherman in #6811
• Fixed issue with topic file emissions in typed processes by @bentsherman in #6688
• Fixed params inclusion across modules in v2 parser by @bentsherman in #6766
• Fixed resolution of nested Groovy class in v2 parser by @bentsherman in #6744
• Fixed type inference in v2 ConfigDsl by @bentsherman in #6800

AWS Batch​

• Fixed AWS Batch spot instance detection by @munishchouhan in #6722
• Fixed isCompleted check in getNumSpotInterruptions by @munishchouhan in #6805

S3​

• Fixed error when checking whether an S3 bucket exists by @jorgee in #6706

Kubernetes​

• Fixed K8s job fallback to not return incorrect zero exit code by @munishchouhan in #6746

General​

• Fixed fetching new remote branch in multi-revision mode by @jorgee in #6733
• Fixed lint error formatting for errors at end of line by @ewels in #6717
• Fixed LogsCheckpoint thread blocking shutdown for up to 90 seconds by @pditommaso in #6787
• Fixed nextflow inspect not applying container settings from config by @adam-novak in #6736
• Fixed spurious WARN when workflow fails before onFlowBegin by @pditommaso in #6816

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.01.0-edge

Feature updates and improvements​

• Added Channel::mix(Value...) by @bentsherman in a2bb57158
• Added spot interruption tracking to trace records by @munishchouhan in #6606

Bug fixes​

• Fixed nextflow inspect not applying container settings from config by @ewels in #6736
• Fixed false error with task ext blocks in strict syntax by @bentsherman in #6569
• Fixed issue with topic file emissions in typed processes by @stekaz in #6688
• Fixed optional param in params block by @bentsherman in #6657
• Fixed validation of numeric types in params block by @bentsherman in #6656
• Fixed ignore multi-revision folder in list command by @jorgee in #6678

Dependencies​

• Bumped nf-amazon@3.4.3
• Bumped nf-google@1.23.4
• Bumped nf-tower@1.17.4

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.3

Feature updates and improvements​

Language features​

• Added listDirectory() to Path type and deprecate listFiles() by @bentsherman in #6581
• Set local task exit status when time limit is exceeded by @bentsherman in #6592

Google Batch​

• Added default maxSpotAttempts for Fusion Snapshots in Google Batch by @fntlnz in #6652
• Refactored Google Batch getExitCode to imperative style by @pditommaso in #6649

Kubernetes​

• Added runtimeClassName to the pod options by @alexpilotti in #6633

Wave​

• Added wave.build.template config option by @pditommaso in #6639

Plugins​

• Added README files for all plugins by @pditommaso in #6660
• Checked Nextflow version before loading plugins by @bentsherman in #6591

General​

• Added onlyJobState option for SLURM executor by @tcutts in #6659
• Added Spot interruption tracking to trace records by @munishchouhan in #6606
• Added URL encoding when revision name is used as HTTP query parameter by @jorgee in #6598
• Added warnings to JSON output in lint command by @ewels in #6625
• Implemented Git multiple revisions by @jorgee in #6620
• Added Nextflow Development Constitution by @pditommaso in #6578
• Added extra warnings as 25.10 is added to Platform by @christopher-hakkaart in #6655
• Added longer NXF_SYNTAX_PARSER descriptions by @christopher-hakkaart in #6637
• Documented best practices for script and config params by @bentsherman in #6631
• Fixed typos by @christopher-hakkaart in #6641
• Improved preview feature warnings in documentation by @pditommaso in #6663
• Updated note about AWS CLI by @christopher-hakkaart in #6626
• Updated NXF_SYNTAX_PARSER callouts by @christopher-hakkaart in #6640

Bug fixes​

Language features​

• Fixed optional param in params block by @bentsherman in #6657
• Fixed validation of numeric types in params block by @bentsherman in #6656

Wave​

• Fixed WaveClient sending Bearer token to public S3 URLs by @pditommaso in #6672

Plugins​

• Fixed String.format error when plugin URL contains percent chars by @pditommaso in #6651

General​

• Fixed GitHub repository provider when providing token with auth property by @jorgee in #6662
• Fixed tolerate spaces in $NXF_TASK_WORKDIR by @TheLostLambda in #6421

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.12.0-edge

Feature updates and improvements​

Configuration​

• Added default value to Apptainer pull timeout config parameter by @jorgee in #6534

Dependencies​

• Bumped logback 1.5.20 by @pditommaso in 904d968
• Bumped nf-amazon@3.4.2 by @pditommaso in 2411115
• Bumped nf-tower@1.17.2 by @pditommaso in 9f13afd

Bug fixes​

Language features​

• Fixed error with dynamic directives with named arguments by @bentsherman in #6550
• Fixed issue with optional workflow output by @bentsherman in #6519

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

Fusion​

• Fixed Fusion license JWT token refresh by reusing TowerClient by @jorgee in 561ed6c

Configuration​

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

Plugins​

• Reverted 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

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.1

Feature updates and improvements​

Dependencies​

• Bumped nf-tower@1.17.3 by @pditommaso in 5c4aab6

Bug fixes​

General​

• Fixed TowerJsonGenerator thread-safety issue by @pditommaso in #6619

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.2

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

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

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