19 posts tagged with "nextflow"

Feature updates and improvements​

Language features​

• Hardened ProcessEntryHandler types and added test for dot-notation conflicts by @pditommaso in #6966
• Added print workflow outputs on run completion by @bentsherman in #6875
• Used destructuring syntax for process record/tuple inputs by @pditommaso in #6912

General​

• Added -project-dir option to lint command by @bentsherman in #6728
• Added platform-related metadata to WorkflowRun lineage record by @jorgee in #6545
• Added request timeout to tower client by @jorgee in #6950
• Added support for Java 26 by @pditommaso in #6969
• Improved module command: enabled logging for module run, fixed info URL and search output by @pditommaso in #6961
• Skipped launch metadata fetch for CLI-submitted runs by @pditommaso in #6975
• Used -d flag for bkill in LSF executor by @cgoina in #6784

Bug fixes​

Language features​

• Fixed handling of empty publishedValues in PublishOp.onComplete for optional outputs by @jorgee in #6979
• Fixed incorrect evaluation of secret process directive by @bentsherman in #6934
• Fixed params block in included module by @bentsherman in #6940

S3​

• Fixed download of empty files in old MinIO-based S3 transfers by @jorgee in #6944

AWS Batch​

• Fixed AWS Batch machine type trace for new instance families by @FloWuenne in #6952

Plugins​

• Fixed jackson-databind dependency in nf-amazon by @pditommaso in #6941

Dependencies​

• Fixed netty and jackson vulnerabilities by @jorgee in #6955
• Fixed security vulnerabilities by @jorgee in #6938

General​

• Fixed AgentLogObserver printing [SUCCESS] on failed runs by @pditommaso in #6962
• Fixed LogsCheckpoint thread interrupt race condition by @pditommaso in #6939
• Fixed module run CLI params cast to declared meta.yml input types by @jorgee in #6968
• Fixed typo in TowerRetryPolicy: maxAttemps → maxAttempts by @robsyme in #6949

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.03.1-edge

Feature updates and improvements​

Language features​

• Added module system by @pditommaso in #6650
• Added multi-arch support to arch process directive by @pditommaso in #6897
• Added record types by @bentsherman in #6679
• Propagated errors from workflow outputs by @bentsherman in #6876

Configuration​

• Added provider option to Seqera executor config by @pditommaso in #6908

Google Batch​

• Added support for GCP Ops Agent by @ejseqera in #6608
• Added support for latest-generation Google Cloud machine families by @sosoihd in #6841

Fusion​

• Defaulted Fusion to v2.6 for Seqera executor by @pditommaso in #6933

General​

• Added NVMe disk allocation and diskMountPath support by @pditommaso in #6879
• Added logStreamId to Tower task record by @pditommaso in #6877
• Excluded container from task trace when containers are not enabled by @bentsherman in #6824
• Increased tasks.cloudZone width from 15 to 25 by @ramonamela in #6907

Bug fixes​

Language features​

• Fixed formatting bug with map key expression by @bentsherman in #6893
• Fixed path traversal, resource leak, and race condition in module system by @pditommaso in #6929
• Fixed remote modules when base dir is not the current working directory by @jorgee in #6932
• Fixed stageAs method signature in typed process by @bentsherman in #6915

Configuration​

• Fixed type detection of CLI params in v2 config parser by @bentsherman in #6765

Google Batch​

• Fixed Google Batch exit code when spot claim is successfully retried by @jorgee in #6926

Kubernetes​

• Fixed K8s token refresh by caching K8sClient at executor level by @pditommaso in #6925

Plugins​

• Fixed HttpPluginRepository empty plugin list check by @pditommaso in #6650

General​

• Fixed TraceFileObserver NPE when trace file already exists by @robsyme in #6891

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.03.0-edge

Feature updates and improvements​

Language features​

• Allowed boolean params to implicitly default to false by @bentsherman in #6764

Azure Batch​

• Handled Azure Batch ActiveJobAndScheduleQuotaReached with retry by @adamrtalbot in #6874
• Updated default Azure Batch VM image to Ubuntu 24.04 by @adamrtalbot in #6844

Google Batch​

• Reported actual GCP zone in Google Batch trace records by @pditommaso in #6855

LSF​

• Treated LSF job status UNKWN as HOLD by @bentsherman in #5756
• Used explicit memory units for LSF executor by @bentsherman in #5217

General​

• Added agent output mode (NXF_AGENT_MODE) by @edmundmiller in eae9f7d
• Ensured main script is first in the WorkflowRun lineage record by @jorgee in #6845
• Implemented sched core (alpha1) by @pditommaso in #6242

Bug fixes​

S3​

• Fixed S3 delete throwing DirectoryNotEmptyException due to eventual consistency by @pditommaso in #6833
• Fixed S3 lookup unbounded pagination with double call by @jorgee in #6851

General​

• Fixed AgentLogObserver println clash with Groovy GDK method by @pditommaso in c6314d7
• Fixed AnsiLogObserver sticky messages duplicated when lines wrap by @pditommaso in #6852
• Fixed missing space before revision in launch info by @pditommaso in #6834
• Fixed ResourcesAggregator deadlock with virtual thread executor by @pditommaso in #6840
• Fixed vertical alignment in timeline report by @PeterKneale in #6794

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.02.0-edge

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