26 posts tagged with "nextflow"

• chore: pin dependency python to 3.14.5 (#7152) [ec74f3d28]
• Fix module run to allow optional path inputs (#7163) [4fd28fd5b]
• Fix azure rnaseq-nf test (#7143) [e4f92906d]
• Fix destructured record input in module run (#7164) [0498ca6c5]
• Fix function calls in typed process outputs (#7148) [7e0908c66]
• Fix strict parser to include params refs in task hash (#7165) [785e801ad]
• GitHub Actions - security updates (#7138) [5e2ef5762]
• Honor token field in BitbucketServerRepositoryProvider (#7120) [6bf6e8d1e]
• Normalize TaskPath -> Path in typed process outputs (#7090) [38c072395]
• Pick up force-pushed branches in multi-revision repo strategy (#7103) [091f93f05]
• Release HTTP sockets when reading HTTP attributes to avoid 503 throttling [f2b0284e6]
• Tighten CI security and remove dead code in workflows (#7139) [2bec40277]
• Update guidelines for strict parser (#7134) [3aa26a7d4]
• Validate module spec against JSON schema (#7094) [6a6ea9fe6]
• Bump nf-azure@1.22.4
• Bump nf-k8s@1.5.3
• Bump nf-seqera@0.20.0

https://github.com/nextflow-io/nextflow/releases/tag/v26.04.2

Feature updates and improvements​

General​

• Updated migration docs now that 26.04 is released by @ewels in #7085

Dependencies​

• Bumped ch.qos.logback:logback-classic to v1.5.32 by @seqeralabs-renovate in #7126
• Bumped nf-amazon@3.9.1 by @pditommaso in 816c0774
• Bumped nf-azure@1.22.3 by @pditommaso in 78fa5013
• Bumped nf-codecommit@0.5.2 by @pditommaso in 4ae5c872
• Bumped nf-seqera@0.19.1 by @pditommaso in 764003a9

Bug fixes​

General​

• Fixed module binaries on nextflow module run via session flag by @pditommaso in #7089

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.1

Feature updates and improvements​

Dependencies​

• Bumped nf-tower@1.17.6 by @pditommaso

Bug fixes​

Language features​

• Fixed formatting bug with map key expression by @bentsherman in #6893
• Fixed incorrect evaluation of secret process directive by @bentsherman in #6934
• Fixed params block in included module by @bentsherman in #6940
• Fixed params inclusion across modules in v2 parser by @bentsherman in #6766

Configuration​

• Fixed resolution of params in resolved config text by @jorgee in #7072

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.5

Feature updates and improvements​

Configuration​

• Renamed nextflow.preview.types feature flag to nextflow.enable.types by @pditommaso in #7067
• Added support for validation of collection params with record types by @bentsherman in #7025

General​

• Added -user-secret and -workspace-secret flags to nextflow launch by @rnaidu-seqera in #7040

Bug fixes​

Language features​

• Fixed runtime type reflection in nf-lang by @bentsherman in #7077

General​

• Fixed ANSI colors in error messages by @ewels in #7078

Dependencies​

• Bumped nf-tower@1.27.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.0

Feature updates and improvements​

Language features​

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

Dependencies​

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

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

AWS Batch​

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

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/v26.03.4-edge

Feature updates and improvements​

Language features​

• Added option to disable printing workflow outputs by @bentsherman in #7018
• Resolved structured process input types by @bentsherman in #7014

S3​

• Applied socket timeout to S3 CRT connections by @jorgee in #7024
• Managed AWS SDK exceptions to convert to the appropriate IO exceptions by @jorgee in #6707

Plugins​

• Updated missing pf4j updates by @jorgee in #7016

Fusion​

• Added Fusion GPU metrics collection by @pditommaso in #7022
• Used Fusion trace metrics to replace bash command-trace wrapper by @pditommaso in #7041

General​

• Added -files-from option to lint command to avoid ARG_MAX limit by @adamrtalbot in #6858
• Added 26.04 migration docs by @bentsherman in #7000
• Allowed cloning from local Git repositories when --offline by @MatthiasZepper in #7035
• Allowed running pipeline from URL and main script path by @jorgee in #6602
• Filtered autoLabels to selected workflow-metadata fields by @pditommaso in #7049
• Honored process.resourceLabels in nf-seqera executor by @pditommaso in #7048
• Renamed module info subcommand to module view by @pditommaso in #7052
• Simplified demo module README template by @pditommaso in #7051
• Suppressed lint progress logging with -q flag by @ewels in #6880

Bug fixes​

Language features​

• Fixed formatting issues with complex expressions by @bentsherman in #7027

S3​

• Fixed S3FileSystemProvider.newInputStream() draining full object on close by @jorgee in #7046

Plugins​

• Fixed inconsistent indentation in nf-amazon by @bentsherman in #7047
• Fixed nextflowVersion for nf-tower and nf-seqera plugins by @pditommaso in cbc0a2d8e

General​

• Fixed generated process name in module create command by @jorgee in #7008
• Fixed module info formatting separator by @pditommaso in #7033
• Fixed resolution of -with-tower with TOWER_API_ENDPOINT by @bentsherman in #7045
• Fixed saveCacheFiles early return skipping log file uploads by @munishchouhan in #7015

Dependencies​

• Bumped org.bouncycastle:bcpkix-jdk18on from 1.79 to 1.84 by @dependabot in #7042
• Bumped nf-amazon@3.8.3
• Bumped nf-k8s@1.5.2
• Bumped nf-seqera@0.18.0
• Bumped nf-tower@1.25.0
• Bumped nf-wave@1.19.1

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.03.3-edge

Feature updates and improvements​

Language features​

• Added typed workflows by @bentsherman in #6881

Modules​

• Added module create subcommand by @pditommaso in #6992
• Added module spec command by @jorgee in #6859
• Added module validate subcommand by @pditommaso in #6993
• Replaced custom ModuleRegistryClient with npr-client API by @pditommaso in #7012

General​

• Added compute env ID and provider support to Seqera executor by @pditommaso in #6906
• Added resourceAllocation field to trace record by @pditommaso in #6973
• Replaced Auth0 with Platform OIDC PKCE for auth login by @pditommaso in #6953
• Used inline metadata from trace create response by @pditommaso in #6976

Bug fixes​

General​

• Fixed NPE in GitLab/Gitea getGitCredentials when password is null but token is set by @robsyme in #7007
• Fixed missing version for junit-platform-launcher dependency by @pditommaso in #7011

Dependencies​

• Bumped nf-amazon@3.8.2
• Bumped nf-seqera@0.17.0
• Bumped nf-tower@1.24.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.03.2-edge

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