29 posts tagged with "nextflow"

Feature updates and improvements​

Plugins​

• Bumped the default plugin create template to v0.4.0 by @pditommaso in #7234

General​

• Added Nextflow module info to lineage TaskRun entry by @jorgee in #7160

Bug fixes​

Language features​

• Fixed "No such variable" in typed output block with job arrays by @jorgee in #7221
• Fixed cast and instanceof with record types by @bentsherman in #7185
• Fixed staging of Path fields of included record types by @robsyme in #7226

Plugins​

• Preserved order of plugin declarations in config by @jagedn in #7227

General​

• Fixed workflow completion handler being called twice by @bentsherman in #7191
• Fixed nxf_date for uutils coreutils (Ubuntu 26.04+) by @robsyme in #7118
• Fixed nxf_date to sample seconds and nanoseconds atomically by @pditommaso in #7207

Dependencies​

• Bumped nf-amazon@3.9.2
• Bumped nf-azure@1.22.6
• Bumped nf-codecommit@0.5.3
• Bumped nf-seqera@0.21.0
• Bumped nf-tower@1.28.1

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.4

Feature updates and improvements​

Azure​

• Updated default Azure Batch pool image to Ubuntu 24.04 by @pditommaso in 114d0e4c

General​

• Pinned rnaseq-nf to v2.3 in Azure validation script by @pditommaso in 8f7e5780

Bug fixes​

S3​

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

General​

• Fixed world-readable seqera-auth.config credential file by @arnaualcazar in #7182
• Fixed LogsCheckpoint thread interrupt race condition by @pditommaso in #6939

Dependencies​

• Bumped nf-amazon@3.4.5 by @pditommaso in b9074b2d
• Bumped nf-tower@1.17.7 by @pditommaso in da09f092
• Bumped nf-azure@1.20.3 by @pditommaso in 1e000afe

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.6

Feature updates and improvements​

Language features​

• Improved the error message when enabling types with syntax parser v1 by @jorgee in #7173

Plugins​

• Made plugin metadata prefetch resilient to registry rate limiting by @pditommaso in #7181

Fusion​

• Added support for fetching local files in FUSION_CONTAINER_CONFIG_URL by @alberto-miranda in #7142

Bug fixes​

S3​

• Fixed bucket cleanup in S3 test by @bentsherman in #7172

General​

• Fixed docs CI on Python 3.14 by upgrading Sphinx by @jorgee in #7175

Dependencies​

• Bumped nf-azure@1.22.5
• Bumped nf-google@1.27.3
• Bumped nf-k8s@1.5.4
• Bumped nf-seqera@0.20.1
• Bumped nf-tower@1.28.0
• Bumped nf-wave@1.21.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.3

Feature updates and improvements​

Language features​

• Validated module spec against JSON schema by @pditommaso in #7094
• Updated guidelines for strict parser by @bentsherman in #7134

General​

• Honored token field in BitbucketServerRepositoryProvider by @jorgee in #7120
• Picked up force-pushed branches in multi-revision repo strategy by @jorgee in #7103
• Tightened CI security and removed dead code in workflows by @ewels in #7139
• Updated GitHub Actions with security updates by @ewels in #7138

Dependencies​

• Pinned python to 3.14.5 by @seqeralabs-renovate in #7152
• Bumped nf-azure@1.22.4 by @pditommaso in 2bcc6e8c
• Bumped nf-k8s@1.5.3 by @pditommaso in b2ea7492
• Bumped nf-seqera@0.20.0 by @pditommaso in 4d55e81e

Bug fixes​

Language features​

• Fixed module run to allow optional path inputs by @bentsherman in #7163
• Fixed destructured record input in module run by @bentsherman in #7164
• Fixed function calls in typed process outputs by @bentsherman in #7148
• Fixed strict parser to include params refs in task hash by @bentsherman in #7165
• Normalized TaskPath to Path in typed process outputs by @stekaz in #7090

Azure​

• Fixed Azure rnaseq-nf test by @bentsherman in #7143

General​

• Released HTTP sockets when reading HTTP attributes to avoid 503 throttling by @jorgee in f2b0284e

Full changelog: 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