34 posts tagged with "nextflow"

Feature updates and improvements​

Language features​

• Added a Semantics reference page to the docs by @bentsherman in #7271

Configuration​

• Added the docker.cpuLimits config option by @bentsherman in #7289
• Added the seqera.executor.providerConfig option by @pditommaso in #7335

Google Batch​

• Added a docs note about IAM roles for google.batch.serviceAccountEmail by @bentsherman in #7291

Plugins​

• Sent pipeline-secret references to the Seqera Scheduler from nf-seqera by @pditommaso in #7314
• Skipped nf-tower when superseded by nf-seqera by @jorgee in #7283
• Reverted "Consolidate nf-tower plugin into nf-seqera (#7252)" by @pditommaso in da5afcfe9
• Reverted "Skip nf-tower when superseded by nf-seqera (#7283)" by @pditommaso in c5dec3b4e

General​

• Added a graceful fallback for the array directive with unsupported executors by @bentsherman in #7296
• Added two Indian scientists to NameGenerator by @deepmind11 in #7079
• Clarified Bitbucket API token auth requirements in the docs by @pditommaso in #7279
• Clarified the override behavior of the resourceLabels directive in the docs by @bentsherman in #7287
• Dropped the dead oss.sonatype.org repository by @pditommaso in #7282
• Showed the absolute path in the missing main script error by @bentsherman in #7286
• Used the scheduler API exit code, falling back to the .exitcode file by @jordeu in #7273

Dependencies​

• Bumped jackson 2.21.1 to 2.21.4 to fix high-severity CVEs by @pditommaso in #7274
• Bumped jackson-databind to patched versions to fix deserialization CVEs by @jorgee in #7322
• Replaced the discontinued bcprov-ext with bcprov-jdk18on 1.84 to fix CVE-2025-14813 by @pditommaso in #7284
• Used the wiremock self-contained distribution to drop vulnerable handlebars by @pditommaso in #7275
• Pinned Docusaurus dependencies by @seqeralabs-renovate in #7324
• Updated the actions/checkout action to v6.0.3 by @seqeralabs-renovate in #7325
• Updated the anthropics/claude-code-action action to v1.0.168 by @seqeralabs-renovate in #7326
• Updated ch.qos.logback:logback-classic to v1.5.37 by @seqeralabs-renovate in #7327
• Updated ch.qos.logback:logback-core to v1.5.35 (security) by @seqeralabs-renovate in #7297
• Updated com.azure:azure-compute-batch to v1.0.0-beta.6 by @seqeralabs-renovate in #7128
• Bumped nf-amazon@3.10.1
• Bumped nf-azure@1.23.1
• Bumped nf-google@1.27.4
• Bumped nf-k8s@1.5.5
• Bumped nf-seqera@0.23.0
• Bumped nf-tower@1.29.1
• Bumped nf-wave@1.21.1

Bug fixes​

Language features​

• Fixed error checking in workflow emits by @bentsherman in #7058
• Fixed path input for exec processes by @bentsherman in #7272

Configuration​

• Excluded null config environment entries from the task environment by @bentsherman in #7294

AWS Batch​

• Fixed containerOptions --opt=value parsing for AWS Batch by @bentsherman in #7288
• Rounded up CPUs to the nearest valid value for AWS Batch Fargate by @bentsherman in #7295

Azure​

• Tolerated stale or transient resize errors on autoscale Azure Batch pools by @jorgee in #7312

Fusion​

• Keyed the Fusion license token cache by product and version by @robsyme in #7320

General​

• Fixed a high-severity form-data CRLF injection in the docs site by @pditommaso in #7276
• Fixed a Kryo deserialization error with enum types by @bentsherman in #7277
• Fixed URL percent-encoding lost on resume for HTTP/FTP paths by @bentsherman in #7333
• Force-created staged input symlinks to allow task re-runs by @bentsherman in #7285

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.07.0-edge

Dependencies​

• Bumped nf-seqera@0.21.1
• Bumped nf-tower@1.28.2

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.6

Feature updates and improvements​

General​

• Added GPU metrics to workflow-level execution summary by @cristianrcv in #7229
• Propagated Seqera Intelligent Compute scheduler run identifier to Platform by @jorgee in #7228

Bug fixes​

Language features​

• Fixed flatMap tuple error for dataflow value by @bentsherman in #7254

Dependencies​

• Bumped nf-seqera@0.22.0
• Bumped nf-tower@1.29.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.5

Feature updates and improvements​

Language features​

• Clarified storeDir caveats with env, eval, and stdout outputs by @bentsherman in #7235

Azure​

• Added docs tip for relocating Docker storage on Azure Batch nodes by @adamrtalbot in #6937

Fusion​

• Added a clear error when Fusion is enabled without an access token by @jorgee in #7263

Plugins​

• Consolidated the nf-tower plugin into nf-seqera by @pditommaso in #7252

General​

• Added Fibonacci and Pareto to the run name generator by @bentsherman in #7255
• Normalized version callouts in the docs by @bentsherman in #7256
• Propagated the Seqera Intelligent Compute scheduler run identifier to Platform by @jorgee in #7228
• Removed uncommitted specs by @bentsherman in #7267

Dependencies​

• Bumped nf-seqera@1.0.0

Bug fixes​

Language features​

• Fixed docs example for record operations by @bentsherman in #7250
• Fixed flatMap tuple error for dataflow value by @bentsherman in #7254

General​

• Fixed failing unit tests with clean build by @bentsherman in #7264
• Lowered trace-access.nf memory to fit CI runner capacity by @pditommaso in #7266

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.06.0-edge

Feature updates and improvements​

Language features​

• Removed the deprecated echo process directive by @pditommaso in #7206
• Added support for record type input with dot-notation CLI params by @jorgee in #7170

Azure​

• Improved Azure Batch VM image diagnostics and fixed stale 24.04 docs by @pditommaso in #7200

Plugins​

• Added workflow DAG reporting to the nf-tower plugin by @ewels in #7218
• Allowed the plugin version to be specified when running a plugin command by @JosuaCarl in #7113
• Added subcommand listing to nextflow plugins -help by @ewels in #7197

General​

• Added -help as an alias for -h in top-level CLI options by @ewels in #7238
• Added GPU metrics to the workflow-level execution summary by @cristianrcv in #7229
• Added hidden plural/singular aliases for noun subcommands by @ewels in #7239
• Added Nextflow module info to the lineage TaskRun entry by @jorgee in #7160
• Added seqera:// data-links support to the nf-tower filesystem by @jorgee in #7070
• Added a shellEnabled option and per-task prediction model to the Seqera executor by @pditommaso in #7204
• Added the nextflow logfile command by @ewels in #7177
• Added a data lineage architecture decision record (ADR) by @bentsherman in #7187
• Changed stdout outputs to stderr to avoid breaking piped output by @ewels in #7121
• Clarified the distinction between modules and script inclusion in the docs by @bentsherman in #7217
• Migrated the docs to the new build by @christopher-hakkaart in #7119
• Improved Tower telemetry error handling on transient gateway failures by @pditommaso in #7190
• Mirrored test containers to public.cr.seqera.io to harden CI against quay.io outages by @pditommaso in #7195
• Promoted the latest stable channel by version comparison instead of branch name by @pditommaso in b5ac62e0c
• Refactored changelog.txt to CHANGELOG.md by @ewels in #7179
• Added support for the accelerator directive in the local executor by @bentsherman in #5850
• Used a stop flag instead of a thread interrupt to shut down the logs checkpoint by @pditommaso in #7193

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 the order of plugin declarations in config by @jagedn in #7227

General​

• Fixed workflow completion handler being called twice by @bentsherman in #7191
• Fixed lineage records for stub-run and eval outputs by @jorgee in #7211
• Fixed netty CVE-2026-44249 via an AWS SDK bump and azure-core-http-netty pin by @jorgee in #7223
• 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@3.10.0
• Bumped nf-azure@1.23.0
• Bumped nf-codecommit@0.6.0
• Bumped nf-seqera@0.22.0
• Bumped nf-tower@1.29.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.05.0-edge

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