48 posts tagged with "nextflow"

Feature updates and improvements​

Language features​

• Allowed a list of columns for the splitCsv header in the type checker by @bentsherman in #7871
• Checked equality between records, maps, lists, and tuples by @bentsherman in #7852
• Detected input file name collisions in typed processes by @bentsherman in #7859
• Highlighted the entire token on parse error by @bentsherman in #7877
• Staged files in record collection inputs by @bentsherman in #7866

Configuration​

• Typed the process.secret config option as a list by @bentsherman in #7911

Plugins​

• Documented -patchN plugin versions for stable releases and hardened the release job by @bentsherman in #7876
• Preserved the generic return type in plugin function specs by @bentsherman in #7910

Wave​

• Made Wave optional for the Seqera executor and skipped the Wave Fusion layer by @pditommaso in #7744
• Retried Wave validation tasks when Docker exits 125 by @edmundmiller in #7898

General​

• Built plain and dind launchers for e2e tests by @pditommaso in #7835
• Capped the lifetime of Azure Batch jobs created by CI by @pinin4fjords in #7935
• Improved redaction of sensitive values in logs by @jorgee in #7879
• Prevented leaking environment secrets in CI by @jorgee in #7873

Bug fixes​

Language features​

• Fixed task hash of records returned by typed functions by @bentsherman in #7887
• Fixed type checking of comparator closures on lists of tuples by @bentsherman in #7869
• Fixed type checking of key and value properties on map entries by @bentsherman in #7875

Azure​

• Fixed Azure Batch pool creation when the pool does not exist by @pinin4fjords in #7904

Google Batch​

• Stripped trailing slash from task output paths on GCS by @bentsherman in #7888

Plugins​

• Fixed serial input files metrics computation in nf-seqera by @jordeu in #7899

Dependencies​

• Bumped nf-azure@1.24.3
• Bumped nf-k8s@1.6.2
• Bumped nf-seqera@0.26.1
• Bumped nf-tower@1.32.2
• Bumped nf-wave@1.22.4
• Bumped sched-client to 0.111.0 in nf-seqera

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.4

Feature updates and improvements​

General​

• Improved redaction of sensitive values in logs by @jorgee in #7879

Dependencies​

• Bumped nf-google@1.27.3-patch1
• Bumped nf-k8s@1.5.4-patch1

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.9

Bug fixes​

General​

• Removed the Bitbucket API token from git clone URLs and logs by @bentsherman in #7870
• Prevented leaking environment secrets in CI by @jorgee in #7873

Dependencies​

• Bumped nf-azure@1.20.4
• Bumped nf-k8s@1.2.3
• Bumped nf-tower@1.17.8

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.9

Bug fixes​

General​

• Removed the Bitbucket API token from git clone URLs and logs by @bentsherman in #7870
• Prevented leaking environment secrets in CI by @jorgee in #7873

Dependencies​

• Bumped nf-azure@1.22.8
• Bumped nf-k8s@1.5.6
• Bumped nf-tower@1.28.4

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.8

Bug fixes​

Language features​

• Applied Harshil alignment to trailing comments, not annotations by @bentsherman in #7832
• Fixed cascading type errors from inconsistently typed expressions by @bentsherman in #7851
• Fixed hang in preview mode with workflow outputs by @bentsherman in #7838
• Fixed onError section in entry workflow by @bentsherman in #7831
• Fixed stdlib typos by @bentsherman in #7863
• Fixed type checking of function calls that omit default params by @bentsherman in #7860
• Fixed type of task.label in language definitions by @bentsherman in #7857

Configuration​

• Fixed unrecognized config warnings for nextflow.retryPolicy options by @pditommaso in #7843

General​

• Escaped control characters in task metadata and job names by @arnaualcazar in #7764
• Removed the Bitbucket API token from git clone URLs and logs by @bentsherman in #7870

Dependencies​

• Updated Grengine to 3.1.2 (group ID and package ch.grengine) by @alainstalder in #7842

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.3

Feature updates and improvements​

Google Batch​

• Fetched Google Batch task status once per trace record by @bentsherman in #7807
• Retried INTERNAL errors from the Google Batch API by @bentsherman in #7805

Plugins​

• Loaded the config files in the plugin commands session by @pditommaso in #7815

General​

• Retried foreign file staging on connection reset by @pditommaso in #7799

Bug fixes​

Language features​

• Fixed file-handling bugs in native processes by @bentsherman in #7789
• Fixed workflow output path closure returning an empty map by @bentsherman in #7823
• Fixed workflow variables named published or owner by @pinin4fjords in #7814

Google Batch​

• Fixed Google Batch array job deleted when a single array task is killed by @pditommaso in #7808

Fusion​

• Skipped Fusion .fusion directories when publishing directories by @pditommaso in #7811

General​

• Fixed unit tests that depend on global state from other tests by @bentsherman in #7804

Dependencies​

• Bumped nf-amazon@3.12.1
• Bumped nf-azure@1.24.2
• Bumped nf-google@1.29.1

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.1

Feature updates and improvements​

Plugins​

• Built plugin commands config in the CLI by @pditommaso in #7834

Bug fixes​

Language features​

• Fixed formatter treating comment-like GString text as a comment by @bentsherman in #7828

Dependencies​

• Bumped nf-tower@1.32.1
• Bumped nf-wave@1.22.3

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.2

Feature updates and improvements​

Language features​

• Addressed limitations in agent inputs and outputs by @bentsherman in #7750
• Checked typed output names and allowed single named outputs by @bentsherman in #7769
• Deprecated the process when section in favor of the process.when config setting by @bentsherman in #7746
• Inferred the element type of empty channels, lists, and maps from first use by @bentsherman in #7774
• Made exit() graceful and reported an error for return statements in the workflow body by @bentsherman in #7570

Configuration​

• Allowed run-level cpus and memory limits for grid executors by @raphaelbetschart in #7783

General​

• Added a deprecations page to the docs by @bentsherman in #7766
• Improved the error message for local paths in module commands by @bentsherman in #7779

Bug fixes​

Language features​

• Fixed nullable workflow emits wrapping null in a dataflow value by @bentsherman in #7760
• Fixed static typing issues found while migrating a pipeline by @bentsherman in #7722

Google Batch​

• Fixed Google Batch array status polling for arrays of 500+ tasks by @robsyme in #7767
• Fixed Google Batch array task status cache never matching by @robsyme in #7778
• Fixed Google Batch task listing not retrying errors after the first page by @robsyme in #7768
• Fixed retried Google Batch job submissions failing with ALREADY_EXISTS by @pditommaso in #7762

General​

• Fixed interactive CLI prompts when stdin is not a terminal by @pditommaso in #7641
• Fixed the main thread exiting before the flow completes when aborted on another thread by @stefanoboriero in #7781
• Fixed IllegalThreadStateException aborting the session on task timeout by @Mohit-Ak in #7571
• Fixed invalid JSON sent to Seqera Platform when a value fails to serialize in TowerJsonGenerator by @pinin4fjords in #7772

Dependencies​

• Bumped nf-agent@0.2.0
• Bumped nf-agent-pi@0.6.0
• Bumped nf-amazon@3.12.0
• Bumped nf-google@1.29.0
• Bumped nf-tower@1.32.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.0

Bug fixes​

Language features​

• Fixed error checking in workflow emits by @bentsherman in #7058
• Fixed the formatter dropping the main: label when onComplete: or onError: is present by @ewels in #7346

Configuration​

• Fixed config rendering of nested closures by @bentsherman in #7375

S3​

• Fixed S3 directory upload skipping symbolic links by @jorgee in #7515

Dependencies​

• Bumped vulnerable dependencies to patched releases by @jorgee in #7598
• Bumped nf-amazon@3.9.3
• Bumped nf-azure@1.22.7
• Bumped nf-codecommit@0.5.4
• Bumped nf-google@1.27.4
• Bumped nf-k8s@1.5.5
• Bumped nf-seqera@0.21.2
• Bumped nf-tower@1.28.3

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.7

Feature updates and improvements​

Language features​

• Added pipeline composition by @bentsherman in #7213
• Allowed any return type for a closure with a boolean signature by @bentsherman in #7688
• Added type checking for the type arguments of call arguments by @bentsherman in #7728
• Improved lint errors for common gotchas by @bentsherman in #7742
• Moved v1 process output resolution to TaskOutputResolverV1 by @bentsherman in #7036
• Published workflow outputs with FilePublisher by @bentsherman in #7745
• Added recognition of Record::subMap() in the type checker by @bentsherman in #7743
• Added an error for a closure or function that returns no value by @bentsherman in #7714
• Added an error for a missing return statement in a closure or function by @bentsherman in #7738
• Changed invalid script definitions to report the real syntax error by @bentsherman in #7675
• Added a type error for record field assignment by @bentsherman in #7718
• Skipped argument checks for plugin functions in typed scripts by @bentsherman in #7726
• Added support for a map of source-to-target pairs in the output path directive by @bentsherman in #7646
• Changed unnamed typed process outputs to use the inferred type by @pditommaso in #7757
• Added runtime validation of record fields for process record inputs by @bentsherman in #7692

Configuration​

• Added the seqera.executor.machineRequirement.onDemandCostRatio option by @pditommaso in #7710

Wave​

• Added conda/micromamba:v2-fast and conda/pixi:v1-fast to the wave.build.template docs by @pditommaso in #7727

General​

• Centralized shared dependency versions in gradle.properties by @pditommaso in #7704
• Made HashBuilder.isAssetFile public by @jorgee in #7723
• Changed CSV output to quote values only when required by @xHaMMaDy in #7377
• Changed lineage to record only tasks that completed by @jorgee in #7664
• Replaced LockManager with Guava Striped locks by @pditommaso in #7736
• Changed sched multi-attempt tasks to report the final attempt's start time by @pditommaso in #7755
• Changed the console log to go to stderr when ANSI logging is disabled by @bentsherman in #7741
• Added CI validation of agent examples against a staged runner image by @pditommaso in #7761

Bug fixes​

Language features​

• Fixed formatting of directives with a list argument by @bentsherman in #7679
• Fixed lineage path references for typed processes by @jorgee in #7713
• Fixed an NPE when all publish statements in a workflow output are no-ops by @bentsherman in #7674
• Fixed an NPE when publishing an external file with a publish statement by @bentsherman in #7721
• Fixed record cast of non-local Path values by @bentsherman in #7684
• Fixed serialization of dataflow params by @pinin4fjords in #7759
• Fixed the params block breaking piped operators in the entry workflow by @bentsherman in #7405

Plugins​

• Fixed plugin functions that return or take a channel by @bentsherman in #7715

General​

• Fixed a grep broken pipe error when reading the CPU model in the trace script by @bentsherman in #7672
• Fixed stale ANSI log lines when COLUMNS does not match the terminal width by @pditommaso in #7705
• Fixed the launcher Java version cache and md5 fallback by @ewels in #7695
• Fixed LsfExecutor.parseJobId() swallowing submit failures by @Arthur031221 in #7730
• Fixed the validate.sh image override with a relative results directory and Wave images by @pditommaso in #7763

Dependencies​

• Bumped Jackson to 2.21.7 and 2.18.11 to fix security advisories by @jorgee in #7732
• Bumped nf-agent-pi to 0.5.4 with pi-coding-agent 1.0.2 so the catalog includes GPT-6 Luna by @edmundmiller in #7748
• Bumped pi-coding-agent to 0.86.1 to fix undici advisories by @jorgee in #7733
• Bumped sched-client to 0.100.0 in nf-seqera by @pditommaso in fe446ce6d
• Bumped slf4j to 2.0.20 by @pditommaso in #7703
• Bumped nf-agent@0.1.2
• Bumped nf-agent-pi@0.5.4
• Bumped nf-azure@1.24.1
• Bumped nf-google@1.28.2
• Bumped nf-seqera@0.26.0
• Bumped nf-tower@1.31.0
• Bumped nf-wave@1.22.2

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.09.2-edge