Merge branch 'master' into backport-mysql-version-warnings

Author: justinegeffen

.github/workflows/check-internal-links.yml

@@ -27,4 +27,5 @@ jobs:
       - name: Build Docusaurus website
         env:
           FAIL_ON_BROKEN_LINKS: true
+          TYPESENSE_SEARCH_API_KEY: ${{ secrets.TYPESENSE_SEARCH_API_KEY }}
         run: npm run build

changelog/nextflow/v25.11.0-edge.md

@@ -8,12 +8,12 @@ tags: [nextflow]
 
 ### Google Batch
 
-- Added Google Batch LogsPolicy PATH option for logging to GCS by @dglazer in [#6431](https://github.com/nextflow-io/nextflow/pull/6431)
+- Added Google Batch `LogsPolicy` `PATH` option for logging to GCS by @dglazer in [#6431](https://github.com/nextflow-io/nextflow/pull/6431)
 - Optimized exit code handling by relying on scheduler status for successful executions by @jorgee in [#6484](https://github.com/nextflow-io/nextflow/pull/6484)
 
 ### Kubernetes
 
-- Changed log level from warn1 to debug1 for K8s Job Pod Warnings by @BioWilko in [#6523](https://github.com/nextflow-io/nextflow/pull/6523)
+- Changed log level from `warn1` to `debug1` for K8s Job Pod Warnings by @BioWilko in [#6523](https://github.com/nextflow-io/nextflow/pull/6523)
 
 ### Language features
 
@@ -41,12 +41,12 @@ tags: [nextflow]
 - Improved error message for invalid contribution type in manifest contributors by @bentsherman in [#6593](https://github.com/nextflow-io/nextflow/pull/6593)
 - Moved task error formatting logic into separate class by @bentsherman in [#6551](https://github.com/nextflow-io/nextflow/pull/6551)
 - Removed unused BatchHelper class by @pditommaso in [#6547](https://github.com/nextflow-io/nextflow/pull/6547)
-- Removed wiremock-groovy dependency and updated tests using this dependency by @jorgee in [#6611](https://github.com/nextflow-io/nextflow/pull/6611)
+- Removed `wiremock-groovy` dependency and updated tests using this dependency by @jorgee in [#6611](https://github.com/nextflow-io/nextflow/pull/6611)
 - Updated bundled Docker runtime to 19.03.15 by @yarikoptic in [#6565](https://github.com/nextflow-io/nextflow/pull/6565)
 - Updated trace table columns in Reports page by @JustinBellavance in [#6483](https://github.com/nextflow-io/nextflow/pull/6483)
 - Upgraded from Apache Commons Lang 2.6 to Commons Lang3 3.18.0 by @pditommaso in [#6511](https://github.com/nextflow-io/nextflow/pull/6511)
 - Added admonition to inputs and index words by @christopher-hakkaart in [#6461](https://github.com/nextflow-io/nextflow/pull/6461)
-- Improved task previousTrace documentation by @rnaidu in [#6538](https://github.com/nextflow-io/nextflow/pull/6538)
+- Improved task `previousTrace` documentation by @rnaidu in [#6538](https://github.com/nextflow-io/nextflow/pull/6538)
 - Updated feature flags page by @christopher-hakkaart in [#6504](https://github.com/nextflow-io/nextflow/pull/6504)
 - Updated task directives by @christopher-hakkaart in [#6506](https://github.com/nextflow-io/nextflow/pull/6506)
 
@@ -68,12 +68,12 @@ tags: [nextflow]
 
 ### Kubernetes
 
-- Fixed Do not delete K8s jobs when ttlSecondsAfterFinished is set by @bentsherman in [#6597](https://github.com/nextflow-io/nextflow/pull/6597)
-- Fixed K8sTaskHandlerTest method name typos by @pditommaso in [bcf81d9](https://github.com/nextflow-io/nextflow/commit/bcf81d90)
+- Fixed Do not delete K8s jobs when `ttlSecondsAfterFinished` is set by @bentsherman in [#6597](https://github.com/nextflow-io/nextflow/pull/6597)
+- Fixed `K8sTaskHandlerTest` method name typos by @pditommaso in [bcf81d9](https://github.com/nextflow-io/nextflow/commit/bcf81d90)
 
 ### Fusion
 
-- Fixed Fusion license JWT token refresh by reusing TowerClient by @jorgee in [498125d](https://github.com/nextflow-io/nextflow/commit/498125d2)
+- Fixed Fusion license JWT token refresh by reusing `TowerClient` by @jorgee in [498125d](https://github.com/nextflow-io/nextflow/commit/498125d2)
 
 ### S3
 
@@ -83,29 +83,29 @@ tags: [nextflow]
 ### Language features
 
 - Fixed Invalid type error detection by @pditommaso in [9e3aeed](https://github.com/nextflow-io/nextflow/commit/9e3aeed1)
-- Fixed csv splitter when skipping empty lines by @bentsherman in [#6586](https://github.com/nextflow-io/nextflow/pull/6586)
+- Fixed CSV splitter when skipping empty lines by @bentsherman in [#6586](https://github.com/nextflow-io/nextflow/pull/6586)
 - Fixed documentation of `unique` operator by @bentsherman in [#6541](https://github.com/nextflow-io/nextflow/pull/6541)
 - Fixed error with dynamic directives with named arguments by @bentsherman in [#6550](https://github.com/nextflow-io/nextflow/pull/6550)
-- Fixed false error with task ext blocks in strict syntax by @bentsherman in [#6569](https://github.com/nextflow-io/nextflow/pull/6569)
+- Fixed false error with task `ext` blocks in strict syntax by @bentsherman in [#6569](https://github.com/nextflow-io/nextflow/pull/6569)
 - Fixed invalid cache write when cacheable split operation fails by @bentsherman in [#6588](https://github.com/nextflow-io/nextflow/pull/6588)
 - Fixed issue with optional workflow output by @bentsherman in [#6519](https://github.com/nextflow-io/nextflow/pull/6519)
-- Fixed issues with rsync stage-out mode by @bentsherman in [#6587](https://github.com/nextflow-io/nextflow/pull/6587)
+- Fixed issues with `rsync` stage-out mode by @bentsherman in [#6587](https://github.com/nextflow-io/nextflow/pull/6587)
 
 ### Configuration
 
 - Fixed false config validation warnings for process selectors by @bentsherman in [#6542](https://github.com/nextflow-io/nextflow/pull/6542)
 
 ### Plugins
 
-- Fixed Plugins.init() in run command to original location by @jorgee in [#6568](https://github.com/nextflow-io/nextflow/pull/6568)
+- Fixed `Plugins.init()` in run command to original location by @jorgee in [#6568](https://github.com/nextflow-io/nextflow/pull/6568)
 
 ### General
 
 - Fixed asset detection when item is not a sibling of the executed script by @DriesSchaumont in [#6605](https://github.com/nextflow-io/nextflow/pull/6605)
-- Fixed security vulnerabilities in org.json dependency by @pditommaso in [c7161c2](https://github.com/nextflow-io/nextflow/commit/c7161c2a)
-- Fixed TowerJsonGenerator thread-safety issue by @pditommaso in [#6619](https://github.com/nextflow-io/nextflow/pull/6619)
-- Fixed security vulnerabilities for wiremock by @jorgee in [#6607](https://github.com/nextflow-io/nextflow/pull/6607)
+- Fixed security vulnerabilities in `org.json` dependency by @pditommaso in [c7161c2](https://github.com/nextflow-io/nextflow/commit/c7161c2a)
+- Fixed `TowerJsonGenerator` thread-safety issue by @pditommaso in [#6619](https://github.com/nextflow-io/nextflow/pull/6619)
+- Fixed security vulnerabilities for `wiremock` by @jorgee in [#6607](https://github.com/nextflow-io/nextflow/pull/6607)
 - Fixed replace complete plotly bundle with smaller more specific one by @mashehu in [#6527](https://github.com/nextflow-io/nextflow/pull/6527)
-- Fixed stageFileEnabled flag to control `.command.stage` file creation by @pditommaso in [#6618](https://github.com/nextflow-io/nextflow/pull/6618)
+- Fixed `stageFileEnabled` flag to control `.command.stage` file creation by @pditommaso in [#6618](https://github.com/nextflow-io/nextflow/pull/6618)
 
 **Full changelog**: https://github.com/nextflow-io/nextflow/releases/tag/v25.11.0-edge

changelog/nextflow/v25.12.0-edge.md

@@ -13,16 +13,16 @@ tags: [nextflow]
 
 ### Google Batch
 
-- Added default maxSpotAttempts for fusion snapshots in Google Batch by @fntlnz in [#6652](https://github.com/nextflow-io/nextflow/pull/6652)
-- Refactored Google Batch getExitCode to imperative style by @pditommaso in [#6649](https://github.com/nextflow-io/nextflow/pull/6649)
+- Added default `maxSpotAttempts` for Fusion Snapshots in Google Batch by @fntlnz in [#6652](https://github.com/nextflow-io/nextflow/pull/6652)
+- Refactored Google Batch `getExitCode` to imperative style by @pditommaso in [#6649](https://github.com/nextflow-io/nextflow/pull/6649)
 
 ### Kubernetes
 
-- Added runtimeClassName to the pod options by @alexpilotti in [#6633](https://github.com/nextflow-io/nextflow/pull/6633)
+- Added `runtimeClassName` to the pod options by @alexpilotti in [#6633](https://github.com/nextflow-io/nextflow/pull/6633)
 
 ### Wave
 
-- Added wave.build.template config option by @pditommaso in [#6639](https://github.com/nextflow-io/nextflow/pull/6639)
+- Added `wave.build.template` config option by @pditommaso in [#6639](https://github.com/nextflow-io/nextflow/pull/6639)
 
 ### Plugins
 
@@ -31,19 +31,19 @@ tags: [nextflow]
 
 ### General
 
-- Added onlyJobState option for SLURM executor by @tcutts in [#6659](https://github.com/nextflow-io/nextflow/pull/6659)
-- Added spot interruption tracking to trace records by @munishchouhan in [#6606](https://github.com/nextflow-io/nextflow/pull/6606)
+- Added `onlyJobState` option for SLURM executor by @tcutts in [#6659](https://github.com/nextflow-io/nextflow/pull/6659)
+- Added Spot interruption tracking to trace records by @munishchouhan in [#6606](https://github.com/nextflow-io/nextflow/pull/6606)
 - Added URL encoding when revision name is used as HTTP query parameter by @jorgee in [#6598](https://github.com/nextflow-io/nextflow/pull/6598)
 - Added warnings to JSON output in lint command by @ewels in [#6625](https://github.com/nextflow-io/nextflow/pull/6625)
 - Implemented Git multiple revisions by @jorgee in [#6620](https://github.com/nextflow-io/nextflow/pull/6620)
 - Added Nextflow Development Constitution by @pditommaso in [#6578](https://github.com/nextflow-io/nextflow/pull/6578)
-- Added extra warnings as 25.10 is added to platform by @christopher-hakkaart in [#6655](https://github.com/nextflow-io/nextflow/pull/6655)
-- Added longer NXF_SYNTAX_PARSER descriptions by @christopher-hakkaart in [#6637](https://github.com/nextflow-io/nextflow/pull/6637)
+- Added extra warnings as 25.10 is added to Platform by @christopher-hakkaart in [#6655](https://github.com/nextflow-io/nextflow/pull/6655)
+- Added longer `NXF_SYNTAX_PARSER` descriptions by @christopher-hakkaart in [#6637](https://github.com/nextflow-io/nextflow/pull/6637)
 - Documented best practices for script and config params by @bentsherman in [#6631](https://github.com/nextflow-io/nextflow/pull/6631)
 - Fixed typos by @christopher-hakkaart in [#6641](https://github.com/nextflow-io/nextflow/pull/6641)
 - Improved preview feature warnings in documentation by @pditommaso in [#6663](https://github.com/nextflow-io/nextflow/pull/6663)
 - Updated note about AWS CLI by @christopher-hakkaart in [#6626](https://github.com/nextflow-io/nextflow/pull/6626)
-- Updated NXF_SYNTAX_PARSER callouts by @christopher-hakkaart in [#6640](https://github.com/nextflow-io/nextflow/pull/6640)
+- Updated `NXF_SYNTAX_PARSER` callouts by @christopher-hakkaart in [#6640](https://github.com/nextflow-io/nextflow/pull/6640)
 
 ## Bug fixes
 
@@ -54,15 +54,15 @@ tags: [nextflow]
 
 ### Wave
 
-- Fixed WaveClient sending Bearer token to public S3 URLs by @pditommaso in [#6672](https://github.com/nextflow-io/nextflow/pull/6672)
+- Fixed `WaveClient` sending Bearer token to public S3 URLs by @pditommaso in [#6672](https://github.com/nextflow-io/nextflow/pull/6672)
 
 ### Plugins
 
-- Fixed String.format error when plugin URL contains percent chars by @pditommaso in [#6651](https://github.com/nextflow-io/nextflow/pull/6651)
+- Fixed `String.format` error when plugin URL contains percent chars by @pditommaso in [#6651](https://github.com/nextflow-io/nextflow/pull/6651)
 
 ### General
 
-- Fixed GitHub repository provider when providing token with auth property by @jorgee in [#6662](https://github.com/nextflow-io/nextflow/pull/6662)
+- Fixed GitHub repository provider when providing token with `auth` property by @jorgee in [#6662](https://github.com/nextflow-io/nextflow/pull/6662)
 - Fixed tolerate spaces in `$NXF_TASK_WORKDIR` by @TheLostLambda in [#6421](https://github.com/nextflow-io/nextflow/pull/6421)
 
 **Full changelog**: https://github.com/nextflow-io/nextflow/releases/tag/v25.12.0-edge

changelog/nextflow/v26.01.0-edge.md

@@ -0,0 +1,87 @@
+---
+title: Nextflow 26.01.0-edge
+date: 2026-02-08
+tags: [nextflow]
+---
+
+## Feature updates and improvements
+
+### Language features
+
+- Allowed `collection-type` params to be loaded from files by @bentsherman in [#6675](https://github.com/nextflow-io/nextflow/pull/6675)
+- Enabled v2 syntax parser by default by @bentsherman in [#6643](https://github.com/nextflow-io/nextflow/pull/6643)
+- Improved config syntax errors by @bentsherman in [#6721](https://github.com/nextflow-io/nextflow/pull/6721)
+- Improved error message for invalid config statements by @bentsherman in [#6804](https://github.com/nextflow-io/nextflow/pull/6804)
+- Improved error messages for workflow outputs by @bentsherman in [#6785](https://github.com/nextflow-io/nextflow/pull/6785)
+- Moved task hashing logic to TaskHasher class by @bentsherman in [#6572](https://github.com/nextflow-io/nextflow/pull/6572)
+
+### AWS Batch
+
+- Added `aws.batch.forceGlacierTransfer` config option by @munishchouhan in [#6700](https://github.com/nextflow-io/nextflow/pull/6700)
+
+### Google Batch
+
+- Refactored `GoogleBatchTaskHandler.newSubmitRequest` for reduced complexity by @pditommaso in [#6687](https://github.com/nextflow-io/nextflow/pull/6687)
+
+### Kubernetes
+
+- Added time-based caching for `K8sConfig.getClient()` by @munishchouhan in [#6742](https://github.com/nextflow-io/nextflow/pull/6742)
+
+### Configuration
+
+- Supported multiple config option types in config spec by @bentsherman in [#6720](https://github.com/nextflow-io/nextflow/pull/6720)
+
+### General
+
+- Added accelerator request to trace record by @munishchouhan in [#6703](https://github.com/nextflow-io/nextflow/pull/6703)
+- Added `CloudCacheConfig` to register `cloudcache` config options by @pditommaso in [#6774](https://github.com/nextflow-io/nextflow/pull/6774)
+- Added markdown output mode to lint command by @ewels in [#6715](https://github.com/nextflow-io/nextflow/pull/6715)
+- Added missing provider credentials when updating the bare repo in multi-revision assets by @jorgee in [#6698](https://github.com/nextflow-io/nextflow/pull/6698)
+- Added warning stats to lint summary output by @ewels in [#6714](https://github.com/nextflow-io/nextflow/pull/6714)
+- Added workflow manifest metadata to execution report by @bentsherman in [#6689](https://github.com/nextflow-io/nextflow/pull/6689)
+- Detected conda explicit files by content instead of extension by @bentsherman in [#6713](https://github.com/nextflow-io/nextflow/pull/6713)
+- Excluded nf-test.config from lint by default by @ewels in [#6716](https://github.com/nextflow-io/nextflow/pull/6716)
+- Used `conda-forge` and `bioconda` channels by default by @Midnighter in [#5423](https://github.com/nextflow-io/nextflow/pull/5423)
+
+### Dependencies
+
+- Bumped Groovy to 4.0.30 by @pditommaso in [#6747](https://github.com/nextflow-io/nextflow/pull/6747)
+- Bumped Spock 2.4 by @pditommaso in [#6681](https://github.com/nextflow-io/nextflow/pull/6681)
+
+## Bug fixes
+
+### Language features
+
+- Fixed caching of task ext properties with the strict parser by @bentsherman in [#6696](https://github.com/nextflow-io/nextflow/pull/6696)
+- Fixed compiler error in v2 parser with enums by @bentsherman in [#6781](https://github.com/nextflow-io/nextflow/pull/6781)
+- Fixed different task hash with v2 parser by @bentsherman in [#6789](https://github.com/nextflow-io/nextflow/pull/6789)
+- Fixed false error in v2 parser when including config file from http url by @bentsherman in [#6753](https://github.com/nextflow-io/nextflow/pull/6753)
+- Fixed false error with multi-line tuple assignment in v2 parser by @bentsherman in [#6786](https://github.com/nextflow-io/nextflow/pull/6786)
+- Fixed false error with optional param by @bentsherman in [#6811](https://github.com/nextflow-io/nextflow/pull/6811)
+- Fixed issue with topic file emissions in typed processes by @bentsherman in [#6688](https://github.com/nextflow-io/nextflow/pull/6688)
+- Fixed params inclusion across modules in v2 parser by @bentsherman in [#6766](https://github.com/nextflow-io/nextflow/pull/6766)
+- Fixed resolution of nested Groovy class in v2 parser by @bentsherman in [#6744](https://github.com/nextflow-io/nextflow/pull/6744)
+- Fixed type inference in v2 `ConfigDsl` by @bentsherman in [#6800](https://github.com/nextflow-io/nextflow/pull/6800)
+
+### AWS Batch
+
+- Fixed AWS Batch spot instance detection by @munishchouhan in [#6722](https://github.com/nextflow-io/nextflow/pull/6722)
+- Fixed `isCompleted` check in `getNumSpotInterruptions` by @munishchouhan in [#6805](https://github.com/nextflow-io/nextflow/pull/6805)
+
+### S3
+
+- Fixed error when checking whether an S3 bucket exists by @jorgee in [#6706](https://github.com/nextflow-io/nextflow/pull/6706)
+
+### Kubernetes
+
+- Fixed K8s job fallback to not return incorrect zero exit code by @munishchouhan in [#6746](https://github.com/nextflow-io/nextflow/pull/6746)
+
+### General
+
+- Fixed fetching new remote branch in multi-revision mode by @jorgee in [#6733](https://github.com/nextflow-io/nextflow/pull/6733)
+- Fixed lint error formatting for errors at end of line by @ewels in [#6717](https://github.com/nextflow-io/nextflow/pull/6717)
+- Fixed `LogsCheckpoint` thread blocking shutdown for up to 90 seconds by @pditommaso in [#6787](https://github.com/nextflow-io/nextflow/pull/6787)
+- Fixed `nextflow inspect` not applying container settings from config by @adam-novak in [#6736](https://github.com/nextflow-io/nextflow/pull/6736)
+- Fixed spurious WARN when workflow fails before `onFlowBegin` by @pditommaso in [#6816](https://github.com/nextflow-io/nextflow/pull/6816)
+
+**Full changelog**: https://github.com/nextflow-io/nextflow/releases/tag/v26.01.0-edge

changelog/nextflow/v26.01.1-edge.md

@@ -0,0 +1,30 @@
+---
+title: Nextflow 26.01.1-edge
+date: 2026-02-11
+tags: [nextflow]
+---
+
+## Feature updates and improvements
+
+### General
+
+- Added OSC 8 hyperlinks to task hashes in progress output by @bentsherman in [#6799](https://github.com/nextflow-io/nextflow/pull/6799)
+- Improved documentation of workflow outputs by @bentsherman in [#6822](https://github.com/nextflow-io/nextflow/pull/6822)
+
+### Dependencies
+
+- Bumped ch.qos.logback@1.5.26 to fix false version mismatch warning in shadow JAR by @pditommaso in [0b97f4a](https://github.com/nextflow-io/nextflow/commit/0b97f4a84)
+- Bumped ch.qos.logback@1.5.25 (CVE-2026-1225) by @pditommaso in [97dec3a](https://github.com/nextflow-io/nextflow/commit/97dec3af6)
+- Bumped com.gradleup.shadow@9.3.1 (CVE-2025-68161) by @pditommaso in [d31e6ed](https://github.com/nextflow-io/nextflow/commit/d31e6edc7)
+
+## Bug fixes
+
+### Language features
+
+- Fixed `listDirectory()` to follow symbolic links by @bentsherman in [#6821](https://github.com/nextflow-io/nextflow/pull/6821)
+
+### General
+
+- Fixed JGit resources not being closed in CLI commands by @pditommaso in [#6795](https://github.com/nextflow-io/nextflow/pull/6795)
+
+**Full changelog**: https://github.com/nextflow-io/nextflow/releases/tag/v26.01.1-edge

changelog/wave/v1.32.3.md

@@ -0,0 +1,21 @@
+---
+title: Wave v1.32.3
+date: 2026-02-10
+tags: [wave]
+---
+
+## Feature updates and improvements
+
+### Dependencies
+
+- Bumped libseqera dependencies by @pditommaso in [#978](https://github.com/seqeralabs/wave/pull/978)
+
+## Bug fixes
+
+None.
+
+### General
+
+- Closed pairing session on heartbeat when record is missing from Redis by @pditommaso in [#977](https://github.com/seqeralabs/wave/pull/977)
+
+**Full changelog**: https://github.com/seqeralabs/wave/compare/v1.32.2...v1.32.3