Nextflow

- Improve Google Batch executor stability and error handling (5690) [1a9e8bf5]
- Fix Mount input file buckets in task arrays for Google Batch (5739) [0d98442d]
- Fix Google Batch task array causes process to fail (5780) [d4c1ba12]
- Fixing bug when execution with stub and no stub defined (5473) [ba5ab069]
- Fix Conda directive is not honoured by task array (5704) [63124eb8]
- Fix Use unbound queue for transfer thread pool (5700) [d57a85d0]
- Bump nf-google1.15.4 [ee9c1fd4]

25.01.0-edge - 12 Feb 2025
- Add DeadlineExceededException to Google Batch retryable exceptions [944f48f9]
- Add Fusion token validation (5614) [1dcb18d6]
- Add stub flag to task hash only if task has a stub (5750) [deec443d]
- Add traceparent header to wave & tower clients (5725) [7eea9f2d]
- Allow Azure Batch tasks to be submitted to different pools (5766) [76790d2a]
- Configure target java version alongside gradle toolchain (5676) [2153abb1]
- Disable cleanup on remote work dir (5742) [ef67b81e]
- Do not skip integration tests on PRs [4caf6ef8]
- Fail the run if publish thread pool times out (5578) [5325e5a6]
- Fix Check for number of low priority nodes in Azure Batch before raising a pool resize error (5576) [9b528c11]
- Fix Conda directive is not honoured by task array (5704) [f8c3b63c]
- Fix Create parent directory for DAG report (5752) [62263a35]
- Fix Google Batch task array causes process to fail (5780) [7ad7a237]
- Fix Mount input file buckets in task arrays for Google Batch (5739) [ba171fd1]
- Fix bugs with workflow outputs (5502) [ab59d30f]
- Fix first collection method [a0ca6e4f]
- Fix stub templates (5751) [13072d64]
- Ignore tests when smoke mode is enabled [3eb6efad]
- Improve Google Batch executor stability and error handling (5690) [b64087fc]
- Preserve attributes of published files (take 2) (5660) [422f2898]
- Remove compileJava options [28e03a21]
- Remove redundant exception handling [00376aa3]
- Revert "Fix the cleanup of local secret file" (5697) [55f25b34]
- Strengthen shell directive validation (5689) [039c8f30]
- Update HyperQueue CLI option (5730) [BREAKING] [b582cb57]
- Update azure deps [b163da95]
- Use unbound queue for transfer thread pool (5700) [90319681]
- Bump Fusion to version 2.5 (2nd attempt) [a7f09ae4]
- Bump gradle 8.12.1 [1fffb85c]
- Bump groovy 4.0.25 [19c40a4a]
- Bump io.netty:netty-handler:4.1.118.Final [db4a9037]
- Bump net.minidev:json-smart:2.5.2 [b5c4faf4]
- Bump netty-common:4.1.118.Final [8574e243]

- Fix CLI params normalization (5661) [42a9d8a0]
- Fix azure repos when clone URL is used (5667) [eb092c9f]
- Fix Prevent the use existing work dir (5682) [7ed233ea]

24.12.0-edge - 20 Jan 2025
- Add Warning when Cloudinfo fails in Google Batch machine type selection (5649) [5aef532f]
- Add rate limiter to wave requests (5608) [ecf68294]
- Allow named parameters with plugin subcommand (5643) [f81da8cf]
- Customise mermaid diagram theme in DAG template (5553) [54713a16]
- Deprecate -with-weblog CLI opt [aa258b4a]
- Disable AWS SDK v1 warning [cd00a26d]
- Dump threads only with trace log level [87df7cd4]
- Ensure job is killed when exception in task status check (5561) [9eefd207]
- Fix CLI params normalization (5661) [e2e prod] [b5d43adc]
- Fix Execution may hang reading trace file (5683) [17d7a083]
- Fix Google Batch hang when internal error during scheduling (5567) [18f7de13]
- Fix GroovyCompiler source and target compability [6dd92e3a]
- Fix Only close the cache db if it is not null (5631) [93860828]
- Fix Azure repos when clone URL is used (5667) [dc6cc414]
- Fix shell directive with trace command in wrapper script (4292) [8342889e]
- Fixing getRepositoryUrl when project name is not provided (5560) [335701e3]
- Handle attribute caching with Lustre filesystem (5650) [61674d2b]
- Improve Fargate + Wave docs (5562) [12be47ef]
- Improve inspect mode (5605) [8e2056e7]
- Include all processes in inspect command (5580) [0aa76aff]
- Prevent the use existing work dir (5682) [e14fc998]
- Remove 'defaults' conda channel from docs (5607) [8b541814]
- Update Google Batch docs to clarify spot retry behaviour (5644) [18788361]
- Update flux job id regular expression (5662) [58a0b344]
- Use printf instead of echo to write trace file (5397) [c6434d46]
- Bump groovy 4.0.24 missing deps [40670f7e]
- Bump jgit to version 7.1.0 (5587) [3d714683]
- Bump logback 1.5.13 + slf4j 2.0.16 [cc0163ac]
- Bump logback 1.5.16 [5ac91f00]
- Bump nf-wave1.9.0 [182ddd46]
- Bump nf-tower1.9.4 [4d949d16]
- Bump nf-google1.17.0 [741d0f38]
- Bump nf-console1.1.5 [958820fd]
- Bump nf-codecommit0.2.3 [fdc32c71]
- Bump nf-cloudcache0.4.3 [c173c535]
- Bump nf-azure1.12.0 [b747dcfa]
- Bump nf-amazon2.11.0 [2650f07a]

24.11.0-edge - 3 Dec 2024
- Add GHA to submit dependencies to dependabot (5440) [80395a6d]
- Add NotFoundException to retry condition for Google Batch [aa4d19cc]
- Add Rahel Hirsch to run name generator (5442) [ff2bc6ae]
- Add `env()` function (5506) [fa0e8e0f]
- Add more scientists to run name generator (5447) [38d9eda0]
- Add `singularity.libraryDir` to config page (5498) [b5e31bb0]
- Add RepositoryProvider.revision now public property (5500) [f0a4c526]
- Deprecate process `shell` block (5508) [6f527551]
- Detecting errors in data unstaging (5345) [3c8e602d]
- Disable virtual threads on CI tests [ci slip] [69d07dbc]
- Fix Fargate warning on memory check (5475) [bdf0ad00]
- Fix `isContainerReady` when wave is disabled (5509) [3215afa8]
- Fix missing wave response (5547) [ee252173]
- Fix overlapping conda lock file (5540) [9248c04d]
- Fix overlapping conda lock exception (5489) [eaaeb3de]
- Fix possible deadlock in dynamic `maxRetry` resolution (5474) [25bbb621]
- Fix Wave GCP integration test (5490) [ad56c89b]
- Fixing bug when execution with stub and no stub defined (5473) [f7fd56db]
- Fix Incorrect CPU value in Azure example (5549) [fc5e2c2a]
- Improve docs for using the GPU accelerator directive (5488) [4b908524]
- Improve groupTuple docs with scatter/gather example (5520) [b5c63a9f]
- Prevent NPE with null AWS Batch response [12fc1d60]
- Target Java 17 as minimal Java version (5045) [0140f954]
- Update 'nexus-staging' plugin to latest version (5462) [07934513]
- Update gradle 'shadow' plugin version to 8.3.5 (5463) [2a5f15f0]
- Update install docs to reflect change from 'all' to 'dist' (5496) [c9115659]
- Update process snippets to comply with strict syntax (5526) [be1694bf]
- Update Wave dependencies [09ccd295]
- Bump aws sdk 1.12.777 (5458) [8bad0b4b]
- Bump bouncycastle to jdk18on:1.78.1 (5467) [cd8c385f]
- Bump com.azure:azure-identity from 1.11.3 to 1.12.2 (5449) [cb70f1df]
- Bump commons-io:2.15.1 [767e4a0a]
- Bump groovy 4.0.24 [dd71ad31]
- Bump netty-common to version 4.1.115.Final [d1bbd3d0]
- Bump nf-amazon2.10.0 [2b653b07]
- Bump nf-azure1.11.0 [6af7198d]
- Bump nf-google1.16.0 [9494f970]
- Bump nf-google1.8.0 [7e2c8d82]
- Bump protobuf-java:3.25.5 to nf-google [488b7906]

- Prevent NPE with null AWS Batch response [3d491934]
- Fix overlapping conda lock file (5540) [df66deaa]
- Fix missing wave response (5547) [eb85cda8]
- Bump nf-wave1.7.4 [93d09404]
- Bump nf-amazon2.9.2 [469a35dd]

- Fix overlapping file lock exception (5489) [a2566d54]
- Fix isContainerReady when wave is disabled (5509) [c69e3711]
- Bump nf-wave1.7.3 [e7709a0f]
- Bump nf-azure1.10.2 [54496ac4]
- Bump nf-amazon2.9.1 [fa227933]
- Bump netty-common to version 4.1.115.Final [90623c1e]

- Add `manifest.contributors` config option (5322) [cf0f9690]
- Add wave mirror and scan config [92e69776]
- Add wave mirror vs module bundles conflicst warning [b37a8a5b]
- Add Workflow output definition (second preview) (5185) [ea128463]
- Demote azure batch task status log level to trace (5416) [d6c684bb]
- Document formal script syntax (5336) [a48ac589]
- Add Expose trace record meta info in the task context (5402) [ffdd3819]
- Fix NextflowMeta compilation error [500f49c0]
- Fix XFileSystem serialization issue (5411) [711864fd]
- Fix closure rendering in yaml and json config (5408) [d3a85ceb]
- Fix failing docs snippet (5430) [a818f4b8]
- Fix http files stream (5405) [e2e stage] [718dcbe6]
- Fix nf-tower plugin to upload logs when early failures (5434) [4222442a]
- Fix support for micromamba (4302) [12431302]
- Harmonise documentation for hybrid cloud execution (5362) [a69407d2]
- Prevent NPE when containerInfo is null [368a266a]
- Remove invalid equals char (5414) [7f39e6ed]
- Bump nf-azure1.10.1 [f67e157a]
- Bump nf-tower1.9.3 [7a572a12]
- Bump nf-wave1.7.2 [6524d8dc]

24.09.2-edge - 14 Oct 2024
- Add Google LS deprecation notice (5400) [0ee1d9bc]
- Add hybrid workflow documentation for Azure (5361) [f81f27de]
- Add more out formats to config command (5399) [8acdb6e8]
- Change to scan.levels to scan.allowedLevels (5401) [88a1b1b5]
- Fix inspect concretize option [0ee29a87]
- Manage moduleBinaries feature flag in the pipeline script (5348) [dd5fd20f]
- Bump nf-wave1.7.1 [94273967]
- Bump nf-google1.15.2 [fab01d58]

24.09.1-edge - 13 Oct 2024
- Add retry policy in Channel.fromSRA factory (5389) [fb1c8b2e]
- Add retry policy to Google batch describe task (5356) [64bb5a92]
- Add support for Wave container status API (5384) [873703ad] [9ed18a88]
- Fix Identify default git branch when downloading pipelines (3593) (5375) [4f74fc37]
- Fix issue when retrying with stub (5359) [324b611f]
- Fix include aborted in the ProgressRecord total count (5365) [8eb0c393]
- Redirect logs to stderr during app bootstrap (5206) [94918105]
- Remove unused reportsOpts (5379) [e794e868]
- Sunsetting Spack support in Wave [3a54cb3b] [7bbba67b]
- Bump nf-google1.15.1 [4204435e]
- Bump nf-wave1.7.0 [cdecb3f5]

24.09.0-edge - 2 Oct 2024
- Add Fusion version pinning info to Fusion config scope (5294) [be1cac37]
- Add container tip in the task error report (5299) [62e26043]
- Add support for Java 23 (5329) [6e10c372]
- Add Platform workflow prefix in AWS Batch job names (5318) [42dd4ba8]
- Fix AWS spot attempts with zero value (5331) [bac2da12]
- Fix Azure Fusion env misses credentials when no key or SAS provided (5328) [e11382c8]
- Fix CI build taking only the commit msg header [9e702c4d]
- Fix Inconsistency with camelCase and kebab-case config params 4702 (solve 4033) [349f4f6f]
- Fix XPath default de-serializer issue (5339) [290f2d07]
- Fix failOnIgnore causes task monitor to stop submitting tasks (5293) [d6870335]
- Fix large mermaid diagrams (5302) [a46edfa0]
- Improve Wave build timeout handling (5304) [05bef7e4]
- Include additional fields to manifest (5314) [33fab52d]
- Remove `mini` from Flux submit command (5229) [a0f69025]
- Update container handling with charliecloud (5300) [8e6068db]
- Update Documentation structure (4766) [25e5eba0]
- Update nextflow install docs (5198) [7c453815]
- Bump groovy 4.0.23 (5303) [fe3e3ac7]
- Bump nf-wave1.6.0 [179093dc]
- Bump nf-azure1.10.0 [41d37fa8]
- Bump nf-amazon2.9.0 [e38980fb]

24.08.0-edge - 4 Sep 2024
- Add Google Batch warning when for conflicting disk image config (5279) [96cb57cb]
- Add support for Google Batch used specified boot images (5268) [0aaa6482]
- Disable AWS spot retry (5215) [f28fcb25]
- Disable Google Batch automatic spot retries (5223) [aad21533]
- Disable automatic detection of virtual threads (5270) [b3ba2c2d]
- Fix missing .command.env when eval is used and task runs on a cloud env [4a6b54aa]
- Fix job array syntax for PBS/Torque executor (5281) [d59f5fae]
- Fix k8s client status cond is possible null in podState (5264) [46672415]
- Fix non-determinist behaviour of join operator with bag array as key (5189) [e7dc0d69]
- Fix stage retry on corrupted HTTP downloads (5275) [bf0cd326]
- Support Azure Managed Identities in Fusion configuration logic (5278) [a0bf8b40]
- Use public.cr.seqera.io in place of AWS ECR [5a01f277]
- Wave client logs improvement [5a37e617]
- Bump amazoncorretto:21-al2023 [59aed581]
- Bump nf-wave1.5.1 [97c4e08f]
- Bump nf-google1.15.0 [24133f2a]
- Bump nf-azure1.9.0 [29f49ba7]
- Bump nf-amazon2.8.0 [bbc3adca]

24.07.0-edge - 8 Aug 2024
- Add runtime error for missing channel factory (5170) [1f9210ab]
- Apply k8s.cpuLimits to kuberun driver pod (5160) [4300adf1]
- Await build completion for all Wave containers [2b8117e9]
- Deprecate module addParams() and params() (5200) [82c97f8c]
- Remove capsule launcher dependencies (3395) [f15e4246]
- Fix AWS Cloudwatch access when using custom log group name [30195838]
- Fix Invalid AWS Fargate CPUs usage error reporting [d9c50e59]
- Fix Prevent AwS Batch retry the job execution when the container does not exist [4e218f22]
- Fix Prevent negative cpus values [af2e4ef7]
- Fix ProcessUnrecoverableException detection [17ec6c96]
- Fix aws logs group name (5146) [643b16b0]
- Fix readAllBytes with http files (5202) [7e90ce62]
- Improve Google Batch 5000x error class handling (5141) [61b2205f]
- Improve docs [7703f0d0]
- Improve error message for topic channel feature flag (5161) [c4d407fb]
- Improve fusion docs (5166) [abdd78f1]
- Improve queue docs (5154) [bc2fb409]
- Improve version checking [e7a879de]
- Link to other docs on the failOnIgnore option (5122) [572f2116]
- Make Google Batch auto retry codes configurable (5148) [e562ce06]
- More robust parsing of shm-size containerOptions (5177) [b56802a3]
- Prevent default output/error logs for job arrays (5152) [71f6ed0b]
- Bump amazon sdk to version 1.12.766 [cc6ec314]
- Bump gradle 8.9 [a437e97f]
- Bump jgit 6.10.0 [177dc474]
- Bump nf-amazon2.7.0 [46c69d77]
- Bump nf-azure1.8.1 [26dcb604]
- Bump nf-cloudchare0.4.2 [c171b601]
- Bump nf-codecommit0.2.2 [d7dd4611]
- Bump nf-console1.1.4 [c1175157]
- Bump nf-google1.14.0 [1eda221a]
- Bump nf-tower1.9.2 [257bebfd]
- Bump nf-wave1.5.0 [e8d643c2]
- Bump pf4j to version 3.12.0 [96117b9a]
- Bump wave-api to 0.11.1 [96ec4ded]

- Fix parsing of shm-size containerOptions (5177) [98cf0068]
- Fix aws logs group name (5146) [b2ab651c]
- Update Azure batch deps [72576648]
- Bump nf-wave1.4.2-patch1 [19a7272f]
- Bump nf-codecommit0.2.1 [f2bcce99]
- Bump nf-azure1.6.1 [0ea1f102]
- Bump nf-amazon2.5.3 [b13b5548]
- Bump wave-api to 0.11.1 [87828afd]
- Bump amazon sdk to version 1.12.766 [5ce42b79]
- Bump pf4j to version 3.12.0 [1a8f086a]
- Bump jgit 6.10.0 [cc2ccd81]