Nextflow

- 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]

- Add ability to override failOnError setting default via env variable (5117) [6852429c]
- Fix normalization of consecutive slashes in uri path (5114) [3f366b7e]
- Fix executions hangs on finalisation exception (5070) [4c207c23]
- Bump nf-google1.13.2-patch1 [55ec5ec5]

24.06.0-edge - 8 Jul 2024
- Add ability to override failOnError setting default via env variable (5117) [72d78425]
- Add retry options to Azure Blob client (5098) [7d5e5d2b]
- Add support for HyperQueue 0.17.0 or later [BREAKING] [b45f7c48]
- Adds example of error strategies to documentation (5121) [e82b0dee]
- Fix docs for `failOnDuplicate` and `failOnMismatch` (5113) [7d5c4824]
- Fix normalization of consecutive slashes in uri path (5114) [18ec484f]
- Update Azure VMs and regions for 2024-07-01 (5100) [12b027ee]
- Bump Fusion 2.4 (5080) [0a8a484e]
- Bump Groovy 4.0.22 [284a6606]
- Bump nf-azure1.8.0 [28122b70]
- Bump nf-google1.13.4 [a1c2a814]
- Bump nf-wave1.4.4 [a3dfba54]
- Bump amazoncorretto:17-al2023 to Dockerfile [5e03a7b7]

24.05.0-edge - 17 Jun 2024
- Add Managed Identity to Azure authentication documentation (5062) [ab5b3eb2]
- Add support for Azure managed identity (4897) [21ca16e6]
- Add support for EC-encrypted private keys for K8s executor [4dbb5193]
- Add workflow.failOnIgnore config option (4686) [172edc38]
- Allow requester pays for S3 buckets (5027) [0070c1b0]
- Dump threads on abort condition [e3740977]
- Enable build with Java 21 (5030) [4c54db6a]
- Fix Azure system-assigned managed identity [a639a17d]
- Fix Java 22 version in launcher [29d6f1df]
- Fix executions hangs on finalisation exception (5070) [38434b82]
- Fix support for Azure managed identity clientId [306814e7]
- Fix support for s5cmd 2.2.2 (5069) [7e78bd4d]
- Fix the cleanup of local secret file (5061) [e28537ca]
- Fix typo in error message [f5c2355b]
- Fix unique operator hangs when applied to value (5053) [88b8ab0c]
- Improve retry strategy for Google cloud errors when writing task helper files (5037) [f8b324ab]
- Remove GA4GH plugin (5056) [0471b2e1]
- Remove ending slashes for publish targets [891ed117]
- Bump Gradle 8.8 final [ee54606c]
- Bump aws-sdk 1.12.740 [acad2a1f]
- Bump azure-compute-batch:1.0.0-beta.2 [c08dc49b]
- Bump azure-storage-blob 12.26.1 [c76ff5e7]
- Bump nf-wave1.4.3 [01922f13]
- Bump nf-google1.13.3 [c064d209]
- Bump nf-azure1.7.0 [eeca7d67]
- Bump nf-amazon2.6.0 [d3f53c19]

- Fix handling of tags with slash on Bitbucket (5031) [76cd305f]
- Fix the default for async finalizer (5013) [f5fba709]
- Fix the invocation of function with gstring (5020) [04317f0d]
- Fix escapes dollar char in local secret provider (5021) [d8f8bf56]
- Improve Charliecloud registry handling (5018) [42496dbc]
- Enable the use of Java 22 (4970) [cbf24f9b]