Version 24.09.2-edge

• Add Google LS deprecation notice (#5400) [0ee1d9b]
• Add hybrid workflow documentation for Azure (#5361) [f81f27d]
• Add more out formats to config command (#5399) [8acdb6e]
• Change to scan.levels to scan.allowedLevels (#5401) [88a1b1b]
• Fix inspect concretize option [0ee29a8]
• Manage moduleBinaries feature flag in the pipeline script (#5348) [dd5fd20]
• Bump [email protected] [9427396]
• Bump [email protected] [fab01d5]

Version 24.09.1-edge

• Add retry policy in Channel.fromSRA factory (#5389) [fb1c8b2]
• Add retry policy to Google batch describe task (#5356) [64bb5a9]
• Add support for Wave container status API (#5384) [873703a] [9ed18a8]
• Fix Identify default git branch when downloading pipelines (#3593) (#5375) [4f74fc3]
• Fix issue when retrying with stub (#5359) [324b611]
• Fix include aborted in the ProgressRecord total count (#5365) [8eb0c39]
• Redirect logs to stderr during app bootstrap (#5206) [9491810]
• Remove unused reportsOpts (#5379) [e794e86]
• Sunsetting Spack support in Wave [3a54cb3] [7bbba67]
• Bump [email protected] [4204435]
• Bump [email protected] [cdecb3f]

Version 24.09.0-edge

• Add Fusion version pinning info to Fusion config scope (#5294) [be1cac3]
• Add container tip in the task error report (#5299) [62e2604]
• Add support for Java 23 (#5329) [6e10c37]
• Add Platform workflow prefix in AWS Batch job names (#5318) [42dd4ba]
• Fix AWS spot attempts with zero value (#5331) [bac2da1]
• Fix Azure Fusion env misses credentials when no key or SAS provided (#5328) [e11382c]
• Fix CI build taking only the commit msg header [9e702c4]
• Fix Inconsistency with camelCase and kebab-case config params #4702 (solve #4033) [349f4f6]
• Fix XPath default de-serializer issue (#5339) [290f2d0]
• Fix failOnIgnore causes task monitor to stop submitting tasks (#5293) [d687033]
• Fix large mermaid diagrams (#5302) [a46edfa]
• Improve Wave build timeout handling (#5304) [05bef7e]
• Include additional fields to manifest (#5314) [33fab52]
• Remove mini from Flux submit command (#5229) [a0f6902]
• Update container handling with charliecloud (#5300) [8e6068d]
• Update Documentation structure (#4766) [25e5eba]
• Update nextflow install docs (#5198) [7c45381]
• Bump groovy 4.0.23 (#5303) [fe3e3ac]
• Bump [email protected] [179093d]
• Bump [email protected] [41d37fa]
• Bump [email protected] [e38980f]

Version 24.08.0-edge

• Add Google Batch warning when for conflicting disk image config (#5279) [96cb57c]
• Add support for Google Batch used specified boot images (#5268) [0aaa648]
• Disable AWS spot retry (#5215) [f28fcb2]
• Disable Google Batch automatic spot retries (#5223) [aad2153]
• Disable automatic detection of virtual threads (#5270) [b3ba2c2]
• Fix missing .command.env when eval is used and task runs on a cloud env [4a6b54a]
• Fix job array syntax for PBS/Torque executor (#5281) [d59f5fa]
• Fix k8s client status cond is possible null in podState (#5264) [4667241]
• Fix non-determinist behaviour of join operator with bag array as key (#5189) [e7dc0d6]
• Fix stage retry on corrupted HTTP downloads (#5275) [bf0cd32]
• Support Azure Managed Identities in Fusion configuration logic (#5278) [a0bf8b4]
• Use public.cr.seqera.io in place of AWS ECR [5a01f27]
• Wave client logs improvement [5a37e61]
• Bump amazoncorretto:21-al2023 [59aed58]
• Bump [email protected] [97c4e08]
• Bump [email protected] [24133f2]
• Bump [email protected] [29f49ba]
• Bump [email protected] [bbc3adc]

Version 24.07.0-edge

• Add runtime error for missing channel factory (#5170) [1f9210a]
• Apply k8s.cpuLimits to kuberun driver pod (#5160) [4300adf]
• Await build completion for all Wave containers [2b8117e]
• Deprecate module addParams() and params() (#5200) [ci fast] [82c97f8]
• Remove capsule launcher dependencies (#3395) [f15e424]
• Fix AWS Cloudwatch access when using custom log group name [3019583]
• Fix Invalid AWS Fargate CPUs usage error reporting [d9c50e5]
• Fix Prevent AwS Batch retry the job execution when the container does not exist [4e218f2]
• Fix Prevent negative cpus values [af2e4ef]
• Fix ProcessUnrecoverableException detection [17ec6c9]
• Fix aws logs group name (#5146) [643b16b]
• Fix readAllBytes with http files (#5202) [7e90ce6]
• Improve Google Batch 5000x error class handling (#5141) [61b2205]
• Improve docs [7703f0d]
• Improve error message for topic channel feature flag (#5161) [c4d407f]
• Improve fusion docs (#5166) [abdd78f]
• Improve queue docs (#5154) [bc2fb40]
• Improve version checking [e7a879d]
• Link to other docs on the failOnIgnore option (#5122) [572f211]
• Make Google Batch auto retry codes configurable (#5148) [e562ce0]
• More robust parsing of shm-size containerOptions (#5177) [b56802a]
• Prevent default output/error logs for job arrays (#5152) [71f6ed0]
• Bump amazon sdk to version 1.12.766 [cc6ec31]
• Bump gradle 8.9 [a437e97]
• Bump jgit 6.10.0 [177dc47]
• Bump [email protected] [46c69d7]
• Bump [email protected] [26dcb60]
• Bump [email protected] [c171b60]
• Bump [email protected] [d7dd461]
• Bump [email protected] [c117515]
• Bump [email protected] [1eda221]
• Bump [email protected] [257bebf]
• Bump [email protected] [e8d643c]
• Bump pf4j to version 3.12.0 [96117b9]
• Bump wave-api to 0.11.1 [96ec4de]

Breaking changes

• Grape dependencies management via @Grab annotation is not supported anymore. Custom code requiring third parties libraries should be migrated to a custom plugin

Version 24.04.4

• Fix parsing of shm-size containerOptions (#5177) [98cf006]
• Fix aws logs group name (#5146) [b2ab651]
• Update Azure batch deps [7257664]
• Bump [email protected] [19a7272]
• Bump [email protected] [f2bcce9]
• Bump [email protected] [0ea1f10]
• Bump [email protected] [b13b554]
• Bump wave-api to 0.11.1 [87828af]
• Bump amazon sdk to version 1.12.766 [5ce42b7]
• Bump pf4j to version 3.12.0 [1a8f086]
• Bump jgit 6.10.0 [cc2ccd8]

Version 23.10.4

• Add docker launcher [474427a]
• Update Azure batch deps [e0c6d77]
• Bump [email protected] [5468361]
• Bump [email protected] [084092f]
• Bump [email protected] [de43b17]
• Bump amazon sdk to version 1.12.766 [189f58e]
• Bump pf4j to version 3.12.0 [8dfa407]
• Bump jgit 6.10.0 [4cf6b9f]

Version 24.04.3

• Add ability to override failOnError setting default via env variable (#5117) [ci fast] [6852429]
• Fix normalization of consecutive slashes in uri path (#5114) [3f366b7]
• Fix executions hangs on finalisation exception (#5070) [4c207c2]
• Bump [email protected] [55ec5ec]

Version 24.06.0-edge

• Add ability to override failOnError setting default via env variable (#5117) [72d7842]
• Add retry options to Azure Blob client (#5098) [7d5e5d2]
• Add support for HyperQueue 0.17.0 or later [BREAKING] [b45f7c4]
• Adds example of error strategies to documentation (#5121) [e82b0de]
• Fix docs for failOnDuplicate and failOnMismatch (#5113) [7d5c482]
• Fix normalization of consecutive slashes in uri path (#5114) [18ec484]
• Update Azure VMs and regions for 2024-07-01 (#5100) [12b027e]
• Bump Fusion 2.4 (#5080) [0a8a484]
• Bump Groovy 4.0.22 [284a660]
• Bump [email protected] [28122b7]
• Bump [email protected] [a1c2a81]
• Bump [email protected] [a3dfba5]
• Bump amazoncorretto:17-al2023 to Dockerfile [5e03a7b]

Version 24.05.0-edge

• Add Managed Identity to Azure authentication documentation (#5062) [ab5b3eb]
• Add support for Azure managed identity (#4897) [21ca16e]
• Add support for EC-encrypted private keys for K8s executor [4dbb519]
• Add workflow.failOnIgnore config option (#4686) [ci fast] [172edc3]
• Allow requester pays for S3 buckets (#5027) [0070c1b]
• Dump threads on abort condition [e374097]
• Enable build with Java 21 (#5030) [4c54db6]
• Fix Azure system-assigned managed identity [a639a17]
• Fix Java 22 version in launcher [29d6f1d]
• Fix executions hangs on finalisation exception (#5070) [38434b8]
• Fix support for Azure managed identity clientId [306814e]
• Fix support for s5cmd 2.2.2 (#5069) [7e78bd4]
• Fix the cleanup of local secret file (#5061) [e28537c]
• Fix typo in error message [f5c2355]
• Fix unique operator hangs when applied to value (#5053) [88b8ab0]
• Improve retry strategy for Google cloud errors when writing task helper files (#5037) [f8b324a]
• Remove GA4GH plugin (#5056) [0471b2e]
• Remove ending slashes for publish targets [891ed11]
• Bump Gradle 8.8 final [ee54606]
• Bump aws-sdk 1.12.740 [acad2a1]
• Bump azure-compute-batch:1.0.0-beta.2 [c08dc49]
• Bump azure-storage-blob 12.26.1 [c76ff5e]
• Bump [email protected] [01922f1]
• Bump [email protected] [c064d20]
• Bump [email protected] [eeca7d6]
• Bump [email protected] [d3f53c1]