Version 24.11.0-edge

• Add GHA to submit dependencies to dependabot (#5440) [80395a6]
• Add NotFoundException to retry condition for Google Batch [aa4d19c]
• Add Rahel Hirsch to run name generator (#5442) [ff2bc6a]
• Add env() function (#5506) [fa0e8e0]
• Add more scientists to run name generator (#5447) [38d9eda]
• Add singularity.libraryDir to config page (#5498) [b5e31bb]
• Add RepositoryProvider.revision now public property (#5500) [f0a4c52]
• Deprecate process shell block (#5508) [6f52755]
• Detecting errors in data unstaging (#5345) [3c8e602]
• Disable virtual threads on CI tests [ci slip] [69d07db]
• Fix Fargate warning on memory check (#5475) [bdf0ad0]
• Fix isContainerReady when wave is disabled (#5509) [3215afa]
• Fix missing wave response (#5547) [ee25217]
• Fix overlapping conda lock file (#5540) [9248c04]
• Fix overlapping conda lock exception (#5489) [eaaeb3d]
• Fix possible deadlock in dynamic maxRetry resolution (#5474) [25bbb62]
• Fix Wave GCP integration test (#5490) [ad56c89]
• Fixing bug when execution with stub and no stub defined (#5473) [f7fd56d]
• Fix Incorrect CPU value in Azure example (#5549) [fc5e2c2]
• Improve docs for using the GPU accelerator directive (#5488) [4b90852]
• Improve groupTuple docs with scatter/gather example (#5520) [b5c63a9]
• Prevent NPE with null AWS Batch response [12fc1d6]
• Target Java 17 as minimal Java version (#5045) [0140f95]
• Update 'nexus-staging' plugin to latest version (#5462) [0793451]
• Update gradle 'shadow' plugin version to 8.3.5 (#5463) [2a5f15f]
• Update install docs to reflect change from 'all' to 'dist' (#5496) [c911565]
• Update process snippets to comply with strict syntax (#5526) [be1694b]
• Update Wave dependencies [09ccd29]
• Bump aws sdk 1.12.777 (#5458) [8bad0b4]
• Bump bouncycastle to jdk18on:1.78.1 (#5467) [cd8c385]
• Bump com.azure:azure-identity from 1.11.3 to 1.12.2 (#5449) [cb70f1d]
• Bump commons-io:2.15.1 [767e4a0]
• Bump groovy 4.0.24 [dd71ad3]
• Bump netty-common to version 4.1.115.Final [d1bbd3d]
• Bump [email protected] [2b653b0]
• Bump [email protected] [6af7198]
• Bump [email protected] [9494f97]
• Bump [email protected] [7e2c8d8]
• Bump protobuf-java:3.25.5 to nf-google [488b790]

Version 24.10.2

• Prevent NPE with null AWS Batch response [3d49193]
• Fix overlapping conda lock file (#5540) [df66dea]
• Fix missing wave response (#5547) [eb85cda]
• Bump [email protected] [93d0940]
• Bump [email protected] [469a35d]

Version 24.10.1

• Fix overlapping file lock exception (#5489) [a2566d5]
• Fix isContainerReady when wave is disabled (#5509) [c69e371]
• Bump [email protected] [e7709a0]
• Bump [email protected] [54496ac]
• Bump [email protected] [fa22793]
• Bump netty-common to version 4.1.115.Final [90623c1]

Version 24.10.0

• Add manifest.contributors config option (#5322) [cf0f969]
• Add wave mirror and scan config [92e6977]
• Add wave mirror vs module bundles conflicts warning [b37a8a5]
• Add Workflow output definition (second preview) (#5185) [ea12846]
• Demote azure batch task status log level to trace (#5416) [d6c684b]
• Document formal script syntax (#5336) [a48ac58]
• Add Expose trace record meta info in the task context (#5402) [ffdd381]
• Fix NextflowMeta compilation error [500f49c]
• Fix XFileSystem serialization issue (#5411) [711864f]
• Fix closure rendering in yaml and json config (#5408) [d3a85ce]
• Fix failing docs snippet (#5430) [a818f4b]
• Fix http files stream (#5405) [e2e stage] [718dcbe]
• Fix nf-tower plugin to upload logs when early failures (#5434) [4222442]
• Fix support for micromamba (#4302) [1243130]
• Harmonise documentation for hybrid cloud execution (#5362) [a69407d]
• Prevent NPE when containerInfo is null [368a266]
• Remove invalid equals char (#5414) [7f39e6e]
• Bump [email protected] [f67e157]
• Bump [email protected] [7a572a1]
• Bump [email protected] [6524d8d]

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]