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changelog.txt
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NEXTFLOW CHANGE-LOG
===================
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 [email protected] [2b653b07]
- Bump [email protected] [6af7198d]
- Bump [email protected] [9494f970]
- Bump [email protected] [7e2c8d82]
- Bump protobuf-java:3.25.5 to nf-google [488b7906]
24.10.2 - 27 Nov 2024
- Prevent NPE with null AWS Batch response [3d491934]
- Fix overlapping conda lock file (#5540) [df66deaa]
- Fix missing wave response (#5547) [eb85cda8]
- Bump [email protected] [93d09404]
- Bump [email protected] [469a35dd]
24.10.1 - 18 Nov 2024
- Fix overlapping file lock exception (#5489) [a2566d54]
- Fix isContainerReady when wave is disabled (#5509) [c69e3711]
- Bump [email protected] [e7709a0f]
- Bump [email protected] [54496ac4]
- Bump [email protected] [fa227933]
- Bump netty-common to version 4.1.115.Final [90623c1e]
24.10.0 - 27 Oct 2024
- 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 [email protected] [f67e157a]
- Bump [email protected] [7a572a12]
- Bump [email protected] [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 [email protected] [94273967]
- Bump [email protected] [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 [email protected] [4204435e]
- Bump [email protected] [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 [email protected] [179093dc]
- Bump [email protected] [41d37fa8]
- Bump [email protected] [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 [email protected] [97c4e08f]
- Bump [email protected] [24133f2a]
- Bump [email protected] [29f49ba7]
- Bump [email protected] [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 [email protected] [46c69d77]
- Bump [email protected] [26dcb604]
- Bump [email protected] [c171b601]
- Bump [email protected] [d7dd4611]
- Bump [email protected] [c1175157]
- Bump [email protected] [1eda221a]
- Bump [email protected] [257bebfd]
- Bump [email protected] [e8d643c2]
- Bump pf4j to version 3.12.0 [96117b9a]
- Bump wave-api to 0.11.1 [96ec4ded]
24.04.4 - 1 Aug 2024
- Fix parsing of shm-size containerOptions (#5177) [98cf0068]
- Fix aws logs group name (#5146) [b2ab651c]
- Update Azure batch deps [72576648]
- Bump [email protected] [19a7272f]
- Bump [email protected] [f2bcce99]
- Bump [email protected] [0ea1f102]
- Bump [email protected] [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]
23.10.4 - 31 Jul 2024
- Add docker launcher [474427a5]
- Update Azure batch deps [e0c6d77d]
- Bump [email protected] [54683615]
- Bump [email protected] [084092f1]
- Bump [email protected] [de43b17e]
- Bump amazon sdk to version 1.12.766 [189f58ed]
- Bump pf4j to version 3.12.0 [8dfa4076]
- Bump jgit 6.10.0 [4cf6b9f7]
24.04.3 - 9 Jul 2024
- 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 [email protected] [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 [email protected] [28122b70]
- Bump [email protected] [a1c2a814]
- Bump [email protected] [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 [email protected] [01922f13]
- Bump [email protected] [c064d209]
- Bump [email protected] [eeca7d67]
- Bump [email protected] [d3f53c19]
23.10.3 - 11 Jun 2024
- Bump [email protected] [6960daab]
- Bump [email protected] [fbd3c1b4]
- Bump [email protected] [f5b95820]
- Fix security vulnerabilities (#5057) [6d8765b8]
24.04.2 - 29 May 2024
- 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]
23.10.2 - 28 May 2024
- Update Platform API endpoint (#4855) [04cedce0]
- Fix semaphore in parallel polling monitor (#4927) [d173ceab]
- Fix security vulnerabilities (#5014) [a28b404c]
- Bump [email protected] [3852dd1e]
- Bump [email protected] [d692711b]
- Bump [email protected] [b48a1423]
- Bump [email protected] [911c1624]
- Bump [email protected] [9d6b64c3]
- Bump [email protected] [f43964f8]
- Bump [email protected] [fb9059c7]
- Bump [email protected] [8c398620]
- Bump [email protected] [1d3726db]
24.04.1 - 20 May 2024
- Fix nf-google plugin dependency [725e2860]
- Fix nf-amazon plugin dependency [c234b09f]
- Bump [email protected] [633989a6]
- Bump [email protected] [e31f70e0]
24.04.0 - 20 May 2024
- Add 'preview' to workflow runtime metadata (#4985) [935bb1e5]
- Add enabled property to output dsl (#5008) [284415b1]
- Fix Taskbar API is not supported error [0ea09ccc]
- Fix inspect should not write history entry [c713ad51]
- Fix unexpected container resolution [a5ecf8a4]
- Improve icon loading error handling [c72e16f8]
- Remove Fusion symlink resolution (#5004) [071ea74c]
- Remove `seqera` and `defaults` from Conda default channels (#5003) [ec5ebd0b]
- Use protected visibility for updateStatus method [6871ba06]
- Workflow output definition (#4784) [cf0546b1]
- Bump Fusion 2.3 (#5005) [7176c113]
- Bump groovy-console 4.0.21-patch.2 [eb97831f]
- Bump [email protected] [96ee633d]
- Bump [email protected] [e8359042]
- Bump [email protected] [5dcb4c7a]
- Bump [email protected] [73c668a6]
24.04.0-edge - 13 May 2024
- Add Wave and Fusion info to workflow metadata (#4945) [bb7e1c8e]
- Add `k8s.cpuLimits` config option (#3027) [3c6e96d0]
- Add account config option for grid executors (#4975) [a09e37dd]
- Add git to docs deps [aa9e1273]
- Add resourceLimits directive (#2911) [7c9d965e]
- Add support for Job arrays (#3892) [ca9bc9d4]
- Add support for clusterOptions as a list of values (#4993) [dd173e33]
- Add threads dump for troubleshooting purposes [8992ebde]
- Fix Gstring casting exception when clusterOptions is a closure [74004fbd]
- Fix Missing error code when no entry is specified [f507e9a4]
- Fix NPE in LogsCheckpoint class [deb3076d]
- Fix Prevent maxForks less than zero [7676dd9c]
- Fix Use fully qualified S3 uris in error message (#4923) [f1cffd1b]
- Fix Wave container resolution with singularity and ociMode [54ad6241]
- Fix collectFile saving to GCS with sort: false (#4965) [1418553a]
- Fix console "Plugin manager not initialised" warn (#4989) [5ff44538]
- Fix console icon (#4991) [b8a23706]
- Fix docs formatting [c02e58c7]
- Fix docs snippet [6499649d]
- Fix flaky docs test (#4957) [ea8246f6]
- Fix groovy console issue (#4988) [b9bf6410]
- Fix job array docs (#4984) [6a3347ee]
- Fix missing include error message (#4981) [aad100e1]
- Fix script error text alignment (#4681) [1dc4e4e4]
- Fix security vulnerability in logback (#4947) [0ffcc4ca]
- Fix semaphore in parallel polling monitor (#4927) [5c37fcc2]
- Fix remove commented out test lines in Azure Batch Pool opts tests. (#4914) [cb607f07]
- Guarantees K8s pod name is unique on resume (#4959) [361cef84]
- Improve config resolution docs (#4950) [019eb86c]
- Improve documentation about azcopy installation requirements for custom Azure Batch worker pools (#4911) [5c410db8]
- Improve error message for image pull time-out for Singularity/Apptainer/Charliecloud (#4974) [73015fbd]
- Remove unused const [6e91285d]
- Run task finalisation asynchronously (#4890) [e0e94227]
- Strip auth secret from logs [acf63e0e]
- Update TES executor to TES API v1.1 (#4195) [7b32c2d6]
- Update aws.md to include Cluster access (#4951) [459d725b]
- Update developer diagrams (#4922) [dcff41a5]
- Update operator return types (#4976) [a614fbe7]
- Update stale documentation in overview.md (#4968) [6a58c6d7]
- Use for instead eachLine in error formatting [4a821f46]
- azure batch autopool feature more comprehensive documentation (#4941) [adbd8903]
- Bump Gradle 8.7 [8b5cf3cc]
- Bump [email protected] [830b032c]
- Bump [email protected] [163683c2]
- Bump [email protected] [6d99a22a]
- Bump [email protected] [89695ed3]
- Bump [email protected] [357b143a]
- Bump [email protected] [6c62a60a]
24.03.0-edge - 15 Apr 2024
- Add custom jobName for Google Batch [df40d55f]
- Add escher to name generator class [2e6496e2]
- Add retry policy to Google Batch client [c4981dcc]
- Add retry strategy for publishing (#4839) [c9c7032c]
- Add support for Azure custom startTask (#4913) [27d01e3a]
- Add task tip extension point [eadad5b8]
- Allow secrets to be used in pipeline script (#4171) [df866a24]
- Do not print a new line when stdout is empty (#4892) [658a5ec8]
- Fix Azure pool creation [2ee4d11e]
- Fix Use of secrets in the includeConfig path [00c9f226]
- Fix coloured ANSI log bug (#4898) [a04d6983]
- Fix eval output type via bash -c wrapping (#4887) [2165a14d]
- Fix exception handling in local executor [74d7d7a8]
- Fix support for GCS requester pays bucket option [d9d61cff]
- Fix test when missing Google secret [33dc3ce0]
- Improve Charliecloud support (#4879) [287471c0]
- Improve control on azcopy install (#4883) [01447d5c]
- Improve error message when Google creds file is corrupted [a550e52f]
- Improve getting started docs (#4764) [b59111b3]
- Improve retry logic for AWS Batch executor [62926c28]
- Nextflow launch script: improving search for JAVA_CMD (#4830) [ebbbe9e7]
- Publish built-in reports as Tower reports (#4760) [b710d923]
- Remove not needed dsl=2 + error in example (#4812) [7c5779d7]
- Remove unused code from AssetManager [77365165]
- Revert "Fix failing CI tests (#4861)" [7ba2e253]
- Update NameGenerator (#4907) [248201af]
- Update Platform API endpoint (#4855) [4842423a]
- Update Wave to API v1alpha2 (#4906) [9c350872]
- Update docs (#4852) [6e2d1a94]
- Updated docs on Google Cloud setup and credentials (#4896) [7e8b5e26]
- Updated dodcs note on singularity default command (#4825) [567f5334]
- Bump groovy 4.0.20 [66c1a164]
- Bump groovy 4.0.21 [9e08390b]
- Bump [email protected] [fc70dc8c]
- Bump [email protected] [b0c4e2c5]
- Bump [email protected] [6ae25fad]
- Bump [email protected] [967c2ac8]
- Bump [email protected] [ddda969e]
24.02.0-edge - 10 Mar 2024
- Add K8s job ttlSecondsAfterFinished option (#4434) [93627be6]
- Add NXF_CACHE_DIR environment var (#4655) [4b00170a]
- Add colours to ansi logs (#4573) [5e2ce9ed]
- Add eval output type (#4493) [df978113]
- Fix Always emit publish event for symlinks on resume (#4790) [bb5c4f9d]
- Fix Do not create local plugin path in embedded mode [9d6dd6a0]
- Fix Error while publishing S3 file with blanks [b74c0227]
- Fix Missing dependency for console command [baf29110]
- Fix typo in Azure Batch docs ('Azore') (#4735) [192bf8df]
- Fix typo in error message [a7f23305]
- Remove experimental admonition for podman [17d0dced]
- Remove square brackets from job name in LSF executor (#4799) [6e0ac72d]
- Remove unneeded const [09c957fb]
- Rename Tower -> Seqera Platform in docs and log messages (#4727) [7caffef9]
- Update Azure dependencies [1bcbaf0d]
- Update copyright info [e3089f0e]
- Use alias for HistoryFile.Record [17217a1c]
- minor cli docstring fix (#4759) [ee4b4a25]
- Bump Grengine 3.0.2 [42ca2b6f]
- Bump groovy 4.0.19 [854dc1f0]
- Bump snakeyaml 2.2 [07480779]
- Bump [email protected] [0eb84071]
- Bump [email protected] [d63be8c0]
- Bump [email protected] [57b7004e]
- Bump [email protected] [b7f703f5]
- Bump [email protected] [b8ffb180]
- Bump [email protected] [0c542eda]
- Bump amazoncorretto 17.0.10-al2023 [3e695ad9]
24.01.0-edge - 5 Feb 2024
- Add support for custom fuse device plugin (#4612) [a1e33193]
- Fix Ignore stored process message when ansi log is enabled (#4645) [f9ba47ef]
- Fix Wave container replicable checksum [da382ddf]
- Fix azure retry policy (#4638) [85bab699]
- Fix handling of wave.s5cmdConfigUrl setting (#4707) [3a19386d]
- Fix typo in Hyperqueue section (#4635) [d5a6a963]
- Fix typo in OCI mode warning message (#4633) [e216a876]
- Fix typo in the docs (#4636) [ci-skip] [4727f174]
- Improve detection of sys home variable [8812138f]
- Improve handling of publish error (#4703) [fc9f7685]
- LocalSecretsProvider: invalid permissions tests made more robust (#4663) [682a6806]
- Remove Glacier auto-retrieval (#4705) [5f0ec50d]
- Remove preview from cmd secret [dc040226]
- Set scratch default to false when using Fusion (#4675) [9d17e407]
- Slight change in wording for error message about userEmulation (#4680) [a9c8a841]
- Truncate max size exceeded error message (#4644) [36090b70]
- Use AZURE_STORAGE_SAS_TOKEN environment variable (#4627) [2e02afbf]
- Use canonical init method for plugins initialization [e7a20aff]
- Bump [email protected] [8b9905c7]
- Bump [email protected] [bfc94e46]
- Bump [email protected] [01ff0353]
- Bump [email protected] [3df34188]
- Bump [email protected] [e90d73a7]
- Bump [email protected] [4379c941]
- Bump [email protected] [2bc698c7]
- Bump [email protected] [07415ce1]
- Bump [email protected] [b991e14b]
- Bump Groovy 4 (#4443) [9d32503b]
- Bump actions/checkout@v4 [d1b3195e]
- Bump [email protected] + [email protected] [331ff425]
- Bump nextflow 23.12.0-edge as min version [63e83702]
- Bump tj-actions/changed-files from 35 to 41 in /.github/workflows (#4622) [d67aef5f]
23.10.1 - 12 Jan 2023
- Fix bug with Fusion symlink resolution (#4593) [f28c9e48]
- Fix Fusion symlinks when publishing files (#4348) [1fa5878a]
- Fix Inspect command fails with Singularity [25883df3]
- Fix Allow the use of error built-in function in onComplete handler (#4458) [4be10cd3]
- Fix Harden regular expression to used to strip secrets in logs (#4563) [0102d4d6]
- Fix custom notification template [40980bcb]
- Fix container environment with special chars (#4594) [f4e00601]
- Fix AZURE_STORAGE_SAS_TOKEN environment variable (#4627) [2e1cb413]
- Fix azure retry policy (#4638) [2bc3cf0e]
- Fix BitBucket get source API with custom branch [5ef75e32]
- Improve error details for AbortOperationException [9e795a62]
- Bump [email protected] [206f2614]
- Bump [email protected] [50bcad59]
23.04.5 - 12 Jan 2023
- Fix container environment with special chars (#4594) [663b2936]
23.12.0-edge - 20 Dec 2023
- Add AWS_SESSION_TOKEN to Fusion environment (#4581) [552f29b0]
- Add ability to disable Cloudinfo service (#4606) [f7251895]
- Add experimental support for Fargate compute type for AWS Batch (#3474) [47cf335b]
- Add support for Instance template to Google Batch [df7ed294]
- Add support for Singularity/Apptainer auto pull mode for OCI containers [b7f1a192]
- Fix BitBucket get source API with custom branch [58937831]
- Fix Fusion tags documentation (#4551) [687e2e96]
- Fix Harden regular expression to used to strip secrets in logs (#4563) [832bff24]
- Fix bug with Fusion symlink resolution (#4593) [09e85582]
- Fix container environment with special chars (#4594) [e0fe952f]
- Fix custom notification template [ccf4f59e]
- Fix fusion symlink test (#4604) [681ace86]
- Fix smoke tests [d3c2f330]
- Improve GLS tests [58590b1c]
- Load nf-amazon when AWS SES is enabled [887f06f4]
- Move build num & timestamp to BuildInfo class [ec8083d4]
- Move app version to BuildInfo class [c7d749e8]
- Remove deprecated Wave observer [0e009ef7]
- Remove undocumented userEmulation mode (#4596) [f6c79788]
- Remove unused DSL2 check [e9ee3b2c]
- Replace each iterator with class for [f7662e68]
- Bump [email protected] [0b40b7b9]
- Bump [email protected] [bcb20fcf]
- Bump [email protected] [aa981814]
- Bump [email protected] and [email protected] [9cb50035]
- Build optimizations (#4579) [5ad41e44]
23.11.0-edge - 24 Nov 2023
- Add `fusion.cacheSize` config option (#4518) [2faadc22]
- Add Topic channel type (experimental) (#4459) [921313d1]
- Add Google Batch native retry on spot termination (#4500) [ea1c1b70]
- Add Retry policy to Google Storage (#4524) [c271bb18]
- Add ability detect Google Batch spot interruption (#4462) [d49f02ae]
- Add doc tests, move some snippets to separate files (#3959) [0ff3b305]
- Add docs section on container requirements (#4501) [3fb29f78]
- Add labels field in Job request for Google Batch (#4538) [627c595e]
- Add note about limitations of glacier auto retrieval (#4514) [82e56799]
- Add note about local executor and enforcing resource limits (#4468) [6a0626f7]
- Add section about sharing modules (#4482) [3e66fba4]
- Add section on process directives to plugin docs (#4477) [d9ee9870]
- Add support for Azure low-priority pool (#4527) [8320ea10]
- Add support for FUSION_AWS_REGION (#4481) [8f8b09fa]
- Add support for Fusion when using Singularity OCI mode (#4508) [4f3aa631]
- Add support for K8s schedulerName pod spec (#4485) [dfc7b7c8]
- Add support for Singularity OCI mode (#4440) [f5362a7b]
- Allow the use of error built-in function in onComplete handler (#4458) [35a4424b]
- Fix Bug in JsonSplitter ordering [8ec14dd2]
- Fix Bypass Google Batch Price query if task cpus and memory are defined (#4521) [7f8f20d3]
- Fix Checkout remote tag if checkout remote branch fails (#4247) [b8907ccb]
- Fix Fusion symlinks when publishing files (#4348) [89f09fe0]
- Fix Inspect command fails with Singularity [f5bb829f]
- Fix ParamsMap copyWith param aliases (#4188) [b480ee0e]
- Fix Singularity docs [e952299f]
- Fix container hashing for Singularity + Wave containers [4c6f2e85]
- Fix detection of Conda local path made by Wave client (#4532) [4d5bc216]
- Fix doc tests to fail on test failure (#4505) [4d326551]
- Fix errors when NXF_HOME contains spaces (#4456) [fe5bea99]
- Fix Google Batch network/subnetwork docs (#4475) [27d132f3]
- Fix rounding error with long durations (#4496) [0356178b]
- Fix security vulnerabilities (#4513) [a310c777]
- Fix Use consistently NXF_TASK_WORKDIR (#4484) [48ee3c64]
- Improve error details for AbortOperationException [35609cb0]
- Improve operator docs (#4502) [38210e11]
- Makefile clean to also remove buildSrc/build (#4517) [2ccb05d0]
- Minor test improvements [171831ea]
- Minor types improvement for mix operator [91c1ab15]
- Normalise channel docs [b641d677]
- Remove deprecated TowerArchiver feature [ff8e06a3]
- Remove dsl1 deprecated code (part 2) [159effb1]
- Remove dsl1 deprecated code [2b433a52]
- Remove incorrect note about workflow inputs (#4509) [54bc0b7d]
- Return error if plugin version is not specified in offline mode (#4487) [f5d7246e]
- Update README.md with new branding color for Nextflow (#4412) [7a13b18b]
- Update background color of docs status badges (#4411) [3cb1c53c]
- Update logging filter for Google Batch provider. (#4488) [66a3ed19]
- Bump Gradle 8.4 and test vs Java 21 (#4450) [8cb2702c]
- Bump [email protected] [8e2d7879]
- Bump [email protected] [7c47d090]
- Bump [email protected] [65240b75]
- Bump [email protected] [725f0510]
- Bump [email protected] [a307686c]
- Bump [email protected] [e54ea007]
- Bump [email protected] [033ec92c]
- Bump [email protected] [836a44a5]
- Bump [email protected] [620523ef]
23.10.0 - 15 Oct 2023
- Add support for K8s hostPath [10c32325]
- Add AWS SES docs [b83e7148]
- Add -with-cloudcache instead of -cloudcache [ef530263]
- Add inspect command validation tests [882f369e]
- Improve warning complaining about tuple but mentioning set (#4400) [0ef48735]
- Improve `-dump-hashes` output adding json format (#4369) [5bdaac94]
- Improve error message on invalid file url prefix [82a3f405]
- Fix conda channels order [6672c6d7]
- Docs: Incorporate DSL2 features (#3793) [efd041cb]
- Docs: aws.batch.retrymode = 'built-in' (#4229) [d5a8098f]
- Docs: Update logos, fonts, and colors (#4407) [7814822c]
- Changelog minor changes [dfb5bf09]
- Bump [email protected] [795849d7]
23.09.3-edge - 10 Oct 2023
- Add -cloudcache CLI option (#4385) [73fda582]
- Add bioconda and seqera Conda default channels (#4359) [ff012dcd]
- Add codespell: config, workflow and have typos fixed (#4324) [e044b7a5]
- Add docs page on caching and resuming (#4371) [21190a3c]
- Add example of using the transpose operator with multiple items in element (#4364) [0bce2be0]
- Add setting to enable the use of sync command [f0d5cc5c]
- Improve S3 endpoint validation [2b9ae6aa]
- Improve Wave config validation [7d5a21b0]
- Improve Wave error handling [d47e8b07]
- Fix Google Batch do not stop running jobs (#4381) [3d6b7358]
- Incorporate README content into Nextflow docs (#4263) [74a0f998]
- Never say (nearly) Oops again (#4356) [4a39542b]
- Remove unsupported K8s device capability [be0cf0c2]
- Remove unused -dsl2 option [3cb91a15]
- Rename Microsoft AAD to Microsoft Entra (#4362) [5e3f2c0a]
- Return -1 when exitcode file is empty (#4354) [d26c42be]
- Support for Fusion unprivileged execution (#4387) [035e6e7b]
- Use HistoryFile.Record instead of Record type conflict [11c3aac5]
- Bump [email protected] [a84208a8]
- Bump [email protected] [b37b4014]
- Bump [email protected] [b4eb8b96]
- Bump [email protected] [5681ab13]
- Bump [email protected] [de1de6c7]
23.09.2-edge - 28 Sep 2023
- Add conda.enabled to conda config scope docs (#4320) [0b74c4e2]
- Add developer docs (#4065) [06843d87]
- Add fs stat command [a79056b7]
- Add more tests to container name [da7a1942]
- Add procps by default to Conda-based Wave builds [66b2d2d2]
- Add support for Java 21 (#4338) [ac1fc9ee]
- Add Mermaid diagram in HTML DAG (#4337) [0f3e263f]
- Default Conda basePackages to "conda-forge::procps-ng" [367af52f]
- Disable Tower container field for multiple images [b53936b0]
- Document `NXF_DISABLE_CHECK_LATEST` environment var (#4327) [4e3e9aca]
- Document `fs` CLI command (#4328) [1a680495]
- Document source of `vol_ctxt` and `inv_ctxt` trace metrics (#4333) [6525b0a1]
- Document when process directives are evaluated (#4217) [731a29a2]
- Fix List of S3 bucket for custom endpoint [4327fa58]
- Fix Prevent false positive resumable task [144e0a8a]
- Fix Prevent multi attempts to retrieve AWS creds [b30efe36]
- Fix allow_other vulnerability preventing google-batch submissions (#4332) [9b3741e3]
- Fix fs list command [29ab2f24]
- Fix minor typos in changelogs/source code (#4319) [4ce9f1df]
- Fix support for S3 custom endpoint with anonymous access [03752815]
- Fix use of GITHUB_TOKEN variable to access GitHub repo [afe3dc4f]
- Fix Wave does not support 'null' container engine [f3eba3d7]
- Fix Retry TimeoutException in azure file system (#4295) [79248355]
- Improve K8s unit tests (#4196) [5a43a32b]
- Improve Mermaid DAG rendering (#4070) [19587f40]
- Improve error report when exception is thrown in operator ctx [16f54a9c]
- Improve wave container name validation [73eb5a02]
- Minor improvements [fff3d7bd]
- Prevent cache invalidation for task directives (#4339) [aabb6c19]
- Remove line endings from container box id (#4334) [df41e54a]
- Bump Apache 2.0 license to tower client [e4a878b6]
- Bump [email protected] [3311172f]
- Bump [email protected] [a9b735ce]
- Bump [email protected] [7219d7f2]
- Bump [email protected] [91a935f9]
- Bump [email protected] [0cf2476c]
- Bump [email protected] [d0c47d49]
23.04.4 - 25 Sep 2023
- Fix use of GITHUB_TOKEN variable to access GitHub repo [108c6b55]
- Fix allow_other vulnerability preventing google-batch submissions (#4332) [4895d547]
- Fix Prevent false positive resumable task [aae87715]
- Fix Always emit publish event for cached task outputs (#4227) [c4cd53c2]
- Fix Too long Http connection pool timeout [ce5e9930]
- Bump [email protected] [d881728c]
23.09.1-edge - 11 Sep 2023
- Revert "Allow setting shell directive when using the trace file (#4210)" [9f9edcdc]
23.09.0-edge - 10 Sep 2023
- Add check for latest version (#4194) [3e8cd488]
- Add inspect command (#4069) [090c31ce]
- Add maxSubmitAwait (#3736) [5686bf1d]
- Add scripts logging for troubleshooting [c056a74e]
- Add support for Spack to Singularity builds [23c4ec1d]
- Add support for Wave native build for Singularity [8a434893]
- Add support for inputs and outputs arity [42504d3c]
- Add support for remote debug (#4266) [87e0648a]
- Add warning about using clusterOptions with process directives (#4248) [a68c1a3e]
- Add which to dockerfile build [817aa05b]
- Align Singularity experience with Docker (#4230) [a1e1d3ca] [c1cc60dd]
- Allow setting shell directive when using the trace file (#4210) [7d6ad624]
- Always emit publish event for cached task outputs (#4227) [62686ce8]
- Deprecated Wave report feature [80c5cb27]
- Disable staging script for remote work dir (#4282) [80f7cd46]
- Disable version check on CI tests [db79e13f]
- Docs improvement to clarify the usage of the bin dir (#4121) [2daa4172]
- Document API differences of process path inputs (#4189) [c37e00bc]
- Document use of local variables in closures (#4251) [05ff784a]
- Fix IOException should be thrown when failing to creare Azure directory [b0bdfd79]
- Fix Parallel execution of Conda corrupts data and packages (#4253) [976c282c]
- Fix Parse negative CLI params as numbers (#4238) [1ae70d5d]
- Fix Too long Http connection pool timeout [fa961e7f]
- Fix Wave build for Singularity files [a60ef72b]
- Fix Wave build when Conda package name is quoted [d19cb0b7]
- Fix failing test [2785ffe9]
- Fix fs cp command with remote file [366eedec]
- Fix printf command with negative exit code (#4213) [465468b0]
- Fix security deps in nf-azure plugin [c30d5211]
- Fix setting `executor.queueSize = 0` is ignored (#4228) [6664b578]
- Improve Wave handing of Conda envs [736ab9bb]
- Improve pod options documentation (#4274) [c3aa26e1]
- Make TraceRecord@store field public accessible [07582f0b]
- Remove -dsl1 and -dsl1 rub cli options [b6721b71]
- Remove experimental -dockerize option /2 [7def5542]
- Remove experimental -dockerize option [937c8fb7]
- Report an error on duplicate workflow name definitions (#4088) [fce9702e]
- Undocument internal NXF_DEBUG variable [7955db8d]
- Update AZ File share doc (#4235) [69d317b6]
- Update docs about splitCsv() operator (#4163) [1dfb621c]
- Update documentation of NXF_DEBUG (#4187) [a88a4245]
- Use sipHash24 in place of deprecated murmur32 for script aliasing [bb96763f]
- Bump groovy 3.0.19 [cb411208]
- Bump [email protected] [7e5d414e]
- Bump [email protected] [83410f39]
- Bump [email protected] [a9f6dd65]
23.08.1-edge - 17 Aug 2023
- Add 429 http status code to Wave retriable errors [8eb5f305]
- Add resource labels support for Azure Batch (#4178) [7b5e50a1]
- Apply K8s Pod metadata to Job (#4057) [4d918627]
- Document error about trailing backslash with space (#4180) [245afa5d]
- Enable cloud cache based on environment variable (#4160) [a66b0e63]
- Escape semicolons in paths (#4193) [552501ce]
- FIx nested InvocationTargetException (#4192) [67980f19]
- Fix Execution should fail if report or timeline file already exists [b238d7e2]
- Fix Process hangs when using flatten and finish errorStrategy [d99b3432]
- Fix `workflow.container` map resolution (#4190) [96ab8a69]
- Fix checkpoint thread termination (#4166) [2b449daa]
- Fix env output when changing task workdir [8e4d7fed]
- Fix if-guard on log.trace in trask processor inner class [50f6f6d5]
- Fix typos in source code comments (#4173) [e78bc37e]
- Improve Conda build error report [7b19fb03]
- Improve handling of name-only container env variables [3051cd13]
- Minor changes [7e58c945]
- Remove dockerize launcher classpath file (#4191) [2bae5198]
- Remove lock file from cloudcache (#4167) [6e6ea579]
- Update AWS instructions for creating a custom AMI (#4174) [563bff13]
- Update changelog [98f88a50]
- Update tip about modifying maps (#4153) [30036dbf]
- Use root user in Wave container based on micromamba (#4038) [a3a75ea2]
- Bump [email protected] [6670bb06]
- Bump [email protected] [fb8f6681]
- Bump [email protected] [d06b8365]
- Bump [email protected] [7555b17d]
23.04.3 - 11 Aug 2023
- Increase Wave client max attempts [8c67610a]
- Fix log typo [03e19ea2]
- Add 429 http status code to Wave retriable errors [a8b8c6c5]
- Improve handling Wave server errors [621c9665]
- Bump [email protected] [d7fa3f26]
- Bump corretto 17.0.8 [7a73a78f]
23.08.0-edge - 5 Aug 2023
- Add `-value` option to `config` command (#4142) [57e3100b]
- Add `deleteTasksOnCompletion` to Azure Batch configuration (#4114) [b14674dc]
- Add Tower logs checkpoint (#4132) [71dfecc2]
- Allow use virtual threads in Wave client [dd32f80a]
- Allow workflow entry from module import (#4128) [51f5c842]
- Disable cache backup/restore if cloudcache is used (#4125) [46e828e1]
- Document behavior of withName selector with included aliases (#4129) [8b7e3d48]
- Fix Option fixOwnership traverse parent directories [f2a2ea35]
- Fix Redirection http redirection across different hosts [fcdeec02]
- Fix Wave disable flag [8579e7a4]
- Fix bug with K8s resource labels (#4147) eu-west-1[3f4b8557]
- Fix glob resolution for remove files [19a72c40]
- Fix incorrect error message on missing comma (#4085) eu-west-1[a59af39f]
- Fix missing changelog for version 23.07.0-edge eu-west-1[9a33e936]
- Fix strict mode docs (#4150) [6b46b507]
- Improve plugin docs (#3957) [22638d46]
- Improve Wave config logging [547fad62]
- Improve TaskPollingMonitor logging [077ed5dd]
- Improve Wave and Fusion docs (#4149) [d2229bde]
- Increase Wave client max attempts [fe5dd497]
- Remove module all components import [a6d08c04]
- Restore Tower CacheManager for backward compatibility [6d269070]
- Bump amazoncorretto:17.0.8 [00eb145c]
- Bump [email protected] [78e4b278]
- Bump [email protected] [41c8c164]
- Bump [email protected] [5f33ac17]
- Bump [email protected] [981315ad]
23.07.0-edge - 23 Jul 2023
- Add CPU model name to trace files and traceRecord (#3946) [e0d91bf7]
- Add ability to disable CLI params type detection [9a1c584d]
- Add cloudcache plugin (#4097) [ac90cc26]
- Add missing header to Wave container await [d39866e6]
- Add remote bin support for TES in a workdir (#3990) [8a22168a]
- Add retry logic to wave image await [9fc1d3bd]
- Add rule to build Nextflow docker image for ARM (#4020) [705d55f5]
- Add support for AWS SSO credentials provider (#4045) [53e33cde]
- Add support for Wave container freeze [9a5903e6]
- Add support legacy Wave retry [73a1e7d4]
- Allow SLURM executor option `--mem-per-cpu` (#4023) [96c04e3b]
- Allow disabling the Wave requirement when Fusion is enabled [9180d633]
- Disable Singularity and Apptainer home mount by default (#4056) [a0ee4657]
- Document `NXF_WRAPPER_STAGE_FILE_THRESHOLD` environment variable (#4113) [bda47567]
- Fix AzFileSystem retry policy [ba9b6d18] [c2f3cc96]
- Fix Improve error message for invalid Azure URI [0f4d8867]
- Fix Treat HTTP headers as case insensitive (#4116) [97fd3358]
- Fix invalid detection of hierarchical namespace stub blobs as files (#4046) [ce06c877]
- Fix stage script in Fusion script launcher (#4109) [0933f47e]
- Ignore accelerator type for AWS Batch (#4043) [263ecca8]
- Implement Weblog feature as an external plugin [f9f2c338]
- Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf0]
- Improve Azure retry logging [de58697a]
- Improve description of channels and channel types (#4120) [8975734d]
- Improve handling Wave server errors [84f7a61a]
- Increase Azure min retry delay to 250ms [2e77e5e4]
- Remove default arch from wave request [f0e5c0c1]
- Remove logging of report JSON data (#4098) [099e5039]
- Wait for all child processes in nxf_parallel (#4050) [60a5f1a7]
- Bump Groovy 3.0.18 [207eb535]
- Bump micromamba 1.4.9 [6307f9b5]
- Bump [email protected] [57464746]
- Bump [email protected] [e1512f6a]
- Bump [email protected] [27e7f663]
- Bump [email protected] [1895efc4]
- Bump [email protected] [cb6242c4]
- Bump [email protected] [f98feb77]
- Bump [email protected] [6aede7c0]
- Bump [email protected] [3278d798]
- Bump [email protected] [2998db5d]
23.06.0-edge - 14 Jun 2023
- Add AWS Kms integration test [19449bf4]
- Add Wave containers reports (preview) [9d9e2758]
- Add disk resource with type option for google batch (#3861) [166b3638]
- Add httpConnectTimeout and httpReadTimeout to Google options (#3974) [49fa15f7]
- Add plugin cmd help description [d3788f9f]
- Add retry policy on Az blob operations [295bc1ff]
- Add retry policy to Wave http client [1daebeef]
- Add support for AWS SES as mail sending provider [df85d443]
- Add support for arch auto-detection to Wave [7b5fdaf0]
- Add wave.httpClient.connectTimeout config option [dd999a3c]
- Clarify tip about groupTuple size and groupKey (#3949) [e60d327f]
- Consolidate Wave retryPolicy options [7d7464fe]
- Enhanced support for Spack + Wave (#3998) [63ac03b3]
- Fix Google Batch default instance family types (#3960) [b5257cd7]
- Fix S3 path normalization [b75ec444]
- Fix access to public S3 bucket when no creds are provided (#3992) [cf8ba466] [680f0a90]
- Fix containerOptions when using Fusion [dcde7b7f]
- Fix dump pretty print to not modify input (#3955) [46c17ee3]
- Fix invalid machine type setting when no valid machine type is found (#3961) [5eb93971]
- Fix matching symlink files [d63af784]
- Fix missing options for JsonSplitter creation (#3958) [f991fe9e]
- Fix non-deterministic null container engine error [f227f2e5]
- Fix packing all including Wave [735b8d9c]
- Fix static compiler errors [f48a473c]
- Improve documentation on Nextflow scripts (#3953) [80050c03]
- Improve description of channels and channel types (#4120) [8975734d]
- Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf0]
- Minor change in Wave config [4da0442a]
- Prevent null exit code when Google batch is unable to access exit status [f68a39ec]
- Refactor Conda and Spack support for Wave to Java [36b9e226]
- Remove `--no-home` default option from charliecloud builder (#3956) [915074a4]
- Update workflow.revision max length to match the one in Tower (#4010) [1433a903]
- Bump amazocorretto:17.0.7 [c8aa1214]
- Bump azure-storage-blob:12.22.1 [2a36fa77]
- Bump [email protected] [2998db5d]
- Bump [email protected] [3278d798]
- Bump [email protected] [6aede7c0]
- Bump [email protected] [f98feb77]
- Bump [email protected] [1895efc4]
- Bump [email protected] [57464746]
- Bump [email protected] [cb6242c4]
23.04.2 - 8 Jun 2023
- Fix non-deterministic null container engine error [f93221ab]
- Add retry policy to Wave client [2f1532f6]
- Fix wave build docs [34a73022]
- Bump [email protected] [350201b5]
23.05.0-edge - 15 May 2023
- Add support for custom custom root directory to resolve relative paths (#3942) [f06bb1f7]
- Add `arch` directive support for Spack (#3786) [62dfc482]
- Add clone deep option to run and pull commands [b44b6453]
- Add fusion.exportStorageCredentials option [acb6aedf]
- Add groovy-yaml to core runtime [003e1f70]
- Add missing test env variables to CI build [a0e501bf]
- Add splitJson Operator (#3830) [4f58f695]
- Add support for Java 20 [3788a689]
- Add support for `time` directive in Azure Batch (#3869) [5c11a0d4]
- Add support for the Spack recipes to Wave build (#3636) [b03cbe70]
- Add Preview support for virtual threads (#3871) [5c429046]
- Convert docs to Markdown (#3196) [3cad402f]
- Deprecate DSL1 syntax for tap operator (#3004) [2be0edfe]
- Enable static compilation to missing classes (#3906) [c3c4b2f0]
- Fix -with-conda option in the docs (#3867) [9b350ba8]
- Fix AWS SSE env propagation to Fusion [e24608c3]
- Fix Apptainer rendering by removing superfluous space [36607ed1]
- Fix Azure jobs correctly deleted after completion (#3927) [b173a983]
- Fix Azure pool creation when using scaling formula (#3868) [79984a87]
- Fix DSL2 support in nextflow console (#3864) [0253f8d7]
- Fix K8s handling PodUnschedulableException (#3938) [5b756c63]
- Fix `interval` channel factory (#3848) [d001e4c7]
- Fix invalid warning on func import (#3807) [bb836960]
- Fix minor typo in nextflow subcommand (#3853) [dd3be3d1]
- Fix misleading error message on NoSuchFileException [f3dceba6]
- Fix missing SAS token fusion env for Azure [43015029]
- Fix problem args were not correctly represented in debug yaml (#3904) [eeb4b5c8]
- Fix string comparison in S3 client (#3875) [9344d294]
- Fix use of remote dir with local exec statement [850bc3d9]
- Fix Quote Singularity/Apptainer env values [586417ac]
- Improve handling default out param [91471970]
- Improve plugin test detection [29794bf4]
- Improve plugin updater err handling [f3d72f22]
- Improve task out redirect remove the use of mkfifo (#3863) [efedec74]
- Improve Use Docker stop instead of docker kill [32e6fd85]
- Improve Use separate script for long stage/unstage commands (#3851) [4343e333]
- Increase Azure default maxRetries to 10 [a017139f]
- Keep plugins-info content sorted [d5552ee6]
- Minor change on Docker-spack templates [e0e24bda]
- Refactor the AWS configuration (#3498) [a74e42d9]
- Remove `Channel.from` in favor of `Channel.of` from tests and docs (#3670) [aa8b72fa]
- Rename AmazonS3Client to S3Client [cc59596a]
- Rename com.upplication.s3fs package to nextflow.cloud.aws.nio [a2f3bb24]
- Run build CI tests on push to branches starting with `test*` or `dev*` (#3852) [7032e17c]
- Security fixes [973b7bea]
- Support enums in cache helper (#3901) [e4b977a4]
- Bump slf4j 2.0.7 and logback 1.4.6 [d7eae86e]
- Bump JGit 6.5 and use depth 1 when cloning repos [eda0845c]
- Bump aws-java-sdk-s3:1.12.429 [465171f5]
- Bump fusion 2.2 [f1ebe29a]
- Bump groovy 3.0.17 [cfe4ba56]
- Bump gson:2.10.1 [be555683]
- Bump micromamba:1.4.2 [334df1e0]
- Bump [email protected] [7d6d0108]
- Bump [email protected] [b06ffd0c]
- Bump [email protected] [2e0a15cd]
- Bump [email protected] [0c8fd7df]
- Bump [email protected] [a733b818]
- Bump [email protected] [12edf0e6]
- Bump [email protected] [69b6edde]
- Bump [email protected] [d05d51b4]
23.04.1 - 15 Apr 2023
- Add support for Java 20 [f6933db7]
- Fix use of remote dir with local exec statement [6ea1f68c]
- Fix Azure pool creation when using scaling formula (#3868) [84a808a5]
- Fix interval channel factory (#3848) [82ccf6ad]
- Fix invalid warning on func import (#3807) [4678ffe3]
- Improve plugin test detection [57cfb0d9]
- Improve plugin updater err handling [5627c69a]
- Security fixes [83e8fd6a]
- Bump [email protected] [d8cb763c]
- Bump [email protected] [b2354380]
- Bump [email protected] [22a68cfe]
- Bump gson:2.10.1 [83ca1e32]
- Bump [email protected] [b40b5165]
- Bump [email protected] [98a89154]
- Bump aws-java-sdk-s3:1.12.429 [b71ee0a3]
- Bump [email protected] [a5da54d3]
- Bump [email protected] [c90553c9]
22.10.8 - 15 Apr 2023
- Security fixes [fc2627bb]
- Add support for testing custom plugin uri [718d4562]
- Improve plugin updater err handling [84042082]
- Improve plugin test detection [e6c60a6c]
- Bump [email protected] [26b01b83]
- Bump [email protected] [2a886fe0]
- Bump [email protected] [b8769f1a]
- Bump [email protected] [89d902ec]
- Bump [email protected] [9b0f4bfb]
- Bump [email protected] [f7aaddc6]
- Bump [email protected] [7898cc04]
23.04.0 - 1 Apr 2023
- Add several names to the name generator feat:(#3790) [dfa2f6ca]
- Add support for Fusion to Azure Batch executor (#3209) [3d3cbfa2]
- Add support for testing custom plugin uri [227910ab]
- Add warnings for Azure named pools (#3819) [a2c71acf]
- Enable new pid namespace with Singularity & Apptainer [3601b014]
- Fix NoSuchMethodError String.stripIndent with Java 11 [308eafe6]
- Fix issue checking Google Batch script launcher type [39c3a517]
- Fix resolution of module resources [2c5a6878]
- Fix Relax caching across task retries [840e8432]
- Fix Java version for tests [7ce05c15]
- Remove extra context from workflow error message [38c8bd33]
- Revert "Enable Fusion on Google Batch tests" [2ba7ea54]
- Bump micromamba 1.4.1 [ec1439e6]
- Bump [email protected] [0f98b245]
- Bump [email protected] [e1732be9]
- Bump [email protected] [99477f79]
- Bump [email protected] [939195b5]
- Bump [email protected] [b7b5d4c9]
23.03.0-edge - 19 Mar 2023
- Add Azure batch pool virtualNetwork option (#3723) [e3917b8e]
- Add basePackages option to Wave config [7e827810]
- Add error message for missing container image with Google Batch (#3747) [6419e68f]
- Add notifyFilePublish optional source argument (#3737) [a65a9ff7]
- Add retry strategy on Bash wrapper write logic [1e38274a]
- Add support for AWS S3 Glacier Retrieval Tier (#3680) [fab6bd5e]
- Add sync invocation on job completion (#3678) [e29c4e4b]
- Add workflowId to Wave request [025ff9d0]
- Add Clone result list objects before output binding [38762080]
- Add plugins option to kuberun command (#3766) [6515294f]
- Fix Google Batch logging exception [d7e38e9e]
- Fix Java Matcher serialization [6aecc4ed]
- Fix Logger failure type detection [f1b89c1f]
- Fix Orphaned processes when using Singularity [7236f830]
- Fix groupTuple with mismatching tuple cardinality [1d32e2c2]
- Fix special chars escaping in container env [b93634e9]
- Fix commit revision type for Azure DevOps repos (#3721) [fb71767e]
- Improve DAG API (#3703) [21afb358]
- Improve Wave docs [7299dac9]
- Improve `fair` directive docs (#3677) [7ca7520f]
- Improve transpose and groupTuple examples in the docs (#3685) [7870dfc8]
- Increase pwd obfuscation min length [ba23d036]
- Make GroupKey cloneable (#3738) [0760b0fd]