Nextflow

- 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]

- Fix nf-google plugin dependency [725e2860]
- Fix nf-amazon plugin dependency [c234b09f]
- Bump nf-google1.13.2 [633989a6]
- Bump nf-amazon2.5.2 [e31f70e0]

- 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 nf-amazon2.5.1 [96ee633d]
- Bump nf-console1.1.3 [e8359042]
- Bump nf-google1.13.1 [5dcb4c7a]
- Bump nf-wave1.4.2 [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 nf-wave1.4.1 [830b032c]
- Bump nf-tower1.9.1 [163683c2]
- Bump nf-google1.13.0 [6d99a22a]
- Bump nf-ga4gh1.3.0 [89695ed3]
- Bump nf-console1.1.2 [357b143a]
- Bump nf-amazon2.5.0 [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 nf-wave1.4.0 [fc70dc8c]
- Bump nf-tower1.9.0 [b0c4e2c5]
- Bump nf-google1.12.0 [6ae25fad]
- Bump nf-azure1.6.0 [967c2ac8]
- Bump nf-amazon2.4.2 [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 nf-amazon2.4.1 [0eb84071]
- Bump nf-azure1.5.1 [d63be8c0]
- Bump nf-cloudcache0.4.1 [57b7004e]
- Bump nf-console1.1.1 [b7f703f5]
- Bump nf-tower1.8.1 [b8ffb180]
- Bump nf-wave1.3.1 [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 nf-wave1.3.0 [8b9905c7]
- Bump nf-tower1.8.0 [bfc94e46]
- Bump nf-google1.11.0 [01ff0353]
- Bump nf-ga4gh1.2.0 [3df34188]
- Bump nf-console1.1.0 [e90d73a7]
- Bump nf-codecommit0.2.0 [4379c941]
- Bump nf-cloudcache0.4.0 [2bc698c7]
- Bump nf-azure1.5.0 [07415ce1]
- Bump nf-amazon2.4.0 [b991e14b]
- Bump Groovy 4 (4443) [9d32503b]
- Bump actions/checkoutv4 [d1b3195e]
- Bump logback1.4.12 + guava33.0.0-jre [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]