Nextflow Versions Save

• 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]

• 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]

• 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) [ci fast] [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 build-in function in onComplete handler (#4458) [ci fast] [4be10cd3]
• Fix Harden regular expression used to strip secrets in logs (#4563) [ci fast] [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]

• Fix container environment with special chars (#4594) [663b2936]

• 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]

• 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) [ci fast] [dfc7b7c8]
• Add support for Singularity OCI mode (#4440) [f5362a7b]
• Allow the use of error built-in function in onComplete handler (#4458) [ci fast] [35a4424b]
• Fix Bug in JsonSplitter ordering [ci fast] [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 [ci fast] (#4532) [4d5bc216]
• Fix doc tests to fail on test failure (#4505) [4d326551]
• Fix errors when NXF_HOME contains spaces (#4456) [ci fast] [fe5bea99]
• Fix Google Batch network/subnetwork docs (#4475) [27d132f3]
• Fix rounding error with long durations (#4496) [ci fast] [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 [ci fast] [171831ea]
• Minor types improvement for mix operator [ci fast] [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]

• 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]

From previous egde releases

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 conflic [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]

23.09.1-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]

23.08.0-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]

23.05.0-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]

• 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 not stopping 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]

• 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]