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changelog.txt
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NEXTFLOW CHANGE-LOG
===================
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 nf-amazon@2.3.0 [0b40b7b9]
- Bump nf-google@1.10.0 [bcb20fcf]
- Bump nf-wave@1.2.0 [aa981814]
- Bump wave-utils@0.8.1 and micromamba@1.5.5 [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 nf-amazon@2.2.0 [8e2d7879]
- Bump nf-azure@1.4.0 [7c47d090]
- Bump nf-cloudcache@0.3.1 [65240b75]
- Bump nf-codecommit@0.1.6 [725f0510]
- Bump nf-console@1.0.7 [a307686c]
- Bump nf-ga4gh@1.1.1 [e54ea007]
- Bump nf-google@1.9.0 [033ec92c]
- Bump nf-tower@1.7.0 [836a44a5]
- Bump nf-wave@1.1.0 [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 nf-wave@1.0.0 [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 conflic [11c3aac5]
- Bump nf-amazon@2.1.4 [a84208a8]
- Bump nf-cloudcache@0.3.0 [b37b4014]
- Bump nf-google@1.8.3 [b4eb8b96]
- Bump nf-tower@1.6.3 [5681ab13]
- Bump nf-wave@0.14.0 [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 nf-amazon@2.1.3 [3311172f]
- Bump nf-azure@1.3.2 [a9b735ce]
- Bump nf-google@1.8.2 [7219d7f2]
- Bump nf-tower@1.6.2 [91a935f9]
- Bump nf-wave@0.13.0 [0cf2476c]
- Bump wave-utils@0.7.8 [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 nf-amazon@2.1.2 [7e5d414e]
- Bump nf-azure@1.3.1 [83410f39]
- Bump nf-wave@0.12.0 [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 nf-azure@1.3.0 [6670bb06]
- Bump nf-cloudcache@0.2.0 [fb8f6681]
- Bump nf-tower@1.6.1 [d06b8365]
- Bump nf-wave@0.11.2 [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 nf-wave@0.8.4 [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 nf-wave@0.11.1 [78e4b278]
- Bump nf-tower@1.6.0 [41c8c164]
- Bump nf-azure@1.2.0 [5f33ac17]
- Bump nf-amazon@2.1.1 [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 nf-amazon@2.1.0 [57464746]
- Bump nf-azure@1.1.2 [e1512f6a]
- Bump nf-azure@1.1.3 [27e7f663]
- Bump nf-azure@1.1.4 [1895efc4]
- Bump nf-cloudcache@0.1.0 [cb6242c4]
- Bump nf-ga4gh@1.1.0 [f98feb77]
- Bump nf-google@1.8.1 [6aede7c0]
- Bump nf-tower@1.5.15 [3278d798]
- Bump nf-wave@0.11.0 [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 nf-wave@0.11.0 [2998db5d]
- Bump nf-tower@1.5.15 [3278d798]
- Bump nf-google@1.8.1 [6aede7c0]
- Bump nf-ga4gh@1.1.0 [f98feb77]
- Bump nf-azure@1.1.4 [1895efc4]
- Bump nf-amazon@2.1.0 [57464746]
- Bump nf-cloudcache@0.1.0 [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 nf-wave@0.8.3 [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 nf-wave@0.9.0 [7d6d0108]
- Bump nf-tower@1.5.13 [b06ffd0c]
- Bump nf-google@1.7.4 [2e0a15cd]
- Bump nf-ga4gh@1.0.6 [0c8fd7df]
- Bump nf-console@1.0.6 [a733b818]
- Bump nf-codecommit@0.1.5 [12edf0e6]
- Bump nf-amazon@2.0.0 [69b6edde]
- Bump nf-azure@1.1.0 [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 nf-wave@0.8.2 [d8cb763c]
- Bump nf-tower@1.5.12 [b2354380]
- Bump nf-google@1.7.3 [22a68cfe]
- Bump gson:2.10.1 [83ca1e32]
- Bump nf-ga4gh@1.0.5 [b40b5165]
- Bump nf-codecommit@0.1.4 [98a89154]
- Bump aws-java-sdk-s3:1.12.429 [b71ee0a3]
- Bump nf-azure@1.0.1 [a5da54d3]
- Bump nf-amazon@1.16.2 [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 nf-google@1.4.6 [26b01b83]
- Bump nf-wave@0.5.5 [2a886fe0]
- Bump nf-ga4gh@1.0.5 [b8769f1a]
- Bump nf-tower@1.5.7-patch0 [89d902ec]
- Bump nf-azure@0.14.3 [9b0f4bfb]
- Bump nf-amazon@1.11.5 [f7aaddc6]
- Bump amazoncorretto@17.0.6 [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 nf-amazon@1.16.1 [0f98b245]
- Bump nf-azure@1.0.0 [e1732be9]
- Bump nf-google@1.7.2 [99477f79]
- Bump nf-wave@0.8.1 [939195b5]
- Bump nf-tower@1.5.11 [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]
- Prepare Nextflow for the CWS Plugin (#3727) [fd8bf709]
- Remove DNAnexus page from docs (#3695) [fa58c18c]
- Remove outdated FAQ page from docs (#3683) [e59c7fbb]
- Remove unused classes [9fa8d75b]
- Update Azure VM sizes (#3751) [1d06e9a6]
- Enable Fusion on Google Batch tests [2f1b1094]
- Bump groovy 3.0.16 [d3ff5dcb]
- Bump nf-wave@0.8.0 [aa1b065d]
- Bump nf-google@1.7.1 [2aaaf2a7]
- Bump nf-azure@0.16.0 [f358b008]
- Bump nf-amazon@1.16.0 [2395187d]
23.02.1-edge - 26 Feb 2023
- Add Fusion logs and tags config [09192078]
- Add support for NXF_DEBUG to K8s task handler [828583dc]
- Add support for Mamba HTTP based lock files [7fe88c84]
- Add container name validation [c3b6d9ab]
- Add Fusion for Google storage docs [34fcfe06]
- Improve K8s auth token discovery [44f8cc07]
- Bump nf-wave@0.7.2 [1c697ab5]
- Bump amazoncorretto:17.0.6 [a33a6f47]
23.02.0-edge - 21 Feb 2023
- Add Fusion support for Google Batch (#3577) [d5fbab4f]
- Add Header provider to Google Batch client [20979929]
- Add Wave integration tests [c5faf971]
- Add errorStrategy validation [954cd921]
- Add Java install recommendations to docs (#3617) [7e9bee1e]
- Add nextflow tags to AWS Batch job def [b465ac52] [BREAKING]
- Add readOnlyInputs option for CharliecloudBuilder (#3590) [8ae001fc]
- Add refresh token to Wave request [41510e87]
- Add requirements for container images to run with Nextflow (#3586) [7af1cb66]
- Add support for Fusion to Slurm and LSF executors (#3516) [fbc95e6b]
- Add support for Fusion tags (#3609) [8385ec22] [BREAKING]
- Add support for the Spack package manager (#3580) [a5df62f6]
- Add the fcp tool option to file copy strategy (#3556) [2a224258]
- Add Fusion integration test
- Add Wave + Fusion test with Google Batch [b541c061]
- Add support for entryless Fusion configuration and Singularity support (#3584) [34a27733]
- Improve Fusion config [a1d08463]
- Ignore resource directives if -l option is specified in PBS executor (#3015) [28a67969]
- Improve K8s securityContext support [3f76240b]
- Improve AWS Batch error logging [8f4884c1]
- Improve secrets docs [9a3b4214]
- Improve Wave debug-task plugin command [cf3fd747]
- Improve Wave logging [fced3761]
- Increase Wave token duration to 30 mins [e1a712c2]
- Fix -with-apptainer cli option (#3621) [8c9588fe]
- Fix GH action tests step [bb890d9a]
- Fix Spack failing test [868374d3]
- Fix Tower doc links, fix typos (#3647) [1278e1a5]
- Fix Wave cli messages [10cf414b]
- Fix collectFile cache over remote storage [762ba19c]
- Fix output env var tokenize [40d56735]
- Fix plugin install version [59e9a91b]
- Fix race condition on Wave requests [f57fae2c]
- Fix serialization of S3 paths with spaces (#3565) [ce487624]
- Fix string literal method names with parens (#3604) [8278078a]
- Fix submit command in error message for grid executors that pipe wrapper script (#3548) [40ebd308]
- Fix typos in the documentation (#3640) [eccc1130]
- Fix unique fingerprint for Wave bundle resources [b59fa728]
- Log exception when an unexpected occurs (#3603) [9aeca99f]
- Minor change on container resolution [23d47ded]
- Refactor httpfs configuration [445218a8]
- Remove deprecated buckets field [0a355ac3]
- Remove leading/trailing special chars from tag [7d3cc707]
- Remove unused `-with-k8s` CLI option (#3624) [85b6e7d3]
- Update config.rst (#3655) [1555e188]
- Update Fusion docs [12782eeb]
- Bump Fusion 2.1 [f48ef5b3]
- Bump Groovy 3.0.15 [7a3ebc7d]
- Bump Micromamba 1.3.1 [aa2bf37e]
- Bump Spock 2.3 [9f0dac31]
- Bump nf-wave@0.7.1 [b797fac2]
- Bump nf-tower@1.5.10 [dd2f69dd]
- Bump nf-google@1.7.0 [8cb9fa35]
- Bump nf-amazon@1.15.0 [7ccca430]
22.10.7 - 18 Feb 2023
- Fix plugin install version [895e4f34]
- Fix unique fingerprint for wave bundle resources [7c55aa37]
- Fix race condition on wave requests [7f76d19b]
- Fix serialization of S3 paths with spaces (#3565) [935df949]
- Improve aws batch error logging [1eddeea7]
- Improve wave logging [94415914]
- Increase Wave token duration to 30 mins [8d5fbefe]
- Update fusion docs [b24ee138]
- Bump nf-wave@0.5.4 [f466b266]
- Bump nf-amazon@1.11.4 [d5f6c125]
22.10.6 - 24 Jan 2023
- backport: Add refresh token to wave request [47a7408b]
- backport:Add tower endpoint to wave [fe24b422]
- backport:Fix Wave layer invalid checksum due to not closed stream [20df6400]
- Bump nf-wave@0.5.3 [c1ec759f]
23.01.0-edge - 14 Jan 2023
- Add support for rclone as stageOutMode option [fde2ac27]
- Add queueGlobalStatus config setting [f3339541]
- Add support for bearer token to GithubRepositoryProvider [c4d39384] [a2d2cbf60]
- Add -with-fusion cli option [d22337cd]
- Add support for Fusion container custom options [56e29d35]
- Add `schedulingPriority` option to AWS Batch (use with `shareIdentifier`) (#3505) [06960bb2]
- Fix support for AWS ACL for Batch #2671 [a9644919]
- Fix Java options.release in Gradle build [b362d6f6]
- Fix nf-httpfs module name in build file [568e47f6]
- Fix GitHub creds in CI build [4c4d3f81]
- Fix FilePorter concurrency issue (#3511) [11ccfa26]
- Fix watchPath hang shutdown execution [bac0cedf]
- Fix "no such file" error message to "no such file or directory" (#3547) [c292d84e]
- Improve local exec workdir validation [4a3a2720]
- Improve container native executor configuration [03126371]
- Improve AWS batch exit code reporting [d1bb2fe2]
- Improve channel factories error message [0215b9fc]
- Improve Google Batch executor [c0a25fc2]
- Improve Fusion config [902e5b34] [52f4c5d5]
- Improve redirection on Wave client [124cfb3e]
- Remove unnecessary Fusion env var [dfa47556]
- Remove deprecated method 'just' [d17b3c46]
- Remove deprecated methods [75e65035]
- Remove DSL1 deprecated code [5d290a47]
- Cleanup build from tmp manifests [326b3839]
- Minor compilation improvements [4188a6ac]
- Migrate all tests to DSL2 [14257d49]
- Bump 23.01.0-edge version [9ec31444]
- Bump groovy 3.0.14 [7c204236] [6f3ed6e8]
- Bump Grengine 3.0 [c0b1a7a6]
- Bump nf-wave@0.7.0 [45d274e3]
- Bump nf-tower@1.5.9 [db0ebe72]
- Bump nf-google@1.6.0 [a663fe16]
- Bump nf-console@1.0.5 [45fd53ad]
- Bump nf-codecommit@0.1.3 [cf39ef8f]
- Bump nf-azure@0.15.1 [7a6a78aa]
- Bump nf-amazon@1.14.0 [41fdcc72]
22.10.5 - 14 Jan 2023
- Fix FilePorter concurrency issue (#3511) [0f757156]
- Fix watchPath hang shutdown execution [e03d9ca6]
- Add `schedulingPriority` option to AWS Batch (use with `shareIdentifier`) (#3505) [543ee7b1]
22.12.0-edge - 13 Dec 2022
- Add `fair` process directive [60d34cfd]
- Add support for singularity registry setting [37c1aeb9]
- Add AWS profile config setting [66f4669f]
- Add support for AWS profile when resolving region [d8947707]
- Add support for Sarus container engine (#3470) [54673f18]
- Add support for Fusion ARM64 client [d073c538]
- Add allowedLocations option to google batch (#3453) [c619eb81]
- Add support for AWS config profile in NF config [37112672]
- Add warning on Google Logs failure [bdbcdde9]
- Add possible values of `status` in `trace.txt` to the documentation (#3451) [2425fcfb]
- Add support for AWS Glacier restore [b6110766]
- Add support for S3 storageClass to publishDir [066f9203]
- Add MathHelper utility class [7eecb266]
- Fix Wave layer invalid checksum due to not closed stream [e188bbf9]
- Fix Fusion test [2245a1c7]
- Fix Run fails when home is a symlink [9ff820f4]
- Fix math overflow when copying large AWS S3 files [f32ea0ba]
- Fix Quote the logName in the Cloud Logging filter (#3464) [b3975063]
- Fix Google Batch cloud logging (#3443) [e2bbcf15]
- Fix Tower plugin min nextflow requirement [1713a1cd]
- Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [46af18e5]
- Error & info messages, code comments language fixes (#3475) [29ae36ca]
- Replace `egrep` with `grep -E` (#3485) [ac0c3035]
- Gradle build optimizations (#3483) [19182a57]
- Refactor virtual FS schemes to XPath class [fd59b943]
- Update concat operator description (#3426) [e8d8c3b5]
- Clarify usage of additional options for path qualifier (#3405) [0b70acb1]
- Clarify limitation of `-with-docker` in the docs (#3408) [79afc85d]
- Expose process queue as K8s pod label [4df8c8d2]
- Prefix nextflow K8s labels with `nextflow.io` prefix [9951fcd9]
- Remove deprecated code [c0b164f2]
- Rewrite fetchIamRole and fetchRegion to use AWS SDK (#3425) [e350f319]
- Improve Wave config error reporting [ae502668]
- Improve K8s retry on transient failures [d86ddc36]
- Remove DSL1 output mode [fa400d5f]
- Remove support for DSL1 multi into [f664af45]
- Bump nf-amazon@1.13.0 [ccaab713]
- Bump nf-google@1.5.0 [c07dcec2]
- Bump nf-wave@0.6.3
- Bump nf-tower@1.5.8 [652d0880]
- Bump fusion version URLs 0.6 [a160a8b1]
- Bump AWS sdk version 1.12.351 [4dd82b66]
22.10.4 - 9 Dec 2022
- Fix math overflow when copying large AWS S3 files [07f7cb72]
- Bump nf-amazon@1.11.2 [d96ca4c3]
22.11.1-edge - 29 Nov 2022
- Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [53e6348c]
- Fix tower plugin min nextflow requirement [103dbf74]
- Fix typos in the documentation (#3441) [ae95d90d]
- Add support for Java 19 [811e7ca8]
- Add support for custom conda channels (#3435) [0884e80e]
- Add time directive to AWS Batch, clean language (#3436) [1ed2640a]
- Update err message [ab5bd81b]
- Fix Flux executor config (#3432) [68b45c92]
- Bump nf-wave@0.6.1 [fe669152]
- Bump nf-tower@1.5.7 [2dbf9906]
22.11.0-edge - 23 Nov 2022
- Add support for Apptainer container engine (#3345) [29f98975]
- Add Flux executor to nextflow (#3412) [cc9fc3f0] [3711cef0]
- Add support for Wave containerPlatform [10d56ca1]
- Add CSI ephemeral volume for K8s (#2988) [f18f6e81]
- Add support for disk directive and emptyDir to K8s (#2998) [b548e1c7]
- Add Fusion support for custom S3 endpoints [fba9b649]
- Add support for Tower refresh token for dataset (#3366) [a19e055a]
- Prevent infinite loop while fetching git tags and branches [aa974d44]
- Improve file porter logging [626420b6]
- Improve script err logging [2714770e]
- Extend onFilePublish notification adding source path (#3284) [81acc3ef]
- Remove cpu limits from K8s pod spec builder (#3338) [dc7f78bf]
- Improve task name logging [5ddb7e3f]
- Add tower endpoint to wave [b725ddc4]
- Add Azure SAS token validation [e2244b48]
- Use cpus-shares for container resources (#3383) [b38c3880]
- Report full path scheme on error [4089ba65]
- Allow identity based authentication on Azure Batch (#3132) [a08611be]
- Fix support for remote file mail attachment (#3384) [6b496bb9]
- Fix task cache logging [ed37c4fd]
- Fix unexpected error on task resume [1c3f4685]
- Fix stripIndent failure with java 17 (#3377) [2b115c50]
- Fix -dockerized execution #3137 (#3148) [64a81a58]
- Improve default value in cli help of `nextflow log -s` (#3371) [2141f96e]
- upgrade jsoup and snakeyaml version (#3374) [6e2ca454]
- Bump Java 17 lang version + Java 11 as target [34f133e2]
- Bump nf-amazon@1.12.0 [e307912e]
- Bump nf-azure@0.15.0 [07391d96]
- Bump nf-wave@0.6.0 [4d787561]
22.10.3 - 21 Nov 2022
- Prevent infinite loop while fetching git tags/branches [73a59d33]
- Bump nf-amazon@1.11.1 [f9b54ce3]
- Improve S3 thread pool config [01541b0a]
22.10.2 - 13 Nov 2022
- Fix initialize the plugin once it's defined (#3360) [dd150b92]
- Fix tags typo in docs (#3355) [b82df4e0]
- Fix unexpected error on task resume [e02e8c27]
- Fix template script in trace record [cf828a68]
- Fix ip v6 support for K8s executor [53af5a7c]
- Fix refresh token for tower served resources [9dec2b66] #3366
- Fix full path scheme on error [1399f451]
- Add note to some process implicit variables (#3373) [0374f63a]
- Add retry policy on plugin download failure [e8dbec3f]
- Add examples of when dynamic output filenames are important (#3275) [72a17306]
- Update google batch java sdk, add serviceAccountEmail and installGpuDrivers (#3324) [7f7007a8]
- Update github actions to v3 (#3376) [d3b4a837]
- Update error messages and docs with new report filename behavior [f5725480]
- Bump nf-tower@1.5.6 [164edf7c]
- Bump nf-google@1.4.5 [30cb118d]
22.10.1 - 27 Oct 2022
- Fix mount pwd in the container when work dir is a symlink [ca397181] [b5b7d3cd] <Paolo Di Tommaso>
- Fix secrets command name in the CLI (#3320) [321486df] <Marcel Ribeiro Dantas>
- Fix ver num rendering #3226 [5312a25e] <Paolo Di Tommaso>
- Fix K8s config namespace is not applied [b3d33e3b] <Paolo Di Tommaso>
- Fix log fetching from remote storage [be356939] [3efa1a20] <Paolo Di Tommaso>
- Update docs about default mail ssl protocol (#3299) [15ffffc1] <Ben Sherman>
- Update docs repeated words from documentation (#3311) [d59ea186] <Marcel Ribeiro Dantas>
- Update docs to clarify the difference between collect and toList (#3276) [7ee2b008] <Marcel Ribeiro Dantas>
- Update docs [516a7441] <Paolo Di Tommaso>
- Update docs adding Fusion [11eac707] <Paolo Di Tommaso>
22.10.0 - 13 Oct 2022
- Fix timestamp encoding [47a3a3c4]
- Minor type change in Bridge executor [1f446ee1]
- Bump nf-wave@0.5.2 [326803ff]
22.10.0-RC3 - 7 Oct 2022
- Fix K8s context selection [58b354e6]
22.10.0-RC2 - 7 Oct 2022
- Improve K8s labels/annotation validation [a569afdf]
- Bump fusion final url [80398880]
- Bump nf-wave@0.5.1 [a2b44c4d]
- Update docs
22.10.0-RC1 - 3 Oct 2022
- Add module binaries enabling flag + docs [c50e178f] <Paolo Di Tommaso>
- Add timestamp and fingerprint to wave request [a5a7e138] <Paolo Di Tommaso>
- Add missing inputs to the incremental task "test" (#1442) [f85d59a6] <Thodoris Sotiropoulos>
- Add support for refresh token to Wave [ed9f25f1] <Paolo Di Tommaso>
- Add pretty option to dump operator [4218b299] <Paolo Di Tommaso>
- Add support for custom S3 content type [02afa332] <Paolo Di Tommaso>
- Get rid of file name rolling for report files [a762ed59] <Paolo Di Tommaso>
- Ignore JGit warning when missing git tool [a94fa9c1] <Paolo Di Tommaso>
- Remove jobname limit to HyperQueue executor (#3251) [99604ccb] <Henrik Nortamo>
- Rename baseImage to mambaImage [50086028] <Paolo Di Tommaso>
- Fix failing test [e6790003] <Paolo Di Tommaso>
- Fix K8s cluster token when using serviceAccount [c3364d0f] <Paolo Di Tommaso>
- Fix hanging test [44c04874] <Paolo Di Tommaso>
- Improve docs (#3212) [5d80388c] <Marcel Ribeiro Dantas>
- Bump fusion snapshot [8e03f655] <Paolo Di Tommaso>
- Bump wave endpoint [a044cc6a] <Paolo Di Tommaso>
- Bump nf-wave@0.4.5 [7424dc4b] <Paolo Di Tommaso>
- Bump fusion config v0.5.1 [4dbdf112] <Paolo Di Tommaso>
- Bump nf-wave@0.5.0
- Bump nf-tower@1.5.5
- Bump nf-amazon@1.11.0
22.09.7-edge - 28 Sep 2022
- Fix Issue copying file bigger than 5gb to S3 [18fd9a44]
- Fix chmod command to accommodate hidden files in bindir (or empty bindir) (#3247) [a0fcc7b0] <Abhinav Sharma>
- Bump nf-amazon@1.10.7 [f7f96e6f]
22.09.6-edge - 26 Sep 2022
- Add SocketTimeoutException to k8s client request retry [527e0d5d]
- Add MaxErrorRetry to K8s config [58be2128]
- Add tags propagation to AWS Batch [d64eeffc]
- Fix task resume when updating fusion layer [f38fd2db]
- Fix Channel merge still deprecated for DSL2 (#3220) [d27384d2] <Kibubu>
- Apply GCP resourceLabels to the VirtualMachine (#3234) [2275c03c] <Doug Daniels>
- Update Google Batch mount point with the requirements [5aec28ac]
- Improve wave error reporting [73842215]
- Bump fusion 0.4.x [26f1f896]
22.09.5-edge - 21 Sep 2022
- Use default wave strategy [abbfa7f4]
- Handle errors reported by tower report writer [0e814647]
- Fix AWS S3 copy object [b3b90d23]
22.09.4-edge - 19 Sep 2022
- Add Fusion display name [f789d457]
- Add container cleanup [cd2ae7dc]
- Add Wave interactive debug session [ce7fa651]
- Add support for wave build and cache repositories[692043ff]
- Add shutdown to Google Batch client [8f413cf7]
- Add native_id to Google Batch handler [352b4239]
- Add java sts library to enable use of IRSA in k8s (#3207) [62df42c3] <Vishwas>
- Add support for module custom bin dirs [77f55262]
- Add support for tower token to wave client [928d5b04]
- Update CLI docs (#3200) [8acebee6] <Marcel Ribeiro Dantas>
- Fix issue with empty report file [9cc4f079]
- Do not return resource bundle for root module [775c7ed9]
- Improve tower config [ee03c243]
- Bump groovy 3.0.13 [4a17e198]
22.09.3-edge - 10 Sep 2022
- Add fusion support to K8s executor (#3142) [6bb27b32]
- Fix shutdown/cleanup hooks invocation [f4185070]
- Fix Use smaller buffer size for S3 stream uploader [8c643074] [9926d15d]
- Fix Azure NPE on missing pool opts [d5c0aabd]
- Fix handling of targetDir when using Fusion fs [2091b272]
- Document aws.batch.retryMode config (#3195) [56f75e0c] <Abhinav Sharma>
22.09.2-edge - 7 Sep 2022
- Fix thread pool race condition on shutdown [8d2b0587]
- Fix Intermediate multipart upload requires a minimum size (#3193) [0b66aed6] <Jorge Aguilera>
- Fix fusion enable detection [3ef91512]
- Add before-afterScript warning to docs (#3167) [09464590] <Kibubu>
- Add httpReadTimeout and httpConnectTimeout config to K8s client [064f9bc4]
- Add support for Wave build & cache repos [98a275ba]
- Finalise secrets feature (#3161) [49021b82]
- Update executor retry config docs (#3001) [aed6c234]
- Change Azure test pool name [0c724504]
- Improve Wave error reporting [b11d0f11]
- Remove unneeded launcher file remapping [a255118d] <Paolo Di Tommaso>
- Update Azure vm types [80f5fbe4]
- Update docs logos (#3174) [529bad81] <Phil Ewels>
22.09.1-edge - 1 Sep 2022
- Add support for Charliecloud v0.28 (#3116) [84f43a33] <Patrick Hüther>
- Add Support for EC-encrypted keys for K8s client [fd759d09]
- Add support for Bridge batch scheduler (#3106) [343c17e6] <Eric Bonnet>
- Add fusion support to local executor [17160bb0] [6cfb51e7]
- Add getTags and getBranches to BitBucketServer [53bd89cd]
- Add retry strategy to httpfs client [55f9c87b]
- Add support for project resources [c2ad6566]
- Add mamba build options [987a13cb] <Paolo Di Tommaso>
- Fix Do not override tower endpoint in the config [41fb1ad0]
- Fix Hyperqueue job names must be less than 40 chars #3151 [8e43670b]
- Fix typo in ConfigBuilder.groovy (#3143) [659e6108] <Mike Lee>
- Fix Resume for dynamic resolved containers [13483ff2]
- Improve fusion env handling [10f35b60]
- Improve foreign file(s) cache detection logic [3a9352c8]
- Rename ModuleBundle to ResourcesBundle [0e51dc0f]
- Use quiet output mode for hyperqueue executor (#3103) [70a91fdf] <Ben Sherman>
- Wave improve conda settings [6f087fec]
- Improve secrets cmd (#3158) [115b2f3d] <Jorge Aguilera>
- Improve Wave resolution strategy [2eb700c6]
- Improve Az Batch err handling and testing [85d31e8d] <Paolo Di Tommaso>
- Bump google-cloud-batch 0.2.2
- Bump spock 2.2
22.09.0-edge - [SKIPPED]
22.08.2-edge - 16 Aug 2022
- Fix queueSize setting is not honoured by AWS Batch executor (again) #3117 [1733bb2e]
- Add `files()` method to docs (#3123) [00bb8896] <Ben Sherman>
- Refactor wave packing [bc876986]
- Improve logging [aa380d5f]
- Update dockerfile [e6329282]
22.08.1-edge - 11 Aug 2022
- Add support for disabling config include [e0859a12]
- Add experimental fusion support [1854f1f2]
- Add support for plugin provided function extension (#3079) [16230c2b] <Jorge Aguilera>
- Add support for AWS Batch logs group (#3092) [4ef043ac] <Ben Sherman>
- Add share identifier to Aws Batch (#3089) [c0253aba] <Ben Sherman>
- Improve Tower cache manager [0091afc5]
- Improve S3 copy via xfer manager [02d2beae]
- Reports a warning when using NXF vars in the config [009ec256] <Marcel Ribeiro Dantas>
- Make wake token cache duration config [5f955fc9]
- Patch unable to start non-core plugin [a55f58ff]
- Increase S3 upload chunk size to 100 MB [9c94a080]
- Change Google Batch disk directive to override boot disk size (#3097) [7e1c0686] <Ben Sherman>
- Fix queueSize setting is not honoured by AWS Batch executor (#3093) [d07bb52b] <Ben Sherman>
- Fix Allow disabling scratch with Google Batch [e8e5c721]
- Fix Emit relative path when relative parameter is set (#3072) [39797759] <Jorge Aguilera>
- Bump nf-wave@0.3.0 [e46d341d]
- Bump nf-tower@1.5.1 [cdc2be53]
- Bump nf-google@1.4.1 [c39935a5]
- Bump nf-amazon@1.10.0 [ccdf62d0]
22.08.0-edge - 1 Aug 2022
- Add warning to env config docs (#3083) [ca933c16] <Ben Sherman>
- Add -with-conda CLI option (#3073) [98b2ac80]
- Add simple wave plugin cli commands [8888b866]
- Add default wave plugin [7793a0ec]
- Add boot disk, cpu platform to google batch (#3058) [17a8483d] <Ben Sherman>
- Add support for GPU accelerator to Google Batch (#3056) [f34ad7f6] <Ben Sherman>
- Add support for archive dir to tower plugin [c234681a]
- Add support tower cache backup/restore [bc2f9d13]
- Add disk directive to google batch (#3057) [ec6e290c] <Ben Sherman>
- Add retry when Azure submit fails with OperationTimedOut [6a3f9742]
- Add warning when Google Batch quota is exceeded (#3066) [6b9c52ad] <Ben Sherman>
- Allow fully disabling history file [0a45f858]
- Allow the support function overloading and default parameters (#3011) [042d3857] <Jorge Aguilera>
- Improve S3 file upload/download via Transfer manager [7e8d2a5a] <Jorge Aguilera>
- Prevent overriding container entrypoint [b3a4bf85]
- Update FileTransfer pool settings [503aafce]
- Remove deprecated commands [93228b4b]
- Prevent nextflow config to break tower launch [e059a724]
- Refactor Google Batch executor to use Java API (#3044) [31a6e85c] <Ben Sherman>
- Fix Unable to disable scratch attribute with AWS Batch [1770f73a]
- Fix unit test setting explicit permissions for test files [1c821139] <Jorge Aguilera>
- Fix Default plugins are overridden by config plugins [46cf3bfa] <Paolo Di Tommaso>
- Fix S3 transfer download directory [b7bf9fe5]
- Fix NPE while setting S3 ObjectMetadata #3031 [d6163431] <Jorge Aguilera>
- Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b]
- Fix AWS Batch job definition conflict (#3048) [e5084418]
- Fix JAVA_TOOL_OPTIONS breaking launch #1716 [0e7b416d]
- Fix add ps shared objects to Dockerfile (#3033) [1c23b40a] <Ben Sherman>
- Parallelize build integration tests [807800a3]
- Bump google-cloud-nio:0.124.8 [dfaa9d19]
- Bump groovy 3.0.12 [5c900b91]
- Bump Moment.js 2.29.4 [a9ced868]
- Bump gson@2.9.0 [12f17176]
- Bump nf-azure@0.13.4
- Bump nf-google@1.4.0
- Bump nf-tower@1.5.0
- Bump nf-wave@0.2.1
- Bump nf-amazon@1.9.0
22.04.5 - 15 Jul 2022
- Allow fully disabling history file [1a36c9bc]
22.07.1-edge - 13 Jul 2022
- Add support for Google Batch API v1 [4c116d58] [e85d87ee]
- Add time directive support for K8s executor (#2948) [2b6f70a8] <romanaduraciova>
- Add docs aws.client.s3PathStyleAccess config (#3000) [20005500] <Abhinav Sharma>
- Allow to override lsf.conf settings with nextflow config #2862 [dae191a1] <Paolo Di Tommaso>
- Allow hybrid containers execution [0af1bcb3]
- Improve error msg when script file cannot be read [52c2780e]
- Improve error reporting for custom function [877c7931] <Jorge Aguilera>
- Improve error message for missing plugin extension [4a43db84]
- Improve test #3019 [7c37e0be] <Paolo Di Tommaso>
- Rename kuberun -pod-image to -head-image [2576ba62] <Ben Sherman>
- Externalise sqldb plugin source code [17e80b4f] <Paolo Di Tommaso>
- Fix escape unstage outputs with double quotes #2912 #2904 #2790 [49ff02a6] <Ben Sherman>
- Fix Exception when settings AWS Batch containerOptions #3019 [89312ad8] <Paolo Di Tommaso>
- Fix Missing query param in http file (#2918) [43cc8511] <Paolo Di Tommaso>
- Fix Publish copy mode for S3 based path [085f6b2b]
- Fix Fail fast uploads to S3 (#2969) [7fd1a6e1] <Jorge Aguilera>
- Fix null script name in launch info [7118849f]
- Bump commons-code@1.15 [a06b4442]
- Bump jgit@6.2.0 [3331826f]
- Bump snakeyaml@1.30 [de62fd3f]
- Bump gson@2.8.9 [3234ddd5]
22.07.0-edge - [SKIPPED]
22.04.4 - 19 Jun 2022