Version 23.04.4

• Fix use of GITHUB_TOKEN variable to access GitHub repo [108c6b5]
• Fix allow_other vulnerability preventing google-batch submissions (#4332) [4895d54]
• Fix Prevent false positive resumable task [aae8771]
• Fix Always emit publish event for cached task outputs (#4227) [c4cd53c]
• Fix Too long Http connection pool timeout [ce5e993]
• Bump [email protected] [d881728]

Version 23.09.1-edge

• Revert "Allow setting shell directive when using the trace file (#4210)" [9f9edcd]

Version 23.09.0-edge

• Add check for latest version (#4194) [3e8cd48]
• Add inspect command (#4069) [090c31c]
• Add maxSubmitAwait (#3736) [5686bf1]
• Add scripts logging for troubleshooting [c056a74]
• Add support for Spack to Singularity builds [23c4ec1]
• Add support for Wave native build for Singularity [8a43489]
• Add support for inputs and outputs arity [42504d3]
• Add support for remote debug (#4266) [87e0648]
• Add warning about using clusterOptions with process directives (#4248) [a68c1a3]
• Add which to dockerfile build [817aa05]
• Align Singularity experience with Docker (#4230) [a1e1d3c] [c1cc60d]
• Allow setting shell directive when using the trace file (#4210) [7d6ad62]
• Always emit publish event for cached task outputs (#4227) [62686ce]
• Deprecated Wave report feature [80c5cb2]
• Disable staging script for remote work dir (#4282) [80f7cd4]
• Disable version check on CI tests [db79e13]
• Docs improvement to clarify the usage of the bin dir (#4121) [2daa417]
• Document API differences of process path inputs (#4189) [c37e00b]
• Document use of local variables in closures (#4251) [05ff784]
• Fix IOException should be thrown when failing to creare Azure directory [b0bdfd7]
• Fix Parallel execution of Conda corrupts data and packages (#4253) [976c282]
• Fix Parse negative CLI params as numbers (#4238) [1ae70d5]
• Fix Too long Http connection pool timeout [fa961e7]
• Fix Wave build for Singularity files [a60ef72]
• Fix Wave build when Conda package name is quoted [d19cb0b]
• Fix failing test [2785ffe]
• Fix fs cp command with remote file [366eede]
• Fix printf command with negative exit code (#4213) [465468b]
• Fix security deps in nf-azure plugin [c30d521]
• Fix setting executor.queueSize = 0 is ignored (#4228) [6664b57]
• Improve Wave handing of Conda envs [736ab9b]
• Improve pod options documentation (#4274) [c3aa26e]
• Make TraceRecord@store field public accessible [07582f0]
• Remove -dsl1 and -dsl1 rub cli options [b6721b7]
• Remove experimental -dockerize option /2 [7def554]
• Remove experimental -dockerize option [937c8fb]
• Report an error on duplicate workflow name definitions (#4088) [fce9702]
• Undocument internal NXF_DEBUG variable [7955db8]
• Update AZ File share doc (#4235) [69d317b]
• Update docs about splitCsv() operator (#4163) [1dfb621]
• Update documentation of NXF_DEBUG (#4187) [a88a424]
• Use sipHash24 in place of deprecated murmur32 for script aliasing [bb96763]
• Bump groovy 3.0.19 [cb41120]
• Bump [email protected] [7e5d414]
• Bump [email protected] [83410f3]
• Bump [email protected] [a9f6dd6]

Version 23.08.1-edge

• Add 429 http status code to Wave retriable errors [8eb5f30]
• Add resource labels support for Azure Batch (#4178) [7b5e50a]
• Apply K8s Pod metadata to Job (#4057) [4d91862]
• Document error about trailing backslash with space (#4180) [245afa5]
• Enable cloud cache based on environment variable (#4160) [a66b0e6]
• Escape semicolons in paths (#4193) [552501c]
• FIx nested InvocationTargetException (#4192) [67980f1]
• Fix Execution should fail if report or timeline file already exists [b238d7e]
• Fix Process hangs when using flatten and finish errorStrategy [d99b343]
• Fix workflow.container map resolution (#4190) [96ab8a6]
• Fix checkpoint thread termination (#4166) [2b449da]
• Fix env output when changing task workdir [8e4d7fe]
• Fix if-guard on log.trace in trask processor inner class [50f6f6d]
• Fix typos in source code comments (#4173) [e78bc37]
• Improve Conda build error report [7b19fb0]
• Improve handling of name-only container env variables [3051cd1]
• Minor changes [7e58c94]
• Remove dockerize launcher classpath file (#4191) [2bae519]
• Remove lock file from cloudcache (#4167) [6e6ea57]
• Update AWS instructions for creating a custom AMI (#4174) [563bff1]
• Update changelog [98f88a5]
• Update tip about modifying maps (#4153) [30036db]
• Use root user in Wave container based on micromamba (#4038) [a3a75ea]
• Bump [email protected] [6670bb0]
• Bump [email protected] [fb8f668]
• Bump [email protected] [d06b836]
• Bump [email protected] [7555b17]

Version 23.04.3

• Add 429 http status code to Wave retriable errors [a8b8c6c]
• Increase Wave client max attempts [8c67610]
• Improve handling Wave server errors [621c966]
• Fix log typo [03e19ea]
• Bump [email protected] [d7fa3f2]
• Bump corretto 17.0.8 [7a73a78]

Version 23.08.0-edge

• Add -value option to config command (#4142) [57e3100]
• Add deleteTasksOnCompletion to Azure Batch configuration (#4114) [b14674d]
• Add Tower logs checkpoint (#4132) [71dfecc]
• Allow use virtual threads in Wave client [dd32f80]
• Allow workflow entry from module import (#4128) [51f5c84]
• Disable cache backup/restore if cloudcache is used (#4125) [46e828e]
• Document behavior of withName selector with included aliases (#4129) [8b7e3d4]
• Fix Option fixOwnership traverse parent directories [f2a2ea3]
• Fix Redirection http redirection across different hosts [fcdeec0]
• Fix Wave disable flag [8579e7a]
• Fix bug with K8s resource labels (#4147) eu-west-1[3f4b855]
• Fix glob resolution for remove files [19a72c4]
• Fix incorrect error message on missing comma (#4085) eu-west-1[a59af39]
• Fix missing changelog for version 23.07.0-edge eu-west-1[9a33e93]
• Fix strict mode docs (#4150) [6b46b50]
• Improve plugin docs (#3957) [22638d4]
• Improve Wave config logging [547fad6]
• Improve TaskPollingMonitor logging [077ed5d]
• Improve Wave and Fusion docs (#4149) [d2229bd]
• Increase Wave client max attempts [fe5dd49]
• Remove module all components import [a6d08c0]
• Restore Tower CacheManager for backward compatibility [6d26907]
• Bump amazoncorretto:17.0.8 [00eb145]
• Bump [email protected] [78e4b27]
• Bump [email protected] [41c8c16]
• Bump [email protected] [5f33ac1]
• Bump [email protected] [981315a

Version 23.07.0-edge

23.07.0-edge - 23 Jul 2023

• Add CPU model name to trace files and traceRecord (#3946) [e0d91bf]
• Add ability to disable CLI params type detection [9a1c584]
• Add cloudcache plugin (#4097) [ac90cc2]
• Add missing header to Wave container await [d39866e]
• Add remote bin support for TES in a workdir (#3990) [8a22168]
• Add retry logic to wave image await [9fc1d3b]
• Add rule to build Nextflow docker image for ARM (#4020) [705d55f]
• Add support for AWS SSO credentials provider (#4045) [53e33cd]
• Add support for Wave container freeze [9a5903e]
• Add support legacy Wave retry [73a1e7d]
• Allow SLURM executor option --mem-per-cpu (#4023) [96c04e3]
• Allow disabling the Wave requirement when Fusion is enabled [9180d63]
• Disable Singularity and Apptainer home mount by default (#4056) [a0ee465]
• Document NXF_WRAPPER_STAGE_FILE_THRESHOLD environment variable (#4113) [ci skip] [bda4756]
• Fix AzFileSystem retry policy [ba9b6d1] [c2f3cc9]
• Fix Improve error message for invalid Azure URI [0f4d886]
• Fix Treat HTTP headers as case insensitive (#4116) [97fd335]
• Fix invalid detection of hierarchical namespace stub blobs as files (#4046) [ce06c87]
• Fix stage script in Fusion script launcher (#4109) [0933f47]
• Ignore accelerator type for AWS Batch (#4043) [263ecca]
• Implement Weblog feature as an external plugin [f9f2c33]
• Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf]
• Improve Azure retry logging [de58697]
• Improve description of channels and channel types (#4120) [8975734]
• Improve handling Wave server errors [84f7a61]
• Increase Azure min retry delay to 250ms [2e77e5e]
• Remove default arch from wave request [f0e5c0c]
• Remove logging of report JSON data (#4098) [099e503]
• Wait for all child processes in nxf_parallel (#4050) [60a5f1a]
• Bump Groovy 3.0.18 [207eb53]
• Bump micromamba 1.4.9 [6307f9b]
• Bump [email protected] [5746474]
• Bump [email protected] [e1512f6]
• Bump [email protected] [27e7f66]
• Bump [email protected] [1895efc]
• Bump [email protected] [cb6242c]
• Bump [email protected] [f98feb7]
• Bump [email protected] [6aede7c]
• Bump [email protected] [3278d79]
• Bump [email protected] [2998db5]

Version 23.06.0-edge

• Add Wave containers reports (preview) [9d9e275]
• Add disk resource with type option for Google batch (#3861) [166b363]
• Add httpConnectTimeout and httpReadTimeout to Google options (#3974) [49fa15f]
• Add plugin cmd help description [d3788f9]
• Add retry policy on Az blob operations [295bc1f]
• Add retry policy to Wave HTTP client [1daebee]
• Add support for AWS SES as mail sending provider [df85d44]
• Add support for arch auto-detection to Wave [7b5fdaf]
• Add wave.httpClient.connectTimeout config option [dd999a3]
• Clarify tip about groupTuple size and groupKey (#3949) [e60d327]
• Consolidate Wave retryPolicy options [7d7464f]
• Enhanced support for Spack + Wave (#3998) [63ac03b]
• Fix Google Batch default instance family types (#3960) [b5257cd]
• Fix S3 path normalization [b75ec44]
• Fix access to public S3 bucket when no creds are provided (#3992) [cf8ba46] [680f0a9]
• Fix containerOptions when using Fusion [dcde7b7]
• Fix dump pretty print not to modify input (#3955) [46c17ee]
• Fix invalid machine type setting when no valid machine type is found (#3961) [5eb9397]
• Fix matching symlink files [d63af78]
• Fix missing options for JsonSplitter creation (#3958) [f991fe9]
• Fix non-deterministic null container engine error [f227f2e]
• Fix packing all, including Wave [735b8d9]
• Fix static compiler errors [f48a473]
• Improve documentation on Nextflow scripts (#3953) [80050c0]
• Minor change in Wave config [4da0442]
• Prevent null exit code when Google batch is unable to access exit status [f68a39e]
• Refactor Conda and Spack support for Wave to Java [36b9e22]
• Remove --no-home default option from charliecloud builder (#3956) [915074a]
• Update workflow.revision max length to match the one in Tower (#4010) [1433a90]
• Bump amazocorretto:17.0.7 [c8aa121]
• Bump azure-storage-blob:12.22.1 [2a36fa7]
• Bump [email protected] [0872fba]
• Bump [email protected] [64bf311]
• Bump [email protected] [7ca7d80]
• Bump [email protected] [afd368c]
• Bump [email protected] [58c332a]

Version 23.04.2

• Fix non-deterministic null container engine error [f93221a]
• Add retry policy to Wave client [2f1532f]
• Fix wave build docs [34a7302]
• Bump [email protected] [350201b]

Version 23.05.0-edge

23.05.0-edge - 15 May 2023

• Add support for custom custom root directory to resolve relative paths (#3942) [f06bb1f]
• Add arch directive support for Spack (#3786) [62dfc48]
• Add clone deep option to run and pull commands [b44b645]
• Add fusion.exportStorageCredentials option [acb6aed]
• Add groovy-yaml to core runtime [003e1f7]
• Add missing test env variables to CI build [a0e501b]
• Add splitJson Operator (#3830) [4f58f69]
• Add support for Java 20 [3788a68]
• Add support for time directive in Azure Batch (#3869) [5c11a0d]
• Add support for the Spack recipes to Wave build (#3636) [b03cbe7]
• Add Preview support for virtual threads (#3871) [5c42904]
• Convert docs to Markdown (#3196) [3cad402]
• Deprecate DSL1 syntax for tap operator (#3004) [2be0edf]
• Enable static compilation to missing classes (#3906) [c3c4b2f]
• Fix -with-conda option in the docs (#3867) [9b350ba]
• Fix AWS SSE env propagation to Fusion [e24608c]
• Fix Apptainer rendering by removing superflous space [36607ed]
• Fix Azure jobs correctly deleted after completion (#3927) [b173a98]
• Fix Azure pool creation when using scaling formula (#3868) [79984a8]
• Fix DSL2 support in nextflow console (#3864) [0253f8d]
• Fix K8s handling PodUnschedulableException (#3938) [5b756c6]
• Fix interval channel factory (#3848) [d001e4c]
• Fix invalid warning on func import (#3807) [bb83696]
• Fix minor typo in nextflow subcommand (#3853) [dd3be3d]
• Fix misleading error message on NoSuchFileException [f3dceba]
• Fix missing SAS token fusion env for Azure [4301502]
• Fix problem args were not correctly represented in debug yaml (#3904) [eeb4b5c]
• Fix string comparison in S3 client (#3875) [9344d29]
• Fix use of remote dir with local exec statement [850bc3d]
• Fix Quote Singularity/Apptainer env values [586417a]
• Improve handling default out param [9147197]
• Improve plugin test detection [29794bf]
• Improve plugin updater err handling [f3d72f2]
• Improve task out redirect remove the use of mkfifo (#3863) [efedec7]
• Improve Use Docker stop instead of docker kill [32e6fd8]
• Improve Use separate script for long stage/unstage commands (#3851) [4343e33]
• Increase Azure default maxRetries to 10 [a017139]
• Keep plugins-info content sorted [d5552ee]
• Minor change on Docker-spack templates [e0e24bd]
• Refactor the AWS configuration (#3498) [a74e42d]
• Remove Channel.from in favor of Channel.of from tests and docs (#3670) [aa8b72f]
• Rename AmazonS3Client to S3Client [cc59596]
• Rename com.upplication.s3fs package to nextflow.cloud.aws.nio [a2f3bb2]
• Run build CI tests on push to branches starting with test* or dev* (#3852) [7032e17]
• Security fixes [973b7be]
• Support enums in cache helper (#3901) [e4b977a]
• Bump slf4j 2.0.7 and logback 1.4.6 [d7eae86]
• Bump JGit 6.5 and use depth 1 when cloning repos [eda0845]
• Bump aws-java-sdk-s3:1.12.429 [465171f]
• Bump fusion 2.2 [f1ebe29]
• Bump groovy 3.0.17 [cfe4ba5]
• Bump gson:2.10.1 [be55568]
• Bump micromamba:1.4.2 [334df1e]
• Bump [email protected] [7d6d010]
• Bump [email protected] [b06ffd0]
• Bump [email protected] [2e0a15c]
• Bump [email protected] [0c8fd7d]
• Bump [email protected] [a733b81]
• Bump [email protected] [12edf0e]
• Bump [email protected] [69b6edd]
• Bump [email protected] [d05d51b]