nextflow

• 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]

• Fix use of GITHUB_TOKEN variable to access GitHub repo [108c6b55]
• Fix allow_other vulnerability preventing google-batch submissions (#4332) [4895d547]
• Fix Prevent false positive resumable task [aae87715]
• Fix Always emit publish event for cached task outputs (#4227) [c4cd53c2]
• Fix Too long Http connection pool timeout [ce5e9930]
• Bump [email protected] [d881728c]

• Revert "Allow setting shell directive when using the trace file (#4210)" [9f9edcdc]

• 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]

• 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]

• Add 429 http status code to Wave retriable errors [a8b8c6c5]
• Increase Wave client max attempts [8c67610a]
• Improve handling Wave server errors [621c9665]
• Fix log typo [03e19ea2]
• Bump [email protected] [d7fa3f26]
• Bump corretto 17.0.8 [7a73a78f]

• 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) [ci skip] [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]

• 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 not to 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]
• 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] [0872fba5]
• Bump [email protected] [64bf3115]
• Bump [email protected] [7ca7d808]
• Bump [email protected] [afd368c4]
• Bump [email protected] [58c332a1]

• Fix non-deterministic null container engine error [f93221ab]
• Add retry policy to Wave client [2f1532f6]
• Fix wave build docs [34a73022]
• Bump [email protected] [350201b5]

23.05.0-edge - 15 May 2023

• Add support for custom custom root directory to resolve relative paths (#3942) [f06bb1f7]
• Add arch directive support for Spack (#3786) [62dfc482]
• Add clone deep option to run and pull commands [b44b6453]
• Add fusion.exportStorageCredentials option [acb6aedf]
• Add groovy-yaml to core runtime [003e1f70]
• Add missing test env variables to CI build [a0e501bf]
• Add splitJson Operator (#3830) [4f58f695]
• Add support for Java 20 [3788a689]
• Add support for time directive in Azure Batch (#3869) [5c11a0d4]
• Add support for the Spack recipes to Wave build (#3636) [b03cbe70]
• Add Preview support for virtual threads (#3871) [5c429046]
• Convert docs to Markdown (#3196) [3cad402f]
• Deprecate DSL1 syntax for tap operator (#3004) [2be0edfe]
• Enable static compilation to missing classes (#3906) [c3c4b2f0]
• Fix -with-conda option in the docs (#3867) [9b350ba8]
• Fix AWS SSE env propagation to Fusion [e24608c3]
• Fix Apptainer rendering by removing superflous 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]

• Security fixes [fc2627bb]
• Add support for testing custom plugin uri [718d4562]
• Improve plugin updater err handling [84042082]
• Improve plugin test detection [ci fast] [e6c60a6c]
• Bump [email protected] [26b01b83]
• Bump [email protected] [2a886fe0]
• Bump [email protected] [b8769f1a]
• Bump [email protected] [89d902ec]
• Bump [email protected] [9b0f4bfb]
• Bump [email protected] [f7aaddc6]
• Bump [email protected] [7898cc04]

• Add support for Java 20 [f6933db7]
• Fix use of remote dir with local exec statement [6ea1f68c]
• Fix Azure pool creation when using scaling formula (#3868) [84a808a5]
• Fix interval channel factory (#3848) [82ccf6ad]
• Fix invalid warning on func import (#3807) [4678ffe3]
• Improve plugin test detection [57cfb0d9]
• Improve plugin updater err handling [5627c69a]
• Security fixes [83e8fd6a]
• Bump [email protected] [d8cb763c]
• Bump [email protected] [b2354380]
• Bump [email protected] [22a68cfe]
• Bump gson:2.10.1 [83ca1e32]
• Bump [email protected] [b40b5165]
• Bump [email protected] [98a89154]
• Bump aws-java-sdk-s3:1.12.429 [b71ee0a3]
• Bump [email protected] [a5da54d3]
• Bump [email protected] [c90553c9]

• Add several names to the name generator feat:(#3790) [dfa2f6ca]
• Add support for Fusion to Azure Batch executor (#3209) [3d3cbfa2]
• Add support for testing custom plugin uri [227910ab]
• Add warnings for Azure named pools (#3819) [a2c71acf]
• Enable new pid namespace with Singularity & Apptainer [3601b014]
• Fix NoSuchMethodError String.stripIndent with Java 11 [308eafe6]
• Fix issue checking Google Batch script launcher type [39c3a517]
• Fix resolution of module resources [2c5a6878]
• Fix Relax caching across task retries [840e8432]
• Fix Java version for tests [7ce05c15]
• Remove extra context from workflow error message [38c8bd33]
• Revert "Enable Fusion on Google Batch tests" [2ba7ea54]
• Bump micromamba 1.4.1 [ec1439e6]
• Bump [email protected] [0f98b245]
• Bump [email protected] [e1732be9]
• Bump [email protected] [99477f79]
• Bump [email protected] [939195b5]
• Bump [email protected] [b7b5d4c9]

From previous edge releases

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 [email protected] [aa1b065d]
• Bump [email protected] [2aaaf2a7]
• Bump [email protected] [f358b008]
• Bump [email protected] [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 [email protected] [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 [skip ci] (#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 [email protected] [b797fac2]
• Bump [email protected] [dd2f69dd]
• Bump [email protected] [8cb9fa35]
• Bump [email protected] [7ccca430]

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 [email protected] [45d274e3]
• Bump [email protected] [db0ebe72]
• Bump [email protected] [a663fe16]
• Bump [email protected] [45fd53ad]
• Bump [email protected] [cf39ef8f]
• Bump [email protected] [7a6a78aa]
• Bump [email protected] [41fdcc72]

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 [email protected] [ccaab713]
• Bump [email protected] [c07dcec2]
• Bump [email protected]
• Bump [email protected] [652d0880]
• Bump fusion version URLs 0.6 [a160a8b1]
• Bump AWS sdk version 1.12.351 [4dd82b66]

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 [email protected] [fe669152]
• Bump [email protected] [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 [email protected] [e307912e]
• Bump [email protected] [07391d96]
• Bump [email protected] [4d787561]

• 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 [email protected] [aa1b065d]
• Bump [email protected] [2aaaf2a7]
• Bump [email protected] [f358b008]
• Bump [email protected] [2395187d]

• Add Fusion logs and tags config [09192078]
• Add support for NXF_DEBUG to K8s task handler [ci fast] [828583dc]
• Add support for Mamba HTTP-based lock files [ci fast] [7fe88c84]
• Add container name validation [c3b6d9ab]
• Add Fusion for Google storage docs [34fcfe06]
• Improve K8s auth token discovery [ci fast] [44f8cc07]
• Bump [email protected] [1c697ab5]
• Bump amazoncorretto:17.0.6 [a33a6f47]

• 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]
• 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 [skip ci] (#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 [email protected] [b797fac2]
• Bump [email protected] [dd2f69dd]
• Bump [email protected] [8cb9fa35]
• Bump [email protected] [7ccca430]

Breaking changes

• Using the AWS Batch executor, Nextflow requires the permission batch:TagResource when creating Batch job permissions
• Using the AWS Batch executor with Fusion file system, Nextflow requires s3:PutObjectTagging permission on the S3 objects created by job executions

• 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 [email protected] [f466b266]
• Bump [email protected] [d5f6c125]

• 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 [email protected] [c1ec759f]