- 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-wave1.0.0 [795849d7]
**From previous egde releases**
23.09.3-edge - 10 Oct 2023
- Add -cloudcache CLI option (4385) [73fda582]
- Add bioconda and seqera Conda default channels (4359) [ff012dcd]
- Add codespell: config, workflow and have typos fixed (4324) [e044b7a5]
- Add docs page on caching and resuming (4371) [21190a3c]
- Add example of using the transpose operator with multiple items in element (4364) [0bce2be0]
- Add setting to enable the use of sync command [f0d5cc5c]
- Improve S3 endpoint validation [2b9ae6aa]
- Improve Wave config validation [7d5a21b0]
- Improve Wave error handling [d47e8b07]
- Fix Google Batch do not stop running jobs (4381) [3d6b7358]
- Incorporate README content into Nextflow docs (4263) [74a0f998]
- Never say (nearly) Oops again (4356) [4a39542b]
- Remove unsupported K8s device capability [be0cf0c2]
- Remove unused -dsl2 option [3cb91a15]
- Rename Microsoft AAD to Microsoft Entra (4362) [5e3f2c0a]
- Return -1 when exitcode file is empty (4354) [d26c42be]
- Support for Fusion unprivileged execution (4387) [035e6e7b]
- Use HistoryFile.Record instead of Record type conflic [11c3aac5]
- Bump nf-amazon2.1.4 [a84208a8]
- Bump nf-cloudcache0.3.0 [b37b4014]
- Bump nf-google1.8.3 [b4eb8b96]
- Bump nf-tower1.6.3 [5681ab13]
- Bump nf-wave0.14.0 [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-amazon2.1.3 [3311172f]
- Bump nf-azure1.3.2 [a9b735ce]
- Bump nf-google1.8.2 [7219d7f2]
- Bump nf-tower1.6.2 [91a935f9]
- Bump nf-wave0.13.0 [0cf2476c]
- Bump wave-utils0.7.8 [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 TraceRecordstore 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-amazon2.1.2 [7e5d414e]
- Bump nf-azure1.3.1 [83410f39]
- Bump nf-wave0.12.0 [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-azure1.3.0 [6670bb06]
- Bump nf-cloudcache0.2.0 [fb8f6681]
- Bump nf-tower1.6.1 [d06b8365]
- Bump nf-wave0.11.2 [7555b17d]
23.08.0-edge - 5 Aug 2023
- Add `-value` option to `config` command (4142) [57e3100b]
- Add `deleteTasksOnCompletion` to Azure Batch configuration (4114) [b14674dc]
- Add Tower logs checkpoint (4132) [71dfecc2]
- Allow use virtual threads in Wave client [dd32f80a]
- Allow workflow entry from module import (4128) [51f5c842]
- Disable cache backup/restore if cloudcache is used (4125) [46e828e1]
- Document behavior of withName selector with included aliases (4129) [8b7e3d48]
- Fix Option fixOwnership traverse parent directories [f2a2ea35]
- Fix Redirection http redirection across different hosts [fcdeec02]
- Fix Wave disable flag [8579e7a4]
- Fix bug with K8s resource labels (4147) eu-west-1[3f4b8557]
- Fix glob resolution for remove files [19a72c40]
- Fix incorrect error message on missing comma (4085) eu-west-1[a59af39f]
- Fix missing changelog for version 23.07.0-edge eu-west-1[9a33e936]
- Fix strict mode docs (4150) [6b46b507]
- Improve plugin docs (3957) [22638d46]
- Improve Wave config logging [547fad62]
- Improve TaskPollingMonitor logging [077ed5dd]
- Improve Wave and Fusion docs (4149) [d2229bde]
- Increase Wave client max attempts [fe5dd497]
- Remove module all components import [a6d08c04]
- Restore Tower CacheManager for backward compatibility [6d269070]
- Bump amazoncorretto:17.0.8 [00eb145c]
- Bump nf-wave0.11.1 [78e4b278]
- Bump nf-tower1.6.0 [41c8c164]
- Bump nf-azure1.2.0 [5f33ac17]
- Bump nf-amazon2.1.1 [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-amazon2.1.0 [57464746]
- Bump nf-azure1.1.2 [e1512f6a]
- Bump nf-azure1.1.3 [27e7f663]
- Bump nf-azure1.1.4 [1895efc4]
- Bump nf-cloudcache0.1.0 [cb6242c4]
- Bump nf-ga4gh1.1.0 [f98feb77]
- Bump nf-google1.8.1 [6aede7c0]
- Bump nf-tower1.5.15 [3278d798]
- Bump nf-wave0.11.0 [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-wave0.11.0 [2998db5d]
- Bump nf-tower1.5.15 [3278d798]
- Bump nf-google1.8.1 [6aede7c0]
- Bump nf-ga4gh1.1.0 [f98feb77]
- Bump nf-azure1.1.4 [1895efc4]
- Bump nf-amazon2.1.0 [57464746]
- Bump nf-cloudcache0.1.0 [cb6242c4]
23.05.0-edge - 15 May 2023
- Add support for custom custom root directory to resolve relative paths (3942) [f06bb1f7]
- Add `arch` directive support for Spack (3786) [62dfc482]
- Add clone deep option to run and pull commands [b44b6453]
- Add fusion.exportStorageCredentials option [acb6aedf]
- Add groovy-yaml to core runtime [003e1f70]
- Add missing test env variables to CI build [a0e501bf]
- Add splitJson Operator (3830) [4f58f695]
- Add support for Java 20 [3788a689]
- Add support for `time` directive in Azure Batch (3869) [5c11a0d4]
- Add support for the Spack recipes to Wave build (3636) [b03cbe70]
- Add Preview support for virtual threads (3871) [5c429046]
- Convert docs to Markdown (3196) [3cad402f]
- Deprecate DSL1 syntax for tap operator (3004) [2be0edfe]
- Enable static compilation to missing classes (3906) [c3c4b2f0]
- Fix -with-conda option in the docs (3867) [9b350ba8]
- Fix AWS SSE env propagation to Fusion [e24608c3]
- Fix Apptainer rendering by removing superfluous space [36607ed1]
- Fix Azure jobs correctly deleted after completion (3927) [b173a983]
- Fix Azure pool creation when using scaling formula (3868) [79984a87]
- Fix DSL2 support in nextflow console (3864) [0253f8d7]
- Fix K8s handling PodUnschedulableException (3938) [5b756c63]
- Fix `interval` channel factory (3848) [d001e4c7]
- Fix invalid warning on func import (3807) [bb836960]
- Fix minor typo in nextflow subcommand (3853) [dd3be3d1]
- Fix misleading error message on NoSuchFileException [f3dceba6]
- Fix missing SAS token fusion env for Azure [43015029]
- Fix problem args were not correctly represented in debug yaml (3904) [eeb4b5c8]
- Fix string comparison in S3 client (3875) [9344d294]
- Fix use of remote dir with local exec statement [850bc3d9]
- Fix Quote Singularity/Apptainer env values [586417ac]
- Improve handling default out param [91471970]
- Improve plugin test detection [29794bf4]
- Improve plugin updater err handling [f3d72f22]
- Improve task out redirect remove the use of mkfifo (3863) [efedec74]
- Improve Use Docker stop instead of docker kill [32e6fd85]
- Improve Use separate script for long stage/unstage commands (3851) [4343e333]
- Increase Azure default maxRetries to 10 [a017139f]
- Keep plugins-info content sorted [d5552ee6]
- Minor change on Docker-spack templates [e0e24bda]
- Refactor the AWS configuration (3498) [a74e42d9]
- Remove `Channel.from` in favor of `Channel.of` from tests and docs (3670) [aa8b72fa]
- Rename AmazonS3Client to S3Client [cc59596a]
- Rename com.upplication.s3fs package to nextflow.cloud.aws.nio [a2f3bb24]
- Run build CI tests on push to branches starting with `test*` or `dev*` (3852) [7032e17c]
- Security fixes [973b7bea]
- Support enums in cache helper (3901) [e4b977a4]
- Bump slf4j 2.0.7 and logback 1.4.6 [d7eae86e]
- Bump JGit 6.5 and use depth 1 when cloning repos [eda0845c]
- Bump aws-java-sdk-s3:1.12.429 [465171f5]
- Bump fusion 2.2 [f1ebe29a]
- Bump groovy 3.0.17 [cfe4ba56]
- Bump gson:2.10.1 [be555683]
- Bump micromamba:1.4.2 [334df1e0]
- Bump nf-wave0.9.0 [7d6d0108]
- Bump nf-tower1.5.13 [b06ffd0c]
- Bump nf-google1.7.4 [2e0a15cd]
- Bump nf-ga4gh1.0.6 [0c8fd7df]
- Bump nf-console1.0.6 [a733b818]
- Bump nf-codecommit0.1.5 [12edf0e6]
- Bump nf-amazon2.0.0 [69b6edde]
- Bump nf-azure1.1.0 [d05d51b4]
v23.09.3-edge
- 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]
v23.09.2-edge
- 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-amazon2.1.3 [3311172f]
- Bump nf-azure1.3.2 [a9b735ce]
- Bump nf-google1.8.2 [7219d7f2]
- Bump nf-tower1.6.2 [91a935f9]
- Bump nf-wave0.13.0 [0cf2476c]
- Bump wave-utils0.7.8 [d0c47d49]