nextflow-io/nextflow v23.10.0 on GitHub

Add support for K8s hostPath [10c3232]
Add AWS SES docs [b83e714]
Add -with-cloudcache instead of -cloudcache [ef53026]
Add inspect command validation tests [882f369]
Improve warning complaining about tuple but mentioning set (#4400) [0ef4873]
Improve -dump-hashes output adding json format (#4369) [5bdaac9]
Improve error message on invalid file url prefix [82a3f40]
Fix conda channels order [6672c6d]
Docs: Incorporate DSL2 features (#3793) [efd041c]
Docs: aws.batch.retrymode = 'built-in' (#4229) [d5a8098]
Docs: Update logos, fonts, and colors (#4407) [7814822]
Changelog minor changes [dfb5bf0]
Bump nf-wave@1.0.0 [795849d]

From previous egde releases

23.09.3-edge - 10 Oct 2023

Add -cloudcache CLI option (#4385) [73fda58]
Add bioconda and seqera Conda default channels (#4359) [ff012dc]
Add codespell: config, workflow and have typos fixed (#4324) [e044b7a]
Add docs page on caching and resuming (#4371) [21190a3]
Add example of using the transpose operator with multiple items in element (#4364) [0bce2be]
Add setting to enable the use of sync command [f0d5cc5]
Improve S3 endpoint validation [2b9ae6a]
Improve Wave config validation [7d5a21b]
Improve Wave error handling [d47e8b0]
Fix Google Batch do not stop running jobs (#4381) [3d6b735]
Incorporate README content into Nextflow docs (#4263) [74a0f99]
Never say (nearly) Oops again (#4356) [4a39542]
Remove unsupported K8s device capability [be0cf0c]
Remove unused -dsl2 option [3cb91a1]
Rename Microsoft AAD to Microsoft Entra (#4362) [5e3f2c0]
Return -1 when exitcode file is empty (#4354) [d26c42b]
Support for Fusion unprivileged execution (#4387) [035e6e7]
Use HistoryFile.Record instead of Record type conflic [11c3aac]
Bump nf-amazon@2.1.4 [a84208a]
Bump nf-cloudcache@0.3.0 [b37b401]
Bump nf-google@1.8.3 [b4eb8b9]
Bump nf-tower@1.6.3 [5681ab1]
Bump nf-wave@0.14.0 [de1de6c]

23.09.2-edge - 28 Sep 2023

Add conda.enabled to conda config scope docs (#4320) [0b74c4e]
Add developer docs (#4065) [06843d8]
Add fs stat command [a79056b]
Add more tests to container name [da7a194]
Add procps by default to Conda-based Wave builds [66b2d2d]
Add support for Java 21 (#4338) [ac1fc9e]
Add Mermaid diagram in HTML DAG (#4337) [0f3e263]
Default Conda basePackages to "conda-forge::procps-ng" [367af52]
Disable Tower container field for multiple images [b53936b]
Document NXF_DISABLE_CHECK_LATEST environment var (#4327) [4e3e9ac]
Document fs CLI command (#4328) [1a68049]
Document source of vol_ctxt and inv_ctxt trace metrics (#4333) [6525b0a]
Document when process directives are evaluated (#4217) [731a29a]
Fix List of S3 bucket for custom endpoint [4327fa5]
Fix Prevent false positive resumable task [144e0a8]
Fix Prevent multi attempts to retrieve AWS creds [b30efe3]
Fix allow_other vulnerability preventing google-batch submissions (#4332) [9b3741e]
Fix fs list command [29ab2f2]
Fix minor typos in changelogs/source code (#4319) [4ce9f1d]
Fix support for S3 custom endpoint with anonymous access [0375281]
Fix use of GITHUB_TOKEN variable to access GitHub repo [afe3dc4]
Fix Wave does not support 'null' container engine [f3eba3d]
Fix Retry TimeoutException in azure file system (#4295) [7924835]
Improve K8s unit tests (#4196) [5a43a32]
Improve Mermaid DAG rendering (#4070) [19587f4]
Improve error report when exception is thrown in operator ctx [16f54a9]
Improve wave container name validation [73eb5a0]
Minor improvements [fff3d7b]
Prevent cache invalidation for task directives (#4339) [aabb6c1]
Remove line endings from container box id (#4334) [df41e54]
Bump Apache 2.0 license to tower client [e4a878b]
Bump nf-amazon@2.1.3 [3311172]
Bump nf-azure@1.3.2 [a9b735c]
Bump nf-google@1.8.2 [7219d7f]
Bump nf-tower@1.6.2 [91a935f]
Bump nf-wave@0.13.0 [0cf2476]
Bump wave-utils@0.7.8 [d0c47d4]

23.09.1-edge - 11 Sep 2023

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

23.09.0-edge - 10 Sep 2023

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 nf-amazon@2.1.2 [7e5d414]
Bump nf-azure@1.3.1 [83410f3]
Bump nf-wave@0.12.0 [a9f6dd6]

23.08.1-edge - 17 Aug 2023

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 nf-azure@1.3.0 [6670bb0]
Bump nf-cloudcache@0.2.0 [fb8f668]
Bump nf-tower@1.6.1 [d06b836]
Bump nf-wave@0.11.2 [7555b17]

23.08.0-edge - 5 Aug 2023

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 nf-wave@0.11.1 [78e4b27]
Bump nf-tower@1.6.0 [41c8c16]
Bump nf-azure@1.2.0 [5f33ac1]
Bump nf-amazon@2.1.1 [981315a]

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) [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 nf-amazon@2.1.0 [5746474]
Bump nf-azure@1.1.2 [e1512f6]
Bump nf-azure@1.1.3 [27e7f66]
Bump nf-azure@1.1.4 [1895efc]
Bump nf-cloudcache@0.1.0 [cb6242c]
Bump nf-ga4gh@1.1.0 [f98feb7]
Bump nf-google@1.8.1 [6aede7c]
Bump nf-tower@1.5.15 [3278d79]
Bump nf-wave@0.11.0 [2998db5]

23.06.0-edge - 14 Jun 2023

Add AWS Kms integration test [19449bf]
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 to not 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]
Improve description of channels and channel types (#4120) [8975734]
Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf]
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 nf-wave@0.11.0 [2998db5]
Bump nf-tower@1.5.15 [3278d79]
Bump nf-google@1.8.1 [6aede7c]
Bump nf-ga4gh@1.1.0 [f98feb7]
Bump nf-azure@1.1.4 [1895efc]
Bump nf-amazon@2.1.0 [5746474]
Bump nf-cloudcache@0.1.0 [cb6242c]

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 superfluous 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 nf-wave@0.9.0 [7d6d010]
Bump nf-tower@1.5.13 [b06ffd0]
Bump nf-google@1.7.4 [2e0a15c]
Bump nf-ga4gh@1.0.6 [0c8fd7d]
Bump nf-console@1.0.6 [a733b81]
Bump nf-codecommit@0.1.5 [12edf0e]
Bump nf-amazon@2.0.0 [69b6edd]
Bump nf-azure@1.1.0 [d05d51b]

nextflow-io/nextflow v23.10.0 Version 23.10.0 on GitHub

nextflow-io/nextflow v23.10.0
Version 23.10.0

on GitHub