nextflow-io/nextflow v24.04.0 on GitHub

Add 'preview' to workflow runtime metadata (#4985) [935bb1e]
Add enabled property to output dsl (#5008) [284415b]
Fix Taskbar API is not supported error [0ea09cc]
Fix inspect should not write history entry [c713ad5]
Fix unexpected container resolution [a5ecf8a]
Improve icon loading error handling [c72e16f]
Remove Fusion symlink resolution (#5004) [071ea74]
Remove seqera and defaults from Conda default channels (#5003) [ec5ebd0]
Use protected visibility for updateStatus method [6871ba0]
Workflow output definition (#4784) [cf0546b]
Bump Fusion 2.3 (#5005) [7176c11]
Bump groovy-console 4.0.21-patch.2 [eb97831]
Bump nf-amazon@2.5.1 [96ee633]
Bump nf-console@1.1.3 [e835904]
Bump nf-google@1.13.1 [5dcb4c7]
Bump nf-wave@1.4.2 [73c668a]

24.04.0-edge - 13 May 2024

Add Wave and Fusion info to workflow metadata (#4945) [bb7e1c8]
Add k8s.cpuLimits config option (#3027) [3c6e96d]
Add account config option for grid executors (#4975) [a09e37d]
Add git to docs deps [aa9e127]
Add resourceLimits directive (#2911) [7c9d965]
Add support for Job arrays (#3892) [ca9bc9d]
Add support for clusterOptions as a list of values (#4993) [dd173e3]
Add threads dump for troubleshooting purposes [8992ebd]
Fix Gstring casting exception when clusterOptions is a closure [74004fb]
Fix Missing error code when no entry is specified [f507e9a]
Fix NPE in LogsCheckpoint class [deb3076]
Fix Prevent maxForks less than zero [7676dd9]
Fix Use fully qualified S3 uris in error message (#4923) [f1cffd1]
Fix Wave container resolution with singularity and ociMode [54ad624]
Fix collectFile saving to GCS with sort: false (#4965) [1418553]
Fix console "Plugin manager not initialised" warn (#4989) [5ff4453]
Fix console icon (#4991) [b8a2370]
Fix docs formatting [c02e58c]
Fix docs snippet [6499649]
Fix flaky docs test (#4957) [ea8246f]
Fix groovy console issue (#4988) [b9bf641]
Fix job array docs (#4984) [6a3347e]
Fix missing include error message (#4981) [aad100e]
Fix script error text alignment (#4681) [1dc4e4e]
Fix security vulnerability in logback (#4947) [0ffcc4c]
Fix semaphore in parallel polling monitor (#4927) [5c37fcc]
Fix remove commented out test lines in Azure Batch Pool opts tests. (#4914) [cb607f0]
Guarantees K8s pod name is unique on resume (#4959) [361cef8]
Improve config resolution docs (#4950) [019eb86]
Improve documentation about azcopy installation requirements for custom Azure Batch worker pools (#4911) [5c410db]
Improve error message for image pull time-out for Singularity/Apptainer/Charliecloud (#4974) [73015fb]
Remove unused const [6e91285]
Run task finalisation asynchronously (#4890) [e0e9422]
Strip auth secret from logs [acf63e0]
Update TES executor to TES API v1.1 (#4195) [7b32c2d]
Update aws.md to include Cluster access (#4951) [459d725]
Update developer diagrams (#4922) [dcff41a]
Update operator return types (#4976) [a614fbe]
Update stale documentation in overview.md (#4968) [6a58c6d]
Use for instead eachLine in error formatting [4a821f4]
azure batch autopool feature more comprehensive documentation (#4941) [adbd890]
Bump Gradle 8.7 [8b5cf3c]
Bump nf-wave@1.4.1 [830b032]
Bump nf-tower@1.9.1 [163683c]
Bump nf-google@1.13.0 [6d99a22]
Bump nf-ga4gh@1.3.0 [89695ed]
Bump nf-console@1.1.2 [357b143]
Bump nf-amazon@2.5.0 [6c62a60]

24.03.0-edge - 15 Apr 2024

Add custom jobName for Google Batch [df40d55]
Add escher to name generator class [2e6496e]
Add retry policy to Google Batch client [c4981dc]
Add retry strategy for publishing (#4839) [c9c7032]
Add support for Azure custom startTask (#4913) [27d01e3]
Add task tip extension point [eadad5b]
Allow secrets to be used in pipeline script (#4171) [df866a2]
Do not print a new line when stdout is empty (#4892) [658a5ec]
Fix Azure pool creation [2ee4d11]
Fix Use of secrets in the includeConfig path [00c9f22]
Fix coloured ANSI log bug (#4898) [a04d698]
Fix eval output type via bash -c wrapping (#4887) [2165a14]
Fix exception handling in local executor [74d7d7a]
Fix support for GCS requester pays bucket option [d9d61cf]
Fix test when missing Google secret [33dc3ce]
Improve Charliecloud support (#4879) [287471c]
Improve control on azcopy install (#4883) [01447d5]
Improve error message when Google creds file is corrupted [a550e52]
Improve getting started docs (#4764) [b59111b]
Improve retry logic for AWS Batch executor [62926c2]
Nextflow launch script: improving search for JAVA_CMD (#4830) [ebbbe9e]
Publish built-in reports as Tower reports (#4760) [b710d92]
Remove not needed dsl=2 + error in example (#4812) [7c5779d]
Remove unused code from AssetManager [7736516]
Revert "Fix failing CI tests (#4861)" [7ba2e25]
Update NameGenerator (#4907) [248201a]
Update Platform API endpoint (#4855) [4842423]
Update Wave to API v1alpha2 (#4906) [9c35087]
Update docs (#4852) [6e2d1a9]
Updated docs on Google Cloud setup and credentials (#4896) [7e8b5e2]
Updated dodcs note on singularity default command (#4825) [567f533]
Bump groovy 4.0.20 [66c1a16]
Bump groovy 4.0.21 [9e08390]
Bump nf-wave@1.4.0 [fc70dc8]
Bump nf-tower@1.9.0 [b0c4e2c]
Bump nf-google@1.12.0 [6ae25fa]
Bump nf-azure@1.6.0 [967c2ac]
Bump nf-amazon@2.4.2 [ddda969]

24.02.0-edge - 10 Mar 2024

Add K8s job ttlSecondsAfterFinished option (#4434) [93627be]
Add NXF_CACHE_DIR environment var (#4655) [4b00170]
Add colours to ansi logs (#4573) [5e2ce9e]
Add eval output type (#4493) [df97811]
Fix Always emit publish event for symlinks on resume (#4790) [bb5c4f9]
Fix Do not create local plugin path in embedded mode [9d6dd6a]
Fix Error while publishing S3 file with blanks [b74c022]
Fix Missing dependency for console command [baf2911]
Fix typo in Azure Batch docs ('Azore') (#4735) [192bf8d]
Fix typo in error message [a7f2330]
Remove experimental admonition for podman [17d0dce]
Remove square brackets from job name in LSF executor (#4799) [6e0ac72]
Remove unneeded const [09c957f]
Rename Tower -> Seqera Platform in docs and log messages (#4727) [7caffef]
Update Azure dependencies [1bcbaf0]
Update copyright info [e3089f0]
Use alias for HistoryFile.Record [17217a1]
minor cli docstring fix (#4759) [ee4b4a2]
Bump Grengine 3.0.2 [42ca2b6]
Bump groovy 4.0.19 [854dc1f]
Bump snakeyaml 2.2 [0748077]
Bump nf-amazon@2.4.1 [0eb8407]
Bump nf-azure@1.5.1 [d63be8c]
Bump nf-cloudcache@0.4.1 [57b7004]
Bump nf-console@1.1.1 [b7f703f]
Bump nf-tower@1.8.1 [b8ffb18]
Bump nf-wave@1.3.1 [0c542ed]
Bump amazoncorretto 17.0.10-al2023 [3e695ad]

24.01.0-edge - 5 Feb 2024

Add support for custom fuse device plugin (#4612) [a1e3319]
Fix Ignore stored process message when ansi log is enabled (#4645) [f9ba47e]
Fix Wave container replicable checksum [da382dd]
Fix azure retry policy (#4638) [85bab69]
Fix handling of wave.s5cmdConfigUrl setting (#4707) [3a19386]
Fix typo in Hyperqueue section (#4635) [d5a6a96]
Fix typo in OCI mode warning message (#4633) [e216a87]
Fix typo in the docs (#4636) [ci-skip] [4727f17]
Improve detection of sys home variable [8812138]
Improve handling of publish error (#4703) [fc9f768]
LocalSecretsProvider: invalid permissions tests made more robust (#4663) [682a680]
Remove Glacier auto-retrieval (#4705) [5f0ec50]
Remove preview from cmd secret [dc04022]
Set scratch default to false when using Fusion (#4675) [9d17e40]
Slight change in wording for error message about userEmulation (#4680) [a9c8a84]
Truncate max size exceeded error message (#4644) [36090b7]
Use AZURE_STORAGE_SAS_TOKEN environment variable (#4627) [2e02afb]
Use canonical init method for plugins initialization [e7a20af]
Bump nf-wave@1.3.0 [8b9905c]
Bump nf-tower@1.8.0 [bfc94e4]
Bump nf-google@1.11.0 [01ff035]
Bump nf-ga4gh@1.2.0 [3df3418]
Bump nf-console@1.1.0 [e90d73a]
Bump nf-codecommit@0.2.0 [4379c94]
Bump nf-cloudcache@0.4.0 [2bc698c]
Bump nf-azure@1.5.0 [07415ce]
Bump nf-amazon@2.4.0 [b991e14]
Bump Groovy 4 (#4443) [9d32503]
Bump actions/checkout@v4 [d1b3195]
Bump logback@1.4.12 + guava@33.0.0-jre [331ff42]
Bump nextflow 23.12.0-edge as min version [63e8370]
Bump tj-actions/changed-files from 35 to 41 in /.github/workflows (#4622) [d67aef5]

23.12.0-edge - 20 Dec 2023

Add AWS_SESSION_TOKEN to Fusion environment (#4581) [552f29b]
Add ability to disable Cloudinfo service (#4606) [f725189]
Add experimental support for Fargate compute type for AWS Batch (#3474) [47cf335]
Add support for Instance template to Google Batch [df7ed29]
Add support for Singularity/Apptainer auto pull mode for OCI containers [b7f1a19]
Fix BitBucket get source API with custom branch [5893783]
Fix Fusion tags documentation (#4551) [687e2e9]
Fix Harden regular expression to used to strip secrets in logs (#4563) [832bff2]
Fix bug with Fusion symlink resolution (#4593) [09e8558]
Fix container environment with special chars (#4594) [e0fe952]
Fix custom notification template [ccf4f59]
Fix fusion symlink test (#4604) [681ace8]
Fix smoke tests [d3c2f33]
Improve GLS tests [58590b1]
Load nf-amazon when AWS SES is enabled [887f06f]
Move build num & timestamp to BuildInfo class [ec8083d]
Move app version to BuildInfo class [c7d749e]
Remove deprecated Wave observer [0e009ef]
Remove undocumented userEmulation mode (#4596) [f6c7978]
Remove unused DSL2 check [e9ee3b2]
Replace each iterator with class for [f7662e6]
Bump nf-amazon@2.3.0 [0b40b7b]
Bump nf-google@1.10.0 [bcb20fc]
Bump nf-wave@1.2.0 [aa98181]
Bump wave-utils@0.8.1 and micromamba@1.5.5 [9cb5003]
Build optimizations (#4579) [5ad41e4]

23.11.0-edge - 24 Nov 2023

Add fusion.cacheSize config option (#4518) [2faadc2]
Add Topic channel type (experimental) (#4459) [921313d]
Add Google Batch native retry on spot termination (#4500) [ea1c1b7]
Add Retry policy to Google Storage (#4524) [c271bb1]
Add ability detect Google Batch spot interruption (#4462) [d49f02a]
Add doc tests, move some snippets to separate files (#3959) [0ff3b30]
Add docs section on container requirements (#4501) [3fb29f7]
Add labels field in Job request for Google Batch (#4538) [627c595]
Add note about limitations of glacier auto retrieval (#4514) [82e5679]
Add note about local executor and enforcing resource limits (#4468) [6a0626f]
Add section about sharing modules (#4482) [3e66fba]
Add section on process directives to plugin docs (#4477) [d9ee987]
Add support for Azure low-priority pool (#4527) [8320ea1]
Add support for FUSION_AWS_REGION (#4481) [8f8b09f]
Add support for Fusion when using Singularity OCI mode (#4508) [4f3aa63]
Add support for K8s schedulerName pod spec (#4485) [dfc7b7c]
Add support for Singularity OCI mode (#4440) [f5362a7]
Allow the use of error built-in function in onComplete handler (#4458) [35a4424]
Fix Bug in JsonSplitter ordering [8ec14dd]
Fix Bypass Google Batch Price query if task cpus and memory are defined (#4521) [7f8f20d]
Fix Checkout remote tag if checkout remote branch fails (#4247) [b8907cc]
Fix Fusion symlinks when publishing files (#4348) [89f09fe]
Fix Inspect command fails with Singularity [f5bb829]
Fix ParamsMap copyWith param aliases (#4188) [b480ee0]
Fix Singularity docs [e952299]
Fix container hashing for Singularity + Wave containers [4c6f2e8]
Fix detection of Conda local path made by Wave client (#4532) [4d5bc21]
Fix doc tests to fail on test failure (#4505) [4d32655]
Fix errors when NXF_HOME contains spaces (#4456) [fe5bea9]
Fix Google Batch network/subnetwork docs (#4475) [27d132f]
Fix rounding error with long durations (#4496) [0356178]
Fix security vulnerabilities (#4513) [a310c77]
Fix Use consistently NXF_TASK_WORKDIR (#4484) [48ee3c6]
Improve error details for AbortOperationException [35609cb]
Improve operator docs (#4502) [38210e1]
Makefile clean to also remove buildSrc/build (#4517) [2ccb05d]
Minor test improvements [171831e]
Minor types improvement for mix operator [91c1ab1]
Normalise channel docs [b641d67]
Remove deprecated TowerArchiver feature [ff8e06a]
Remove dsl1 deprecated code (part 2) [159effb]
Remove dsl1 deprecated code [2b433a5]
Remove incorrect note about workflow inputs (#4509) [54bc0b7]
Return error if plugin version is not specified in offline mode (#4487) [f5d7246]
Update README.md with new branding color for Nextflow (#4412) [7a13b18]
Update background color of docs status badges (#4411) [3cb1c53]
Update logging filter for Google Batch provider. (#4488) [66a3ed1]
Bump Gradle 8.4 and test vs Java 21 (#4450) [8cb2702]
Bump nf-amazon@2.2.0 [8e2d787]
Bump nf-azure@1.4.0 [7c47d09]
Bump nf-cloudcache@0.3.1 [65240b7]
Bump nf-codecommit@0.1.6 [725f051]
Bump nf-console@1.0.7 [a307686]
Bump nf-ga4gh@1.1.1 [e54ea00]
Bump nf-google@1.9.0 [033ec92]
Bump nf-tower@1.7.0 [836a44a]
Bump nf-wave@1.1.0 [620523e]

nextflow-io/nextflow v24.04.0 Version 24.04.0 on GitHub

nextflow-io/nextflow v24.04.0
Version 24.04.0

on GitHub