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Releases: nextflow-io/nextflow

Version 25.01.0-edge

12 Feb 14:10
e2ae8a9
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Version 25.01.0-edge Pre-release
Pre-release
  • Add DeadlineExceededException to Google Batch retryable exceptions [944f48f]
  • Add Fusion token validation (#5614) [1dcb18d]
  • Add stub flag to task hash only if task has a stub (#5750) [deec443]
  • Add traceparent header to wave & tower clients (#5725) [7eea9f2]
  • Allow Azure Batch tasks to be submitted to different pools (#5766) [76790d2]
  • Configure target java version alongside gradle toolchain (#5676) [2153abb]
  • Disable cleanup on remote work dir (#5742) [ef67b81]
  • Do not skip integration tests on PRs [4caf6ef]
  • Fail the run if publish thread pool times out (#5578) [5325e5a]
  • Fix Check for number of low priority nodes in Azure Batch before raising a pool resize error (#5576) [9b528c1]
  • Fix Conda directive is not honoured by task array (#5704) [f8c3b63]
  • Fix Create parent directory for DAG report (#5752) [62263a3]
  • Fix Google Batch task array causes process to fail (#5780) [7ad7a23]
  • Fix Mount input file buckets in task arrays for Google Batch (#5739) [ba171fd]
  • Fix bugs with workflow outputs (#5502) [ab59d30]
  • Fix first collection method [a0ca6e4]
  • Fix stub templates (#5751) [13072d6]
  • Ignore tests when smoke mode is enabled [3eb6efa]
  • Improve Google Batch executor stability and error handling (#5690) [b64087f]
  • Preserve attributes of published files (take 2) (#5660) [422f289]
  • Remove compileJava options [28e03a2]
  • Remove redundant exception handling [00376aa]
  • Revert "Fix the cleanup of local secret file" (#5697) [55f25b3]
  • Strengthen shell directive validation (#5689) [039c8f3]
  • Update HyperQueue CLI option (#5730) [BREAKING] [b582cb5]
  • Update azure deps [b163da9]
  • Use unbound queue for transfer thread pool (#5700) [9031968]
  • Bump Fusion to version 2.5 (2nd attempt) [a7f09ae]
  • Bump gradle 8.12.1 [1fffb85]
  • Bump groovy 4.0.25 [19c40a4]
  • Bump io.netty:netty-handler:4.1.118.Final [db4a903]
  • Bump net.minidev:json-smart:2.5.2 [b5c4faf]
  • Bump netty-common:4.1.118.Final [8574e24]

Version 24.12.0-edge

20 Jan 16:22
24faeee
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Version 24.12.0-edge Pre-release
Pre-release
  • Add Warning when Cloudinfo fails in Google Batch machine type selection (#5649) [5aef532]
  • Add rate limiter to wave requests (#5608) [ecf6829]
  • Allow named parameters with plugin subcommand (#5643) [f81da8c]
  • Customise mermaid diagram theme in DAG template (#5553) [54713a1]
  • Deprecate -with-weblog CLI opt [aa258b4]
  • Disable AWS SDK v1 warning [cd00a26]
  • Dump threads only with trace log level [87df7cd]
  • Ensure job is killed when exception in task status check (#5561) [9eefd20]
  • Fix CLI params normalization (#5661) [e2e prod] [b5d43ad]
  • Fix Execution may hang reading trace file (#5683) [17d7a08]
  • Fix Google Batch hang when internal error during scheduling (#5567) [18f7de1]
  • Fix GroovyCompiler source and target compability [6dd92e3]
  • Fix Only close the cache db if it is not null (#5631) [9386082]
  • Fix Azure repos when clone URL is used (#5667) [dc6cc41]
  • Fix shell directive with trace command in wrapper script (#4292) [8342889]
  • Fixing getRepositoryUrl when project name is not provided (#5560) [335701e]
  • Handle attribute caching with Lustre filesystem (#5650) [61674d2]
  • Improve Fargate + Wave docs (#5562) [12be47e]
  • Improve inspect mode (#5605) [8e2056e]
  • Include all processes in inspect command (#5580) [0aa76af]
  • Prevent the use existing work dir (#5682) [e14fc99]
  • Remove 'defaults' conda channel from docs (#5607) [8b54181]
  • Update Google Batch docs to clarify spot retry behaviour (#5644) [1878836]
  • Update flux job id regular expression (#5662) [58a0b34]
  • Use printf instead of echo to write trace file (#5397) [c6434d4]
  • Bump groovy 4.0.24 missing deps [40670f7]
  • Bump jgit to version 7.1.0 (#5587) [3d71468]
  • Bump logback 1.5.13 + slf4j 2.0.16 [cc0163a]
  • Bump logback 1.5.16 [5ac91f0]
  • Bump nf-wave@1.9.0 [182ddd4]
  • Bump nf-tower@1.9.4 [4d949d1]
  • Bump nf-google@1.17.0 [741d0f3]
  • Bump nf-console@1.1.5 [958820f]
  • Bump nf-codecommit@0.2.3 [fdc32c7]
  • Bump nf-cloudcache@0.4.3 [c173c53]
  • Bump nf-azure@1.12.0 [b747dcf]
  • Bump nf-amazon@2.11.0 [2650f07]

Version 24.10.4

20 Jan 17:03
56ad7db
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Version 24.10.3

16 Dec 16:42
6183fdf
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  • Fix Google Batch hang when internal error during scheduling (#5567) [79374c5]
  • Fixing getRepositoryUrl when project name is not provided (#5560) [9910cec]
  • Bump nf-google@1.15.3 [e80ded3]

Version 24.11.0-edge

03 Dec 10:43
6e231be
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Version 24.11.0-edge Pre-release
Pre-release
  • Add GHA to submit dependencies to dependabot (#5440) [80395a6]
  • Add NotFoundException to retry condition for Google Batch [aa4d19c]
  • Add Rahel Hirsch to run name generator (#5442) [ff2bc6a]
  • Add env() function (#5506) [fa0e8e0]
  • Add more scientists to run name generator (#5447) [38d9eda]
  • Add singularity.libraryDir to config page (#5498) [b5e31bb]
  • Add RepositoryProvider.revision now public property (#5500) [f0a4c52]
  • Deprecate process shell block (#5508) [6f52755]
  • Detecting errors in data unstaging (#5345) [3c8e602]
  • Disable virtual threads on CI tests [ci slip] [69d07db]
  • Fix Fargate warning on memory check (#5475) [bdf0ad0]
  • Fix isContainerReady when wave is disabled (#5509) [3215afa]
  • Fix missing wave response (#5547) [ee25217]
  • Fix overlapping conda lock file (#5540) [9248c04]
  • Fix overlapping conda lock exception (#5489) [eaaeb3d]
  • Fix possible deadlock in dynamic maxRetry resolution (#5474) [25bbb62]
  • Fix Wave GCP integration test (#5490) [ad56c89]
  • Fixing bug when execution with stub and no stub defined (#5473) [f7fd56d]
  • Fix Incorrect CPU value in Azure example (#5549) [fc5e2c2]
  • Improve docs for using the GPU accelerator directive (#5488) [4b90852]
  • Improve groupTuple docs with scatter/gather example (#5520) [b5c63a9]
  • Prevent NPE with null AWS Batch response [12fc1d6]
  • Target Java 17 as minimal Java version (#5045) [0140f95]
  • Update 'nexus-staging' plugin to latest version (#5462) [0793451]
  • Update gradle 'shadow' plugin version to 8.3.5 (#5463) [2a5f15f]
  • Update install docs to reflect change from 'all' to 'dist' (#5496) [c911565]
  • Update process snippets to comply with strict syntax (#5526) [be1694b]
  • Update Wave dependencies [09ccd29]
  • Bump aws sdk 1.12.777 (#5458) [8bad0b4]
  • Bump bouncycastle to jdk18on:1.78.1 (#5467) [cd8c385]
  • Bump com.azure:azure-identity from 1.11.3 to 1.12.2 (#5449) [cb70f1d]
  • Bump commons-io:2.15.1 [767e4a0]
  • Bump groovy 4.0.24 [dd71ad3]
  • Bump netty-common to version 4.1.115.Final [d1bbd3d]
  • Bump nf-amazon@2.10.0 [2b653b0]
  • Bump nf-azure@1.11.0 [6af7198]
  • Bump nf-google@1.16.0 [9494f97]
  • Bump nf-google@1.8.0 [7e2c8d8]
  • Bump protobuf-java:3.25.5 to nf-google [488b790]

Version 24.10.2

27 Nov 21:39
62fc001
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Version 24.10.1

18 Nov 14:17
65941da
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  • Fix overlapping file lock exception (#5489) [a2566d5]
  • Fix isContainerReady when wave is disabled (#5509) [c69e371]
  • Bump nf-wave@1.7.3 [e7709a0]
  • Bump nf-azure@1.10.2 [54496ac]
  • Bump nf-amazon@2.9.1 [fa22793]
  • Bump netty-common to version 4.1.115.Final [90623c1]

Version 24.10.0

27 Oct 20:24
a019ef8
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  • Add manifest.contributors config option (#5322) [cf0f969]
  • Add wave mirror and scan config [92e6977]
  • Add wave mirror vs module bundles conflicts warning [b37a8a5]
  • Add Workflow output definition (second preview) (#5185) [ea12846]
  • Demote azure batch task status log level to trace (#5416) [d6c684b]
  • Document formal script syntax (#5336) [a48ac58]
  • Add Expose trace record meta info in the task context (#5402) [ffdd381]
  • Fix NextflowMeta compilation error [500f49c]
  • Fix XFileSystem serialization issue (#5411) [711864f]
  • Fix closure rendering in yaml and json config (#5408) [d3a85ce]
  • Fix failing docs snippet (#5430) [a818f4b]
  • Fix http files stream (#5405) [e2e stage] [718dcbe]
  • Fix nf-tower plugin to upload logs when early failures (#5434) [4222442]
  • Fix support for micromamba (#4302) [1243130]
  • Harmonise documentation for hybrid cloud execution (#5362) [a69407d]
  • Prevent NPE when containerInfo is null [368a266]
  • Remove invalid equals char (#5414) [7f39e6e]
  • Bump nf-azure@1.10.1 [f67e157]
  • Bump nf-tower@1.9.3 [7a572a1]
  • Bump nf-wave@1.7.2 [6524d8d]

Version 24.09.2-edge

14 Oct 21:39
0c9b333
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Version 24.09.2-edge Pre-release
Pre-release
  • Add Google LS deprecation notice (#5400) [0ee1d9b]
  • Add hybrid workflow documentation for Azure (#5361) [f81f27d]
  • Add more out formats to config command (#5399) [8acdb6e]
  • Change to scan.levels to scan.allowedLevels (#5401) [88a1b1b]
  • Fix inspect concretize option [0ee29a8]
  • Manage moduleBinaries feature flag in the pipeline script (#5348) [dd5fd20]
  • Bump nf-wave@1.7.1 [9427396]
  • Bump nf-google@1.15.2 [fab01d5]

Version 24.09.1-edge

13 Oct 13:06
34cdac3
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Version 24.09.1-edge Pre-release
Pre-release