Releases: nextflow-io/nextflow
Releases · nextflow-io/nextflow
Version 25.01.0-edge
- 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
- 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
Version 24.10.3
Version 24.11.0-edge
- 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
Version 24.10.1
Version 24.10.0
- 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
- 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
- Add retry policy in Channel.fromSRA factory (#5389) [fb1c8b2]
- Add retry policy to Google batch describe task (#5356) [64bb5a9]
- Add support for Wave container status API (#5384) [873703a] [9ed18a8]
- Fix Identify default git branch when downloading pipelines (#3593) (#5375) [4f74fc3]
- Fix issue when retrying with stub (#5359) [324b611]
- Fix include aborted in the ProgressRecord total count (#5365) [8eb0c39]
- Redirect logs to stderr during app bootstrap (#5206) [9491810]
- Remove unused reportsOpts (#5379) [e794e86]
- Sunsetting Spack support in Wave [3a54cb3] [7bbba67]
- Bump nf-google@1.15.1 [4204435]
- Bump nf-wave@1.7.0 [cdecb3f]