Releases | Open Source Science

io.nextflow:nextflow - Version 25.07.0-edge

Add -template option to plugin create command and improve class name normalization (#6334) [c2c879d7]
Add read permissions to nextflow launcher (#6288) [3614aea1]
Add support for Bitbucket API tokens instead of access tokens (#6337) [1d73b87f]
Add token support for BitBucket, Gitea and Gitlab repository providers (#6212) [9d8943e1]
Add version, kind, and spec to lineage schema (#6075) [63286135]
Add warning for Azure Batch lowPriority pools (#6261) [a32fd50c]
Add Workflow onComplete and onError sections (#6275) [4fd97b9e]
Add custom date time format support with configurable NXFDATEFORMAT (#6013) [163cd37b]
BREAKING: Improve eval output hash with semantic names instead of raw commands (#6346) [d86be1a1]
Fix Fail if splitFastq receives incomplete record (#6268) [0869a34a]
Fix AWS transfer manager anonymous fallback (#6296) [ed5c99e1]
Fix Azure Batch startTask concatenation issue (#6300) (#6305) [81d5c0dc]
Fix AzureRepositoryProvider readBytes operation (#6286) [f6eb2f71]
Fix CSV writer with empty list (#6333) [46ae10df]
Fix ExecutorRetryConfig null pointer exception [ae661026]
Fix Job arrays exceeding queue size limit (#5920) (#6345) [66abf249]
Fix NPE in GoogleBatchMachineTypeSelector when spotPrice is null [a797a795]
Fix Reset terminal color after lint success/failure message (#6323) [17b05bae]
Fix bug in DefaultObserverFactory (#6259) [bec4bf7a]
Fix bug with workflow output index file (#6328) [fa972305]
Fix bugs with workflow output and lineage (#6254) [21a64705]
Fix explicit it closure parameter (#6276) [99f9edf1]
Fix formatting of channel factories (#6282) [f73f87b2]
Fix new plugins registry download when OCI repositories require tokens (#6303) [12fbef34]
Fix silent failure when downloading a directory with AWS SDK v2 (#6266) [2d76d8f0]
Fix submitted count when aborting submitted tasks (#6281) [d0d3e100]
Fix typos (#6291) [18c278b9]
Fix error_action typo (#6283) [cc5a9c98]
Fix GitlabRepositoryProvider now handles leading slashes for content URLs (#6284) [b7fa6f4e]
Fix Invoke workflow complete handler on all workflow errors (#4299) [9d246154]
Fix Improve Fusion license error message (#6313) [c3f397ea]
Migration guide for workflow outputs (#6162) [9a4f79d5]
Move AST transforms to nf-lang (#6247) [824dabbb]
Register fully-qualified process names at compile-time (#6312) [9a70cdbb]
Remove warning on missing config [14be407a]
Rephrase nf-core extension pack description (#6273) [1446e542]
Unify nf-lang config scopes with runtime classes (#6271) [bfa67ca3]
Update AWS Java SDK v2 guide #6269 [4a61e283]
Update Azure and AWS deps (#6343) [ff00e2de]
Update Gitea provider to gitea.com as default server (#6285) [cbfa2323]
Update changelog [e2e prod] [b48c0698]
Update nf-codecommit to AWS SDK v2 with corrected test (#6293) [1557a91a]
Update standard types docs (#6329) [a76b7604]
Update to plugin registry V1 (#6316) [9b1d1b6d]
Update trace observers to V2 (#6257) [544b8c47]
Bump groovy 4.0.28 (#6304) [a468f8ef]
Bump netty-codec-http2:4.1.124.Final [7e690b44]
Bump nextflow registry as default (#6339) [eaf1048f]
Bump org.apache.commons:commons-lang3 from 3.12.0 to 3.18.0 (#6272) [b8ccddb5]
Bump nf-wave@1.14.1 [5ee40f0e]
Bump nf-tower@1.14.0 [fe399deb]
Bump nf-k8s@1.1.1 [821f6996]
Bump nf-google@1.22.2 [9a4e5795]
Bump nf-codecommit@0.3.0 [3ec9e583]
Bump nf-azure@1.19.0 [8a7e0507]
Bump nf-amazon@3.1.0 [2fb0f136]

- Groovy
Published by pditommaso 7 months ago

io.nextflow:nextflow - Version 25.06.0-edge

Add Git response max length check (#6190) [098fe84f]
Add docker.registryOverride option (#6205) [e26abe4f]
Add namespaces to nf-lang (#6176) [c839799b]
Add support for Bitbucket API token (#6209) [f711f24e]
Fix AWS NIO tests [069653dd]
Fix JWT token refresh to Fusion validation request (#6231) [95dfdafd]
Fix Apptainer and singularity --no-https option (#6216) [66ead2c6]
Fix class not found exception Google Life science executor (#6193) [7bfb9358]
Fix false error on nested closure in config process directive (#6203) [481c773b]
Fix false error when using stdin/stdout in a tuple (#6219) [5d7f12ce]
Fix false warning in config schema validator (#6240) [4e55ceeb]
Fix http response err message [1f05451f]
Fix mamba env create stalls at prompt [e7c93791]
Fix null reference error in lint command (#6202) [3e1837e6]
Fix readBytes for non-GitHub providers (#6243) [fa79c12c]
Fix replace List.getFirst with List.get(0) for compatibility [83428ee2]
Fix same Conda env is re-created for same module (#6166) [b46f01f9]
Fix stack overflow error with workflow metadata (#5988) [9d50c495]
Fix Maven publish with aws credentials [34d64ab3]
Implement retry strategy for Git repository provider (#6195) [0f922826]
Implement unordered directory hash (#6197) [a0eeed8d]
Minor Azure Batch disk slot calculation demoted to debug (#6234) [c65955ce]
Remove deprecated GsonHelper class [700faddb]
Remove deprecated nexus-staging plugin [68b449bb]
Rename IncludeModuleNode to IncludeEntryNode (#6217) [1f456d9c]
Replace URLConnection with HttpClient (#6188) [d1e6836e]
Return null result when repository provider has not auth [9d7fd9fc]
Unwrap Failsafe exception cause in Wave client [0cb39df5]
Update Google dependencies (#6229) [8bd42acb]
Update stalebot (#6228) [27174df3]
Update Wave retryPolicy default values (#6222) [b8069a58]
Upgrade AWS instructions to AL2023 (#6183) [ed407095]
Upgrade to AWS Java SDK v2 (#6165) [fc99b447]
Upload Google Batch log on task exit (#6226) [78d9f473]
Bump Google instance type for testing [bde9ef1b]
Bump Logback version 1.5.18 [e3d5cedd]
Bump Slf4j version 2.0.17 [93199e09]
Bump gson version 2.13.1 [ab8e36a2]
Bump nf-wave@1.14.0 [71ecf264]
Bump nf-tower@1.13.0 [53d1bfb4]
Bump nf-google@1.22.1 [cdf56d14]
Bump nf-azure@1.18.0 [fc514062]
Bump nf-amazon@3.0.0 [ffe699bd]

- Groovy
Published by pditommaso 8 months ago

io.nextflow:nextflow - Version 25.04.6

Upload Google Batch log on task exit (#6226) [ci fast] [3f2f85a8]
Bump nf-google@1.21.1 [d145d9fd]

- Groovy
Published by pditommaso 8 months ago

io.nextflow:nextflow - Version 25.04.5

Fix JWT token refresh to Fusion validation request (#6231) [267ee1cf]
Fix null reference error in lint command (#6202) [5347bb72]
Fix false error on nested closure in config process directive (#6203) [d6f4e662]
Fix false error when using stdin/stdout in a tuple (#6219) [159ec370]
Document bucketDir config option (#6191) [e5ed05b1]
Document secrets config variable (#6230) [79f1ad64]
Bump nf-tower@1.11.4 [3cbc2aa7]

- Groovy
Published by pditommaso 8 months ago

io.nextflow:nextflow - Version 24.10.9

Fix JWT token refresh to Fusion validation request (#6231) [716468d6]
Disable latest upload [35b0c5c6]
Bump nf-tower@1.9.3-patch2 [4ed40831]

- Groovy
Published by pditommaso 8 months ago

io.nextflow:nextflow - Version 24.04.6

Fix JWT token refresh to Fusion validation request (#6231) [3ee05c0e]
Disable latest upload [5fd87b29]
Bump nf-tower@1.9.1.patch2 [38908a1d]

- Groovy
Published by pditommaso 8 months ago

io.nextflow:nextflow - Version 25.04.4

Fix bug in generated Groovy code (#6082) [ead2f320]
Fix default imports in included configs (#6096) [831a577b]
Fix variable checking in v2 config parser (#6097) [686ff608]
Sort linter errors/warnings by source location (#6098) [f51f339c]

- Groovy
Published by pditommaso 9 months ago

io.nextflow:nextflow - Version 24.04.5

Add Fusion license validation [cb7210b9]
Bump nf-wave@1.4.2-patch2 [69b63342]
Bump nf-tower@1.9.1-patch1 [8bfdc673]

- Groovy
Published by pditommaso 9 months ago

io.nextflow:nextflow - Version 24.10.8

Add Fusion license validation [02b4dd74]
Bump nf-wave@1.7.5-patch1 [cf6af9c5]
Bump nf-tower@1.9.3-patch1 [bdef2177]

- Groovy
Published by pditommaso 9 months ago

io.nextflow:nextflow - Version 25.04.3

Add Platform info to Fusion license (#6142) [375db65a]
Force overwritting to trace file (#6105) [59e9d88d]
Bump nf-tower@1.11.3 [f7509bce]

- Groovy
Published by pditommaso 9 months ago

io.nextflow:nextflow - Version 25.05.0-edge

- Groovy
Published by pditommaso 9 months ago

io.nextflow:nextflow - Version 25.04.2

Add check subcommand in lineage (#6074) [5ba67bca]
Fix issues with lint console output (#6064) [7405f513]
Remove obsolete conda create --mkdir option (#6010) [9fc44f76]

- Groovy
Published by pditommaso 10 months ago

io.nextflow:nextflow - Version 25.04.1

Add Beta annotation to LinStore [3bd0d731]
Add data lineage guide (#6044) [7f7fb631]
Add more excludes to cmd lint [fc52c843]
Add support for ARM and Snapshots (#6057) [ef4c3865]
Add version to Lineage data model (#6037) [5c2c2834]
Fix IllegalArgumentException on publish operator [ecdbe21b]
Fix linting of output label directive (#6065) [74bf33a2]
Fix selector expression documentation (#6050) [548c87bd]
Improve lineage checksum validation [d708bf09]
Improve not found error in lineage render (#6061) [e55419ad]
Make config parser v2 compatible with AssetManager (#6042) [aab5574b]
Refactor lineage model using v1beta1 package name [63d59154]
Support fromPath with pattern in Lineage Pseudo-FS (#6054) [ce165c0e]
Bump plugin template to v0.2.0 (#6062) [96c88931]
Bump nf-wave@1.12.1 [8cabfd74]

- Groovy
Published by pditommaso 10 months ago

io.nextflow:nextflow - Version 25.04.0

Add Support for Google Batch network tags (#5951) [d6e4d6c2]
Add Trace observer v2 (#6014) [c4437c1a]
Add allowed plugins list (#6049) [e22882e3]
Add azure.batch.jobMaxWallClockTime config option (#5996) [74963fdc]
Add config error checking to run command (#5998) [b0191fa4]
Add lineage to gitignore [02e1a542]
Add plugin create command (#6032) [68865f7f]
Add socketTimeoutException to retryable condition [b676e996]
Add support for Java 24 [a47ceefe]
Add timezone to lineage list timestamp [77736b55]
Add verbose AWS Batch job cleanup logging [504bd2df]
Add Support downloading plugins from OCI registries (#6016) [b41c65d5]
Add Support prefetching plugins metadata from plugins registry (#5887) [37d433d8]
Bring topic channels out of preview (#6030) [4b1b008b]
Data Lineage quick fixes (#6045) [f3cee76b]
Data Lineage workflow outputs fixes (#6041) [2cb49d08]
Data Lineage documentation (#5999) [c0bfc092]
Data Lineage programmatic API (#6003) [85b9d00d]
Fix NPE when params value is null [c7316eaf]
Fix lineage find command arguments validation (#6034) [375dc17c]
Fix concurrent modification error in lint command (#6053) [ccf5705e]
Fix errors in output fragment (#6020) [f947c9b4]
Fix false error in workflow output (#5982) [039ad401]
Fix small formatting inconsistencies (#6024) [c3a47605]
Fix task progress percentage with failed tasks (#5868) [7e931e83]
Fix timeout in failing test [cf3e1661]
Improve plugin template update [d33c5063]
Improve process creation logging [0121670c]
Make plugins log less verbose [38410fd0]
Minor allow null output params and values [53824bb0]
Refactor lineage annotations as list (#6022) [9280b59e]
Remove test constructors or mark as TestOnly (#5216) [d4fadd42]
Replace output labels with label directive (#6035) [f99bcd33]
Separate language and runtime reference docs (#6018) [75ad21d0]
Split standard library docs into multiple pages (#5993) [2f82d236]
Store lineage meta in root location and default to .lineage path [d1cae3be]
Use channel namespace to access channel factories (#6029) [26557f0c]
Use the same antlr4 dep as Groovy 4 (#5990) [bd33a76e]
Bump plugin template v0.1.0 [b54e78f3]
Bump repository provider connection timeout to 60 secs [39aaa831]
Bump nf-google@1.21.0 [b7aba74d]
Bump nf-azure@1.16.0 [e8304c1e]
Bump nf-amazon@2.15.0 [c5100f6d]

- Groovy
Published by pditommaso 10 months ago

io.nextflow:nextflow - Version 24.10.6

- Groovy
Published by pditommaso 10 months ago

io.nextflow:nextflow - Version 25.03.1-edge

Fix lineage packaging (#6001) [c3bb7a51]

- Groovy
Published by pditommaso 10 months ago

io.nextflow:nextflow - Version 25.03.0-edge

Add Google Batch gcsfuseOptions (#5991) [1d4dd574]
Add fs command to CLI help (#5967) [c0566aad]
Add lint command (#5908) [8699cc6b]
Add support for Fusion Snapshots (#5954) [d7f047f8]
Add support for data and execution lineage (#5715) [20e06da7]
Add Workflow outputs (third preview) (#5909) [2e2dea42]
Add Manage AWS Batch Unscheduled jobs (#5936) [44abe60c]
Document process/workflow recursion (#5974) [72bc4c22]
Document release notes (#5975) [368db5c4]
Fix Bash escape in build script [c8750a04]
Fix bugs in workflow outputs (#5978) [c7536c9a]
Fix kebab-case normalization for params file (#5989) [9a045f80]
Fix possible syntax error in Mermaid DAG renderer (#5935) [e3b8ca42]
Fix race condition in unit tests (#5955) [cff7bf8c]
Fix recursion snippets in workflow docs (#5979) [ac71280e]
Fix repeated warning for local executor (#5961) [11999659]
Fix validation of plugin config options (#5952) [60f1d1f6]
Refactor K8s support as core plug-in (#5965) [27ecb89d]
Refactor TraceObserver as interface (#5963) [8826134a]
Removed unused thread pool factory [fac2e4b7]
Revert Bump Fusion to version 2.5 [49b58d2d]
Support dag.direction for dot DAG format (#5941) [834cee48]
Update Azure Batch VM sizes and regions (#5985) [297150b8]
Update shell block deprecation notice (#5972) [fea67859]
Bump Gradle 8.13 [e19aeedb]
Bump nf-wave@1.12.0 [1ec04db5]
Bump nf-googlee@1.20.0 [5fce5092]
Bump nf-azure@1.15.0 [45e76d7d]
Bump nf-amazon@2.14.0 [8615aecb]

- Groovy
Published by pditommaso 10 months ago

io.nextflow:nextflow - Version 25.02.3-edge

Fix container meta deduplication [f4600d2e]
Bump nf-tower@1.11.2 [220e429a]

- Groovy
Published by pditommaso 11 months ago

io.nextflow:nextflow - Version 25.02.2-edge

Add nf-lang module from language-server (#5876) [36153c68]
Add section about include addParams to syntax guide (#5946) [d0842992]
Add tower plugin when fusion is enabled [579873bc]
Fix Nextflow console (#5937) [0206d1f2]
Fix console with v1 parser only [c733b371]
Fix date format in Wave containers meta (#5903) [59536c0a]
Fix grammar for reference to an operator (#5914) [7d3cb2b7]
Fix typo in comments (#5891) [47a0cc1e]
Fix Preserve workflow context in DAG for Mermaid renderer (#5918) [6da5496b]
Chore Improve deprecation warnings (#5939) [ea60dfb4]
Chore Move compile-to-groovy visitors into nf-lang (#5910) [0f588576]
Chore Move foreign file staging after storeDir evaluation (#5759) [2c53d9bd]
Chore Add nf-lang type checking utils (#5913) [4be204fb]
Bump nf-console@1.2.1 [cd3b1f93]
Bump nf-tower@1.11.1 [587d6274]
Bump nf-wave@1.11.1 [e5fb7694]

- Groovy
Published by pditommaso 11 months ago

io.nextflow:nextflow - Version 25.02.1-edge

Fix handling of exit status with Azure Batch and Fusion Fusion (#5806) [7085862d]
Fix false positive Process already defined error (#5894) [4bd0b619]
Fix Specify container platform when creating test deployment [d27df801]
Removing Azure vmList from log [67ffc8ab]
Bump nf-azure@1.14.1 [87ef472a]

- Groovy
Published by pditommaso 11 months ago

io.nextflow:nextflow - Version 25.02.0-edge

Add cpu-shares and memory limits to Azure Batch tasks (#5799) [f9c0cbfd]
Add Config parser v2 (and loader) (#4744) [b019b0bb]
Add Wave container metadata to Platform traces (#5724) [b81178c5]
Add disk directive support in Azure Batch (#5784) [113d7250]
Add example of dynamic directive with input file (#4545) [2ebeb346]
Add static config schema checking (#5816) [2430ea64]
Add update guide for spot retry strategy (#5872) [f053b815]
Add Script parser v2 (#4613) [7e3868df]
Fix Align container platform with arch directive when using Wave (#5847) [b9d23e22]
Fix Fail if glob does not exist with checkIfExists: true (#4224) [ab358dc9]
Fix Consider AWS China as custom endpoint (#5840) [232ce9d1]
Fix Flaky tests using random server port [e25d3092]
Fix Google Batch autoRetryExitCodes bug (#5828) [cfeedd6f]
Fix Ignore Azure pool already exists error (#5721) [e267961b]
Fix Prevent S3 global option when using custom endpoints (#5779) [ed9da469]
Fix bugs with strict config parser (#5854) [8f9fe0a6]
Fix dynamic publish path (#5809) [6a81c015]
Fix false error in variable visitor (#5765) [c3f67db2]
Fix race conditions in e2e tests (#5859) [50812746]
Fix subgraph name collisions in Mermaid DAG (#5843) (#5860) [1d2e7bf7]
Improve GH warning reporting [5ead5ba2]
Improve Google Batch support for GPUs (#5406) [420fb17e]
Improve docs for process path input/output arity (#5842) [15c6f3cf]
Improve fusion-symlink.nf test (#5819) [138a1ff7]
Improve operator summary (#5880) [a5f13799]
Improve params documentation (#5800) [976e0020]
Improve storeDir error message (#5791) [da5f7592]
Remove Spack from Wave (2nd) [076c8237]
Remove Spack from Wave assets [9c554de9]
Remove changed-files GH action due to sec vulnerability [00a53b97]
Remove invalid config option azure.managedIdentity.tenantId (#5846) [6ce8d648]
Remove stack trace from fusion license warn [3e7670f5]
Remove unused DSL1 warning (#3671) [bf18ee82]
Skip wave tests when tower access token is not available [6d2dafc0]
Update Platform token error message [18b69349]
Update config-to-groovy visitor (#5867) [a23f6840]
Update issue and PR templates (#5805) [d8c8151b]
Update metrics tutorial (#5853) [130a9c81]
Use parallelization in Gradle build (#5830) [c02fe91f]
Use semver to pin only major/minor plugin versions (#5435) [80dec141]
Validates Azure region before checking available VMs (#5108) [080893a2]
Bump Ubuntu 22.04 as default SKU for Azure Batch (#5804) [e0ba536d]
Bump groovy 4.0.26 [f740bc56]
Bump nf-amazon@2.13.0 [cca97256]
Bump nf-azure@1.14.0 [38e04354]
Bump nf-console@1.2.0 [98da8413]
Bump nf-google@1.19.0 [b0fc9de6]
Bump nf-tower@1.11.0 [d003e2f2]
Bump nf-wave@1.11.0 [b1df8344]

- Groovy
Published by pditommaso 12 months ago

io.nextflow:nextflow - Version 24.10.5

Improve Google Batch executor stability and error handling (#5690) [1a9e8bf5]
Fix Mount input file buckets in task arrays for Google Batch (#5739) [0d98442d]
Fix Google Batch task array causes process to fail (#5780) [d4c1ba12]
Fixing bug when execution with stub and no stub defined (#5473) [ba5ab069]
Fix Conda directive is not honoured by task array (#5704) [63124eb8]
Fix Use unbound queue for transfer thread pool (#5700) [d57a85d0]
Bump nf-google@1.15.4 [ee9c1fd4]

- Groovy
Published by pditommaso 12 months ago

io.nextflow:nextflow - Version 25.01.0-edge

Add DeadlineExceededException to Google Batch retryable exceptions [944f48f9]
Add Fusion token validation (#5614) [1dcb18d6]
Add stub flag to task hash only if task has a stub (#5750) [deec443d]
Add traceparent header to wave & tower clients (#5725) [7eea9f2d]
Allow Azure Batch tasks to be submitted to different pools (#5766) [76790d2a]
Configure target java version alongside gradle toolchain (#5676) [2153abb1]
Disable cleanup on remote work dir (#5742) [ef67b81e]
Do not skip integration tests on PRs [4caf6ef8]
Fail the run if publish thread pool times out (#5578) [5325e5a6]
Fix Check for number of low priority nodes in Azure Batch before raising a pool resize error (#5576) [9b528c11]
Fix Conda directive is not honoured by task array (#5704) [f8c3b63c]
Fix Create parent directory for DAG report (#5752) [62263a35]
Fix Google Batch task array causes process to fail (#5780) [7ad7a237]
Fix Mount input file buckets in task arrays for Google Batch (#5739) [ba171fd1]
Fix bugs with workflow outputs (#5502) [ab59d30f]
Fix first collection method [a0ca6e4f]
Fix stub templates (#5751) [13072d64]
Ignore tests when smoke mode is enabled [3eb6efad]
Improve Google Batch executor stability and error handling (#5690) [b64087fc]
Preserve attributes of published files (take 2) (#5660) [422f2898]
Remove compileJava options [28e03a21]
Remove redundant exception handling [00376aa3]
Revert "Fix the cleanup of local secret file" (#5697) [55f25b34]
Strengthen shell directive validation (#5689) [039c8f30]
Update HyperQueue CLI option (#5730) [BREAKING] [b582cb57]
Update azure deps [b163da95]
Use unbound queue for transfer thread pool (#5700) [90319681]
Bump Fusion to version 2.5 (2nd attempt) [a7f09ae4]
Bump gradle 8.12.1 [1fffb85c]
Bump groovy 4.0.25 [19c40a4a]
Bump io.netty:netty-handler:4.1.118.Final [db4a9037]
Bump net.minidev:json-smart:2.5.2 [b5c4faf4]
Bump netty-common:4.1.118.Final [8574e243]

- Groovy
Published by pditommaso about 1 year ago

io.nextflow:nextflow - Version 24.10.4

Fix CLI params normalization (#5661) [42a9d8a0]
Fix azure repos when clone URL is used (#5667) [eb092c9f]
Fix Prevent the use existing work dir (#5682) [7ed233ea]

- Groovy
Published by pditommaso about 1 year ago

io.nextflow:nextflow - Version 24.12.0-edge

Add Warning when Cloudinfo fails in Google Batch machine type selection (#5649) [5aef532f]
Add rate limiter to wave requests (#5608) [ecf68294]
Allow named parameters with plugin subcommand (#5643) [f81da8cf]
Customise mermaid diagram theme in DAG template (#5553) [54713a16]
Deprecate -with-weblog CLI opt [aa258b4a]
Disable AWS SDK v1 warning [cd00a26d]
Dump threads only with trace log level [87df7cd4]
Ensure job is killed when exception in task status check (#5561) [9eefd207]
Fix CLI params normalization (#5661) [e2e prod] [b5d43adc]
Fix Execution may hang reading trace file (#5683) [17d7a083]
Fix Google Batch hang when internal error during scheduling (#5567) [18f7de13]
Fix GroovyCompiler source and target compability [6dd92e3a]
Fix Only close the cache db if it is not null (#5631) [93860828]
Fix Azure repos when clone URL is used (#5667) [dc6cc414]
Fix shell directive with trace command in wrapper script (#4292) [8342889e]
Fixing getRepositoryUrl when project name is not provided (#5560) [335701e3]
Handle attribute caching with Lustre filesystem (#5650) [61674d2b]
Improve Fargate + Wave docs (#5562) [12be47ef]
Improve inspect mode (#5605) [8e2056e7]
Include all processes in inspect command (#5580) [0aa76aff]
Prevent the use existing work dir (#5682) [e14fc998]
Remove 'defaults' conda channel from docs (#5607) [8b541814]
Update Google Batch docs to clarify spot retry behaviour (#5644) [18788361]
Update flux job id regular expression (#5662) [58a0b344]
Use printf instead of echo to write trace file (#5397) [c6434d46]
Bump groovy 4.0.24 missing deps [40670f7e]
Bump jgit to version 7.1.0 (#5587) [3d714683]
Bump logback 1.5.13 + slf4j 2.0.16 [cc0163ac]
Bump logback 1.5.16 [5ac91f00]
Bump nf-wave@1.9.0 [182ddd46]
Bump nf-tower@1.9.4 [4d949d16]
Bump nf-google@1.17.0 [741d0f38]
Bump nf-console@1.1.5 [958820fd]
Bump nf-codecommit@0.2.3 [fdc32c71]
Bump nf-cloudcache@0.4.3 [c173c535]
Bump nf-azure@1.12.0 [b747dcfa]
Bump nf-amazon@2.11.0 [2650f07a]

- Groovy
Published by pditommaso about 1 year ago

io.nextflow:nextflow - Version 24.10.3

Fix Google Batch hang when internal error during scheduling (#5567) [79374c58]
Fixing getRepositoryUrl when project name is not provided (#5560) [9910cece]
Bump nf-google@1.15.3 [e80ded36]

- Groovy
Published by pditommaso about 1 year ago

io.nextflow:nextflow - Version 24.11.0-edge

Add GHA to submit dependencies to dependabot (#5440) [80395a6d]
Add NotFoundException to retry condition for Google Batch [aa4d19cc]
Add Rahel Hirsch to run name generator (#5442) [ff2bc6ae]
Add env() function (#5506) [fa0e8e0f]
Add more scientists to run name generator (#5447) [38d9eda0]
Add singularity.libraryDir to config page (#5498) [b5e31bb0]
Add RepositoryProvider.revision now public property (#5500) [f0a4c526]
Deprecate process shell block (#5508) [6f527551]
Detecting errors in data unstaging (#5345) [3c8e602d]
Disable virtual threads on CI tests [ci slip] [69d07dbc]
Fix Fargate warning on memory check (#5475) [bdf0ad00]
Fix isContainerReady when wave is disabled (#5509) [3215afa8]
Fix missing wave response (#5547) [ee252173]
Fix overlapping conda lock file (#5540) [9248c04d]
Fix overlapping conda lock exception (#5489) [eaaeb3de]
Fix possible deadlock in dynamic maxRetry resolution (#5474) [25bbb621]
Fix Wave GCP integration test (#5490) [ad56c89b]
Fixing bug when execution with stub and no stub defined (#5473) [f7fd56db]
Fix Incorrect CPU value in Azure example (#5549) [fc5e2c2a]
Improve docs for using the GPU accelerator directive (#5488) [4b908524]
Improve groupTuple docs with scatter/gather example (#5520) [b5c63a9f]
Prevent NPE with null AWS Batch response [12fc1d60]
Target Java 17 as minimal Java version (#5045) [0140f954]
Update 'nexus-staging' plugin to latest version (#5462) [07934513]
Update gradle 'shadow' plugin version to 8.3.5 (#5463) [2a5f15f0]
Update install docs to reflect change from 'all' to 'dist' (#5496) [c9115659]
Update process snippets to comply with strict syntax (#5526) [be1694bf]
Update Wave dependencies [09ccd295]
Bump aws sdk 1.12.777 (#5458) [8bad0b4b]
Bump bouncycastle to jdk18on:1.78.1 (#5467) [cd8c385f]
Bump com.azure:azure-identity from 1.11.3 to 1.12.2 (#5449) [cb70f1df]
Bump commons-io:2.15.1 [767e4a0a]
Bump groovy 4.0.24 [dd71ad31]
Bump netty-common to version 4.1.115.Final [d1bbd3d0]
Bump nf-amazon@2.10.0 [2b653b07]
Bump nf-azure@1.11.0 [6af7198d]
Bump nf-google@1.16.0 [9494f970]
Bump nf-google@1.8.0 [7e2c8d82]
Bump protobuf-java:3.25.5 to nf-google [488b7906]

- Groovy
Published by pditommaso about 1 year ago

io.nextflow:nextflow - Version 24.10.2

Prevent NPE with null AWS Batch response [3d491934]
Fix overlapping conda lock file (#5540) [df66deaa]
Fix missing wave response (#5547) [eb85cda8]
Bump nf-wave@1.7.4 [93d09404]
Bump nf-amazon@2.9.2 [469a35dd]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.10.1

Fix overlapping file lock exception (#5489) [a2566d54]
Fix isContainerReady when wave is disabled (#5509) [c69e3711]
Bump nf-wave@1.7.3 [e7709a0f]
Bump nf-azure@1.10.2 [54496ac4]
Bump nf-amazon@2.9.1 [fa227933]
Bump netty-common to version 4.1.115.Final [90623c1e]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.10.0

Add manifest.contributors config option (#5322) [cf0f9690]
Add wave mirror and scan config [92e69776]
Add wave mirror vs module bundles conflicts warning [b37a8a5b]
Add Workflow output definition (second preview) (#5185) [ea128463]
Demote azure batch task status log level to trace (#5416) [d6c684bb]
Document formal script syntax (#5336) [a48ac589]
Add Expose trace record meta info in the task context (#5402) [ffdd3819]
Fix NextflowMeta compilation error [500f49c0]
Fix XFileSystem serialization issue (#5411) [711864fd]
Fix closure rendering in yaml and json config (#5408) [d3a85ceb]
Fix failing docs snippet (#5430) [a818f4b8]
Fix http files stream (#5405) [e2e stage] [718dcbe6]
Fix nf-tower plugin to upload logs when early failures (#5434) [4222442a]
Fix support for micromamba (#4302) [12431302]
Harmonise documentation for hybrid cloud execution (#5362) [a69407d2]
Prevent NPE when containerInfo is null [368a266a]
Remove invalid equals char (#5414) [7f39e6ed]
Bump nf-azure@1.10.1 [f67e157a]
Bump nf-tower@1.9.3 [7a572a12]
Bump nf-wave@1.7.2 [6524d8dc]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.09.2-edge

Add Google LS deprecation notice (#5400) [0ee1d9bc]
Add hybrid workflow documentation for Azure (#5361) [f81f27de]
Add more out formats to config command (#5399) [8acdb6e8]
Change to scan.levels to scan.allowedLevels (#5401) [88a1b1b5]
Fix inspect concretize option [0ee29a87]
Manage moduleBinaries feature flag in the pipeline script (#5348) [dd5fd20f]
Bump nf-wave@1.7.1 [94273967]
Bump nf-google@1.15.2 [fab01d58]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.09.1-edge

Add retry policy in Channel.fromSRA factory (#5389) [fb1c8b2e]
Add retry policy to Google batch describe task (#5356) [64bb5a92]
Add support for Wave container status API (#5384) [873703ad] [9ed18a88]
Fix Identify default git branch when downloading pipelines (#3593) (#5375) [4f74fc37]
Fix issue when retrying with stub (#5359) [324b611f]
Fix include aborted in the ProgressRecord total count (#5365) [8eb0c393]
Redirect logs to stderr during app bootstrap (#5206) [94918105]
Remove unused reportsOpts (#5379) [e794e868]
Sunsetting Spack support in Wave [3a54cb3b] [7bbba67b]
Bump nf-google@1.15.1 [4204435e]
Bump nf-wave@1.7.0 [cdecb3f5]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.09.0-edge

Add Fusion version pinning info to Fusion config scope (#5294) [be1cac37]
Add container tip in the task error report (#5299) [62e26043]
Add support for Java 23 (#5329) [6e10c372]
Add Platform workflow prefix in AWS Batch job names (#5318) [42dd4ba8]
Fix AWS spot attempts with zero value (#5331) [bac2da12]
Fix Azure Fusion env misses credentials when no key or SAS provided (#5328) [e11382c8]
Fix CI build taking only the commit msg header [9e702c4d]
Fix Inconsistency with camelCase and kebab-case config params #4702 (solve #4033) [349f4f6f]
Fix XPath default de-serializer issue (#5339) [290f2d07]
Fix failOnIgnore causes task monitor to stop submitting tasks (#5293) [d6870335]
Fix large mermaid diagrams (#5302) [a46edfa0]
Improve Wave build timeout handling (#5304) [05bef7e4]
Include additional fields to manifest (#5314) [33fab52d]
Remove mini from Flux submit command (#5229) [a0f69025]
Update container handling with charliecloud (#5300) [8e6068db]
Update Documentation structure (#4766) [25e5eba0]
Update nextflow install docs (#5198) [7c453815]
Bump groovy 4.0.23 (#5303) [fe3e3ac7]
Bump nf-wave@1.6.0 [179093dc]
Bump nf-azure@1.10.0 [41d37fa8]
Bump nf-amazon@2.9.0 [e38980fb]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.08.0-edge

Add Google Batch warning when for conflicting disk image config (#5279) [96cb57cb]
Add support for Google Batch used specified boot images (#5268) [0aaa6482]
Disable AWS spot retry (#5215) [f28fcb25]
Disable Google Batch automatic spot retries (#5223) [aad21533]
Disable automatic detection of virtual threads (#5270) [b3ba2c2d]
Fix missing .command.env when eval is used and task runs on a cloud env [4a6b54aa]
Fix job array syntax for PBS/Torque executor (#5281) [d59f5fae]
Fix k8s client status cond is possible null in podState (#5264) [46672415]
Fix non-determinist behaviour of join operator with bag array as key (#5189) [e7dc0d69]
Fix stage retry on corrupted HTTP downloads (#5275) [bf0cd326]
Support Azure Managed Identities in Fusion configuration logic (#5278) [a0bf8b40]
Use public.cr.seqera.io in place of AWS ECR [5a01f277]
Wave client logs improvement [5a37e617]
Bump amazoncorretto:21-al2023 [59aed581]
Bump nf-wave@1.5.1 [97c4e08f]
Bump nf-google@1.15.0 [24133f2a]
Bump nf-azure@1.9.0 [29f49ba7]
Bump nf-amazon@2.8.0 [bbc3adca]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.07.0-edge

Add runtime error for missing channel factory (#5170) [1f9210ab]
Apply k8s.cpuLimits to kuberun driver pod (#5160) [4300adf1]
Await build completion for all Wave containers [2b8117e9]
Deprecate module addParams() and params() (#5200) [ci fast] [82c97f8c]
Fix AWS Cloudwatch access when using custom log group name [30195838]
Fix Invalid AWS Fargate CPUs usage error reporting [d9c50e59]
Fix Prevent AwS Batch retry the job execution when the container does not exist [4e218f22]
Fix Prevent negative cpus values [af2e4ef7]
Fix ProcessUnrecoverableException detection [17ec6c96]
Fix aws logs group name (#5146) [643b16b0]
Fix readAllBytes with http files (#5202) [7e90ce62]
Improve Google Batch 5000x error class handling (#5141) [61b2205f]
Improve docs [7703f0d0]
Improve error message for topic channel feature flag (#5161) [c4d407fb]
Improve fusion docs (#5166) [abdd78f1]
Improve queue docs (#5154) [bc2fb409]
Improve version checking [e7a879de]
Link to other docs on the failOnIgnore option (#5122) [572f2116]
Make Google Batch auto retry codes configurable (#5148) [e562ce06]
More robust parsing of shm-size containerOptions (#5177) [b56802a3]
Prevent default output/error logs for job arrays (#5152) [71f6ed0b]
Bump amazon sdk to version 1.12.766 [cc6ec314]
Bump gradle 8.9 [a437e97f]
Bump jgit 6.10.0 [177dc474]
Bump nf-amazon@2.7.0 [46c69d77]
Bump nf-azure@1.8.1 [26dcb604]
Bump nf-cloudchare@0.4.2 [c171b601]
Bump nf-codecommit@0.2.2 [d7dd4611]
Bump nf-console@1.1.4 [c1175157]
Bump nf-google@1.14.0 [1eda221a]
Bump nf-tower@1.9.2 [257bebfd]
Bump nf-wave@1.5.0 [e8d643c2]
Bump pf4j to version 3.12.0 [96117b9a]
Bump wave-api to 0.11.1 [96ec4ded]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.04.4

Fix parsing of shm-size containerOptions (#5177) [98cf0068]
Fix aws logs group name (#5146) [b2ab651c]
Update Azure batch deps [72576648]
Bump nf-wave@1.4.2-patch1 [19a7272f]
Bump nf-codecommit@0.2.1 [f2bcce99]
Bump nf-azure@1.6.1 [0ea1f102]
Bump nf-amazon@2.5.3 [b13b5548]
Bump wave-api to 0.11.1 [87828afd]
Bump amazon sdk to version 1.12.766 [5ce42b79]
Bump pf4j to version 3.12.0 [1a8f086a]
Bump jgit 6.10.0 [cc2ccd81]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 23.10.4

Add docker launcher [474427a5]
Update Azure batch deps [e0c6d77d]
Bump nf-azure@1.3.3-patch3 [54683615]
Bump nf-amazon@2.1.4-patch3 [084092f1]
Bump nf-codecommit@0.1.5-patch2 [de43b17e]
Bump amazon sdk to version 1.12.766 [189f58ed]
Bump pf4j to version 3.12.0 [8dfa4076]
Bump jgit 6.10.0 [4cf6b9f7]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.04.3

Add ability to override failOnError setting default via env variable (#5117) [ci fast] [6852429c]
Fix normalization of consecutive slashes in uri path (#5114) [3f366b7e]
Fix executions hangs on finalisation exception (#5070) [4c207c23]
Bump nf-google@1.13.2-patch1 [55ec5ec5]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.06.0-edge

Add ability to override failOnError setting default via env variable (#5117) [72d78425]
Add retry options to Azure Blob client (#5098) [7d5e5d2b]
Add support for HyperQueue 0.17.0 or later [BREAKING] [b45f7c48]
Adds example of error strategies to documentation (#5121) [e82b0dee]
Fix docs for failOnDuplicate and failOnMismatch (#5113) [7d5c4824]
Fix normalization of consecutive slashes in uri path (#5114) [18ec484f]
Update Azure VMs and regions for 2024-07-01 (#5100) [12b027ee]
Bump Fusion 2.4 (#5080) [0a8a484e]
Bump Groovy 4.0.22 [284a6606]
Bump nf-azure@1.8.0 [28122b70]
Bump nf-google@1.13.4 [a1c2a814]
Bump nf-wave@1.4.4 [a3dfba54]
Bump amazoncorretto:17-al2023 to Dockerfile [5e03a7b7]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.05.0-edge

Add Managed Identity to Azure authentication documentation (#5062) [ab5b3eb2]
Add support for Azure managed identity (#4897) [21ca16e6]
Add support for EC-encrypted private keys for K8s executor [4dbb5193]
Add workflow.failOnIgnore config option (#4686) [ci fast] [172edc38]
Allow requester pays for S3 buckets (#5027) [0070c1b0]
Dump threads on abort condition [e3740977]
Enable build with Java 21 (#5030) [4c54db6a]
Fix Azure system-assigned managed identity [a639a17d]
Fix Java 22 version in launcher [29d6f1df]
Fix executions hangs on finalisation exception (#5070) [38434b82]
Fix support for Azure managed identity clientId [306814e7]
Fix support for s5cmd 2.2.2 (#5069) [7e78bd4d]
Fix the cleanup of local secret file (#5061) [e28537ca]
Fix typo in error message [f5c2355b]
Fix unique operator hangs when applied to value (#5053) [88b8ab0c]
Improve retry strategy for Google cloud errors when writing task helper files (#5037) [f8b324ab]
Remove GA4GH plugin (#5056) [0471b2e1]
Remove ending slashes for publish targets [891ed117]
Bump Gradle 8.8 final [ee54606c]
Bump aws-sdk 1.12.740 [acad2a1f]
Bump azure-compute-batch:1.0.0-beta.2 [c08dc49b]
Bump azure-storage-blob 12.26.1 [c76ff5e7]
Bump nf-wave@1.4.3 [01922f13]
Bump nf-google@1.13.3 [c064d209]
Bump nf-azure@1.7.0 [eeca7d67]
Bump nf-amazon@2.6.0 [d3f53c19]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 23.10.3

Bump nf-google@1.8.3-patch2 [6960daab]
Bump nf-azure@1.3.3-patch2 [fbd3c1b4]
Bump nf-amazon@2.1.4-patch2 [f5b95820]
Fix security vulnerabilities (#5057) [6d8765b8]

- Groovy
Published by pditommaso over 1 year ago

io.nextflow:nextflow - Version 24.04.2

Fix handling of tags with slash on Bitbucket (#5031) [ci fast] [76cd305f]
Fix the default for async finalizer (#5013) [f5fba709]
Fix the invocation of function with gstring (#5020) [04317f0d]
Fix escapes dollar char in local secret provider (#5021) [d8f8bf56]
Improve Charliecloud registry handling (#5018) [ci fast] [42496dbc]
Enable the use of Java 22 (#4970) [ci fast] [cbf24f9b]

- Groovy
Published by pditommaso almost 2 years ago

io.nextflow:nextflow - Version 23.10.2

Update Platform API endpoint (#4855) [04cedce0]
Fix semaphore in parallel polling monitor (#4927) [d173ceab]
Fix security vulnerabilities (#5014) [a28b404c]
Bump nf-wave@1.0.1-patch1 [3852dd1e]
Bump nf-tower@1.6.3-patch1 [d692711b]
Bump nf-google@1.8.3-patch1 [b48a1423]
Bump nf-ga4gh@1.1.0-patch1 [911c1624]
Bump nf-console@1.0.6-patch1 [9d6b64c3]
Bump nf-codecommit@0.1.5-patch1 [f43964f8]
Bump nf-cloudcache@0.3.3-patch1 [fb9059c7]
Bump nf-azure@1.3.3-patch1 [8c398620]
Bump nf-amazon@2.1.4-patch1 [1d3726db]

- Groovy
Published by pditommaso almost 2 years ago

io.nextflow:nextflow - Version 24.04.1

Fix nf-google plugin dependency [725e2860]
Fix nf-amazon plugin dependency [c234b09f]
Bump nf-google@1.13.2 [633989a6]
Bump nf-amazon@2.5.2 [e31f70e0]

- Groovy
Published by pditommaso almost 2 years ago

io.nextflow:nextflow - Version 24.04.0

Add 'preview' to workflow runtime metadata (#4985) [935bb1e5]
Add enabled property to output dsl (#5008) [284415b1]
Fix Taskbar API is not supported error [0ea09ccc]
Fix inspect should not write history entry [c713ad51]
Fix unexpected container resolution [a5ecf8a4]
Improve icon loading error handling [c72e16f8]
Remove Fusion symlink resolution (#5004) [071ea74c]
Remove seqera and defaults from Conda default channels (#5003) [ec5ebd0b]
Use protected visibility for updateStatus method [6871ba06]
Workflow output definition (#4784) [cf0546b1]
Bump Fusion 2.3 (#5005) [7176c113]
Bump groovy-console 4.0.21-patch.2 [eb97831f]
Bump nf-amazon@2.5.1 [96ee633d]
Bump nf-console@1.1.3 [e8359042]
Bump nf-google@1.13.1 [5dcb4c7a]
Bump nf-wave@1.4.2 [73c668a6]

24.04.0-edge - 13 May 2024 - Add Wave and Fusion info to workflow metadata (#4945) [bb7e1c8e] - Add k8s.cpuLimits config option (#3027) [3c6e96d0] - Add account config option for grid executors (#4975) [a09e37dd] - Add git to docs deps [aa9e1273] - Add resourceLimits directive (#2911) [7c9d965e] - Add support for Job arrays (#3892) [ca9bc9d4] - Add support for clusterOptions as a list of values (#4993) [dd173e33] - Add threads dump for troubleshooting purposes [8992ebde] - Fix Gstring casting exception when clusterOptions is a closure [74004fbd] - Fix Missing error code when no entry is specified [f507e9a4] - Fix NPE in LogsCheckpoint class [deb3076d] - Fix Prevent maxForks less than zero [7676dd9c] - Fix Use fully qualified S3 uris in error message (#4923) [f1cffd1b] - Fix Wave container resolution with singularity and ociMode [54ad6241] - Fix collectFile saving to GCS with sort: false (#4965) [1418553a] - Fix console "Plugin manager not initialised" warn (#4989) [5ff44538] - Fix console icon (#4991) [b8a23706] - Fix docs formatting [c02e58c7] - Fix docs snippet [6499649d] - Fix flaky docs test (#4957) [ea8246f6] - Fix groovy console issue (#4988) [b9bf6410] - Fix job array docs (#4984) [6a3347ee] - Fix missing include error message (#4981) [aad100e1] - Fix script error text alignment (#4681) [1dc4e4e4] - Fix security vulnerability in logback (#4947) [0ffcc4ca] - Fix semaphore in parallel polling monitor (#4927) [5c37fcc2] - Fix remove commented out test lines in Azure Batch Pool opts tests. (#4914) [cb607f07] - Guarantees K8s pod name is unique on resume (#4959) [361cef84] - Improve config resolution docs (#4950) [019eb86c] - Improve documentation about azcopy installation requirements for custom Azure Batch worker pools (#4911) [5c410db8] - Improve error message for image pull time-out for Singularity/Apptainer/Charliecloud (#4974) [73015fbd] - Remove unused const [6e91285d] - Run task finalisation asynchronously (#4890) [e0e94227] - Strip auth secret from logs [acf63e0e] - Update TES executor to TES API v1.1 (#4195) [7b32c2d6] - Update aws.md to include Cluster access (#4951) [459d725b] - Update developer diagrams (#4922) [dcff41a5] - Update operator return types (#4976) [a614fbe7] - Update stale documentation in overview.md (#4968) [6a58c6d7] - Use for instead eachLine in error formatting [4a821f46] - azure batch autopool feature more comprehensive documentation (#4941) [adbd8903] - Bump Gradle 8.7 [8b5cf3cc] - Bump nf-wave@1.4.1 [830b032c] - Bump nf-tower@1.9.1 [163683c2] - Bump nf-google@1.13.0 [6d99a22a] - Bump nf-ga4gh@1.3.0 [89695ed3] - Bump nf-console@1.1.2 [357b143a] - Bump nf-amazon@2.5.0 [6c62a60a]

24.03.0-edge - 15 Apr 2024 - Add custom jobName for Google Batch [df40d55f] - Add escher to name generator class [2e6496e2] - Add retry policy to Google Batch client [c4981dcc] - Add retry strategy for publishing (#4839) [c9c7032c] - Add support for Azure custom startTask (#4913) [27d01e3a] - Add task tip extension point [eadad5b8] - Allow secrets to be used in pipeline script (#4171) [df866a24] - Do not print a new line when stdout is empty (#4892) [658a5ec8] - Fix Azure pool creation [2ee4d11e] - Fix Use of secrets in the includeConfig path [00c9f226] - Fix coloured ANSI log bug (#4898) [a04d6983] - Fix eval output type via bash -c wrapping (#4887) [2165a14d] - Fix exception handling in local executor [74d7d7a8] - Fix support for GCS requester pays bucket option [d9d61cff] - Fix test when missing Google secret [33dc3ce0] - Improve Charliecloud support (#4879) [287471c0] - Improve control on azcopy install (#4883) [01447d5c] - Improve error message when Google creds file is corrupted [a550e52f] - Improve getting started docs (#4764) [b59111b3] - Improve retry logic for AWS Batch executor [62926c28] - Nextflow launch script: improving search for JAVA_CMD (#4830) [ebbbe9e7] - Publish built-in reports as Tower reports (#4760) [b710d923] - Remove not needed dsl=2 + error in example (#4812) [7c5779d7] - Remove unused code from AssetManager [77365165] - Revert "Fix failing CI tests (#4861)" [7ba2e253] - Update NameGenerator (#4907) [248201af] - Update Platform API endpoint (#4855) [4842423a] - Update Wave to API v1alpha2 (#4906) [9c350872] - Update docs (#4852) [6e2d1a94] - Updated docs on Google Cloud setup and credentials (#4896) [7e8b5e26] - Updated dodcs note on singularity default command (#4825) [567f5334] - Bump groovy 4.0.20 [66c1a164] - Bump groovy 4.0.21 [9e08390b] - Bump nf-wave@1.4.0 [fc70dc8c] - Bump nf-tower@1.9.0 [b0c4e2c5] - Bump nf-google@1.12.0 [6ae25fad] - Bump nf-azure@1.6.0 [967c2ac8] - Bump nf-amazon@2.4.2 [ddda969e]

24.02.0-edge - 10 Mar 2024 - Add K8s job ttlSecondsAfterFinished option (#4434) [93627be6] - Add NXFCACHEDIR environment var (#4655) [4b00170a] - Add colours to ansi logs (#4573) [5e2ce9ed] - Add eval output type (#4493) [df978113] - Fix Always emit publish event for symlinks on resume (#4790) [bb5c4f9d] - Fix Do not create local plugin path in embedded mode [9d6dd6a0] - Fix Error while publishing S3 file with blanks [b74c0227] - Fix Missing dependency for console command [baf29110] - Fix typo in Azure Batch docs ('Azore') (#4735) [192bf8df] - Fix typo in error message [a7f23305] - Remove experimental admonition for podman [17d0dced] - Remove square brackets from job name in LSF executor (#4799) [6e0ac72d] - Remove unneeded const [09c957fb] - Rename Tower -> Seqera Platform in docs and log messages (#4727) [7caffef9] - Update Azure dependencies [1bcbaf0d] - Update copyright info [e3089f0e] - Use alias for HistoryFile.Record [17217a1c] - minor cli docstring fix (#4759) [ee4b4a25] - Bump Grengine 3.0.2 [42ca2b6f] - Bump groovy 4.0.19 [854dc1f0] - Bump snakeyaml 2.2 [07480779] - Bump nf-amazon@2.4.1 [0eb84071] - Bump nf-azure@1.5.1 [d63be8c0] - Bump nf-cloudcache@0.4.1 [57b7004e] - Bump nf-console@1.1.1 [b7f703f5] - Bump nf-tower@1.8.1 [b8ffb180] - Bump nf-wave@1.3.1 [0c542eda] - Bump amazoncorretto 17.0.10-al2023 [3e695ad9]

24.01.0-edge - 5 Feb 2024 - Add support for custom fuse device plugin (#4612) [a1e33193] - Fix Ignore stored process message when ansi log is enabled (#4645) [f9ba47ef] - Fix Wave container replicable checksum [da382ddf] - Fix azure retry policy (#4638) [85bab699] - Fix handling of wave.s5cmdConfigUrl setting (#4707) [3a19386d] - Fix typo in Hyperqueue section (#4635) [d5a6a963] - Fix typo in OCI mode warning message (#4633) [e216a876] - Fix typo in the docs (#4636) [ci-skip] [4727f174] - Improve detection of sys home variable [8812138f] - Improve handling of publish error (#4703) [fc9f7685] - LocalSecretsProvider: invalid permissions tests made more robust (#4663) [682a6806] - Remove Glacier auto-retrieval (#4705) [5f0ec50d] - Remove preview from cmd secret [dc040226] - Set scratch default to false when using Fusion (#4675) [9d17e407] - Slight change in wording for error message about userEmulation (#4680) [a9c8a841] - Truncate max size exceeded error message (#4644) [36090b70] - Use AZURESTORAGESAS_TOKEN environment variable (#4627) [2e02afbf] - Use canonical init method for plugins initialization [e7a20aff] - Bump nf-wave@1.3.0 [8b9905c7] - Bump nf-tower@1.8.0 [bfc94e46] - Bump nf-google@1.11.0 [01ff0353] - Bump nf-ga4gh@1.2.0 [3df34188] - Bump nf-console@1.1.0 [e90d73a7] - Bump nf-codecommit@0.2.0 [4379c941] - Bump nf-cloudcache@0.4.0 [2bc698c7] - Bump nf-azure@1.5.0 [07415ce1] - Bump nf-amazon@2.4.0 [b991e14b] - Bump Groovy 4 (#4443) [9d32503b] - Bump actions/checkout@v4 [d1b3195e] - Bump logback@1.4.12 + guava@33.0.0-jre [331ff425] - Bump nextflow 23.12.0-edge as min version [63e83702] - Bump tj-actions/changed-files from 35 to 41 in /.github/workflows (#4622) [d67aef5f]

23.12.0-edge - 20 Dec 2023 - Add AWSSESSIONTOKEN to Fusion environment (#4581) [552f29b0] - Add ability to disable Cloudinfo service (#4606) [f7251895] - Add experimental support for Fargate compute type for AWS Batch (#3474) [47cf335b] - Add support for Instance template to Google Batch [df7ed294] - Add support for Singularity/Apptainer auto pull mode for OCI containers [b7f1a192] - Fix BitBucket get source API with custom branch [58937831] - Fix Fusion tags documentation (#4551) [687e2e96] - Fix Harden regular expression to used to strip secrets in logs (#4563) [832bff24] - Fix bug with Fusion symlink resolution (#4593) [09e85582] - Fix container environment with special chars (#4594) [e0fe952f] - Fix custom notification template [ccf4f59e] - Fix fusion symlink test (#4604) [681ace86] - Fix smoke tests [d3c2f330] - Improve GLS tests [58590b1c] - Load nf-amazon when AWS SES is enabled [887f06f4] - Move build num & timestamp to BuildInfo class [ec8083d4] - Move app version to BuildInfo class [c7d749e8] - Remove deprecated Wave observer [0e009ef7] - Remove undocumented userEmulation mode (#4596) [f6c79788] - Remove unused DSL2 check [e9ee3b2c] - Replace each iterator with class for [f7662e68] - Bump nf-amazon@2.3.0 [0b40b7b9] - Bump nf-google@1.10.0 [bcb20fcf] - Bump nf-wave@1.2.0 [aa981814] - Bump wave-utils@0.8.1 and micromamba@1.5.5 [9cb50035] - Build optimizations (#4579) [5ad41e44]

23.11.0-edge - 24 Nov 2023 - Add fusion.cacheSize config option (#4518) [2faadc22] - Add Topic channel type (experimental) (#4459) [921313d1] - Add Google Batch native retry on spot termination (#4500) [ea1c1b70] - Add Retry policy to Google Storage (#4524) [c271bb18] - Add ability detect Google Batch spot interruption (#4462) [d49f02ae] - Add doc tests, move some snippets to separate files (#3959) [0ff3b305] - Add docs section on container requirements (#4501) [3fb29f78] - Add labels field in Job request for Google Batch (#4538) [627c595e] - Add note about limitations of glacier auto retrieval (#4514) [82e56799] - Add note about local executor and enforcing resource limits (#4468) [6a0626f7] - Add section about sharing modules (#4482) [3e66fba4] - Add section on process directives to plugin docs (#4477) [d9ee9870] - Add support for Azure low-priority pool (#4527) [8320ea10] - Add support for FUSIONAWSREGION (#4481) [8f8b09fa] - Add support for Fusion when using Singularity OCI mode (#4508) [4f3aa631] - Add support for K8s schedulerName pod spec (#4485) [dfc7b7c8] - Add support for Singularity OCI mode (#4440) [f5362a7b] - Allow the use of error built-in function in onComplete handler (#4458) [35a4424b] - Fix Bug in JsonSplitter ordering [8ec14dd2] - Fix Bypass Google Batch Price query if task cpus and memory are defined (#4521) [7f8f20d3] - Fix Checkout remote tag if checkout remote branch fails (#4247) [b8907ccb] - Fix Fusion symlinks when publishing files (#4348) [89f09fe0] - Fix Inspect command fails with Singularity [f5bb829f] - Fix ParamsMap copyWith param aliases (#4188) [b480ee0e] - Fix Singularity docs [e952299f] - Fix container hashing for Singularity + Wave containers [4c6f2e85] - Fix detection of Conda local path made by Wave client (#4532) [4d5bc216] - Fix doc tests to fail on test failure (#4505) [4d326551] - Fix errors when NXFHOME contains spaces (#4456) [fe5bea99] - Fix Google Batch network/subnetwork docs (#4475) [27d132f3] - Fix rounding error with long durations (#4496) [0356178b] - Fix security vulnerabilities (#4513) [a310c777] - Fix Use consistently NXFTASK_WORKDIR (#4484) [48ee3c64] - Improve error details for AbortOperationException [35609cb0] - Improve operator docs (#4502) [38210e11] - Makefile clean to also remove buildSrc/build (#4517) [2ccb05d0] - Minor test improvements [171831ea] - Minor types improvement for mix operator [91c1ab15] - Normalise channel docs [b641d677] - Remove deprecated TowerArchiver feature [ff8e06a3] - Remove dsl1 deprecated code (part 2) [159effb1] - Remove dsl1 deprecated code [2b433a52] - Remove incorrect note about workflow inputs (#4509) [54bc0b7d] - Return error if plugin version is not specified in offline mode (#4487) [f5d7246e] - Update README.md with new branding color for Nextflow (#4412) [7a13b18b] - Update background color of docs status badges (#4411) [3cb1c53c] - Update logging filter for Google Batch provider. (#4488) [66a3ed19] - Bump Gradle 8.4 and test vs Java 21 (#4450) [8cb2702c] - Bump nf-amazon@2.2.0 [8e2d7879] - Bump nf-azure@1.4.0 [7c47d090] - Bump nf-cloudcache@0.3.1 [65240b75] - Bump nf-codecommit@0.1.6 [725f0510] - Bump nf-console@1.0.7 [a307686c] - Bump nf-ga4gh@1.1.1 [e54ea007] - Bump nf-google@1.9.0 [033ec92c] - Bump nf-tower@1.7.0 [836a44a5] - Bump nf-wave@1.1.0 [620523ef]

- Groovy
Published by pditommaso almost 2 years ago

io.nextflow:nextflow - Version 24.04.0-edge

Add Wave and Fusion info to workflow metadata (#4945) [bb7e1c8e]
Add k8s.cpuLimits config option (#3027) [3c6e96d0]
Add account config option for grid executors (#4975) [a09e37dd]
Add git to docs deps [aa9e1273]
Add resourceLimits directive (#2911) [7c9d965e]
Add support for Job arrays (#3892) [ca9bc9d4]
Add support for clusterOptions as a list of values (#4993) [dd173e33]
Add threads dump for troubleshooting purposes [8992ebde]
Fix Gstring casting exception when clusterOptions is a closure [74004fbd]
Fix Missing error code when no entry is specified [f507e9a4]
Fix NPE in LogsCheckpoint class [deb3076d]
Fix Prevent maxForks less than zero [7676dd9c]
Fix Use fully qualified S3 uris in error message (#4923) [f1cffd1b]
Fix Wave container resolution with singularity and ociMode [54ad6241]
Fix collectFile saving to GCS with sort: false (#4965) [1418553a]
Fix console "Plugin manager not initialised" warn (#4989) [5ff44538]
Fix console icon (#4991) [b8a23706]
Fix docs formatting [c02e58c7]
Fix docs snippet [6499649d]
Fix flaky docs test (#4957) [ea8246f6]
Fix groovy console issue (#4988) [b9bf6410]
Fix job array docs (#4984) [6a3347ee]
Fix missing include error message (#4981) [aad100e1]
Fix script error text alignment (#4681) [1dc4e4e4]
Fix security vulnerability in logback (#4947) [0ffcc4ca]
Fix semaphore in parallel polling monitor (#4927) [5c37fcc2]
Fix remove commented out test lines in Azure Batch Pool opts tests. (#4914) [cb607f07]
Guarantees K8s pod name is unique on resume (#4959) [361cef84]
Improve config resolution docs (#4950) [019eb86c]
Improve documentation about azcopy installation requirements for custom Azure Batch worker pools (#4911) [5c410db8]
Improve error message for image pull time-out for Singularity/Apptainer/Charliecloud (#4974) [73015fbd]
Remove unused const [6e91285d]
Run task finalisation asynchronously (#4890) [e0e94227]
Strip auth secret from logs [acf63e0e]
Update TES executor to TES API v1.1 (#4195) [7b32c2d6]
Update aws.md to include Cluster access (#4951) [459d725b]
Update developer diagrams (#4922) [dcff41a5]
Update operator return types (#4976) [a614fbe7]
Update stale documentation in overview.md (#4968) [6a58c6d7]
Use for instead eachLine in error formatting [4a821f46]
azure batch autopool feature more comprehensive documentation (#4941) [adbd8903]
Bump Gradle 8.7 [8b5cf3cc]
Bump nf-wave@1.4.1 [830b032c]
Bump nf-tower@1.9.1 [163683c2]
Bump nf-google@1.13.0 [6d99a22a]
Bump nf-ga4gh@1.3.0 [89695ed3]
Bump nf-console@1.1.2 [357b143a]
Bump nf-amazon@2.5.0 [6c62a60a

- Groovy
Published by pditommaso almost 2 years ago

io.nextflow:nextflow - Version 24.03.0-edge

Add custom jobName for Google Batch [df40d55f]
Add escher to name generator class [2e6496e2]
Add retry policy to Google Batch client [c4981dcc]
Add retry strategy for publishing (#4839) [c9c7032c]
Add support for Azure custom startTask (#4913) [27d01e3a]
Add task tip extension point [eadad5b8]
Allow secrets to be used in pipeline script (#4171) [df866a24]
Do not print a new line when stdout is empty (#4892) [658a5ec8]
Fix Azure pool creation [2ee4d11e]
Fix Use of secrets in the includeConfig path [00c9f226]
Fix coloured ANSI log bug (#4898) [a04d6983]
Fix eval output type via bash -c wrapping (#4887) [2165a14d]
Fix exception handling in local executor [74d7d7a8]
Fix support for GCS requester pays bucket option [d9d61cff]
Fix test when missing Google secret [33dc3ce0]
Improve Charliecloud support (#4879) [287471c0]
Improve control on azcopy install (#4883) [01447d5c]
Improve error message when Google creds file is corrupted [a550e52f]
Improve getting started docs (#4764) [b59111b3]
Improve retry logic for AWS Batch executor [62926c28]
Nextflow launch script: improving search for JAVA_CMD (#4830) [ebbbe9e7]
Publish built-in reports as Tower reports (#4760) [b710d923]
Remove not needed dsl=2 + error in example (#4812) [7c5779d7]
Remove unused code from AssetManager [77365165]
Revert "Fix failing CI tests (#4861)" [7ba2e253]
Update NameGenerator (#4907) [248201af]
Update Platform API endpoint (#4855) [4842423a]
Update Wave to API v1alpha2 (#4906) [9c350872]
Update docs (#4852) [6e2d1a94]
Updated docs on Google Cloud setup and credentials (#4896) [7e8b5e26]
Updated dodcs note on singularity default command (#4825) [567f5334]
Bump groovy 4.0.20 [66c1a164]
Bump groovy 4.0.21 [9e08390b]
Bump nf-wave@1.4.0 [fc70dc8c]
Bump nf-tower@1.9.0 [b0c4e2c5]
Bump nf-google@1.12.0 [6ae25fad]
Bump nf-azure@1.6.0 [967c2ac8]
Bump nf-amazon@2.4.2 [ddda969e]

- Groovy
Published by pditommaso almost 2 years ago

io.nextflow:nextflow - Version 24.02.0-edge

Add K8s job ttlSecondsAfterFinished option (#4434) [93627be6]
Add NXFCACHEDIR environment var (#4655) [4b00170a]
Add colours to ansi logs (#4573) [5e2ce9ed]
Add eval output type (#4493) [df978113]
Fix Always emit publish event for symlinks on resume (#4790) [bb5c4f9d]
Fix Do not create local plugin path in embedded mode [9d6dd6a0]
Fix Error while publishing S3 file with blanks [b74c0227]
Fix Missing dependency for console command [baf29110]
Fix typo in Azure Batch docs ('Azore') (#4735) [192bf8df]
Fix typo in error message [a7f23305]
Remove experimental admonition for podman [17d0dced]
Remove square brackets from job name in LSF executor (#4799) [6e0ac72d]
Remove unneeded const [09c957fb]
Rename Tower -> Seqera Platform in docs and log messages (#4727) [7caffef9]
Update Azure dependencies [1bcbaf0d]
Update copyright info [e3089f0e]
Use alias for HistoryFile.Record [17217a1c]
minor cli docstring fix (#4759) [ee4b4a25]
Bump Grengine 3.0.2 [42ca2b6f]
Bump groovy 4.0.19 [854dc1f0]
Bump snakeyaml 2.2 [07480779]
Bump nf-amazon@2.4.1 [0eb84071]
Bump nf-azure@1.5.1 [d63be8c0]
Bump nf-cloudcache@0.4.1 [57b7004e]
Bump nf-console@1.1.1 [b7f703f5]
Bump nf-tower@1.8.1 [b8ffb180]
Bump nf-wave@1.3.1 [0c542eda]
Bump amazoncorretto 17.0.10-al2023 [3e695ad9]

- Groovy
Published by pditommaso almost 2 years ago

io.nextflow:nextflow - Version 24.01.0-edge

Add support for custom fuse device plugin (#4612) [a1e33193]
Fix Ignore stored process message when ansi log is enabled (#4645) [f9ba47ef]
Fix Wave container replicable checksum [da382ddf]
Fix azure retry policy (#4638) [85bab699]
Fix handling of wave.s5cmdConfigUrl setting (#4707) [3a19386d]
Fix typo in Hyperqueue section (#4635) [d5a6a963]
Fix typo in OCI mode warning message (#4633) [e216a876]
Fix typo in the docs (#4636) [ci-skip] [4727f174]
Improve detection of sys home variable [8812138f]
Improve handling of publish error (#4703) [fc9f7685]
LocalSecretsProvider: invalid permissions tests made more robust (#4663) [682a6806]
Remove Glacier auto-retrieval (#4705) [5f0ec50d]
Remove preview from cmd secret [dc040226]
Set scratch default to false when using Fusion (#4675) [9d17e407]
Slight change in wording for error message about userEmulation (#4680) [a9c8a841]
Truncate max size exceeded error message (#4644) [36090b70]
Use AZURESTORAGESAS_TOKEN environment variable (#4627) [2e02afbf]
Use canonical init method for plugins initialization [e7a20aff]
Bump nf-wave@1.3.0 [8b9905c7]
Bump nf-tower@1.8.0 [bfc94e46]
Bump nf-google@1.11.0 [01ff0353]
Bump nf-ga4gh@1.2.0 [3df34188]
Bump nf-console@1.1.0 [e90d73a7]
Bump nf-codecommit@0.2.0 [4379c941]
Bump nf-cloudcache@0.4.0 [2bc698c7]
Bump nf-azure@1.5.0 [07415ce1]
Bump nf-amazon@2.4.0 [b991e14b]
Bump Groovy 4 (#4443) [ci fast] [9d32503b]
Bump actions/checkout@v4 [d1b3195e]
Bump logback@1.4.12 + guava@33.0.0-jre [331ff425]
Bump nextflow 23.12.0-edge as min version [63e83702]
Bump tj-actions/changed-files from 35 to 41 in /.github/workflows (#4622) [d67aef5f]

- Groovy
Published by pditommaso about 2 years ago

io.nextflow:nextflow - Version 23.10.1

23.10.1 - 12 Jan 2023 - Fix bug with Fusion symlink resolution (#4593) [f28c9e48] - Fix Fusion symlinks when publishing files (#4348) [1fa5878a] - Fix Inspect command fails with Singularity [25883df3] - Fix Allow the use of error build-in function in onComplete handler (#4458) [ci fast] [4be10cd3] - Fix Harden regular expression used to strip secrets in logs (#4563) [ci fast] [0102d4d6] - Fix custom notification template [40980bcb] - Fix container environment with special chars (#4594) [f4e00601] - Fix AZURESTORAGESAS_TOKEN environment variable (#4627) [2e1cb413] - Fix azure retry policy (#4638) [2bc3cf0e] - Fix BitBucket get source API with custom branch [5ef75e32] - Improve error details for AbortOperationException [9e795a62] - Bump nf-wave@1.0.1 [206f2614] - Bump nf-azure@1.3.3 [50bcad59]

- Groovy
Published by pditommaso about 2 years ago

io.nextflow:nextflow - Version 23.04.5

Fix container environment with special chars (#4594) [663b2936]

- Groovy
Published by pditommaso about 2 years ago

io.nextflow:nextflow - Version 23.12.0-edge

Add AWSSESSIONTOKEN to Fusion environment (#4581) [552f29b0]
Add ability to disable Cloudinfo service (#4606) [f7251895]
Add experimental support for Fargate compute type for AWS Batch (#3474) [47cf335b]
Add support for Instance template to Google Batch [df7ed294]
Add support for Singularity/Apptainer auto pull mode for OCI containers [b7f1a192]
Fix BitBucket get source API with custom branch [58937831]
Fix Fusion tags documentation (#4551) [687e2e96]
Fix Harden regular expression to used to strip secrets in logs (#4563) [832bff24]
Fix bug with Fusion symlink resolution (#4593) [09e85582]
Fix container environment with special chars (#4594) [e0fe952f]
Fix custom notification template [ccf4f59e]
Fix fusion symlink test (#4604) [681ace86]
Fix smoke tests [d3c2f330]
Improve GLS tests [58590b1c]
Load nf-amazon when AWS SES is enabled [887f06f4]
Move build num & timestamp to BuildInfo class [ec8083d4]
Move app version to BuildInfo class [c7d749e8]
Remove deprecated Wave observer [0e009ef7]
Remove undocumented userEmulation mode (#4596) [f6c79788]
Remove unused DSL2 check [e9ee3b2c]
Replace each iterator with class for [f7662e68]
Bump nf-amazon@2.3.0 [0b40b7b9]
Bump nf-google@1.10.0 [bcb20fcf]
Bump nf-wave@1.2.0 [aa981814]
Bump wave-utils@0.8.1 and micromamba@1.5.5 [9cb50035]
Build optimizations (#4579) [5ad41e44]

- Groovy
Published by pditommaso about 2 years ago

io.nextflow:nextflow - Version 23.11.0-edge

Add fusion.cacheSize config option (#4518) [2faadc22]
Add Topic channel type (experimental) (#4459) [921313d1]
Add Google Batch native retry on spot termination (#4500) [ea1c1b70]
Add Retry policy to Google Storage (#4524) [c271bb18]
Add ability detect Google Batch spot interruption (#4462) [d49f02ae]
Add doc tests, move some snippets to separate files (#3959) [0ff3b305]
Add docs section on container requirements (#4501) [3fb29f78]
Add labels field in Job request for Google Batch (#4538) [627c595e]
Add note about limitations of glacier auto retrieval (#4514) [82e56799]
Add note about local executor and enforcing resource limits (#4468) [6a0626f7]
Add section about sharing modules (#4482) [3e66fba4]
Add section on process directives to plugin docs (#4477) [d9ee9870]
Add support for Azure low-priority pool (#4527) [8320ea10]
Add support for FUSIONAWSREGION (#4481) [8f8b09fa]
Add support for Fusion when using Singularity OCI mode (#4508) [4f3aa631]
Add support for K8s schedulerName pod spec (#4485) [ci fast] [dfc7b7c8]
Add support for Singularity OCI mode (#4440) [f5362a7b]
Allow the use of error built-in function in onComplete handler (#4458) [ci fast] [35a4424b]
Fix Bug in JsonSplitter ordering [ci fast] [8ec14dd2]
Fix Bypass Google Batch Price query if task cpus and memory are defined (#4521) [7f8f20d3]
Fix Checkout remote tag if checkout remote branch fails (#4247) [b8907ccb]
Fix Fusion symlinks when publishing files (#4348) [89f09fe0]
Fix Inspect command fails with Singularity [f5bb829f]
Fix ParamsMap copyWith param aliases (#4188) [b480ee0e]
Fix Singularity docs [e952299f]
Fix container hashing for Singularity + Wave containers [4c6f2e85]
Fix detection of Conda local path made by Wave client ci fast [4d5bc216]
Fix doc tests to fail on test failure (#4505) [4d326551]
Fix errors when NXF_HOME contains spaces (#4456) [ci fast] [fe5bea99]
Fix Google Batch network/subnetwork docs (#4475) [27d132f3]
Fix rounding error with long durations (#4496) [ci fast] [0356178b]
Fix security vulnerabilities (#4513) [a310c777]
Fix Use consistently NXFTASKWORKDIR (#4484) [48ee3c64]
Improve error details for AbortOperationException [35609cb0]
Improve operator docs (#4502) [38210e11]
Makefile clean to also remove buildSrc/build (#4517) [2ccb05d0]
Minor test improvements [ci fast] [171831ea]
Minor types improvement for mix operator [ci fast] [91c1ab15]
Normalise channel docs [b641d677]
Remove deprecated TowerArchiver feature [ff8e06a3]
Remove dsl1 deprecated code (part 2) [159effb1]
Remove dsl1 deprecated code [2b433a52]
Remove incorrect note about workflow inputs (#4509) [54bc0b7d]
Return error if plugin version is not specified in offline mode (#4487) [f5d7246e]
Update README.md with new branding color for Nextflow (#4412) [7a13b18b]
Update background color of docs status badges (#4411) [3cb1c53c]
Update logging filter for Google Batch provider. (#4488) [66a3ed19]
Bump Gradle 8.4 and test vs Java 21 (#4450) [8cb2702c]
Bump nf-amazon@2.2.0 [8e2d7879]
Bump nf-azure@1.4.0 [7c47d090]
Bump nf-cloudcache@0.3.1 [65240b75]
Bump nf-codecommit@0.1.6 [725f0510]
Bump nf-console@1.0.7 [a307686c]
Bump nf-ga4gh@1.1.1 [e54ea007]
Bump nf-google@1.9.0 [033ec92c]
Bump nf-tower@1.7.0 [836a44a5]
Bump nf-wave@1.1.0 [620523ef]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.10.0

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-wave@1.0.0 [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-amazon@2.1.4 [a84208a8] - Bump nf-cloudcache@0.3.0 [b37b4014] - Bump nf-google@1.8.3 [b4eb8b96] - Bump nf-tower@1.6.3 [5681ab13] - Bump nf-wave@0.14.0 [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 allowother 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 GITHUBTOKEN 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-amazon@2.1.3 [3311172f] - Bump nf-azure@1.3.2 [a9b735ce] - Bump nf-google@1.8.2 [7219d7f2] - Bump nf-tower@1.6.2 [91a935f9] - Bump nf-wave@0.13.0 [0cf2476c] - Bump wave-utils@0.7.8 [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 TraceRecord@store 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 NXFDEBUG variable [7955db8d] - Update AZ File share doc (#4235) [69d317b6] - Update docs about splitCsv() operator (#4163) [1dfb621c] - Update documentation of NXFDEBUG (#4187) [a88a4245] - Use sipHash24 in place of deprecated murmur32 for script aliasing [bb96763f] - Bump groovy 3.0.19 [cb411208] - Bump nf-amazon@2.1.2 [7e5d414e] - Bump nf-azure@1.3.1 [83410f39] - Bump nf-wave@0.12.0 [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-azure@1.3.0 [6670bb06] - Bump nf-cloudcache@0.2.0 [fb8f6681] - Bump nf-tower@1.6.1 [d06b8365] - Bump nf-wave@0.11.2 [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-wave@0.11.1 [78e4b278] - Bump nf-tower@1.6.0 [41c8c164] - Bump nf-azure@1.2.0 [5f33ac17] - Bump nf-amazon@2.1.1 [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-amazon@2.1.0 [57464746] - Bump nf-azure@1.1.2 [e1512f6a] - Bump nf-azure@1.1.3 [27e7f663] - Bump nf-azure@1.1.4 [1895efc4] - Bump nf-cloudcache@0.1.0 [cb6242c4] - Bump nf-ga4gh@1.1.0 [f98feb77] - Bump nf-google@1.8.1 [6aede7c0] - Bump nf-tower@1.5.15 [3278d798] - Bump nf-wave@0.11.0 [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-wave@0.11.0 [2998db5d] - Bump nf-tower@1.5.15 [3278d798] - Bump nf-google@1.8.1 [6aede7c0] - Bump nf-ga4gh@1.1.0 [f98feb77] - Bump nf-azure@1.1.4 [1895efc4] - Bump nf-amazon@2.1.0 [57464746] - Bump nf-cloudcache@0.1.0 [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-wave@0.9.0 [7d6d0108] - Bump nf-tower@1.5.13 [b06ffd0c] - Bump nf-google@1.7.4 [2e0a15cd] - Bump nf-ga4gh@1.0.6 [0c8fd7df] - Bump nf-console@1.0.6 [a733b818] - Bump nf-codecommit@0.1.5 [12edf0e6] - Bump nf-amazon@2.0.0 [69b6edde] - Bump nf-azure@1.1.0 [d05d51b4]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.09.3-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]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.09.2-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-amazon@2.1.3 [3311172f]
Bump nf-azure@1.3.2 [a9b735ce]
Bump nf-google@1.8.2 [7219d7f2]
Bump nf-tower@1.6.2 [91a935f9]
Bump nf-wave@0.13.0 [0cf2476c]
Bump wave-utils@0.7.8 [d0c47d49]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.04.4

Fix use of GITHUB_TOKEN variable to access GitHub repo [108c6b55]
Fix allow_other vulnerability preventing google-batch submissions (#4332) [4895d547]
Fix Prevent false positive resumable task [aae87715]
Fix Always emit publish event for cached task outputs (#4227) [c4cd53c2]
Fix Too long Http connection pool timeout [ce5e9930]
Bump nf-google@1.7.3-patch1 [d881728c]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.09.1-edge

Revert "Allow setting shell directive when using the trace file (#4210)" [9f9edcdc]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.09.0-edge

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 TraceRecord@store 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-amazon@2.1.2 [7e5d414e]
Bump nf-azure@1.3.1 [83410f39]
Bump nf-wave@0.12.0 [a9f6dd65]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.08.1-edge

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-azure@1.3.0 [6670bb06]
Bump nf-cloudcache@0.2.0 [fb8f6681]
Bump nf-tower@1.6.1 [d06b8365]
Bump nf-wave@0.11.2 [7555b17d]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.04.3

Add 429 http status code to Wave retriable errors [a8b8c6c5]
Increase Wave client max attempts [8c67610a]
Improve handling Wave server errors [621c9665]
Fix log typo [03e19ea2]
Bump nf-wave@0.8.4 [d7fa3f26]
Bump corretto 17.0.8 [7a73a78f]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.08.0-edge

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-wave@0.11.1 [78e4b278]
Bump nf-tower@1.6.0 [41c8c164]
Bump nf-azure@1.2.0 [5f33ac17]
Bump nf-amazon@2.1.1 [981315ad

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.07.0-edge

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) [ci skip] [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-amazon@2.1.0 [57464746] - Bump nf-azure@1.1.2 [e1512f6a] - Bump nf-azure@1.1.3 [27e7f663] - Bump nf-azure@1.1.4 [1895efc4] - Bump nf-cloudcache@0.1.0 [cb6242c4] - Bump nf-ga4gh@1.1.0 [f98feb77] - Bump nf-google@1.8.1 [6aede7c0] - Bump nf-tower@1.5.15 [3278d798] - Bump nf-wave@0.11.0 [2998db5d]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.06.0-edge

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 not to 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]
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-wave@0.10.0 [0872fba5]
Bump nf-tower@1.5.14 [64bf3115]
Bump nf-google@1.8.0 [7ca7d808]
Bump nf-azure@1.1.1 [afd368c4]
Bump nf-amazon@2.0.1 [58c332a1]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.04.2

Fix non-deterministic null container engine error [f93221ab]
Add retry policy to Wave client [2f1532f6]
Fix wave build docs [34a73022]
Bump nf-wave@0.8.3 [350201b5]

- Groovy
Published by pditommaso over 2 years ago

io.nextflow:nextflow - Version 23.05.0-edge

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 superflous 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-wave@0.9.0 [7d6d0108] - Bump nf-tower@1.5.13 [b06ffd0c] - Bump nf-google@1.7.4 [2e0a15cd] - Bump nf-ga4gh@1.0.6 [0c8fd7df] - Bump nf-console@1.0.6 [a733b818] - Bump nf-codecommit@0.1.5 [12edf0e6] - Bump nf-amazon@2.0.0 [69b6edde] - Bump nf-azure@1.1.0 [d05d51b4]

- Groovy
Published by pditommaso almost 3 years ago

io.nextflow:nextflow - Version 22.10.8

Security fixes [fc2627bb]
Add support for testing custom plugin uri [718d4562]
Improve plugin updater err handling [84042082]
Improve plugin test detection [ci fast] [e6c60a6c]
Bump nf-google@1.4.6 [26b01b83]
Bump nf-wave@0.5.5 [2a886fe0]
Bump nf-ga4gh@1.0.5 [b8769f1a]
Bump nf-tower@1.5.7-patch0 [89d902ec]
Bump nf-azure@0.14.3 [9b0f4bfb]
Bump nf-amazon@1.11.5 [f7aaddc6]
Bump amazoncorretto@17.0.6 [7898cc04]

- Groovy
Published by pditommaso almost 3 years ago

io.nextflow:nextflow - Version 23.04.1

Add support for Java 20 [f6933db7]
Fix use of remote dir with local exec statement [6ea1f68c]
Fix Azure pool creation when using scaling formula (#3868) [84a808a5]
Fix interval channel factory (#3848) [82ccf6ad]
Fix invalid warning on func import (#3807) [4678ffe3]
Improve plugin test detection [57cfb0d9]
Improve plugin updater err handling [5627c69a]
Security fixes [83e8fd6a]
Bump nf-wave@0.8.2 [d8cb763c]
Bump nf-tower@1.5.12 [b2354380]
Bump nf-google@1.7.3 [22a68cfe]
Bump gson:2.10.1 [83ca1e32]
Bump nf-ga4gh@1.0.5 [b40b5165]
Bump nf-codecommit@0.1.4 [98a89154]
Bump aws-java-sdk-s3:1.12.429 [b71ee0a3]
Bump nf-azure@1.0.1 [a5da54d3]
Bump nf-amazon@1.16.2 [c90553c9]

- Groovy
Published by pditommaso almost 3 years ago

io.nextflow:nextflow - Version 23.04.0

Add several names to the name generator feat:(#3790) [dfa2f6ca]
Add support for Fusion to Azure Batch executor (#3209) [3d3cbfa2]
Add support for testing custom plugin uri [227910ab]
Add warnings for Azure named pools (#3819) [a2c71acf]
Enable new pid namespace with Singularity & Apptainer [3601b014]
Fix NoSuchMethodError String.stripIndent with Java 11 [308eafe6]
Fix issue checking Google Batch script launcher type [39c3a517]
Fix resolution of module resources [2c5a6878]
Fix Relax caching across task retries [840e8432]
Fix Java version for tests [7ce05c15]
Remove extra context from workflow error message [38c8bd33]
Revert "Enable Fusion on Google Batch tests" [2ba7ea54]
Bump micromamba 1.4.1 [ec1439e6]
Bump nf-amazon@1.16.1 [0f98b245]
Bump nf-azure@1.0.0 [e1732be9]
Bump nf-google@1.7.2 [99477f79]
Bump nf-wave@0.8.1 [939195b5]
Bump nf-tower@1.5.11 [b7b5d4c9]

From previous edge releases

23.03.0-edge - 19 Mar 2023 - Add Azure batch pool virtualNetwork option (#3723) [e3917b8e] - Add basePackages option to Wave config [7e827810] - Add error message for missing container image with Google Batch (#3747) [6419e68f] - Add notifyFilePublish optional source argument (#3737) [a65a9ff7] - Add retry strategy on Bash wrapper write logic [1e38274a] - Add support for AWS S3 Glacier Retrieval Tier (#3680) [fab6bd5e] - Add sync invocation on job completion (#3678) [e29c4e4b] - Add workflowId to Wave request [025ff9d0] - Add Clone result list objects before output binding [38762080] - Add plugins option to kuberun command (#3766) [6515294f] - Fix Google Batch logging exception [d7e38e9e] - Fix Java Matcher serialization [6aecc4ed] - Fix Logger failure type detection [f1b89c1f] - Fix Orphaned processes when using Singularity [7236f830] - Fix groupTuple with mismatching tuple cardinality [1d32e2c2] - Fix special chars escaping in container env [b93634e9] - Fix commit revision type for Azure DevOps repos (#3721) [fb71767e] - Improve DAG API (#3703) [21afb358] - Improve Wave docs [7299dac9] - Improve fair directive docs (#3677) [7ca7520f] - Improve transpose and groupTuple examples in the docs (#3685) [7870dfc8] - Increase pwd obfuscation min length [ba23d036] - Make GroupKey cloneable (#3738) [0760b0fd] - Prepare Nextflow for the CWS Plugin (#3727) [fd8bf709] - Remove DNAnexus page from docs (#3695) [fa58c18c] - Remove outdated FAQ page from docs (#3683) [e59c7fbb] - Remove unused classes [9fa8d75b] - Update Azure VM sizes (#3751) [1d06e9a6] - Enable Fusion on Google Batch tests [2f1b1094] - Bump groovy 3.0.16 [d3ff5dcb] - Bump nf-wave@0.8.0 [aa1b065d] - Bump nf-google@1.7.1 [2aaaf2a7] - Bump nf-azure@0.16.0 [f358b008] - Bump nf-amazon@1.16.0 [2395187d]

23.02.1-edge - 26 Feb 2023 - Add Fusion logs and tags config [09192078] - Add support for NXF_DEBUG to K8s task handler [828583dc] - Add support for Mamba HTTP based lock files [7fe88c84] - Add container name validation [c3b6d9ab] - Add Fusion for Google storage docs [34fcfe06] - Improve K8s auth token discovery [44f8cc07] - Bump nf-wave@0.7.2 [1c697ab5] - Bump amazoncorretto:17.0.6 [a33a6f47]

23.02.0-edge - 21 Feb 2023 - Add Fusion support for Google Batch (#3577) [d5fbab4f] - Add Header provider to Google Batch client [20979929] - Add Wave integration tests [c5faf971] - Add errorStrategy validation [954cd921] - Add Java install recommendations to docs (#3617) [7e9bee1e] - Add nextflow tags to AWS Batch job def [b465ac52] [BREAKING] - Add readOnlyInputs option for CharliecloudBuilder (#3590) [8ae001fc] - Add refresh token to Wave request [41510e87] - Add requirements for container images to run with Nextflow (#3586) [7af1cb66] - Add support for Fusion to Slurm and LSF executors (#3516) [fbc95e6b] - Add support for Fusion tags (#3609) [8385ec22] [BREAKING] - Add support for the Spack package manager (#3580) [a5df62f6] - Add the fcp tool option to file copy strategy (#3556) [2a224258] - Add Fusion integration test - Add Wave + Fusion test with Google Batch [b541c061] - Add support for entryless Fusion configuration and Singularity support (#3584) [34a27733] - Improve Fusion config [a1d08463] - Ignore resource directives if -l option is specified in PBS executor (#3015) [28a67969] - Improve K8s securityContext support [3f76240b] - Improve AWS Batch error logging [8f4884c1] - Improve secrets docs [9a3b4214] - Improve Wave debug-task plugin command [cf3fd747] - Improve Wave logging [fced3761] - Increase Wave token duration to 30 mins [e1a712c2] - Fix -with-apptainer cli option (#3621) [8c9588fe] - Fix GH action tests step [bb890d9a] - Fix Spack failing test [868374d3] - Fix Tower doc links, fix typos (#3647) [1278e1a5] - Fix Wave cli messages [10cf414b] - Fix collectFile cache over remote storage [762ba19c] - Fix output env var tokenize [40d56735] - Fix plugin install version [59e9a91b] - Fix race condition on Wave requests [f57fae2c] - Fix serialization of S3 paths with spaces (#3565) [ce487624] - Fix string literal method names with parens (#3604) [8278078a] - Fix submit command in error message for grid executors that pipe wrapper script (#3548) [40ebd308] - Fix typos in the documentation skip ci [eccc1130] - Fix unique fingerprint for Wave bundle resources [b59fa728] - Log exception when an unexpected occurs (#3603) [9aeca99f] - Minor change on container resolution [23d47ded] - Refactor httpfs configuration [445218a8] - Remove deprecated buckets field [0a355ac3] - Remove leading/trailing special chars from tag [7d3cc707] - Remove unused -with-k8s CLI option (#3624) [85b6e7d3] - Update config.rst (#3655) [1555e188] - Update Fusion docs [12782eeb] - Bump Fusion 2.1 [f48ef5b3] - Bump Groovy 3.0.15 [7a3ebc7d] - Bump Micromamba 1.3.1 [aa2bf37e] - Bump Spock 2.3 [9f0dac31] - Bump nf-wave@0.7.1 [b797fac2] - Bump nf-tower@1.5.10 [dd2f69dd] - Bump nf-google@1.7.0 [8cb9fa35] - Bump nf-amazon@1.15.0 [7ccca430]

23.01.0-edge - 14 Jan 2023 - Add support for rclone as stageOutMode option [fde2ac27] - Add queueGlobalStatus config setting [f3339541] - Add support for bearer token to GithubRepositoryProvider [c4d39384] [a2d2cbf60] - Add -with-fusion cli option [d22337cd] - Add support for Fusion container custom options [56e29d35] - Add schedulingPriority option to AWS Batch (use with shareIdentifier) (#3505) [06960bb2] - Fix support for AWS ACL for Batch #2671 [a9644919] - Fix Java options.release in Gradle build [b362d6f6] - Fix nf-httpfs module name in build file [568e47f6] - Fix GitHub creds in CI build [4c4d3f81] - Fix FilePorter concurrency issue (#3511) [11ccfa26] - Fix watchPath hang shutdown execution [bac0cedf] - Fix "no such file" error message to "no such file or directory" (#3547) [c292d84e] - Improve local exec workdir validation [4a3a2720] - Improve container native executor configuration [03126371] - Improve AWS batch exit code reporting [d1bb2fe2] - Improve channel factories error message [0215b9fc] - Improve Google Batch executor [c0a25fc2] - Improve Fusion config [902e5b34] [52f4c5d5] - Improve redirection on Wave client [124cfb3e] - Remove unnecessary Fusion env var [dfa47556] - Remove deprecated method 'just' [d17b3c46] - Remove deprecated methods [75e65035] - Remove DSL1 deprecated code [5d290a47] - Cleanup build from tmp manifests [326b3839] - Minor compilation improvements [4188a6ac] - Migrate all tests to DSL2 [14257d49] - Bump 23.01.0-edge version [9ec31444] - Bump groovy 3.0.14 [7c204236] [6f3ed6e8] - Bump Grengine 3.0 [c0b1a7a6] - Bump nf-wave@0.7.0 [45d274e3] - Bump nf-tower@1.5.9 [db0ebe72] - Bump nf-google@1.6.0 [a663fe16] - Bump nf-console@1.0.5 [45fd53ad] - Bump nf-codecommit@0.1.3 [cf39ef8f] - Bump nf-azure@0.15.1 [7a6a78aa] - Bump nf-amazon@1.14.0 [41fdcc72]

22.12.0-edge - 13 Dec 2022 - Add fair process directive [60d34cfd] - Add support for singularity registry setting [37c1aeb9] - Add AWS profile config setting [66f4669f] - Add support for AWS profile when resolving region [d8947707] - Add support for Sarus container engine (#3470) [54673f18] - Add support for Fusion ARM64 client [d073c538] - Add allowedLocations option to google batch (#3453) [c619eb81] - Add support for AWS config profile in NF config [37112672] - Add warning on Google Logs failure [bdbcdde9] - Add possible values of status in trace.txt to the documentation (#3451) [2425fcfb] - Add support for AWS Glacier restore [b6110766] - Add support for S3 storageClass to publishDir [066f9203] - Add MathHelper utility class [7eecb266] - Fix Wave layer invalid checksum due to not closed stream [e188bbf9] - Fix Fusion test [2245a1c7] - Fix Run fails when home is a symlink [9ff820f4] - Fix math overflow when copying large AWS S3 files [f32ea0ba] - Fix Quote the logName in the Cloud Logging filter (#3464) [b3975063] - Fix Google Batch cloud logging (#3443) [e2bbcf15] - Fix Tower plugin min nextflow requirement [1713a1cd] - Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [46af18e5] - Error & info messages, code comments language fixes (#3475) [29ae36ca] - Replace egrep with grep -E (#3485) [ac0c3035] - Gradle build optimizations (#3483) [19182a57] - Refactor virtual FS schemes to XPath class [fd59b943] - Update concat operator description (#3426) [e8d8c3b5] - Clarify usage of additional options for path qualifier (#3405) [0b70acb1] - Clarify limitation of -with-docker in the docs (#3408) [79afc85d] - Expose process queue as K8s pod label [4df8c8d2] - Prefix nextflow K8s labels with nextflow.io prefix [9951fcd9] - Remove deprecated code [c0b164f2] - Rewrite fetchIamRole and fetchRegion to use AWS SDK (#3425) [e350f319] - Improve Wave config error reporting [ae502668] - Improve K8s retry on transient failures [d86ddc36] - Remove DSL1 output mode [fa400d5f] - Remove support for DSL1 multi into [f664af45] - Bump nf-amazon@1.13.0 [ccaab713] - Bump nf-google@1.5.0 [c07dcec2] - Bump nf-wave@0.6.3 - Bump nf-tower@1.5.8 [652d0880] - Bump fusion version URLs 0.6 [a160a8b1] - Bump AWS sdk version 1.12.351 [4dd82b66]

22.11.1-edge - 29 Nov 2022 - Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [53e6348c] - Fix tower plugin min nextflow requirement [103dbf74] - Fix typos in the documentation (#3441) [ae95d90d] - Add support for Java 19 [811e7ca8] - Add support for custom conda channels (#3435) [0884e80e] - Add time directive to AWS Batch, clean language (#3436) [1ed2640a] - Update err message [ab5bd81b] - Fix Flux executor config (#3432) [68b45c92] - Bump nf-wave@0.6.1 [fe669152] - Bump nf-tower@1.5.7 [2dbf9906]

22.11.0-edge - 23 Nov 2022 - Add support for Apptainer container engine (#3345) [29f98975] - Add Flux executor to nextflow (#3412) [cc9fc3f0] [3711cef0] - Add support for Wave containerPlatform [10d56ca1] - Add CSI ephemeral volume for K8s (#2988) [f18f6e81] - Add support for disk directive and emptyDir to K8s (#2998) [b548e1c7] - Add Fusion support for custom S3 endpoints [fba9b649] - Add support for Tower refresh token for dataset (#3366) [a19e055a] - Prevent infinite loop while fetching git tags and branches [aa974d44] - Improve file porter logging [626420b6] - Improve script err logging [2714770e] - Extend onFilePublish notification adding source path (#3284) [81acc3ef] - Remove cpu limits from K8s pod spec builder (#3338) [dc7f78bf] - Improve task name logging [5ddb7e3f] - Add tower endpoint to wave [b725ddc4] - Add Azure SAS token validation [e2244b48] - Use cpus-shares for container resources (#3383) [b38c3880] - Report full path scheme on error [4089ba65] - Allow identity based authentication on Azure Batch (#3132) [a08611be] - Fix support for remote file mail attachment (#3384) [6b496bb9] - Fix task cache logging [ed37c4fd] - Fix unexpected error on task resume [1c3f4685] - Fix stripIndent failure with java 17 (#3377) [2b115c50] - Fix -dockerized execution #3137 (#3148) [64a81a58] - Improve default value in cli help of nextflow log -s (#3371) [2141f96e] - upgrade jsoup and snakeyaml version (#3374) [6e2ca454] - Bump Java 17 lang version + Java 11 as target [34f133e2] - Bump nf-amazon@1.12.0 [e307912e] - Bump nf-azure@0.15.0 [07391d96] - Bump nf-wave@0.6.0 [4d787561]

- Groovy
Published by pditommaso almost 3 years ago

io.nextflow:nextflow - Version 23.03.0-edge

Add Azure batch pool virtualNetwork option (#3723) [e3917b8e]
Add basePackages option to Wave config [7e827810]
Add error message for missing container image with Google Batch (#3747) [6419e68f]
Add notifyFilePublish optional source argument (#3737) [a65a9ff7]
Add retry strategy on Bash wrapper write logic [1e38274a]
Add support for AWS S3 Glacier Retrieval Tier (#3680) [fab6bd5e]
Add sync invocation on job completion (#3678) [e29c4e4b]
Add workflowId to Wave request [025ff9d0]
Add Clone result list objects before output binding [38762080]
Add plugins option to kuberun command (#3766) [6515294f]
Fix Google Batch logging exception [d7e38e9e]
Fix Java Matcher serialization [6aecc4ed]
Fix Logger failure type detection [f1b89c1f]
Fix Orphaned processes when using Singularity [7236f830]
Fix groupTuple with mismatching tuple cardinality [1d32e2c2]
Fix special chars escaping in container env [b93634e9]
Fix commit revision type for Azure DevOps repos (#3721) [fb71767e]
Improve DAG API (#3703) [21afb358]
Improve Wave docs [7299dac9]
Improve fair directive docs (#3677) [7ca7520f]
Improve transpose and groupTuple examples in the docs (#3685) [7870dfc8]
Increase pwd obfuscation min length [ba23d036]
Make GroupKey cloneable (#3738) [0760b0fd]
Prepare Nextflow for the CWS Plugin (#3727) [fd8bf709]
Remove DNAnexus page from docs (#3695) [fa58c18c]
Remove outdated FAQ page from docs (#3683) [e59c7fbb]
Remove unused classes [9fa8d75b]
Update Azure VM sizes (#3751) [1d06e9a6]
Enable Fusion on Google Batch tests [2f1b1094]
Bump groovy 3.0.16 [d3ff5dcb]
Bump nf-wave@0.8.0 [aa1b065d]
Bump nf-google@1.7.1 [2aaaf2a7]
Bump nf-azure@0.16.0 [f358b008]
Bump nf-amazon@1.16.0 [2395187d]

- Groovy
Published by pditommaso almost 3 years ago

io.nextflow:nextflow - Version 23.02.1-edge

Add Fusion logs and tags config [09192078]
Add support for NXF_DEBUG to K8s task handler [ci fast] [828583dc]
Add support for Mamba HTTP-based lock files [ci fast] [7fe88c84]
Add container name validation [c3b6d9ab]
Add Fusion for Google storage docs [34fcfe06]
Improve K8s auth token discovery [ci fast] [44f8cc07]
Bump nf-wave@0.7.2 [1c697ab5]
Bump amazoncorretto:17.0.6 [a33a6f47]

- Groovy
Published by pditommaso about 3 years ago

io.nextflow:nextflow - Version 23.02.0-edge

Add Fusion support for Google Batch (#3577) [d5fbab4f]
Add Header provider to Google Batch client [20979929]
Add Wave integration tests [c5faf971]
Add errorStrategy validation [954cd921]
Add Java install recommendations to docs (#3617) [7e9bee1e]
Add nextflow tags to AWS Batch job def [b465ac52] [BREAKING]
Add readOnlyInputs option for CharliecloudBuilder (#3590) [8ae001fc]
Add refresh token to Wave request [41510e87]
Add requirements for container images to run with Nextflow (#3586) [7af1cb66]
Add support for Fusion to Slurm and LSF executors (#3516) [fbc95e6b]
Add support for Fusion tags (#3609) [8385ec22]
Add support for the Spack package manager (#3580) [a5df62f6]
Add the fcp tool option to file copy strategy (#3556) [2a224258]
Add Fusion integration test
Add Wave + Fusion test with Google Batch [b541c061]
Add support for entryless Fusion configuration and Singularity support (#3584) [34a27733]
Improve Fusion config [a1d08463]
Ignore resource directives if -l option is specified in PBS executor (#3015) [28a67969]
Improve K8s securityContext support [3f76240b]
Improve AWS Batch error logging [8f4884c1]
Improve secrets docs [9a3b4214]
Improve Wave debug-task plugin command [cf3fd747]
Improve Wave logging [fced3761]
Increase Wave token duration to 30 mins [e1a712c2]
Fix -with-apptainer cli option (#3621) [8c9588fe]
Fix GH action tests step [bb890d9a]
Fix Spack failing test [868374d3]
Fix Tower doc links, fix typos (#3647) [1278e1a5]
Fix Wave cli messages [10cf414b]
Fix collectFile cache over remote storage [762ba19c]
Fix output env var tokenize [40d56735]
Fix plugin install version [59e9a91b]
Fix race condition on Wave requests [f57fae2c]
Fix serialization of S3 paths with spaces (#3565) [ce487624]
Fix string literal method names with parens (#3604) [8278078a]
Fix submit command in error message for grid executors that pipe wrapper script (#3548) [40ebd308]
Fix typos in the documentation skip ci [eccc1130]
Fix unique fingerprint for Wave bundle resources [b59fa728]
Log exception when an unexpected occurs (#3603) [9aeca99f]
Minor change on container resolution [23d47ded]
Refactor httpfs configuration [445218a8]
Remove deprecated buckets field [0a355ac3]
Remove leading/trailing special chars from tag [7d3cc707]
Remove unused -with-k8s CLI option (#3624) [85b6e7d3]
Update config.rst (#3655) [1555e188]
Update Fusion docs [12782eeb]
Bump Fusion 2.1 [f48ef5b3]
Bump Groovy 3.0.15 [7a3ebc7d]
Bump Micromamba 1.3.1 [aa2bf37e]
Bump Spock 2.3 [9f0dac31]
Bump nf-wave@0.7.1 [b797fac2]
Bump nf-tower@1.5.10 [dd2f69dd]
Bump nf-google@1.7.0 [8cb9fa35]
Bump nf-amazon@1.15.0 [7ccca430]

Breaking changes

Using the AWS Batch executor, Nextflow requires the permission batch:TagResource when creating Batch job permissions
Using the AWS Batch executor with Fusion file system, Nextflow requires s3:PutObjectTagging permission on the S3 objects created by job executions

- Groovy
Published by pditommaso about 3 years ago

io.nextflow:nextflow - Version 22.10.7

Fix plugin install version [895e4f34]
Fix unique fingerprint for wave bundle resources [7c55aa37]
Fix race condition on wave requests [7f76d19b]
Fix serialization of S3 paths with spaces (#3565) [935df949]
Improve AWS batch error logging [1eddeea7]
Improve wave logging [94415914]
Increase Wave token duration to 30 mins [8d5fbefe]
Update fusion docs [b24ee138]
Bump nf-wave@0.5.4 [f466b266]
Bump nf-amazon@1.11.4 [d5f6c125]

- Groovy
Published by pditommaso about 3 years ago

io.nextflow:nextflow - Version 22.10.6

backport: Add refresh token to wave request [47a7408b]
backport:Add tower endpoint to wave [fe24b422]
backport:Fix Wave layer invalid checksum due to not closed stream [20df6400]
Bump nf-wave@0.5.3 [c1ec759f]

- Groovy
Published by pditommaso about 3 years ago

io.nextflow:nextflow - Version 23.01.0-edge

Add support for rclone as stageOutMode option [fde2ac27]
Add queueGlobalStatus config setting [ci fast] [f3339541]
Add support for bearer token to GithubRepositoryProvider [c4d39384] [a2d2cbf60]
Add -with-fusion cli option [d22337cd]
Add support for Fusion container custom options [56e29d35]
Add schedulingPriority option to AWS Batch (use with shareIdentifier) (#3505) [06960bb2]
Fix support for AWS ACL for Batch #2671 [a9644919]
Fix Java options.release in Gradle build [b362d6f6]
Fix nf-httpfs module name in build file [568e47f6]
Fix GitHub creds in CI build [4c4d3f81]
Fix FilePorter concurrency issue (#3511) [11ccfa26]
Fix watchPath hang shutdown execution [bac0cedf]
Fix "no such file" error message to "no such file or directory" ci fast [c292d84e]
Improve local exec workdir validation [4a3a2720]
Improve container native executor configuration [03126371]
Improve AWS batch exit code reporting [d1bb2fe2]
Improve channel factories error message [0215b9fc]
Improve Google Batch executor [c0a25fc2]
Improve Fusion config [902e5b34] [52f4c5d5]
Improve redirection on Wave client [124cfb3e]
Remove unnecessary Fusion env var [ci fast] [dfa47556]
Remove deprecated method 'just' [d17b3c46]
Remove deprecated methods [75e65035]
Remove DSL1 deprecated code [5d290a47]
Cleanup build from tmp manifests [326b3839]
Minor compilation improvements [4188a6ac]
Migrate all tests to DSL2 [14257d49]
Bump 23.01.0-edge version [9ec31444]
Bump groovy 3.0.14 [7c204236] [6f3ed6e8]
Bump Grengine 3.0 [c0b1a7a6]
Bump nf-wave@0.7.0 [45d274e3]
Bump nf-tower@1.5.9 [db0ebe72]
Bump nf-google@1.6.0 [a663fe16]
Bump nf-console@1.0.5 [45fd53ad]
Bump nf-codecommit@0.1.3 [cf39ef8f]
Bump nf-azure@0.15.1 [7a6a78aa]
Bump nf-amazon@1.14.0 [41fdcc72]

- Groovy
Published by pditommaso about 3 years ago

io.nextflow:nextflow - Version 22.10.5

Fix FilePorter concurrency issue (#3511) [0f757156]
Fix watchPath hang shutdown execution [e03d9ca6]
Add schedulingPriority option to AWS Batch (use with shareIdentifier) (#3505) [543ee7b1]

- Groovy
Published by pditommaso about 3 years ago

io.nextflow:nextflow - Version 22.12.0-edge

Add fair process directive [60d34cfd]
Add support for singularity registry setting [37c1aeb9]
Add AWS profile config setting [66f4669f]
Add support for AWS profile when resolving region [d8947707]
Add support for Sarus container engine (#3470) [54673f18]
Add support for Fusion ARM64 client [d073c538]
Add allowedLocations option to google batch (#3453) [c619eb81]
Add support for AWS config profile in NF config [37112672]
Add warning on Google Logs failure [bdbcdde9]
Add possible values of status in trace.txt to the documentation (#3451) [2425fcfb]
Add support for AWS Glacier restore [b6110766]
Add support for S3 storageClass to publishDir [066f9203]
Add MathHelper utility class [7eecb266]
Fix Wave layer invalid checksum due to not closed stream [e188bbf9]
Fix Fusion test [2245a1c7]
Fix Run fails when home is a symlink [9ff820f4]
Fix math overflow when copying large AWS S3 files [f32ea0ba]
Fix Quote the logName in the Cloud Logging filter (#3464) [b3975063]
Fix Google Batch cloud logging (#3443) [e2bbcf15]
Fix Tower plugin min nextflow requirement [1713a1cd]
Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [46af18e5]
Error & info messages, code comments language fixes (#3475) [29ae36ca]
Replace egrep with grep -E (#3485) [ac0c3035]
Gradle build optimizations (#3483) [19182a57]
Refactor virtual FS schemes to XPath class [fd59b943]
Update concat operator description (#3426) [e8d8c3b5]
Clarify usage of additional options for path qualifier (#3405) [0b70acb1]
Clarify limitation of -with-docker in the docs (#3408) [79afc85d]
Expose process queue as K8s pod label [4df8c8d2]
Prefix nextflow K8s labels with nextflow.io prefix [9951fcd9]
Remove deprecated code [c0b164f2]
Rewrite fetchIamRole and fetchRegion to use AWS SDK (#3425) [e350f319]
Improve Wave config error reporting [ae502668]
Improve K8s retry on transient failures [d86ddc36]
Remove DSL1 output mode [fa400d5f]
Remove support for DSL1 multi into [f664af45]
Bump nf-amazon@1.13.0 [ccaab713]
Bump nf-google@1.5.0 [c07dcec2]
Bump nf-wave@0.6.3
Bump nf-tower@1.5.8 [652d0880]
Bump fusion version URLs 0.6 [a160a8b1]
Bump AWS sdk version 1.12.351 [4dd82b66]

- Groovy
Published by pditommaso about 3 years ago

io.nextflow:nextflow - Version 22.10.4

Fix math overflow when copying large AWS S3 files [07f7cb72]
Bump nf-amazon@1.11.2 [d96ca4c3]

- Groovy
Published by pditommaso about 3 years ago

io.nextflow:nextflow - Version 22.11.1-edge

Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [53e6348c]
Fix tower plugin min nextflow requirement [103dbf74]
Fix typos in the documentation ci skip [ae95d90d]
Add support for Java 19 [811e7ca8]
Add support for custom Conda channels (#3435) [ci fast] [0884e80e]
Add time directive to AWS Batch, clean language (#3436) [ci skip] [1ed2640a]
Update err message [ci fast] [ab5bd81b]
Fix Flux executor config (#3432) [ci fast] [68b45c92]
Bump nf-wave@0.6.1 [fe669152]
Bump nf-tower@1.5.7 [2dbf9906]

- Groovy
Published by pditommaso about 3 years ago

io.nextflow:nextflow - Version 22.11.0-edge

Add support for Apptainer container engine (#3345) [29f98975]
Add Flux executor to nextflow (#3412) [cc9fc3f0] [3711cef0]
Add support for Wave containerPlatform [10d56ca1]
Add CSI ephemeral volume for K8s (#2988) [f18f6e81]
Add support for disk directive and emptyDir to K8s (#2998) [b548e1c7]
Add Fusion support for custom S3 endpoints [fba9b649]
Add support for Tower refresh token for dataset (#3366) [a19e055a]
Prevent infinite loop while fetching git tags and branches [aa974d44]
Improve file porter logging [626420b6]
Improve script err logging [2714770e]
Extend onFilePublish notification adding source path (#3284) [81acc3ef]
Remove cpu limits from K8s pod spec builder (#3338) [dc7f78bf]
Improve task name logging [5ddb7e3f]
Add tower endpoint to wave [ci fast] [b725ddc4]
Add Azure SAS token validation [e2244b48]
Use cpus-shares for container resources (#3383) [b38c3880]
Report full path scheme on error [4089ba65]
Allow identity based authentication on Azure Batch (#3132) [a08611be]
Fix support for remote file mail attachment (#3384) [6b496bb9]
Fix task cache logging [ed37c4fd]
Fix unexpected error on task resume [1c3f4685]
Fix stripIndent failure with java 17 (#3377) [2b115c50]
Fix -dockerized execution #3137 (#3148) [64a81a58]
Improve default value in cli help of nextflow log -s (#3371) [2141f96e]
upgrade jsoup and snakeyaml version (#3374) [6e2ca454]
Bump Java 17 lang version + Java 11 as target [34f133e2]
Bump nf-amazon@1.12.0 [e307912e]
Bump nf-azure@0.15.0 [07391d96]
Bump nf-wave@0.6.0 [4d787561]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.10.3

Prevent infinite loop while fetching git tags/branches [73a59d33]
Bump nf-amazon@1.11.1 [f9b54ce3]
Improve S3 thread pool config [01541b0a]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.10.2

Fix initialize the plugin once it's defined (#3360) [dd150b92]
Fix tags typo in docs (#3355) [b82df4e0]
Fix unexpected error on task resume [e02e8c27]
Fix template script in trace record [cf828a68]
Fix ip v6 support for K8s executor [53af5a7c]
Fix refresh token for tower served resources [9dec2b66] #3366
Fix full path scheme on error [1399f451]
Add note to some process implicit variables (#3373) [0374f63a]
Add retry policy on plugin download failure [e8dbec3f]
Add examples of when dynamic output filenames are important (#3275) [72a17306]
Update google batch java sdk, add serviceAccountEmail and installGpuDrivers (#3324) [7f7007a8]
Update github actions to v3 (#3376) [d3b4a837]
Update error messages and docs with new report filename behavior [f5725480]
Bump nf-tower@1.5.6 [164edf7c]
Bump nf-google@1.4.5 [30cb118d]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.10.1

Fix mount pwd in the container when work dir is a symlink [ca397181] [b5b7d3cd]
Fix secrets command name in the CLI (#3320) [ci fast] [321486df]
Fix ver num rendering [ci fast] #3226 [5312a25e]
Fix K8s config namespace is not applied [b3d33e3b]
Fix log fetching from remote storage [be356939] [3efa1a20]
Update docs about default mail ssl protocol ci skip [15ffffc1]
Update docs repeated words from documentation (#3311) [ci skip] [d59ea186]
Update docs to clarify the difference between collect and toList (#3276) [7ee2b008]
Update docs [516a7441]
Update docs adding Fusion [11eac707]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.10.0

Fix timestamp encoding [47a3a3c4]
Minor type change in Bridge executor [1f446ee1]
Bump nf-wave@0.5.2 [326803ff]

Included in previous RC and edge releases:

22.10.0-RC3 - 7 Oct 2022 - Fix K8s context selection [58b354e6]

22.10.0-RC2 - 7 Oct 2022 - Improve K8s labels/annotation validation [a569afdf] - Bump fusion final url [80398880] - Bump nf-wave@0.5.1 [a2b44c4d] - Update docs

22.10.0-RC1 - 3 Oct 2022 - Add module binaries enabling flag + docs [c50e178f] - Add timestamp and fingerprint to wave request [a5a7e138] - Add missing inputs to the incremental task "test" (#1442) [ci fast] [f85d59a6] - Add support for refresh token to Wave [ed9f25f1] - Add pretty option to dump operator [ci fast] [4218b299] - Add support for custom S3 content type [02afa332] - Get rid of file name rolling for report files [a762ed59] - Ignore JGit warning when missing git tool [a94fa9c1] - Remove jobname limit to HyperQueue executor (#3251) [99604ccb] - Rename baseImage to mambaImage [ci fast] [50086028] - Fix failing test [ci fast] [e6790003] - Fix K8s cluster token when using serviceAccount [c3364d0f] - Fix hanging test [44c04874] - Improve docs (#3212) [ci skip] [5d80388c] - Bump fusion snapshot [ci skip] [8e03f655] - Bump wave endpoint [a044cc6a] - Bump nf-wave@0.4.5 [7424dc4b] - Bump fusion config v0.5.1 [4dbdf112] - Bump nf-wave@0.5.0 - Bump nf-tower@1.5.5 - Bump nf-amazon@1.11.0

22.09.7-edge - 28 Sep 2022 - Fix Issue copying file bigger than 5gb to S3 [18fd9a44] - Fix chmod command to accommodate hidden files in bindir (or empty bindir) (#3247) [a0fcc7b0] - Bump nf-amazon@1.10.7 [f7f96e6f]

22.09.6-edge - 26 Sep 2022 - Add SocketTimeoutException to k8s client request retry [527e0d5d] - Add MaxErrorRetry to K8s config [58be2128] - Add tags propagation to AWS Batch [d64eeffc] - Fix task resume when updating fusion layer [f38fd2db] - Fix Channel merge still deprecated for DSL2 (#3220) [d27384d2] - Apply GCP resourceLabels to the VirtualMachine (#3234) [2275c03c] - Update Google Batch mount point with the requirements [5aec28ac] - Improve wave error reporting [73842215] - Bump fusion 0.4.x [26f1f896]

22.09.5-edge - 21 Sep 2022 - Use default wave strategy [abbfa7f4] - Handle errors reported by tower report writer [0e814647] - Fix AWS S3 copy object [b3b90d23]

22.09.4-edge - 19 Sep 2022 - Add Fusion display name [f789d457] - Add container cleanup [cd2ae7dc] - Add Wave interactive debug session [ce7fa651] - Add support for wave build and cache repositories[692043ff] - Add shutdown to Google Batch client [8f413cf7] - Add native_id to Google Batch handler [352b4239] - Add java sts library to enable use of IRSA in k8s (#3207) [62df42c3] - Add support for module custon bin dirs [77f55262] - Add support for tower token to wave client [928d5b04] - Update CLI docs (#3200) [8acebee6] - Fix issue with empty report file [9cc4f079] - Do not return resource bundle for root module [775c7ed9] - Improve tower config [ee03c243] - Bump groovy 3.0.13 [4a17e198]

22.09.3-edge - 10 Sep 2022 - Add fusion support to K8s executor (#3142) [6bb27b32] - Fix shutdown/cleanup hooks invocation [f4185070] - Fix Use smaller buffer size for S3 stream uploader [8c643074] [9926d15d] - Fix Azure NPE on missing pool opts [d5c0aabd] - Fix handling of targetDir when using Fusion fs [2091b272] - Document aws.batch.retryMode config (#3195) [56f75e0c]

22.09.2-edge - 7 Sep 2022 - Fix thread pool race condition on shutdown [8d2b0587] - Fix Intermediate multipart upload requires a minimum size (#3193) [0b66aed6] - Fix fusion enable detection [3ef91512] - Add before-afterScript warning to docs (#3167) [09464590] - Add httpReadTimeout and httpConnectTimeout config to K8s client [064f9bc4] - Add support for Wave build & cache repos [98a275ba] - Finalise secrets feature (#3161) [49021b82] - Update executor retry config docs (#3001) [aed6c234] - Change Azure test pool name [0c724504] - Improve Wave error reporting [b11d0f11] - Remove unneeded launcher file remapping [a255118d] - Update Azure vm types [80f5fbe4] - Update docs logos (#3174) [529bad81]

22.09.1-edge - 1 Sep 2022 - Add support for Charliecloud v0.28 (#3116) [84f43a33] - Add Support for EC-encrypted keys for K8s client [fd759d09] - Add support for Bridge batch scheduler (#3106) [343c17e6] - Add fusion support to local executor [17160bb0] [6cfb51e7] - Add getTags and getBranches to BitBucketServer [53bd89cd] - Add retry strategy to httpfs client [55f9c87b] - Add support for project resources [c2ad6566] - Add mamba build options [987a13cb] - Fix Do not override tower endpoint in the config [41fb1ad0] - Fix Hyperqueue job names must be less than 40 chars #3151 [8e43670b] - Fix typo in ConfigBuilder.groovy (#3143) [659e6108] - Fix Resume for dynamic resolved containers [13483ff2] - Improve fusion env handling [10f35b60] - Improve foreign file(s) cache detection logic [3a9352c8] - Rename ModuleBundle to ResourcesBundle [0e51dc0f] - Use quiet output mode for hyperqueue executor (#3103) [70a91fdf] - Wave improve conda settings [6f087fec] - Improve secrets cmd (#3158) [115b2f3d] - Improve Wave resolution strategy [2eb700c6] - Improve Az Batch err handling and testing [85d31e8d] - Bump google-cloud-batch 0.2.2 - Bump spock 2.2

22.08.2-edge - 16 Aug 2022 - Fix queueSize setting is not honoured by AWS Batch executor (again) #3117 [1733bb2e] - Add files() method to docs (#3123) [00bb8896] - Refactor wave packing [bc876986] - Improve logging [aa380d5f] - Update dockerfile [e6329282]

22.08.1-edge - 11 Aug 2022 - Add support for disabling config include [e0859a12] - Add experimental fusion support [1854f1f2] - Add support for plugin provided function extension (#3079) [16230c2b] - Add support for AWS Batch logs group (#3092) [4ef043ac] - Add share identifier to Aws Batch (#3089) [c0253aba] - Improve Tower cache manager [0091afc5] - Improve S3 copy via xfer manager [02d2beae] - Reports a warning when using NXF vars in the config [009ec256] - Make wake token cache duration config [5f955fc9] - Patch unable to start non-core plugin [a55f58ff] - Increase S3 upload chunk size to 100 MB [9c94a080] - Change Google Batch disk directive to override boot disk size (#3097) [7e1c0686] - Fix queueSize setting is not honoured by AWS Batch executor (#3093) [d07bb52b] - Fix Allow disabling scratch with Google Batch [e8e5c721] - Fix Emit relative path when relative parameter is set (#3072) [39797759] - Bump nf-wave@0.3.0 [e46d341d] - Bump nf-tower@1.5.1 [cdc2be53] - Bump nf-google@1.4.1 [c39935a5] - Bump nf-amazon@1.10.0 [ccdf62d0]

22.08.0-edge - 1 Aug 2022 - Add warning to env config docs (#3083) [ca933c16] - Add -with-conda CLI option (#3073) [98b2ac80] - Add simple wave plugin cli commands [8888b866] - Add default wave plugin [7793a0ec] - Add boot disk, cpu platform to google batch (#3058) [17a8483d] - Add support for GPU accelerator to Google Batch (#3056) [f34ad7f6] - Add support for archive dir to tower plugin [c234681a] - Add support tower cache backup/restore [bc2f9d13] - Add disk directive to google batch (#3057) [ec6e290c] - Add retry when Azure submit fails with OperationTimedOut [6a3f9742] - Add warning when Google Batch quota is exceeded (#3066) [6b9c52ad] - Allow fully disabling history file [0a45f858] - Allow the support function overloading and default parameters (#3011) [042d3857] - Improve S3 file upload/download via Transfer manager [7e8d2a5a] - Prevent overriding container entrypoint [b3a4bf85] - Update FileTransfer pool settings [503aafce] - Remove deprecated commands [93228b4b] - Prevent nextflow config to break tower launch [e059a724] - Refactor Google Batch executor to use Java API (#3044) [31a6e85c] - Fix Unable to disable scratch attribute with AWS Batch [1770f73a] - Fix unit test setting explicit permissions for test files [1c821139] - Fix Default plugins are overriden by config plugins [46cf3bfa] - Fix S3 transfer download directory [b7bf9fe5] - Fix NPE while setting S3 ObjectMetada #3031 [d6163431] - Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b] - Fix AWS Batch job definition conflict (#3048) [e5084418] - Fix JAVATOOLOPTIONS breaking launch #1716 [0e7b416d] - Fix add ps shared objects to Dockerfile (#3033) [1c23b40a] - Parallelize build integration tests [807800a3] - Bump google-cloud-nio:0.124.8 [dfaa9d19] - Bump groovy 3.0.12 [5c900b91] - Bump Moment.js 2.29.4 [a9ced868] - Bump gson@2.9.0 [12f17176] - Bump nf-azure@0.13.4 - Bump nf-google@1.4.0 - Bump nf-tower@1.5.0 - Bump nf-wave@0.2.1 - Bump nf-amazon@1.9.0

22.07.1-edge - 13 Jul 2022 - Add support for Google Batch API v1 [4c116d58] [e85d87ee] - Add time directive support for K8s executor (#2948) [2b6f70a8] - Add docs aws.client.s3PathStyleAccess config (#3000) [20005500] - Allow to override lsf.conf settings with nextflow config #2862 [dae191a1] - Allow hybrid containers execution [0af1bcb3] - Improve error msg when script file cannot be read [52c2780e] - Improve error reporting for custom function [877c7931] - Improve error message for missing plugin extension [4a43db84] - Improve test #3019 [7c37e0be] - Rename kuberun -pod-image to -head-image [2576ba62] - Externalise sqldb plugin source code [17e80b4f] - Fix escape unstage outputs with double quotes #2912 #2904 #2790 [49ff02a6] - Fix Exception when settings AWS Batch containerOptions #3019 [89312ad8] - Fix Missing query param in http file (#2918) [43cc8511] - Fix Publish copy mode for S3 based path [085f6b2b] - Fix Fail fast uploads to S3 (#2969) [7fd1a6e1] - Fix null script name in launch info [7118849f] - Bump commons-code@1.15 [a06b4442] - Bump jgit@6.2.0 [3331826f] - Bump snakeyaml@1.30 [de62fd3f] - Bump gson@2.8.9 [3234ddd5]

22.07.0-edge - [SKIPPED]

22.06.1-edge - 17 Jun 2022 - Fix CodeCommit creds handling + nf-codecommit@0.1.2 [70fc0745] - Fix typo in log message [a8f8529d] - Add more scientists to the list of random names [8d5b36a2]

22.06.0-edge - 9 Jun 2022 - Add AWS CodeCommit initial support [80fba6e9] - Add support for 307 and 308 HTTP redirection [92382012] - Add DirWatcher v2 [209c82cd] - Add Moriondo in the list of random names [e0abca58] - Add preview CLI option (#2914) [aa8f1aa4] - Fix Git config resultion error [64436697] - Fix StackOverflowError when dump all profiles (#2922) [28cd11a2] - Fix gradle warning message in nf-sqldb (#2921) [b09ceabe] - Fix log for LsfExecutror perTaskReserve attribute [7c3ec874] - Fix external pod deletion for jobs (#2915) [4dd1af7a] - Prevent function overloading in module definition [c0b522ab] - Improve error message of non sensical include (#2623) [285fe49c] - Mount PWD path only when scratch is used [9b3c6e31] - Stripe sensitive data into strings (#2908) [7fa4c86c] - Dump scm content when trace is enabled [c3117ada]

22.05.0-edge 25 May 2022 - Add Hyperqueue executor (#2896) [ffa5712e] - Add support for K8s Job resource [c70eb12d] - Add support for time process directive in GLS executor (#2880) [1402e183] - Add support for priviledge option for K8s containers [7ffe3a02] - Add DSL1 option to docs (#2836) [d30841a5] - Add support for container options to Azure Batch [3f4f00f9] - Add support for move operation to AWS S3 [8c0ddfd5] - Add K8s execution hostname in the trace file (#2828) [ebaef92a] - Add support for AWS S3 encyption using a custom KMS key [c1e45aa9] - Add support for Micromamba [383e023f] - Add jaxb-api dependecy to nf-amazon [c1a09f87] - Add strict mode config setting [ci fast] [696e70b5] - Add -head-prescript option to kuberun (#2830) [9e387055] - Fix missing err message on submit failure 233e67f0 - Fix resolve azure devops repositories when projectId is present [2500ff01] - Fix AthenaJdbc into distribution zip [853a1f2a] [4b3579d5] [70ef7ee3] - Fix Inconsistent bool parsing #2881 [40bf2b2a] - Fix Unable to pull pipeline if config file is not in default branch (#2876) [4ee5b04f] - Fix Prevent crash when scratch dir does not exist (#2888) [9ef44ae5] - Fix DSL1 detection to invalid workflow keyword matching fe0700b0 - Fix Aws Batch retry policy on spot reclaim [6e029b79] - Fix 'false' string in config interpreted as true (#2865) [079a18ce] - Improve Git Provider config logging [d7dbca8ec] - Improve K8s task handler [1822b2ca] - Improve missing workflow err message da101e8f - Include revision in the Azure Repos provider when specified (#2861) [3342c767] - Remove unnecessary change dir echo [372d1f47] - Abort execution when accessing undefined params with strict mode [93836081] - Update docker base image [50cd7956] - Update default SKU for Azure Batch (#2868) [9ea09dba] ] - Update dependencies [405d9545] - Refactoring to prevent name conflict [aba2671b] - Few DSL syntax to explicit declaration of plugin extensions (#2820) [bfc4a067] - Sanitize k8s label and annotation keys, don't sanitize annotation value (#2843) [5287a984] - Docs improvement (#2835) [09e5bca3] - Bump Jgit 6.1 [7186348c] - Bump Spock 2.1 [51100d16] - Bump capsule 1.1.1 [20ec1697]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.10.0-RC3

Fix K8s context selection [58b354e6]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.10.0-RC2

22.10.0-RC2 - 7 Oct 2022 - Improve K8s labels/annotation validation [a569afdf] - Bump fusion final URL [80398880] - Bump nf-wave@0.5.1 [a2b44c4d] - Update docs

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.10.0-RC1

Add module binaries enabling flag + docs [c50e178f]
Add timestamp and fingerprint to wave request [a5a7e138]
Add missing inputs to the incremental task "test" (#1442) [ci fast] [f85d59a6]
Add support for refresh token to Wave [ed9f25f1]
Add pretty option to dump operator [ci fast] [4218b299]
Add support for custom S3 content type [02afa332]
Get rid of file name rolling for report files [a762ed59]
Ignore JGit warning when missing git tool [a94fa9c1]
Remove jobname limit to HyperQueue executor (#3251) [99604ccb]
Rename baseImage to mambaImage [ci fast] [50086028]
Fix failing test [ci fast] [e6790003]
Fix K8s cluster token when using serviceAccount [c3364d0f]
Fix hanging test [44c04874]
Improve docs (#3212) [ci skip] [5d80388c]
Bump fusion snapshot [ci skip] [8e03f655]
Bump wave endpoint [a044cc6a]
Bump nf-wave@0.4.5 [7424dc4b]
Bump fusion config v0.5.1 [4dbdf112]
Bump nf-wave@0.5.0
Bump nf-tower@1.5.5
Bump nf-amazon@1.11.0

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.09.7-edge

Fix Issue copying file bigger than 5gb to S3 [18fd9a44]
Fix chmod command to accommodate hidden files in bindir (or empty bindir) (#3247) [a0fcc7b0]
Bump nf-amazon@1.10.7 [f7f96e6f]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.09.6-edge

Add SocketTimeoutException to k8s client request retry [527e0d5d]
Add MaxErrorRetry to K8s config [58be2128]
Add tags propagation to AWS Batch [d64eeffc]
Fix task resume when updating fusion layer [f38fd2db]
Fix Channel merge still deprecated for DSL2 (#3220) [d27384d2]
Apply GCP resourceLabels to the VirtualMachine (#3234) [2275c03c]
Update Google Batch mount point with the requirements [5aec28ac]
Improve wave error reporting [73842215]
Bump fusion 0.4.x [26f1f896]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.09.5-edge

Use default wave strategy [abbfa7f4]
Handle errors reported by tower report writer [0e814647]
Fix AWS S3 copy object [b3b90d23]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.09.4-edge

Add Fusion display name [f789d457]
Add container cleanup [cd2ae7dc]
Add Wave interactive debug session [ce7fa651]
Add support for wave build and cache repositories[692043ff]
Add shutdown to Google Batch client [8f413cf7]
Add native_id to Google Batch handler [352b4239]
Add java sts library to enable use of IRSA in k8s (#3207) [62df42c3]
Add support for module custon bin dirs [77f55262]
Add support for tower token to wave client [928d5b04]
Update CLI docs (#3200) [8acebee6]
Fix issue with empty report file [9cc4f079]
Do not return resource bundle for root module [775c7ed9]
Improve tower config [ee03c243]
Bump groovy 3.0.13 [4a17e198]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.09.3-edge

Add Fusion support to K8s executor (#3142) [6bb27b32]
Fix shutdown/cleanup hooks invocation [f4185070]
Fix Use smaller buffer size for S3 stream uploader [8c643074] [9926d15d]
Fix Azure NPE on missing pool opts [d5c0aabd]
Fix handling of targetDir when using Fusion fs [2091b272]
Document aws.batch.retryMode config (#3195) [56f75e0c]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.09.2-edge

Fix thread pool race condition on shutdown [8d2b0587]
Fix Intermediate multipart upload requires a minimum size (#3193) [0b66aed6]
Fix fusion enable detection [3ef91512]
Add before-afterScript warning to docs (#3167) [09464590]
Add httpReadTimeout and httpConnectTimeout config to K8s client [064f9bc4]
Add support for Wave build & cache repos [98a275ba]
Finalise secrets feature (#3161) [49021b82]
Update executor retry config docs (#3001) [aed6c234]
Change Azure test pool name [0c724504]
Improve Wave error reporting [b11d0f11]
Remove unneeded launcher file remapping [a255118d]
Update Azure vm types [80f5fbe4]
Update docs logos (#3174) [529bad81]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.09.1-edge

Add support for Charliecloud v0.28 (#3116) [84f43a33]
Add Support for EC-encrypted keys for K8s client [fd759d09]
Add support for Bridge batch scheduler (#3106) [343c17e6]
Add fusion support to local executor [17160bb0] [6cfb51e7]
Add getTags and getBranches to BitBucketServer [53bd89cd]
Add retry strategy to httpfs client [55f9c87b]
Add support for project resources [c2ad6566]
Add mamba build options [987a13cb]
Fix Do not override tower endpoint in the config [41fb1ad0]
Fix Hyperqueue job names must be less than 40 chars #3151 [8e43670b]
Fix typo in ConfigBuilder.groovy (#3143) [659e6108]
Fix Resume for dynamically resolved containers [13483ff2]
Improve fusion env handling [10f35b60]
Improve foreign file(s) cache detection logic [3a9352c8]
Rename ModuleBundle to ResourcesBundle [0e51dc0f]
Use quiet output mode for Hyperqueue executor (#3103) [70a91fdf]
Wave improve Conda settings [6f087fec]
Improve secrets cmd (#3158) [115b2f3d]
Improve Wave resolution strategy [2eb700c6]
Improve Az Batch err handling and testing [85d31e8d]
Bump google-cloud-batch 0.2.2
Bump Spock 2.2

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.08.2-edge

Fix queueSize setting is not honoured by AWS Batch executor (again) #3117 [1733bb2e]
Add files() method to docs (#3123) [00bb8896]
Refactor wave packing [bc876986]
Improve logging [aa380d5f]
Update dockerfile [e6329282]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.08.1-edge

Add support for disabling config include [e0859a12]
Add experimental fusion support [1854f1f2]
Add support for plugin provided function extension (#3079) [16230c2b]
Add support for AWS Batch logs group (#3092) [4ef043ac]
Add share identifier to Aws Batch (#3089) [c0253aba]
Improve Tower cache manager [0091afc5]
Improve S3 copy via xfer manager [02d2beae]
Reports a warning when using NXF vars in the config [009ec256]
Make wake token cache duration config [5f955fc9]
Patch unable to start non-core plugin [a55f58ff]
Increase S3 upload chunk size to 100 MB [9c94a080]
Change Google Batch disk directive to override boot disk size (#3097) [7e1c0686]
Fix queueSize setting is not honoured by AWS Batch executor (#3093) [d07bb52b]
Fix Allow disabling scratch with Google Batch [e8e5c721]
Fix Emit relative path when relative parameter is set (#3072) [39797759]
Bump nf-wave@0.3.0 [e46d341d]
Bump nf-tower@1.5.1 [cdc2be53]
Bump nf-google@1.4.1 [c39935a5]
Bump nf-amazon@1.10.0 [ccdf62d0]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.08.0-edge

22.08.0-edge - 1 Aug 2022

Add warning to env config docs (#3083) [ca933c16]
Add -with-conda CLI option (#3073) [98b2ac80]
Add simple wave plugin cli commands [8888b866]
Add default wave plugin [7793a0ec]
Add boot disk, cpu platform to Google Batch (#3058) [17a8483d]
Add support for GPU accelerator to Google Batch (#3056) [f34ad7f6]
Add support for archive dir to tower plugin [c234681a]
Add support tower cache backup/restore [bc2f9d13]
Add disk directive to google batch (#3057) [ec6e290c]
Add retry when Azure submit fails with OperationTimedOut [6a3f9742]
Add warning when Google Batch quota is exceeded (#3066) [6b9c52ad]
Allow fully disabling history file [0a45f858]
Allow the support function overloading and default parameters (#3011) [042d3857]
Improve S3 file upload/download via Transfer manager [7e8d2a5a]
Prevent overriding container entrypoint [b3a4bf85]
Update FileTransfer pool settings [503aafce]
Remove deprecated commands [93228b4b]
Prevent nextflow config to break tower launch [e059a724]
Refactor Google Batch executor to use Java API (#3044) [31a6e85c]
Fix Unable to disable scratch attribute with AWS Batch [1770f73a]
Fix unit test setting explicit permissions for test files [1c821139]
Fix Default plugins are overriden by config plugins [46cf3bfa]
Fix S3 transfer download directory [b7bf9fe5]
Fix NPE while setting S3 ObjectMetada #3031 [d6163431]
Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b]
Fix AWS Batch job definition conflict (#3048) [e5084418]
Fix JAVATOOLOPTIONS breaking launch #1716 [0e7b416d]
Fix add ps shared objects to Dockerfile (#3033) [1c23b40a]
Parallelize build integration tests [807800a3]
Bump google-cloud-nio:0.124.8 [dfaa9d19]
Bump groovy 3.0.12 [5c900b91]
Bump Moment.js 2.29.4 [a9ced868]
Bump gson@2.9.0 [12f17176]
Bump nf-azure@0.13.4
Bump nf-google@1.4.0
Bump nf-tower@1.5.0
Bump nf-wave@0.2.1
Bump nf-amazon@1.9.0

Breaking changes

The container entrypoint is not overridden anymore with /bin/bash by Nextflow when using Local, Kubernetes and batch scheduler executors. This has been made for consistency with the AWS, Google and Azure Batch executors that do not set it either. Make sure the containers used in your pipeline use sh or bash as the default entry point. If you want to continue to use the old behaviour set the variable NXF_CONTAINER_ENTRYPOINT_OVERRIDE=true in the launch environment
The use of Conda environment defined in the process definition via the conda directive needs to be enabled in an explicit manner using either the CLI option -with-conda or using the config setting conda.enabled=true or setting environment variable NXF_CONDA_ENABLED=true. See https://github.com/nextflow-io/nextflow/pull/3073 for details.

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.04.5

Allow fully disabling history file [1a36c9bc]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.07.1-edge

Add support for Google Batch API v1 [4c116d58] [e85d87ee]
Add time directive support for K8s executor (#2948) [2b6f70a8]
Add docs aws.client.s3PathStyleAccess config (#3000) [20005500]
Allow to override lsf.conf settings with nextflow config #2862 [dae191a1]
Allow hybrid containers execution [0af1bcb3]
Improve error msg when script file cannot be read [52c2780e]
Improve error reporting for custom function [877c7931]
Improve error message for missing plugin extension [4a43db84]
Improve test #3019 [7c37e0be]
Rename kuberun -pod-image to -head-image [2576ba62]
Externalise sqldb plugin source code [17e80b4f]
Fix escape unstage outputs with double quotes #2912 #2904 #2790 [49ff02a6]
Fix Exception when settings AWS Batch containerOptions #3019 [89312ad8]
Fix Missing query param in http file (#2918) [43cc8511]
Fix Publish copy mode for S3 based path [085f6b2b]
Fix Fail fast uploads to S3 (#2969) [7fd1a6e1]
Fix null script name in launch info [7118849f]
Bump commons-code@1.15 [a06b4442]
Bump jgit@6.2.0 [3331826f]
Bump snakeyaml@1.30 [de62fd3f]
Bump gson@2.8.9 [3234ddd5]

- Groovy
Published by pditommaso over 3 years ago

io.nextflow:nextflow - Version 22.04.4

Fix Publish copy mode for s3 based path [bb510ce6]
Add strict mode config setting [b0567e62]
Update docker base image [b00c1418]

- Groovy
Published by pditommaso over 3 years ago

Recent Releases of io.nextflow:nextflow

io.nextflow:nextflow - Version 25.07.0-edge

io.nextflow:nextflow - Version 25.06.0-edge

io.nextflow:nextflow - Version 25.04.6

io.nextflow:nextflow - Version 25.04.5

io.nextflow:nextflow - Version 24.10.9

io.nextflow:nextflow - Version 24.04.6

io.nextflow:nextflow - Version 25.04.4

io.nextflow:nextflow - Version 24.04.5

io.nextflow:nextflow - Version 24.10.8

io.nextflow:nextflow - Version 25.04.3

io.nextflow:nextflow - Version 25.05.0-edge

io.nextflow:nextflow - Version 25.04.2

io.nextflow:nextflow - Version 25.04.1

io.nextflow:nextflow - Version 25.04.0

io.nextflow:nextflow - Version 24.10.6

io.nextflow:nextflow - Version 25.03.1-edge

io.nextflow:nextflow - Version 25.03.0-edge

io.nextflow:nextflow - Version 25.02.3-edge

io.nextflow:nextflow - Version 25.02.2-edge

io.nextflow:nextflow - Version 25.02.1-edge

io.nextflow:nextflow - Version 25.02.0-edge

io.nextflow:nextflow - Version 24.10.5

io.nextflow:nextflow - Version 25.01.0-edge

io.nextflow:nextflow - Version 24.10.4

io.nextflow:nextflow - Version 24.12.0-edge

io.nextflow:nextflow - Version 24.10.3

io.nextflow:nextflow - Version 24.11.0-edge

io.nextflow:nextflow - Version 24.10.2

io.nextflow:nextflow - Version 24.10.1

io.nextflow:nextflow - Version 24.10.0

io.nextflow:nextflow - Version 24.09.2-edge

io.nextflow:nextflow - Version 24.09.1-edge

io.nextflow:nextflow - Version 24.09.0-edge

io.nextflow:nextflow - Version 24.08.0-edge

io.nextflow:nextflow - Version 24.07.0-edge

io.nextflow:nextflow - Version 24.04.4

io.nextflow:nextflow - Version 23.10.4

io.nextflow:nextflow - Version 24.04.3

io.nextflow:nextflow - Version 24.06.0-edge

io.nextflow:nextflow - Version 24.05.0-edge

io.nextflow:nextflow - Version 23.10.3

io.nextflow:nextflow - Version 24.04.2

io.nextflow:nextflow - Version 23.10.2

io.nextflow:nextflow - Version 24.04.1

io.nextflow:nextflow - Version 24.04.0

io.nextflow:nextflow - Version 24.04.0-edge

io.nextflow:nextflow - Version 24.03.0-edge

io.nextflow:nextflow - Version 24.02.0-edge

io.nextflow:nextflow - Version 24.01.0-edge

io.nextflow:nextflow - Version 23.10.1

io.nextflow:nextflow - Version 23.04.5

io.nextflow:nextflow - Version 23.12.0-edge

io.nextflow:nextflow - Version 23.11.0-edge

io.nextflow:nextflow - Version 23.10.0

io.nextflow:nextflow - Version 23.09.3-edge

io.nextflow:nextflow - Version 23.09.2-edge

io.nextflow:nextflow - Version 23.04.4

io.nextflow:nextflow - Version 23.09.1-edge

io.nextflow:nextflow - Version 23.09.0-edge

io.nextflow:nextflow - Version 23.08.1-edge

io.nextflow:nextflow - Version 23.04.3

io.nextflow:nextflow - Version 23.08.0-edge

io.nextflow:nextflow - Version 23.07.0-edge

io.nextflow:nextflow - Version 23.06.0-edge

io.nextflow:nextflow - Version 23.04.2

io.nextflow:nextflow - Version 23.05.0-edge

io.nextflow:nextflow - Version 22.10.8

io.nextflow:nextflow - Version 23.04.1

io.nextflow:nextflow - Version 23.04.0

From previous edge releases

io.nextflow:nextflow - Version 23.03.0-edge

io.nextflow:nextflow - Version 23.02.1-edge

io.nextflow:nextflow - Version 23.02.0-edge

Breaking changes

io.nextflow:nextflow - Version 22.10.7

io.nextflow:nextflow - Version 22.10.6

io.nextflow:nextflow - Version 23.01.0-edge

io.nextflow:nextflow - Version 22.10.5

io.nextflow:nextflow - Version 22.12.0-edge