NEXTFLOW CHANGE-LOG =================== 26.04.0 - 28 Apr 2026 - Add -user-secret and -workspace-secret flags to nextflow launch (#7040) [53045104d] - Error messages: Fix ANSI colours (#7078) [d158b71f6] - Fix runtime type reflection in nf-lang (#7077) [916f029b7] - Rename `nextflow.preview.types` feature flag to `nextflow.enable.types` (#7067) [e6faaed00] - Support validation of collection params with record types (#7025) [297172c63] - Bump nf-tower@1.27.0 26.03.4-edge - 25 Apr 2026 - Abort execution when platform telemetry error (#6827) [b1ad3f720] - Add $schema ref to generated module spec (#7056) [c40d742f3] - Add Apple container engine support (#7073) [2f7a3c455] - Add hints process directive for executor-specific scheduling hints (#7034) [406358e03] - Add Seqera NIO filesystem for datasets and refactor TowerClient/TowerObserver (#6946) [433b10a1f] - Add workspaceId/computeEnvId to nf-seqera auto labels (#7059) [5e8276c00] - Allow `-with-docker` to be used without a default container image (#7054) [41759d36e] - Allow module run to run modules with local path (#7057) [e2c77c6b7] - Default NXF_FUSION_TRACE to false (#7071) [5b4c8f0c1] - Fix IllegalArgumentException when process.resourceLabels is a closure (#7068) [944977e3f] - Fix resolution of params in resolved config text (#7072) [cb7133def] - Propagate task.containerPlatform through Fusion container command (#7074) [b58a590bd] - Remove arch config option from Seqera MachineRequirement (#7063) [da06e9a9d] - Replace current cloud info URL call with cloudInfo client (#7065) [629184251] - Restructure modules docs as a section and add registry steps (#7030) [29370f4bc] - Update workflow outputs tutorial (#7060) [68d144b9c] - Use toUriString for paths in work-dir and FilesEx error messages (#7075) [b535377cc] - Bump nf-amazon@3.9.0 - Bump nf-google@1.27.2 - Bump nf-seqera@0.19.0 - Bump nf-tower@1.26.0 - Bump nf-wave@1.20.0 26.03.3-edge - 20 Apr 2026 - Add -files-from option to lint command to avoid ARG_MAX limit (#6858) [5a3cd830c] - Add 26.04 migration docs (#7000) [89ec31bbf] - Add option to disable printing workflow outputs (#7018) [791bb449c] - Allow cloning from local Git repositories when `--offline` (#7035) [0fa6b5dbd] - Allow running pipeline from URL and main script path (#6602) [83196d4be] - Apply socket timeout to S3 CRT connections (#7024) [6f4a21764] - Filter autoLabels to selected workflow-metadata fields (#7049) [ddc974fe6] - Fix S3FileSystemProvider.newInputStream() draining full object on close (#7046) [cf3867604] - Fix formatting issues with complex expressions (#7027) [ce661d1d8] - Fix generated process name in `module create` command (#7008) [f3d8de796] - Fix inconsistent indentation in nf-amazon (#7047) [df6855d7d] - Fix module info formatting separator (#7033) [44dff8fcc] - Fix nextflowVersion for nf-tower and nf-seqera plugins [cbc0a2d8e] - Fix resolution of `-with-tower` with `TOWER_API_ENDPOINT` (#7045) [ce962e882] - Fix saveCacheFiles early return skipping log file uploads (#7015) [6fb704838] - Fusion GPU metrics collection (#7022) [6289635b8] - Honour process.resourceLabels in nf-seqera executor (#7048) [979f684ff] - Manage AWS SDK exceptions to convert to the appropriate IO exceptions (#6707) [39c755663] - Rename `module info` subcommand to `module view` (#7052) [7fa1109aa] - Resolve structured process input types (#7014) [583935d88] - Simplify demo module README template (#7051) [6d04c9ebc] - Suppress lint progress logging with `-q` flag (#6880) [61793bb6e] - Update missing pf4j updates (#7016) [f38f0067d] - Use Fusion trace metrics to replace bash command-trace wrapper (#7041) [de4376649] - Bump org.bouncycastle:bcpkix-jdk18on from 1.79 to 1.84 (#7042) [59d847d52] - Bump nf-amazon@3.8.3 - Bump nf-k8s@1.5.2 - Bump nf-seqera@0.18.0 - Bump nf-tower@1.25.0 - Bump nf-wave@1.19.1 26.03.2-edge - 7 Apr 2026 - Add `module create` subcommand (#6992) [d6639a5e0] - Add `module spec` command (#6859) [049e2a40e] - Add `module validate` subcommand (#6993) [b2fa370bd] - Add compute env ID and provider support to Seqera executor (#6906) [4c2eb9390] - Add resourceAllocation field to trace record (#6973) [a2742939c] - Fix NPE in GitLab/Gitea getGitCredentials when password is null but token is set (#7007) [0a202d090] - Fix missing version for junit-platform-launcher dependency (#7011) [9e721f205] - Replace Auth0 with Platform OIDC PKCE for auth login (#6953) [f39afea97] - Typed workflows (#6881) [a12bde35e] - Use inline metadata from trace create response (#6976) [58736b7cc] - Use npr-client API instead of custom ModuleRegistryClient (#7012) [8e06945a4] - Bump nf-amazon@3.8.2 - Bump nf-seqera@0.17.0 - Bump nf-tower@1.24.0 26.03.1-edge - 26 Mar 2026 - Add `-project-dir` option to `lint` command (#6728) [1679b9f3a] - Add platform-related metadata to WorkflowRun lineage record (#6545) [fc4d7dd6e] - Add request timeout to tower client (#6950) [ff773ba72] - Add support for Java 26 (#6969) [9c2b9ff0d] - Fix AWS Batch machine type trace for new instance families (#6952) [06e78ba0b] - Fix AgentLogObserver printing [SUCCESS] on failed runs (#6962) [342d27c64] - Fix LogsCheckpoint thread interrupt race condition (#6939) [9d65b9eea] - Fix download of empty files in old minio based S3 transfers (#6944) [ccded1845] - Fix incorrect evaluation of `secret` process directive (#6934) [235329312] - Fix jackson-databind dependency in nf-amazon (#6941) [321c57f88] - Fix netty and jackson vulnerabilities (#6955) [8dafdd95d] - Fix params block in included module (#6940) [bbafcc714] - Fix security vulnerabilities (#6938) [8b1ab40c4] - Fix typo in TowerRetryPolicy: maxAttemps -> maxAttempts (#6949) [97eb0d1b3] - Fix: cast module run CLI params to declared meta.yml input types (#6968) [0c525672f] - Fix: handle empty publishedValues in PublishOp.onComplete for optional outputs (#6979) [a99fb5dc2] - Harden ProcessEntryHandler types and add test for dot-notation conflicts (#6966) [80041612a] - Improve module command: enable logging for module run, fix info URL and search output (#6961) [30c5dca95] - Print workflow outputs on run completion (#6875) [b8752e41f] - Skip launch metadata fetch for CLI-submitted runs (#6975) [3c9875720] - Use -d flag for bkill in LSF Executor (#6784) [19409304e] - Use destructuring syntax for process record/tuple inputs (#6912) [028e4cc1d] 26.03.0-edge - 18 Mar 2026 - Add module system (#6650) [a0ac594ec] - Add multi-arch support to arch process directive (#6897) [c7ca36902] - Add NVMe disk allocation and diskMountPath support (#6879) [6644d3c90] - Add provider option to Seqera executor config (#6908) [c70376d0a] - Add support for GCP Ops Agent (#6608) [247a53bc0] - Add support for latest-generation Google Cloud machine families (#6841) [27785b171] - Add logStreamId to Tower task record (#6877) [df49fdb68] - Default Fusion to v2.6 for Seqera executor (#6933) [8a7e53957] - Don't include container in task trace when containers are not enabled (#6824) [31a2dfa57] - Fix formatting bug with map key expression (#6893) [e0816159d] - Fix Google Batch exit code when spot claim is successfully retried (#6926) [76927c27e] - Fix K8s token refresh by caching K8sClient at executor level (#6925) [3d2e4c4c4] - Fix HttpPluginRepository empty plugin list check (#6650) [ea1f4ea0c] - Fix path traversal, resource leak, and race condition in module system (#6929) [4d36d22c4] - Fix remote modules when base dir is not the current working dir (#6932) [ca1e625ca] - Fix stageAs method signature in typed process (#6915) [021c77c89] - Fix TraceFileObserver NPE when trace file already exists (#6891) [903caead4] - Fix type detection of CLI params in v2 config parser (#6765) [6711a57f9] - Increase tasks.cloudZone width from 15 to 25 (#6907) [a217a459f] - Propagate errors from workflow outputs (#6876) [31f513559] - Record types (#6679) [d54ff29af] 26.02.0-edge - 28 Feb 2026 - Add agent output mode (NXF_AGENT_MODE) [eae9f7d09] - Allow boolean params to implicitly default to false (#6764) [775a0fb87] - Ensure main script is first in the WorkflowRun lineage record (#6845) [ef01581d5] - Fix AgentLogObserver println clash with Groovy GDK method [c6314d7b5] - Fix AnsiLogObserver sticky messages duplicated when lines wrap (#6852) [4a06f705a] - Fix missing space before revision in launch info (#6834) [f30d782f5] - Fix ResourcesAggregator deadlock with virtual thread executor (#6840) [7ac4f3ea9] - Fix S3 delete throwing DirectoryNotEmptyException due to eventual consistency (#6833) [f3ac49754] - Fix S3 lookup unbounded pagination with double call (#6851) [a2e67eb99] - Fix vertical alignment in timeline report (#6794) [bbe0a27c9] - Handle Azure Batch ActiveJobAndScheduleQuotaReached with retry (#6874) [6e66aaa58] - Report actual GCP zone in Google Batch trace records (#6855) [465791294] - Sched core implementation alpha1 (#6242) [870c858af] - Treat LSF job status UNKWN as HOLD (#5756) [63aae8933] - Update default Azure Batch VM image to Ubuntu 24.04 (#6844) [b621fc7cb] - Use explicit memory units for LSF executor (#5217) [a369d6f33] 26.01.1-edge - 11 Feb 2026 - Add OSC 8 hyperlinks to task hashes in progress output (#6799) [8d266c76b] - Fix JGit resources not being closed in CLI commands (#6795) [908e4c70d] - Fix listDirectory() to follow symbolic links (#6821) [1ee59b3d0] - Improve documentation of workflow outputs (#6822) [3f6c6b351] - Bump ch.qos.logback@1.5.26 — fix false version mismatch warning in shadow JAR [0b97f4a84] - Bump ch.qos.logback@1.5.25 (CVE-2026-1225) [97dec3af6] - Bump com.gradleup.shadow@9.3.1 (CVE-2025-68161) [d31e6edc7] 26.01.0-edge - 8 Feb 2026 - Add accelerator request to trace record (#6703) [00f35b3a9] - Add aws.batch.forceGlacierTransfer config option (#6700) [e3bf3153b] - Add CloudCacheConfig to register cloudcache config options (#6774) [ea8fea470] - Add markdown output mode to lint command (#6715) [dad7c5d35] - Add missing provider credentials when updating the bare repo in multi-revision assets (#6698) [e517f4c23] - Add time-based caching for K8sConfig.getClient() (#6742) [73e507558] - Add warning stats to lint summary output (#6714) [1bfc7bfa5] - Add workflow manifest metadata to execution report (#6689) [49425d8c0] - Allow collection-type params to be loaded from files (#6675) [80671456a] - Detect conda explicit files by content instead of extension (#6713) [f141116d8] - Enable v2 syntax parser by default (#6643) [295f17307] - Exclude nf-test.config from lint by default (#6716) [c256c5ff1] - Fix AWS Batch spot instance detection (#6722) [29356f60e] - Fix caching of task ext properties with the strict parser (#6696) [b5278c75a] - Fix compiler error in v2 parser with enums (#6781) [5d36e89d8] - Fix different task hash with v2 parser (#6789) [66b743836] - Fix error when checking whether an S3 bucket exists (#6706) [c1bd552ab] - Fix false error in v2 parser when including config file from http url (#6753) [1732562dc] - Fix false error with multi-line tuple assignment in v2 parser (#6786) [a73f0f9be] - Fix false error with optional param (#6811) [4657cc05f] - Fix fetching new remote branch in multi-revision mode (#6733) [24b858dee] - Fix isCompleted check in getNumSpotInterruptions (#6805) [76558481a] - Fix issue with topic file emissions in typed processes (#6688) [dcf0dec32] - Fix K8s job fallback to not return incorrect zero exit code (#6746) [573067999] - Fix lint error formatting for errors at end of line (#6717) [51e0e0307] - Fix LogsCheckpoint thread blocking shutdown for up to 90 seconds (#6787) [54a595805] - Fix: `nextflow inspect` not applying container settings from config (#6736) [c13f44472] - Fix params inclusion across modules in v2 parser (#6766) [3223ffee4] - Fix resolution of nested Groovy class in v2 parser (#6744) [10dff2540] - Fix spurious WARN when workflow fails before onFlowBegin (#6816) [584003712] - Fix type inference in v2 ConfigDsl (#6800) [ed4716418] - Improve config syntax errors (#6721) [c07cc2e6c] - Improve error message for invalid config statements (#6804) [439695979] - Improve error messages for workflow outputs (#6785) [887443e77] - Move task hashing logic to TaskHasher class (#6572) [29f775f7d] - Refactor GoogleBatchTaskHandler.newSubmitRequest for reduced complexity (#6687) [38c39108c] - Support multiple config option types in config spec (#6720) [ebb089057] - Use `conda-forge` and `bioconda` channels by default (#5423) [48f9e3e85] - Bump Groovy to 4.0.30 (#6747) [ee0032534] - Bump Spock 2.4 (#6681) [15b2aa43f] 25.12.0-edge - 19 Dec 2025 - Add `listDirectory()` to Path type and deprecate `listFiles()` (#6581) [56f0f007] - Add default maxSpotAttempts for fusion snapshots in Google Batch (#6652) [458ef97a] - Add onlyJobState option for SLURM executor (#6659) [3c3e9f52] - Add README files for all plugins (#6660) [bee8cff6] - Add runtimeClassName to the pod options (#6633) [ddcef4f4] - Add spot interruption tracking to trace records (#6606) [eecd8167] - Add URL encoding when revision name is used as HTTP query parameter (#6598) [7894e097] - Add warnings to JSON output in lint command (#6625) [bb066969] - Add wave.build.template config option (#6639) [d08a8952] - Check Nextflow version before loading plugins (#6591) [03da64eb] - Fix GitHub repository provider when providing token with auth property (#6662) [d01cbde1] - Fix optional param in params block (#6657) [bd8de5ca] - Fix String.format error when plugin URL contains percent chars (#6651) [59c4f4e1] - Fix validation of numeric types in params block (#6656) [664a26eb] - Fix WaveClient sending Bearer token to public S3 URLs (#6672) [ffaef0b6] - Fix: tolerate spaces in `$NXF_TASK_WORKDIR` (#6421) [7b386025] - Implementation of Git multiple revisions (#6620) [ce9d7b59] - Refactor Google Batch getExitCode to imperative style (#6649) [addd59e9] - Set local task exit status when time limit is exceeded (#6592) [d3f8e135] - Add Nextflow Development Constitution (#6578) [7047e6be] - docs: Add extra warnings as 25.10 is added to platform (#6655) [ae0e844f] - docs: Add longer NXF_SYNTAX_PARSER descriptions (#6637) [23c277ad] - docs: Document best practices for script and config params (#6631) [3421734d] - docs: Fix typos (#6641) [20f4631e] - docs: Improve preview feature warnings in documentation (#6663) [cdc7a586] - docs: Update note about AWS CLI (#6626) [bb7aecf8] - docs: Update NXF_SYNTAX_PARSER callouts (#6640) [1b284a19] 25.11.0-edge - 28 Nov 2025 - Add Google Batch LogsPolicy PATH option for logging to GCS (#6431) [5b61afe0] - Add default value to Apptainer pull timeout config paramter (#6534) [f4548bd1] - Add test case for printing config with nested includes (#2498) [0876d557] - Allow pre-existing write-protected plugins directory to be used (#6594) [33943b5b] - Change log level from warn1 to debug1 for K8s Job Pod Warnings (#6523) [74d1b786] - Fix Do not delete K8s jobs when ttlSecondsAfterFinished is set (#6597) [51042dbe] - Fix Fusion license JWT token refresh by reusing TowerClient [498125d2] - Fix Invalid type error detection [9e3aeed1] - Fix K8sTaskHandlerTest method name typos [bcf81d90] - Fix asset detection when item is not a sibling of the executed script (#6605) [1ca327c8] - Fix csv splitter when skipping empty lines (#6586) [253666de] - Fix documentation of `unique` operator (#6541) [6b8aedf5] - Fix error with dynamic directives with named arguments (#6550) [064f57f6] - Fix false config validation warnings for process selectors (#6542) [4db05a00] - Fix false error with task ext blocks in strict syntax (#6569) [fe8065ae] - Fix incorrect AWS region when specifying a S3 regional endpoint (#6530) [0989d31c] - Fix invalid cache write when cacheable split operation fails (#6588) [9930e35d] - Fix issue with optional workflow output (#6519) [75e47147] - Fix issues with rsync stage-out mode (#6587) [bcac9010] - Fix security vulnerabilities in org.json dependency [c7161c2a] - Fix unordered completed parts in AWS multipart upload (#6560) [10209528] - Fix TowerJsonGenerator thread-safety issue (#6619) [579cd6e4] - Fix Plugins.init() in run command to original location (#6568) [ba6be77b] - Fix security vulnerabilities for wiremock (#6607) [0f86933a] - Fix replace complete plotly bundle with smaller more specific one (#6527) [fdab3426] - Fix stageFileEnabled flag to control `.command.stage` file creation (#6618) [2d117cb5] - Improve error message for invalid accelerator resource (#6585) [7c40ee5b] - Improve error message for invalid contribution type in manifest contributors (#6593) [d440040e] - Issue templates: add external links via config (#6563) [3f608789] - Move task error formatting logic into separate class (#6551) [7b664ced] - Optimize exit code handling by relying on scheduler status for successful executions (#6484) [454a2ae8] - Remove unnecessary runtime checks with strict syntax (#6539) [9e296b85] - Remove unused BatchHelper class (#6547) [1c543c05] - Remove wiremock-groovy dependency and update tests using this dependecy (#6611) [6f4cf1ac] - Update bundled Docker runtime to 19.03.15 (#6565) [6c081376] - Update migration timeline for plugin registry (#6543) [ecfb62df] - Update trace table columns in Reports page (#6483) [064ef346] - Upgrade from Apache Commons Lang 2.6 to Commons Lang3 3.18.0 (#6511) [9b2ccb8a] - docs: Add admonition to clarify plugin provider and org (#6536) [e9ab1bb7] - docs: Add admonition to inputs and index words (#6461) [4eee1b69] - docs: Improve task previousTrace documentation (#6538) [53c28b85] - docs: Mark Fusion.tags as supported only for S3 (#6601) [cc0d177f] - docs: Update feature flags page (#6504) [4dc9945d] - docs: Update task directives (#6506) [ce680c53] - Bump Fusion to version 2.5 (#6557) [ec228f64] - Bump Gradle 9.2.0 [26575244] - Bump groovy 4.0.29 (#6510) [a30dbbbc] - Bump logback to version 1.5.20 [462eec58] - Bump org.bouncycastle:bcpkix-jdk18on from 1.78.1 to 1.79 (#6537) [ede076b0] - Bump nf-amazon@3.5.0 - Bump nf-azure@1.21.0 - Bump nf-google@1.24.0 - Bump nf-k8s@1.3.0 - Bump nf-tower@1.18.0 - Bump nf-wave@1.17.0 25.10.1 - 28 Nov 2025 - Add default value to Apptainer pull timeout config parameter (#6534) [a124a5ca0] - Fix asset detection when item is not a sibling of the executed script (#6605) [2390d4a8d] - Fix error with dynamic directives with named arguments (#6550) [c58750bf4] - Fix false config validation warnings for process selectors (#6542) [7bfae6db9] - Fix Fusion license JWT token refresh by reusing TowerClient [561ed6c32] - Fix incorrect AWS region when specifying a S3 regional endpoint (#6530) [770bdd3eb] - Fix issue with optional workflow output (#6519) [5444a7879] - Fix unordered completed parts in AWS multipart upload (#6560) [89eb70130] - Revert Plugins.init() in run command to original location (#6568) [1533f7d9e] - Bump logback 1.5.20 - Bump nf-amazon@3.4.2 - Bump nf-tower@1.17.2 25.10.0 - 22 Oct 2025 - Add publish-artifacts step to release process [75d8ebf9b] - Add type checking utils (#6482) [3e9a2c091] - Fix no secrets in AWS Batch jobs (#6499) [c76c32582] - Prioritize Google Batch API exit codes with fallback to .exitcode file (#6498) [6ac2efcba] - Show workspace roles in 'auth status', tweak error message on 403 (#6497) [0633d90d1] - Simplify S3 configuration options (#6496) [0b7f18049] - Track remote input files in lineage (#6490) [b0660caf3] - Bump nf-amazon@3.4.1 [0d5ced94a] - Bump nf-google@1.23.3 [e6c765217] - Bump nf-tower@1.17.1 [2069c9729] 25.09.2-edge - 21 Oct 2025 - Add .command.log redirection in K8s container command (#6455) [e6eed7949] - Add nextflow auth command for Seqera Platform authentication (#6463) [bedf02a99] - Add nextflow launch command (#6491) [7c8fa3d9d] - Bring workflow outputs out of preview (#6487) [c41677b40] - Fix e2e test infrastructure and add config.schema compatibility aliases (#6495) [d3cee2bab] - Fix false error for `executor.jobName` config option (#6375) [81ae62bf2] - Fix false error with storeDir and val outputs (#6408) [1aa8c4468] - Fix type casting in PluginSpec for ConfigScope (#6469) [b00644c9b] - Improve plugin create confirmation prompt (#6473) [215925c47] - Improve release script validation [3e3a938d6] - Limit S3 client connections when using virtual threads (#6369) [295c60b5c] - Migrate SraExplorer to use HxClient for HTTP operations (#6467) [84e3e7873] - Rename `config.schema` package to `config.spec` (#6485) [ef0d2d601] - Typed processes (#6368) [30f3c3c2a] - Update buildInfo on releaseInfo [46a8a2b53] 25.09.1-edge - 9 Oct 2025 - Improve build metadata generation and validation [60225374f] - Fix Missing static type definition [67a532040] - Add rnaseq-nf tutorial (#6440) [a830125c4] 25.09.0-edge - 8 Oct 2025 - Add listDirectory traversal API to RepositoryProvider abstraction (#6430) [1449fdfec] - Add step to claim plugin in Gradle plugin migration docs (#6450) [3b709004b] - Add support for comma-separated file paths in ProcessEntryHandler (#6434) [fe627644d] - Add support for Java 25 (#6419) [dc8d474d6] - Add unit test for invalid workflow entry name error handling (#6409) [249eb1aaa] - Fix cache command to check session cloudCachePath [a88e2cdf2] - Fix cache command to use SysEnv for cloudcache path check (#6432) [771b8b60e] - Fix cookie policy for Seqera Platform JWT token refresh (#6411) [c3959cfc3] - Fix CVE-2025-55163 in nf-google plugin [7d7061797] - Fix default fields in trace config (#6403) [3eddfad68] - Fix pod log warning with Fusion enabled (#6449) [8c78b3126] - Fix SIGTERM forwarding in AWS Batch jobs (#6414) [abbef79b7] - Fix "Strings must not be null" error message (#6404) [24314b112] - Fix unstage controls in command.run when using storeDir (#6364) [a5756da3e] - Generate plugin spec (#6361) [ed6bb6037] - Get exit code from pod to manage OOM in k8s (#6442) [f258a758e] - Limit S3 concurrent downloads to fix Java Heap OOM (#6402) [fd71d0e8c] - Update Gradle build system to version 9.1.0 (#6418) [e2bb2f083] - Bump Google Cloud libraries to latest versions (#6438) [59a63f1ae] - Bump nextflow-gradle-plugin version 1.0.0-beta.10 [812ed7f9f] - Bump nf-amazon@3.3.0 [3561c26e9] - Bump nf-azure@1.20.1 [fae3c2d58] - Bump nf-codecommit@0.5.0 [91514a6f6] - Bump nf-google@1.23.1 [153745a16] - Bump nf-k8s@1.2.1 [c4f4eca9b] - Bump nf-tower@1.16.0 [ef9110407] - Bump nf-wave@1.16.0 [be01d3f96] 25.08.0-edge - 14 Sep 2025 - Add Claude Code GitHub Action integration (#6389) [1073a1da] - Add Value type for dataflow values (value channels) (#6372) [8de2339e] - Add descriptions to plugin MANIFEST.MF files (#6348) [d558ee33] - Add null checks in TowerClient onFlowComplete method (#6384) [de968f03] - Add plugins redirects (#6385) [3fb8a586] - Add test for prefetchMetadata call in pullPlugins method (#6396) [a5c19b89] - Add Type annotations (#6278) [0008707e] - Fix CLI param override in strict config parser (#6377) [e146b412] - Fix GString equality checks with String (#6330) [01e18883] - Fix GitHub Actions commit message parsing to use only first line [5bc91622] - Fix NPE when contributors omit contribution field in manifest (#6383) [dd2154ca] - Fix Platorm refresh token handling [ba78ef74] - Fix duplicate page and redirects in docs (#6386) [efba138f] - Fix false warning for map config options (#6359) [872d124c] - Fix groupTuple operator to handle GString vs String keys consistently (#6400) [206cc015] - Fix incorrect spelling in docs (#6336) [00150f2a] - Fix null reference error in workflow output (#6374) [d1f43c5d] - Fix typo in task config eval (#6392) [e60978f4] - Implement Process Execution with Command-Line Parameter Mapping (#6381) [experimental] [6d5a0bd0] - Improve secret loading documentation and rename ConfigNullProvider to EmptySecretProvider [9e4c975a] - Minor TowerClient improment (#6387) [d7436674] - New executor for Fujitsu Technical Computing Suite (TCS) (#5928) [dd87b2fb] - Preserve method parameter names in nf-lang JAR (#6355) [83160d66] - Refactor Wave and Tower client to use lib-httpx library (#6354) [148a8a13] - Replace custom JWT refresh logic with standardized HxClient (#6398) [c68c1e9e] - Replace custom retry strategy with HxClient in RepositoryProvider (#6351) [af8ba8c8] - Simplify plugin download implementation (#6349) [a3db0f88] - Support standard environment variables for ANSI terminal output (#6362) [ede13441] - Update core plugins to use Nextflow Gradle plugin (#6379) [a7e4ea86] - Warn when file() matches a collection of files (#5507) [726bf484] - Workflow params (#5929) [876d8052] - Bump netty deps to version 4.1.124.Final [9e8d5969] 25.07.0-edge - 15 Aug 2025 - 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 NXF_DATE_FORMAT (#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] 25.06.0-edge - 6 Jul 2025 - 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] 25.04.4 - 16 Jun 2024 - 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] 24.10.8 - 6 Jun 2025 - Add Fusion license validation [02b4dd74] - Bump nf-wave@1.7.5-patch1 [cf6af9c5] - Bump nf-tower@1.9.3-patch1 [bdef2177] 24.04.5 - 6 Jun 2025 - Add Fusion license validation [cb7210b9] - Bump nf-wave@1.4.2-patch2 [69b63342] - Bump nf-tower@1.9.1-patch1 [8bfdc673] 25.05.0-edge - 2 Jun 2025 - Add Failsafe retry mechanism in K8s (#6083) [9e675c6a] - Add Platform info to Fusion license (#6142) [75f1bc52] - Add support for Azure Managed identities on Azure worker nodes with Fusion (#6118) [37981a5f] - Add support for container build compression (#5964) [daeefa0c] - Deprecated condaFile attribute [9e52b2ad] - Fix bug in generated Groovy code (#6082) [f0620656] - Fix default imports in included configs (#6096) [8f790615] - Fix variable checking in v2 config parser (#6097) [c3e9367b] - Force overwritting to trace file (#6105) [b9dace93] - Improve documentation of splitCsv operator (#6131) [f09ae8d7] - Make RepositoryProvider readBytes public (#6138) [9221b112] - Remove Az Fusion environment variable (#6143) [6c595eac] - Remove deprecated spack options [4e5d32a3] - Remove task attempt from hash list and add note (#6123) [9b48df4c] - Return streams in Lineage search and subkeys methods (#6067) [e4af2308] - Sort linter errors/warnings by source location (#6098) [7c52fafb] - Sunset the Google LS executor (#6070) [06e0d426] - Bump Groovy to version 4.0.27 (#6125) [258e1790] - Bump jgit:7.1.1.202505221757-r [16b88aca] - Bump nf-wave@1.13.0 [ab1d2dfe] - Bump nf-tower@1.12.0 [d4d97dfc] - Bump nf-k8s@1.1.0 [14eb7892] - Bump nf-google@1.22.0 [0f6498f1] - Bump nf-azure@1.17.0 [0b491840] 25.04.3 - 2 Jun 2025 - Add Platform info to Fusion license (#6142) [375db65a] - Force overwritting to trace file (#6105) [59e9d88d] - Bump nf-tower@1.11.3 [f7509bce] 25.04.2 - 13 May 2025 - Add check subcommand in lineage (#6074) [5ba67bca] - Fix issues with `lint` console output (#6064) [7405f513] - Remove obsolete conda create --mkdir option (#6010) [9fc44f76] 25.04.1 - 12 May 2025 - 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] 25.04.0 - 8 May 2025 - 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] 24.10.6 - 24 Apr 2025 - Add support for Fusion Snapshots (#5954) [76a997a3] - Bump nf-wave@1.7.5 [3ddf16fb] - Bump nf-amazon@2.9.3 [ccf672fb] 25.03.1-edge - 24 Apr 2025 - Fix lineage packaging (#6001) [c3bb7a51] 25.03.0-edge - 23 Apr 2025 - 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] 25.02.3-edge - 8 Apr 2025 - Fix container meta deduplication [f4600d2e] - Bump nf-tower@1.11.2 [220e429a] 25.02.2-edge - 5 Apr 2025 - 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] 25.02.1-edge - 19 Mar 2025 - 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] 25.02.0-edge - 17 Mar 2025 - 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] 24.10.5 - 4 Mar 2025 - 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] 25.01.0-edge - 12 Feb 2025 - 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] 24.10.4 - 20 Jan 2025 - 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] 24.12.0-edge - 20 Jan 2025 - 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] 24.11.0-edge - 3 Dec 2024 - 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] 24.10.2 - 27 Nov 2024 - 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] 24.10.1 - 18 Nov 2024 - 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] 24.10.0 - 27 Oct 2024 - Add `manifest.contributors` config option (#5322) [cf0f9690] - Add wave mirror and scan config [92e69776] - Add wave mirror vs module bundles conflicst 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] 24.09.2-edge - 14 Oct 2024 - 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] 24.09.1-edge - 13 Oct 2024 - 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] 24.09.0-edge - 2 Oct 2024 - 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] 24.08.0-edge - 4 Sep 2024 - 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] 24.07.0-edge - 8 Aug 2024 - 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) [82c97f8c] - Remove capsule launcher dependencies (#3395) [f15e4246] - 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] 24.04.4 - 1 Aug 2024 - 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] 23.10.4 - 31 Jul 2024 - 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] 24.04.3 - 9 Jul 2024 - Add ability to override failOnError setting default via env variable (#5117) [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] 24.06.0-edge - 8 Jul 2024 - 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] 24.05.0-edge - 17 Jun 2024 - 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) [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] 23.10.3 - 11 Jun 2024 - 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] 24.04.2 - 29 May 2024 - Fix handling of tags with slash on Bitbucket (#5031) [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) [42496dbc] - Enable the use of Java 22 (#4970) [cbf24f9b] 23.10.2 - 28 May 2024 - 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] 24.04.1 - 20 May 2024 - 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] 24.04.0 - 20 May 2024 - 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 NXF_CACHE_DIR 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 AZURE_STORAGE_SAS_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] 23.10.1 - 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 built-in function in onComplete handler (#4458) [4be10cd3] - Fix Harden regular expression to used to strip secrets in logs (#4563) [0102d4d6] - Fix custom notification template [40980bcb] - Fix container environment with special chars (#4594) [f4e00601] - Fix AZURE_STORAGE_SAS_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] 23.04.5 - 12 Jan 2023 - Fix container environment with special chars (#4594) [663b2936] 23.12.0-edge - 20 Dec 2023 - Add AWS_SESSION_TOKEN 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 FUSION_AWS_REGION (#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 NXF_HOME 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 NXF_TASK_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] 23.10.0 - 15 Oct 2023 - 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] 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 conflict [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 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] 23.04.4 - 25 Sep 2023 - 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] 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 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] 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] 23.04.3 - 11 Aug 2023 - Increase Wave client max attempts [8c67610a] - Fix log typo [03e19ea2] - Add 429 http status code to Wave retriable errors [a8b8c6c5] - Improve handling Wave server errors [621c9665] - Bump nf-wave@0.8.4 [d7fa3f26] - Bump corretto 17.0.8 [7a73a78f] 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] 23.04.2 - 8 Jun 2023 - 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] 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] 23.04.1 - 15 Apr 2023 - 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] 22.10.8 - 15 Apr 2023 - Security fixes [fc2627bb] - Add support for testing custom plugin uri [718d4562] - Improve plugin updater err handling [84042082] - Improve plugin test detection [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] 23.04.0 - 1 Apr 2023 - 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] 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 (#3640) [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] 22.10.7 - 18 Feb 2023 - 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] 22.10.6 - 24 Jan 2023 - 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] 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] 22.10.5 - 14 Jan 2023 - Fix FilePorter concurrency issue (#3511) [0f757156] - Fix watchPath hang shutdown execution [e03d9ca6] - Add `schedulingPriority` option to AWS Batch (use with `shareIdentifier`) (#3505) [543ee7b1] 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] 22.10.4 - 9 Dec 2022 - Fix math overflow when copying large AWS S3 files [07f7cb72] - Bump nf-amazon@1.11.2 [d96ca4c3] 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] 22.10.3 - 21 Nov 2022 - Prevent infinite loop while fetching git tags/branches [73a59d33] - Bump nf-amazon@1.11.1 [f9b54ce3] - Improve S3 thread pool config [01541b0a] 22.10.2 - 13 Nov 2022 - 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] 22.10.1 - 27 Oct 2022 - Fix mount pwd in the container when work dir is a symlink [ca397181] [b5b7d3cd] - Fix secrets command name in the CLI (#3320) [321486df] - Fix ver num rendering #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 (#3299) [15ffffc1] - Update docs repeated words from documentation (#3311) [d59ea186] - Update docs to clarify the difference between collect and toList (#3276) [7ee2b008] - Update docs [516a7441] - Update docs adding Fusion [11eac707] 22.10.0 - 13 Oct 2022 - Fix timestamp encoding [47a3a3c4] - Minor type change in Bridge executor [1f446ee1] - Bump nf-wave@0.5.2 [326803ff] 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) [f85d59a6] - Add support for refresh token to Wave [ed9f25f1] - Add pretty option to dump operator [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 [50086028] - Fix failing test [e6790003] - Fix K8s cluster token when using serviceAccount [c3364d0f] - Fix hanging test [44c04874] - Improve docs (#3212) [5d80388c] - Bump fusion snapshot [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 custom 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 22.09.0-edge - [SKIPPED] 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 overridden by config plugins [46cf3bfa] - Fix S3 transfer download directory [b7bf9fe5] - Fix NPE while setting S3 ObjectMetadata #3031 [d6163431] - Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b] - Fix AWS Batch job definition conflict (#3048) [e5084418] - Fix JAVA_TOOL_OPTIONS 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 22.04.5 - 15 Jul 2022 - Allow fully disabling history file [1a36c9bc] 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] 22.04.4 - 19 Jun 2022 - Fix Publish copy mode for s3 based path [bb510ce6] - Add strict mode config setting [b0567e62] - Update docker base image [b00c1418] 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 resolution 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 privilege 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 encryption using a custom KMS key [c1e45aa9] - Add support for Micromamba [383e023f] - Add jaxb-api dependency to nf-amazon [c1a09f87] - Add strict mode config setting [696e70b5] - Add -head-prescript option to kuberun (#2830) [9e387055] - Fix missing err message on submit failure [233e67f0] (#2899) - 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] (#2879) - 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] (#2871) - 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] 22.04.3 - 18 May 2022 - Fix dsl1 detection (#2879) [1a7ea0d1] - Document params-file and improve self-update (#2673) [1e008f47] - Add support for AWS S3 anonymous credentials (#2810) [ae7ba35a] - Add tolerations K8s pod option (#2763) [7f7cdadc] - Add support for batched queries to nf-sqldb plugin [3a9dad8b] - Add `emitColumns` option fromQuery operator [6a6a6eac] - Add mermaid DAG renderer [653f1e57] - Fix missing SSE flag on AWS Batch job submit (#2809) [4b3e946d] - Fix Task execution is not evicted on unexpected execution error (#2787) [05ea0c86] - Document params-file and improve self-update (#2673) [1e008f47] - Improve deprecation message (#2788) [720a84d7] - General docs improvements (#2800) [88acd26b] - Decrease Aws upload chunk size to 20 MB [086138fb] - Improve error reporting (#2658) [e6ef017d] - Improve err reporting for Azure Batch [798bae1f] - Rename echo directive to debug (#2776) [8f906aa5] - Remove embedded Read The Docs theme [728d545f] - Use a remote config in kuberun (#2781) [5485b699] - Start Github Actions also for edited PRs (#2796) [78f5c10f] - Deprecate isDsl2Final method [0f63f1a7] - Document task object [1c83e21e] - Bump nf-sqldb@0.4.0 [a137e93a] - Bump nf-amazon@1.7.1 [912b9bb2] - Bump moment.js version2.29.2 [a229c1ed] 22.03.1-edge - 6 Apr 2022 - Fix default dsl env detection [b9a09bf6] - Handle K8s timeout error - 500 status code (#2756) [89a1a46b] - Honour background option for kuberun command [b1b0ddd9] - Add Aws Batch native retry on spot reclaim [cd95e297] - Improve Aws Batch error reporting [00443510] - Add missing workflow err report [fa687789] - Use local nextflow when packing docker image (#2757) [40271b08] - Add retry policy Azure create job [792820a2] - Fix log message in nf-azure [80a0e937] - Prevent build on tag [5b660c73] - Fix missing linux/amd64 platform on docker build [05f117d7] 22.03.0-edge - 27 Mar 2022 - Add experimental proxy reg [b3836691] - Add api to access config raw value [977f6305] - Add warning for invalid emit names [0045834c] - Add retry policy on grid submit failure #2696 [673f560c] - Add config tests #2422 [885993b1] - Add ability to disable config names check [814a2605] - Add azcopy fine grain config settings [3998a56b] - Add binary compatibility with Java 8 [763ec999] - Add retry policy to Az Batch operations [991c6175] - Make DSL2 default syntax [4e9189ac] [0c80784a] - Fix Reduce task command runner script size [6930408b] - Fix K8s task retry strategy on node termination [bd093081] - Fix use first config in stack when is into profile #2701 [44bdde8d] - Fix Allow comments after nextflow.enable.dsl (#2746) [6988638b] - Fix allow blank spaces in java path (#2690) [a966020e] - Improve AWS Batch job retry on spot termination [bd8f2e26] [72fbda848] - Improve error reporting [55466be7] - Undeprecate merge operation [1649944b] - Bump support for Java 18 [f3a11e4c] - Prevent invalid use of large maxForks values [5de0c200] - Prevent race condition on thread pool creation [3e707a1d] - Refactor AWS batch job unique token generation [d64f5a21] - Decrease log verbosity [9237d587] [d1a5e5a8] - Throw an error if a required secret is missing [8e5129d6] - Wait for pod to stop running before shutdown (#2667) [505c5ad6]) - Restore AZ tests [858a4568] 22.02.1-edge - 3 Mar 2022 - Prevent multiple parsing of params file [38bb1f71] 22.02.0-edge - 25 Feb 2022 - Fix Prevent S3 tagging with empty list [ae7db466] - Fix Azure repos tests [856aacf0] - Fix issue on includeConfig resolution #2675 [6591a9e1] - Fix NPE when accessing not existing Git file [6c79f8fd] - Fix Batch Job name exceed max allowed size [e8b70ca3] - Fix detect and skip bom mark in files (#2645) [02b06ba3] - Feature: Abort session if publish fails (#2643) [79b3836b] - Fix report overwrite cannot be disabled [202b5c9c] #2647 - Fix match bash interpreter irrespective the path [c2d2b9b2] - Fix build warning + plugins assemble (#2634) [00dd143a] - Fix CITATION.cff and add automatic validation of your citation metadata [15698a45] - Bump nf-amazon@1.5.1 [a4496bb2] - Bump nf-amazon@1.5.2 [e51139bb] 22.01.0-edge - 7 Feb 2022 - Add support for Tower reports (#2523) [de3d76349] - Add RateLimitExceededException when GitHub api limit is reached [ff123c605] - Add fetch tags and branches to local git provider [e1de8e0ac] - Add K8s priorityClassName pod option, updated tests (#2585) [51650f8c4] - Add securityContext pod option to docs (#2584) [19f16f0da] - Add automountServiceAccountToken option for k8s executor (#2562) [1b5908e4c] - Add warn about AWS CLI grandparent path in container (#2565) [67073b0c5] - Add affinity option to pod directive (#2522) [640cbed48](3 weeks ago) - Add ability to specify memory/cpu resources for the control pod (#2559) [13f3e036d] - Add `-entry` parameter to pass in k8s executor (#2525) [a96233af6] - Add AWS Athena JDBC driver for nf-sqldb plugin (#2500) [462575f05] - Fix process output 'env' as array (#2624) [0a246dc2c] - Fix make date format to change independent from system locale [d1e5f6e76] - Fix double access of params file [459ebab7b] - Fix Use account SAS token instead of service SAS token (#2576) [d5125975d] - Fix upload of nested directory outputs on azure (#2578) [85ad55225] [744447155] - Fix Docs Typo (#2556) [942be46f6] - Fix NXF_PARAMS_FILE is not recognised #2549 [62f5fe1d9] - Fix failing tests (4 weeks ago) - Fix Unable to use output path with nested properties [ceceb0784] - Fix Nextflow couldn't parse generated nextflow.config under some circumstances (#2496) [2dfbbc63c] - Fix invalid use of `var` keyword [8418cc8d6] - Improve k8s executor throwing NodeTerminationException on node shutdown (#2590) [084c8d6ca] - Improve docs on `include` statements (#2520) [9c140cee3] - Improve core plugins info & logging [dfa544ac9] - Improve Secrets handling [1c0ad4679] [329502d19] [[26b4be906]] - Improve DSL2 documentation [048b026f2] [e2e8b5557] - Improve documentation (#2600) [787a1fd84] - Allow disabling history file unique check [c3677c311] - Make S3 parallel download as default [b490f146d] [03dae9d6e] - Run Azure integration tests only with Java 11 [0890ceeb3] - Prepare for Java >= 11 build [8c0566fc3] [5ba16dd18] [405b67365] - Use Standard_A3 instance type for Azure tests [67e7d3ab3] [b97b0010c] - Refactor cache store using plugins [54bf7a61d] - Update google cloud docs (#2594) [dfa867953] - Update the azure docs for registry [96baf288e] - Update copyright info [807a816a5] - Remove gradle logs about tasks dependencies (#2618) [cae44e00b] - Remove Tika deps for nf-amazon module [95620d42b] - Remove deprecated validExitStatuas directive [b3117e789] [2188d51a0] - Remove support for Apache Ignite [d4dc1cfe1] [64d2773fd] - Bump nf-amazon@1.5.0 as default plugin - Bump Gradle 7.3.3 [f00bfb0d3] - Bump nf-amazon@1.5.0 [40f90aa92] [[2bc16732e]] 21.12.1-edge - 22 Dec 2021 - Add tags attribute to publishDir directive [e78a997b5] - Add ability to disable running jobs cancellation [a13af9a3c] - Add ability to define containerProperties with using AWS Batch #2471 [ac7f1e71e] - Add NXF_JVM_ARGS env variable [7afb2deed] - Improve paths validation [0849d583f] - Include S3FS provider into nf-amazon plugin [3a7bf8c7a] - Fix error reporting on missing script file #1951 [e1a0b240a] - Fix singularity docs #2493 [c66cb3ba7] - Fix cross compilation error cause by ByteBuffer [74916100f] - Fix File staging race condition + beta AWS parallel downloader [b7c262de3] - Fix enableAIAcaIssuers launcher flag [cd780aabd] - Fix task index sequence generation [3447e735b] - Fix Changes process directives invalidates tasks cache [967c1adff] - Fix Interrupted download of staged files cause execution to fail #1552 [847789fad] - Fix plugins start/stop for fs command [88d8be1f4] - Fix for nested params with the same name #2485 [02de4147c] - Fix race condition on plugin autoload status [ab00a50f5] - Fix failing test with Java 17 [1c6183c92] [4daf8d0a1] - Note on Azure Batch inactive pools #2483 [7fc116067] - Remove drip launcher [909f95279] - Update azure test image [de9d5ee8c] - Update logging library [a957db646] - Bump nf-google@1.1.4 [93193a3f3] - Bump version 21.12.0-edge [9cb7ee81f] - Bump AWS sdk 1.12.129 [bd7ba1706] - Bump logback 1.2.9 [29f260717] - Bump Jsoup 1.14.3 [5776c0391] - Bump corretto:17.0.1 [f7e047ea4] 21.12.0-edge - 22 Dec 2021 [SKIPPED] 21.10.6 - 21 Dec 2021 - Bump Slf4j 1.7.32 - Bump Logback 1.2.9 21.10.5 - 8 Dec 2021 - Fix race condition on plugin autoload status [73a0893ce] 21.11.0-edge - 5 Dec 2021 - Add process and workflow recursion (PREVIEW) [9f51155e9] - Fix include no longer works for custom methods [6adfce099] - Fix Azure executor fail to cleanup jobs on completion [533448be4] - Fix Missing AWS SSE encryption for begin and exit task files #2452 [2c6665ef9] - Fix false positive detection of publishDir conflict [6ea54eaea] - Fix execution hang when reading empty error file [414240a1a] - Test with java-17 LTS [c2141e826] - Improve plugins dev root detection [b095bee15] - Change Azure test pool vmType [ad5ad97ab] - Downgrade Google NIO library to version 0.121.2 [896ec3abd] - Bump nf-amazon@1.3.4 - bump nxf-s3fs@1.1.3 (6 days ago) - Bump nf-amazon@1.3.3 nf-google@1.1.3 nf-azure@0.11.2 [92f94bfeb] - Bump gradle 7.3.1 [2c34a3a27] 21.10.4 - 30 Nov 2021 - Fix include no longer works for custom functions #2469 [e17f6155d] - Bump nf-amazon@1.3.4 - bump nxf-s3fs@1.1.3 [be893dcb1] 21.10.3 - 23 Nov 2021 - Fix execution hang when reading empty error file [414240a1a] 21.10.2 - 22 Nov 2021 - Fix Azure executor fail to cleanup jobs on completion [4d5b71370] - Fix Missing AWS SSE encryption for begin and exit task files #2452 [841e6101b] - Fix Azure integration test [a8051bc01] - Fix false positive detection of publishDir conflict [292b439ad] - Make Azure executor logging less verbose [7452e386d] - Change Azure test pool vmType [85682be7d] - Downgrade Google NIO library to version 0.121.2 [66ae98820] - Add java 16 and 17 to the launch.sh for debugging #2457 [3ff0a248e] 21.10.1 - 18 Nov 2021 - Fix Azure batch NPE when missing pool spec [84b2983f4] - Fix Docker bin in image PATH #2445 [d30da377a] - Fix failing test with Java 16 [f2d01888d] - Fix AWS_RETRY_MODE var definition in Batch job [f1a58600d] - Add docs for AWS endpoints for China region [e96c56d1e] - Correct description of cross #2446 [e4c7f3d98] - Dump resolved config when log trace is enabled [2580fb108] - Bump nf-azure@0.11.1 [eb1e6fbd2] - Bump nf-amazon@1.3.2 - bump nxf-s3fs@1.1.2 [ae9e885a8] 21.10.0 - 11 Nov 2021 - Add support for Java 17 [cb207cd64] - Allow override Bash wrapper template files [e6e25ed7c] - Fix issue with plugins local root sync [1d974a4eb] - Fix Nextflow does not recognised Failed pod (#2430) [9c80cdea0] - Fix Error reporting on Bash launcher creation failure [63e01c324] - Fix Channel.fromSRA error one some project ids #2156 [dbcbac139] - Fix Task completion percentage #2440 - Display no workflow warn if no main is defined [0f1295694] - Invalidate task cache on directive change (EXPERIMENTAL) [62ded3421] - Upgrade XmlParser used by SraExplorer [543b582b5] - Use AWS Batch resources requirement for CPUs and memory [1cf2c379c] - Bump Gradle 7.3 stable + GHA cache [4eaa4f25f] 21.09.1-edge - 28 Oct 2021 - Fix issue with config selectors and DSL2 [4d7d3e972] - Fix issue evaluating dynamic errorStrategy with AWS Batch [8c6a5a6e2] [ce4d491b1] - Fix verbose logging [92b113134] - Fix docker image url [ed24a475d] - Fix Temporary directories not deleted in on_exit #2406 [181bdf528] - Fix implicit authentication for resources served by Tower [e30310b4f] - Fix No more of 255 channels can be defined into a workflow context #2417 [7f91ecb39] - Add tip about escaping variables in env scope #2366 - Add K8s env fieldPath option to pod directive #2363 - Improve AWS Batch error report fetching CloudWatch logs [b9f9578f1] [e229700ef] - Improve docs about IAM policies for AWS Batch #2391 - Accommodate token in password field for Gitlab #2389 [ee32b7726] - Report a warning when main workflow is not defined [83aec6e8b] - Bump nf-amazon 1.3.0 - Bump nf-tower@1.3.0 - Bump nf-google@1.1.2 21.09.0-edge - 12 Oct 2021 - Add secrets manager (preview) [da2a5ff1a] [2d66f83ca] - Add Built-in support for Azure File Shares #2285 [a4c3e0ad5] - Add Azure pool node SKU selection #2360 [9afcac756] - Add support for protocol option to fromSRA #2087 [371f858ab] - Add retry on AWS Job definition not-found error [452cae5d8] - Add ability to define templates library at module level #2332 [7e7d52573] - Add missing information for pulling images from private registry in Azure Batch #2355 [040e190bd] - Add $NXF_CLI_OPTS env variable [7d57acca5] - Add NXF_CACHE_MODE env variable [1c345c497] - Fix asset directory consistent hashing via sha256 checksum [4c5c0ef41] - Fix issue invoking extension method with GString params [570e5299c] - Fix Prevent pipeline stopping when K8s pod is evicted [f9db9cc77] - Fix clean command for Google storage [dc9625eb9] - Fix plugins detection in local repo [6441a3882] - Fix S3 canned ACL documentation #2334 [69216e292] - Fix docker image build with recent docker [2aad36897] [1e485b32b] - Fix amazon plugin is not used when using bucketDir option [6a8c50ad4] - Fix Plugin dependency requirement overrides core plugin #2303 [4d1762fb3] - Fix Make K8s ImagePullBackOff and ErrImagePull recoverable #2302 [766ffde40] - Improve cache resume strategy [0b0eae225] - Improve GH action build compressing integration tests [ab9d747d4] - Prevent NPE if session is not set [83bb46d94] - Remove deprecated attribute [50d63b6fb] - Find newest matching plugin #2303 [e6cf79ff3] - Documents noproxy variable #2325 [bc769b1b4] - Bump Groovy 3.0.9 [dee2d6c99] - Bump nf-sqldb@0.2.0 - Bump nf-amazon@1.2.1 - Bump nf-azure@0.11.0 - Bump nf-google@1.1.1 21.08.0-edge - 30 Aug 2021 - Fix plugin updater version logging [d162eb8b4] - Fix Nextflow launcher breaks when java path contains blanks #2265 [8097a2a90] - Fix docker build [efb2f449b] - Fix NPE in AnsiLogObserver #2283 [cffc683df] - Fix run script when fixing ownership in aws batch #2262 - Improve plugins auto start [283144474] - Improve log error reporting [401863085] - Improve handling of K8s node shutdown [67250c041] - Update GitHub docs [4532b8e1e] - Merge nf-sqldb 0.1.0 21.07.0-edge - 6 Aug 2021 - Add support for AWS_MAX_ATTEMPTS variable [3cc543589] - Add app plugin to gradle build [007bc1cb4] - Add self pid to tower client [d2e54ea22] - Add support for head job operationId + log/out files [a7a76cf91] - Add enable CA Issuers option to NF launcher [8f51dc787] - Fix Clean cmd fails removing foreign files [8bf8ab720] - Fix Prevent script var names conflicting with private names #2246 [82bbc180e] - Fix ENA download URL #2239 [befbabbc8] - Fix Tower client is not activated launching all packaging #2145 [c507518c2] - Fix orphaned AWS Batch jobs after pipeline interruption #2169 [65e2a4d05] - Fix Process error report on target exception #1896 [1bac3f17b] - Fix Unexpected bool conversion on publishDir enable/overwrite attributes #2220 [651835d2d] - Fix BatchCleanup toString method [ec9bb5648] - Improve error reporting [49ac01dbb] - Improve Unknown host error message [ad41d1e98] - Improve AWS Batch task handler [eb1aff275] - Use AWS cli standard retry mode by default [f2f1fdea4] - Report warn on cache hashing failures [7bf93de06] [3b579c954] 21.04.3 [stable] - 21 Jl 2021 - Fix Tower client is not activated launching all packaging 21.04.2 [stable] - 12 Jul 2021 - Fix Plugin install lock file is not deleted #2103 [29c3e516c] - Fix Default plugin version lookup [d340a221f] - Fix BatchCleanup toString method [3c67fa3ae] - Implicit variable projectDir breaks caching #2186 [7a4d1f1a2] 21.06.0-edge - 3 Jul 2021 - Add Keep alive option to Google LS executor [994222074] - Add support for FTP proxy and proxy servers authentication [8ec33b04d] - Add support for plugins grouping [aa5bc7d34] - Add More details about the reason why a AWS Batch job has failed #2146 [27a4e88b2] - Add support for extensions priority [ae083f1aa] - Add stubRun attribute to workflow metadata #2164 [86cfc66fd] - Add Run tasks under user accounts in Azure Batch #2157 [1c9fc4a40] - Refactor GLS executor [2c86b79a4] [97fc49c09] - Refactor AWS batch job def creation [89ce364c9] [986894287] - Fix Default plugin version lookup [e0c8151d9] - Fix Negative labels do not work as expected #2155 [491191811] - Fix PublishDir overwriting task output files [190aa4eaf] - Fix directory deletion strategy [b96fcedc8] - Fix Implicit variable projectDir breaks caching #2186 [76417d273] - Fix Prevent empty download array [9492cde5d] - Fix output unstage with glob pattern [2d4c3dfcf] - Fix Connection-reset crashes the workflow [3ee4fd0eb] [1400ded6d] [61bbc240a] [175c66584] - Fix Slurm does not send soft kill message #2163 [f0ccfc7e8] - Fix storeDir directive does not work with S3 #2141 [2e95a6a76] - Fix maven local publish [05cfb7cf7] - Fix GLS transfer attempts opts [f7c705db5] - Fix build exportClasspath task [88d27f0c8] - Fix PbsPro clusterOptions directive priority #2036 [75e3f225e] - Disallow include nested within a workflow block [7dbf64bea] - Upgrade AWS SDK minor version #2167 [296afaa8f] - Improve gsutil transfer throughput [2da120b91] - Improve config error reporting [6aa102430] 21.05.0-edge - 28 May 2021 - Add support for using mamba with conda (#2030) [10c8385b] - Add AWS cli native error fail-over [fd7670ef] - Add support for Container Registry to Az Batch executor (#2078) [12bf2da6] - Add support for Tower workspace (#2097) [8a4dd3ab] - Add support custom service account email in Google Cloud LifeSciences executor (#2044) [a642c9ea] - Add support for Java 16 + Gradle 7 [caace1c5] [e2dd4510] [74e466e0] [1245ab1c] [bfc69fb6] - Improve tower client error reporting [4efb6bf6] - Fix Plugin install lock file is not deleted #2103 [b7fdffac] - Fix Use caller runs policy of default thread pool #2021 [48b4e8ee] - Fix Error reporting for malformed config [68e5ca18] - Decrease max par transfers to 4 [c7ea816a] - Prevent fetching aws instance type when missing container id [f5f96049] - Use default opts for trace file creation [d8ae94bf] - Improve Azure Batch executor error code and messages for failed Tasks (#2099) [1d5fa5d5] - Bump groovy 3.0.8 [aa695e12] - Bump snakeyaml@1.28 [8d361954] 21.04.1 [stable] - 14 May 2021 - Fix nested params file parse #2091 - Fix Malformed config error reporting #2105 - Fix Use default opts for trace file creation [09e6c6ac] 21.04.0 [stable] - 2 May 2021 - Fix NPE when AWS Batch job container is not returned [412b6fde] - Fix execution hang when native task fail to submit #2060 [1253485d] - Update preview message [e1eebdcd] - Fix nf-ignite all packaging [72b6a428] - Fix GS failing tests [be4f91e9] - Fix AWS batch executor fails when using self-contained distribution #2058 [2e344c18] - Fix groupTuple sort criteria with closure #2020 [28a579a9] - Patch invalid double number cli parsing #2039 [4de4670c] [dcadaaeb] - Update sphinx_rtd_theme 0.5.2 [4a165f43] - Disable cpus option when running docker with legacy opt [1a7854a5] 21.04.0-edge - 8 Apr 2021 - Add readOnly flag to k8s volume mounts (#2013) [33bd24ac] - Add Start default plugins on-demand #1964 [cf2a9d73] - Add support for tower workspaceId [e2977688] - Improve support for BitBucket server repos [eb946e27] - Fix toInt/Long/Float/Double operator hangs with value channel [7c35d985] - Fix regression caused by nested params handling #1923 [b25af49b] - Fix Cache invalidation when repo is cloned between runs #1989 [ac526f38] - Fix Invalid setting of TMP var with singularity #1997 [23f80121] [472cfbdd] - Fix issue overriding nested params from cli #1923 [cfe6b1d1] - Fix az path handling curly brackets globs #1969 [c78a1bbf] - Fix Missing git credentials when checking last commit id [f101308e] - Fix plugins version check against local installation [535c2bb5] - Fix local dependent formatting #1962 [2a5cbac1] - Fix Encode path parameter at GitLab getContentUrl [6f80f651] - Fix Only use sudo rm with docker #1956 [f9490423] - Prevent AZ NPE when missing vmtype + better logging #1992 [711362ca] - Refactor params file var binding #1860 #1972 [330f044a] - Prevent jobs names longer than 100 chars OAR exec [6daa21b9] - Bump nf-azure@0.9.6 + nf-amazon@1.0.3 [aff1d355] - Bump nf-amazon@1.0.3 - s3fs@1.0.9 - solve #1830 [b3b221c1] - Bump nf-tower@1.1.0 [29fdd9f7] - Bump nf-amazon@1.0.4 + nxf-s3fs@1.1.0 [c638af80] - Bump nf-azure@0.9.7 [07c59946] 21.03.0-edge - 5 Mar 2021 - Add support for serializable ValueObject [8dfaadf3] - Add abilitity to fetch revisioned git assets - Add support for FixOwnership to AWS batch [24f83741] - Add support for custom network to GLS #1810 [171f4aa8] - Add ability to handle list of az vm types [00ced0b3] - Add tower config scope to docs #1890 f2bd96fa - Add charliecloud container environment from file (#1909) 4553648b - Add azcopy tool install mode opts [9e9337d3] - Update Az default vm type to Standard_D4_v3 [4c6e76b6] - Update NF console dependency [a2d06e15] - Remove CDN from timeline reports and make them offline readable #1927 [c0e5a941] - Fix plugins install failing in some file systems #1882 [8cc43391] - Fix catch failing commands in nxf_parallel #1884 [dd56f6c1] - Fix missing error on empty process script [3607f84e] - Fix GSL path de-serialization issue [c6cf784f] - Fix Memory unit cannot be a negative number #1902 [abd1c9d9] - Fix pod spec labels to start with numbers in addition to alphas [79740edf] - Fix OAR executor log files #1761 [6f2ff4e4] - Fix issue cause by sleep with subsecond argument [c4be8d00] [63974ac6] - Fix az blob storage SAS permissions [18a33213] - Fix sort human-readable tasks in report [6d68f28d] 21.02.0-edge - 1 Feb 2021 - Fix Issue when merging nested cli params #1856 [275e54c4] [fe37da6d] - Fix job status detection on PBS pro #1840 [c1598908] - Fix Issue when merging nested cli params #1856 (19 hours ago) - Revert the CPU/memory options being passed to singularity VM instead of singularity container [0d04e0f9] - Add ability to specify plugins with cli [de91218f] - Decrease upload/download process polling to 0.2secs [6ca2d6ca] - Remove nf-amazon as default [e6810e90] - Make plugin services singleton [cacd9328] [5787be6d] - Make repository provider accessible to subclasses [988bccc6] - Fix error on plugin downloading #1859 [77cabb3c] 21.01.1-edge - 15 Jan 2021 - Plugins stability improvements [8d849ec9] [bf093826] - Charliecloud improvements [2242411a] - Fix issue of FS discovery with dyn plugin loading [bf5e86df] - Fix crash on startup when mem reported < 0 [095236b8] - Fix and stability [e4b8afb5] - Fix launcher on Java11 [c6b78034] - Add plugins custom version manager (4 days ago) - Improve NF version checking [d33ea642] - Bump plugins minor upgrade [f91bc21e] 21.01.0-edge - 04 Jan 2021 - Merge plugins feature [d959bfdb] - Prevent twice access remote scm file [b2798556] - Fix DAG edges not connected correctly #1486 [cece1161] - Fix k8s executor must provide cpu resource requests #1570 [6896e923] - Fix http/ftp read buffer size [a2886baf] - Add support for OAuth Bearer auth [5823c280] - Add support for basic auth for http/s file provider [6027fcba] - Add User-Agent info to httpfs requests [222637de] - Update CPU and RAM for containers (#1833) [ccf5c8ba] - Move test contains to quay.io [7db053eb] [773be707] [c10a7f53] 20.12.0-edge - 12 Dec 2020 - Add support for charliecloud container engine #1809 - Fix glitch on K8s task progress update [668434f6] - Upgrade to groovy 3.0.7 [27056035] 20.11.0-edge - 16 Nov 2020 - Fix Allow nextflow to handle http protocol for Singularity images #1791 - Fix params-file overrides config parameters [b03efcac] - Fix println failing test #1621 [8c6f0f97] [9d2e5850] - Let output env variables be optional (#1740) [3fca3655] - Add stub-run feature #1774 [3de45c22] [e2d6d55b] - Add overwrite option to trace/time/report/dag features #813 [a0615474] - Allow nested CLI params #1182 [19ab8a8f] [df6204e3] - Allow setting google projectId in nextflow config [223b5d6c] - Make binDir accessible from the executor scope [1405a28f] 20.10.0 - 1 Nov 2020 - Add warning for AWS Batch mem request lower than 4 GB [e9240fc9] - Fix issue with docker images tagged by SHA #1777 - Add support for Bitbucket tags and branches retrivial [5083066e] - Add support for Tower client bearer authentication [532282ae] - Fix Skip FS lock when Conda dir exist #1771 - Add support for Java 15 [b1f48884] - Fix build with Gradle 6.7 [8d7227f0] 20.09.1-edge - 15 Oct Sep 2020 - Prevent USR1 signal to stop jobs #1753 - Add -main-script cli option [702ff64c] - Improve Singularity image file caching #1706 [dd92772b] - Fix unexpected default GLS action flags #1749 - Patch unpexpected error on tower serialization [f922324a] 20.09.0-edge - 23 Sep 2020 - Fix invalid error message on missing process #1719 [fc607f11] - Deduplicate GS file + parallel up/downloads [29d37083] - Deduplicate S3 file uploads [0b65d61f] - Fix issue on GS path composition [276f0ed3] - Add NXF_PARAMS_FILE env var [2e3c9232] - Allow configurable container mounts [8dc0adf4] - Refactor common Bash helper functions [22a0ff34] [502309b7] - Fix race condition creating FTP file system #1725 - Fix invalid checkWarn method invocation [ba052a02] - Move makeDigest into build.gradle file [a2b5de8f] - Add variable NXF_CONFIG_FILE [83365aa3] - Patch use of GString for fromSra apiKey option [a8b81ada] - Use repository URL instead of Git clone URL [75a04d90] - Fix Invalid exception capture for missing config [ce427924] - Fix podman issue on duplicate mounts [661a40e9] - Fix FromSra illegal character error [5a86d180] - Fix Allow custom SCM file location #1657 [a90e66e3] 20.08.1-edge - 2 Sep 2020 - Add variable NXF_CONFIG_FILE [d15edcb8] 20.08.0-edge - 24 Aug 2020 - Merge Groovy3 runtime and support for Java 12/13/14 - Use repository URL instead of Git clone URL [102f8b01] - Fix Invalid exception capture for missing config [8c7accca] - Fix podman issue on duplicate mounts #1710 [d0cc38de] - Fix FromSra illegal character error #1700 [a45decfb] - Fix Allow custom SCM file location #1657 [7c27f895] - Fix dynamic executors loading [7b9ce82f] - Fix missing newline on cmd log stdout/err #1705 [1416a388] - Fix k8s timeline start #1687 [24dff871] - Remove unneeded parentheses from stdout declaration [dc029c04] - Merge execution logs command docs [577ec744] - Passing exact memory to TES executor in GiB #1696 [c8a15545] - Improve docs replacing subscribe{println it} with view() [f84ccb6f] [cb2d607d] - Use current environment Bash #1598 #1614 [e70ef87a] - Include GA4GH support into the standalone binary (make pack) #1666 [e2175d45] - Update Bitbucket docs [b9b57f83] - Clone/Pull submodules recursively #1615 [5f20ab6a] - Bump nf-ignite to version 1.1.0 20.07.1 - 24 Jul 2020 - see 20.07.0 and 20.07.0-RC1 20.07.0 - (skipped) - Allow unqualified stdin/stdout definitions with DSL2 [bcdcaab6] 20.07.0-RC1 - 21 Jul 2020 - Add Dsl2 enable flag [08238109] - Add check on invalid scope syntax definition [23c92021] - Add channel as alias for Channel [05c358c9] - Add DSL2 deprecation + clean up syntax [1b4b1307] - Add DOI field to NF manifest #1676 [ec6ee223] - Improve join duplicate detection [33eb9ef5] - Improve mix operator error message [8074d714] - Remove invalid log message [48b1b9f1] - Fix hidden error message on fail fast run [3b4b377c] - Disallow upwrapped includes + hard deprecation [19130f87] - Suppress trap for SIGUSR1 signal #1656 [ca5bcf46] - Improve error reporting on invalid task id [3921de1a] 20.06.0-edge - 5 Jul 2020 - Add more debug logging for AWS helper [2a62fdf7] - Add join options failOnDuplicate and failOnMismatch [387366aa] - Add strict mode flag [4ba5ac18] - Add support for selecting minimum CPU platform on GCP (#1633) [afc4375d] - Add missing trace fields to docs [bf2e1637] - Fix Invalid GLS path composition in staging directories #1654 [e33fff98] - Fix for feature 1647 that allows non gpu k8s accelerator resources. (#1649) [c1efa29d] - Fix Issue accessing S3 bucket #1596 [ffc6f843] - Fix Update getDomain method in ProviderConfig to support local repositories - #1492 (#1624) [651501ac] 20.05.0-edge - 31 May 2020 - Add support for NXF_LOG_NAME env var [cf496615] - Add exception specialiation for ambiguous repo [a34b1d2a] - Add support for tower_workflow_id env var [53188126] - Add config profile names accessor [2784cdb8] - Add support for Google Cloud buckets with Requester Pays set #1466 [bc9db8d8] - Add Git tag and branch retrieval [7c97f23f] - Fix PublishDir error caused by duplicates output files [5f3b69c1] - Fix weird issue on config resolution [0d0fef4b] - Fix resolution of malformed configs [fe213e41] - Fix K8s labels and annotation normalization [6434b9d] #1577 #1584 - Fix minor git path provider ending slash [9888be29] - Fix bugs in GA4GH TES support (#1589) [26708335] 20.04.1-edge - 19 Apr 2020 - Fix AWS auth with temporary security token [6a7b11b8] 20.04.0-edge - 13 Apr 2020 - Add SGE hr status handling (#1558) [f4db0049] - Add moduleDir, projectDir and launchDir vars [7832a697] [576a5694] - Add executor display name rendering [74c90ca9] - Add ability to pipe custom fun [DSL2] [80bb6485] - Add Aws Batch container image validation [e73951fa] - Recognizes more UGE states (#1536) [4dacebbf] - Prevent invalid process tag values [f2da1357] - Report Tower backend error cause on failure [da8ac8f5] - Fix Config cmd should resolve remote projects #889 [c2e0ac0b] - Fix issue applying branch/multiMap to value channel [e69f39fa] - Fix Kill signal is not propagated for Singularity container #1561 - Fix docs typos [d7261d2e] - Fix Minor docs update #1545 - Revert "Bump jline 2.14.9" [ef7040cb] - Deprecate validExitStatus directive #1564 - Improve error message [DSL2] [f8a0ee1c] - Add sluper parse method for Path [a54fd03d] - Report error message when accessing invalid out #1553 [83bd009c] - Remove deprecated $ config syntax [0a31f9df] - Remove deprecated workflow publish [DSL2] [1bd7b4a4] - Remove support for workflow 'get' [d9b91149] - Remove deprecated process output getter [013a323b] - Remove deprecated out cardinal getters [414fae94] - Remove deprecated gpu directive [f48b2c24] - Minor executor logging [7f94299b] - Minor improvement createDirIfNotExists API [34211675] - Bump groovy 2.5.11 20.03.0-edge - 28 Mar 2020 - Add support for GLS private addr #1545 [a481b42b] - Add AWS batch job def normalise function [79239f05] - Fix Escape Singularity env variables #1535 [b651a371] - Add Local executor file system check [ffc92926] - Add Launch Id to Tower client [d768d2d1] - Add workflow progress on completion [aea41f37] - Remove deprecated onFlowStart method [14f12b5f] - Minor method visibility change [43bc9697] - Minor log change [130a963b] - Fix docs broken link [0a1ec9a9] - Fix typo CVS -> CSV #1500 [d89281c3] 20.02.0-edge - 29 Feb 2020 - Fix Unable to create AWS helper class warn #1504 - Fix Ansi log flickers when variable-length tags are used #1288 - Fix Directive maxForks may cause execution to hang #1432 - Fix Missing tag in ansi log #1503 - Fix PBSPRO res req should always include cpus #1510 - Deprecate workflow publish 7f315a63 20.01.0 - 12 Feb 2020 - Fix ansi logging and line count [4f5c7187] - Fix Division by 0 in launcher script with Biocontainers #1488 - Fix Run name validation to 80 chars max #1491 - Add GitHub badge to README - Add Bash version to issue template [78928546] - Bump jline 2.14.9 [5df2b27e] 20.01.0-rc1 - 6 Feb 2020 - Add ability to extend module params #1484 [17c6acca] - Add dsl2 command line opt [1cf544d5] - Add GLS executor docs [574f2098] [7ce2597a] - Add HTCondor detail on data sharing #1473 [f0af66de] - Allow aliased process to inherit config settings [DSL2] [1c447e85] - Allow module inclusion to inherit context params #1484 - Allow multiple inclusion from the same module [DSL2] [a9ae36f9] - Fix Script template fails to render list of files #1478 [2e97bbbc] - Fix process name validation when using legacy script [1543365c] - Fix Early detection Dsl2 declaration #1468 [93a642aa] - Fix Missing script validation checks #1468 [5d0cf145] - Revert "Disable ansi log on non-tty env #1417" [98e6758b] - Minor changes gradle build [619385f1] - Minor AWS Batch api refactor [c20abc11] - Improve foreign file detection [50508684] - Improve GLS location validation [5b89ab50] - Removed unused module flag [cf19cc9c] - Update dsl2 docs [5c57c3a8] 20.01.0-edge - 20 Jan 2020 - Add Prevent negative progress stats [87cdddc6] - Add More cloud tests [7a5dd828] - Add support for UGE throttled jobs (Tr) #1461 [20408e4b] - Add progress stats to tower client [781116a4] [138cf0b0] - Add experimental Podman containers support (#1451) 026866cd - Add support for Gexf format for DAG rendering [28bfe0ee] - Improve ansi logging for multilines output [1ce978c3] [004e23eb] - Improve progress stats and ansi log [0212ba16] - Improve api to enable wr executor #1148 [21088ad3] - Update tower trace client requests [138cf0b0] - Enhance progress execution stats & tracking [a30e2b9a] - Unexpected output when using Google Storage as work dir #1452 - Fix typos and minor changes [fb2f954f] - Fix Operator splitFastq fails with PE option and DSL2 enabled #1390 - Fix Container entrypoint when using GLS executor #1291 - Fix GLS file unstaging #1406 [e67ef3be] - Fix GLS unstage for file patterns #1406 - Fix Scratch directive does not work #1280 [644e9ac7] [6c7291fa] - Fix Resume fails due to LevelDB exception #1358 [28fa3a6c] - Fix Conda env activation #1195 [e3919275] - Fix java command in launch script #1436 [f28b015f] - Rename variable java to JAVA_BIN [086377d8] - Removed unused compile deps [686bcd98] - Bump capsule-maven 1.0.3.2 and fix broken env [004684e3] - Bump capsule-maven 1.0.3.1 and seqera repo [62964eed] 19.12.0-edge - 20 Dec 2019 - Add GLS assigned zone discovery #1406 - Add Google Life sciences (GLS) executor improvements #1406 [ead29c11] [8228e9b4] - Add GLS bootDiskSize support #1331 [f118798c] [af8fe16d] - Add GLS job debugging #1351 - Fix NPE when file pattern is missing [1cbb6e49] - Fix AWS cloud parsing for NVEe storage and tests - Fix Disable ansi log on non-tty env #1417 - Fix Allow Singularity image path with blank #1368 - Fix Shell template invalid caching #1422 - Fix Task vars ordering may invalidate cache #1408 - Fix Join operator not matching gstrings #1394 - Fix sigpipe error caused by runner script #1332 - Fix Google Storage bucket with underscore is not recognized #1069 [85cd0cde] - Fix fromFilePairs can't take list of paths #1405 [c00f5669] - Refactor onFlowInit to onFlowCreate event [c477eeaf] - Improve err msg when input files are remove from output [5d5744a8] - Upgrade to Gradle 6.0.1 [e0c1a3ac] 19.11.0-edge - 2 Dec 2019 - Increase tasks.module to 255 [7332c606] - Fix Allow the output of process env variables #69 [1c1befc7] - Fix docs rounding issue #1350 [af824fc7] - Fix Join operation incorrectly represented in DAG #1346 [9d83ed51] - Fix Tiny typo in docs #1361 - Fix lost trace/report/timeline file name - Fix invalid class exception [4308d6a4] - Fix Invalid dynamic resolution of stageIn/OutMode directive #1374 - Fix No such property stackTraceDepth error #1387 [49450f67] [f5342e71] - Fix Singularity env variables are not accessible #1386 [036af4a6] - Fix PublishDir should not create dir when disabled #1381 - Fix Process hangs for non zero exit status #1344 - Fix Output stdout does not support emit attribute #1373 - Fix False positive warning when importing module #1349 - Fix HTCondor queue status command #1353 [a1addc8f] - Fix Escape file names with blanks #1392 - Fix broken docs tutorial #1366 - Patch Duration unit cannot be a negative number #1384 - Handle ProviderMismatchException in CacheHelper (#1382) [cc584368] [3523f174] - Introduce workflow take in place of get [DSL2] [e8cbbf08] - Disable ansi log when using dockerized run [86bc2ada] - Minor logging change [238b0e6c] [f5342e71] [b707882f] [ce97f073] - Add multiMap in place of fork operator [afd671c8] - Add Show Tower init response message as warning - Add output path includeInputs docs [2ce7e861] - Add metrics fields check #1360 [5b7f42e9] [caf9f137] - Add console command to cli help #1347 - Add OAR executor #1343 - Add graphiviz to Docker image #1370 - Removed unused property [9c65426a] 19.10.0 - 21 Oct 2019 - Merge Use a delete function that doesn't follow symlinks #1337 - Merge Allow multiple mounts for the same K8s claim name [1d288a3d] #1284 - Make Google Pipelines logging less verbose [6edd9954] - Merge Shifterimg workaround for ensuring image pulls #1327 - Merge Add ENDPOINT support for China regions #1323 [636cbfb5] - Add limit on max field lengths sent by Tower [4d5cabc2] - Add retry ability to Tower client for 500 class errors [c7f70fc5] - Add support for Java 12 #1082 [b86b2da0] - Add BitBucket Server provider [6af6a902] #1297 #1309 - Add support for AWS temporary security credentials #934 - Fix Broken container environment when enabling metrics #1289 - Improve resource not found error message [02cf0a55] - Remove route operator #991 19.09.0-edge - 16 Sep 2019 - Add `of` and `fromList` channel factories [cc60b305] - Add nf-tower init request [120ed8ba] - Add support for accelerator directive #997 [624c8e83] - Add support for native shifterimg for shifter engine (#1292) [a106712e] - Add nf-tower subproject [285e09ce] - Add sticky log marker [f9a3c9da] - Add support for config resolution [4754abc6] - Add enable option to publishDir [7b9c2d2f] - Fix race condition on task workdir creation [5bc323a0] - Fix issue when fetching aws profile from env #1248 [ba30b97c] - Fix minor issue when reporting invalid entry error msg [814d6728] - Fix non determinist test failure [a9289e9e] - Throw error cause on InovationTargetException [9e1467d0] - Remove verbos logs on readExitFile check [a5a6a1fc] - Revert "Patch capsule error message" [ac4ac073] - Patch for inconsistent cached task id #1301 [7bfd0008] - Improve flow execution events [335b76d1] 19.08.1-edge - 26 Aug 2019 - Add Process named output channels #1290 [DSL] [6a756fd2] - Add workflow publish directive [DSL2] [287a095e] - Add stageAs option to input path [DSL2] [9b5f55f6] - Add workflow entry option [DSL2] [f29e3e04] - Add extension to module file name instead of simpleName [DSL2] [71a60365] - Add support AWS temporary session token support [15ac3938] - Add support for GCP disk resource [72bb9c41] - Add fork operator #1281 [DSL2] [6f89833a] - Add branch operator #1202 [706a182a] [DSL2] - Add workflow definition and composition #1276 [13f43291] [DSL2] - Add projectName to workflow metadata [55be0762] - Add support for tower [1255f702] - Add support for timezoned timestamp to metadata [6f4a2e28] - Add task pending event [d2d66698]] - Add support for path in/out qualifier [DSL2] #1201 [5552b38a] - Add set chainable operator #1262 [2651a099] - Fix name generator uniq check [0bbf7015] - Fix execution report nested processes aggregation [e4fad827] - Fix nested process names config resolution [ccd8e833] - Fix missing deprecation [8af85189] - Fix broken div structure in html report [3e055a7a] - Fix set operator for multi-channel #1262 [eab39378] [DSL2] - Fix typo in the `delete` file docs [38fa2dca] - Fix test #1276 [cc03d76b] - Fix classpath resolving when launched from foreign path [04024fe6] - Fix console cmd throws runtime exception #1273 [2f78d943] - Fix process names validation fails for included modules #1175 [75b96aa8] [DSL2] - Fix issue with `set` as operator #1262 - Fix misleading name when throwing multiple in/out channel [e7c8cdb9] - Fix Combine operation incorrectly represented in DAG #1268 [6e86e28a] - Fix docs collectFile `size` vs `skip` option [8cfb5a64] - Fix K8s TaskHandler updates its status correctly to 'RUNNING' (#1256) [a1457a1c] - Remove potential sensitive environment vars #1075 [a413b967] - Enable use AWS profiles other than `default` (#1248) [d7434773] - Relax deprecation messages #1269 [454e78f1] [fd11f8d8] - Defer process start and channel emission [DSL2] [f5eef256] - Rename ChannelFactory helper to CH [4b5b3c7e] - Improve modules error checking and reporting [aa650b9e] [DSL2] - Increase build test max heap size [daca896e] - Upgrade Gradle to version 5.5.1 [027cb16b] - Enforce process execution in `workflow` scope` [DSL2] [bca15a91] [0a582240] - Replace InterruptedException with TimeoutException in GCP test [a6d3c24c] - Explicitly check whether module path does not end with .nf (#1254) [8253608a] - Minor improvement AWS Batch docs [bd56ea44] - Upgrade Groovy to version 2.5.8 [36dffa18] - Enhance execution report [ab5f8d98] - Enhance simple http client [2e0f5c2b] - Refactor resource metrics collector [fec86ed2] - Refactor observers plugin system [9dab8f08] - Replace input/output set type with tuple [DSL2] #1207 [5e19f72f] - Convert any simple object to a value channel [DSL2] [86b0469d] - Improve logging [5adc2c09] 19.07.0 - 27 Jul 2019 - Add support for K8s annotations #1240 [8eeb7f9f] - Add support for Moab resource manager #1224 [3ba51a19] - Add Pbs Pro execution documentation [1d39ab31] - Add code of conduct document - Fix missing LFS executor register invocation #1234 [b1b7ab1] - Fix "invalid pod status" when running scripts with the kubernetes executor #1242 [11caac68] - Revert Fix Environment activation fails with recent versions of Conda #1195 [98c0d1f8] - (includes changes from `19.07.0-edge`, `19.05.0-edge` and `19.05.0-edge`) 19.07.0-edge - 9 Jul 2019 - Fix Remote input file download slowdown submission rate #1206 [b710e21e] - Fix serial publishDir uploads #856 [14774854] - Fix Trace file option is not honoured #1217 - Fix Custom lib path is not added to the classpath #1213 - Fix Discovery executor tracing error [3e26c146] - Add megabyte unit to Slurm memory requirement #1216 [efabdd2f] - Add support for GCP dynamic machine type #1198 [5c2c7665] - Add setCredentialsProvider for submodules #1205 [e2460414] - Improve google pipelines docs [aed407ed] - Improve FileTransfer await termination log #1206 [cb968da7] - Allow trace logging for `com.upplication.s3fs` package [d71b94e1] - Upgrade s3fs lib to version 1.0.6 #856 19.06.0-edge - 21 Jun 2019 - Fix Nextflow indefinitely waiting for killed jobs #981 - Fix Suppress Unknown hashing type logging message #1178 [a005b1b0] - Fix a typo in AWS docs (#1171) - Fix Invalid response cause Google pipelines exec to crash #1163 - Fix kuberun doesn't delete config maps #1165 - Fix Disable ansi logging when using kuberun command #1161 - Fix comparable test with groovy 2.5.8 [3d1c0833] - Fix Unexpected config selector warning #1167 [52e70e31] - Fix Kuberun should honour `-bg` (background) option #1159 [4b160b7b] - Add S3 download retry (#1164) - Upgrade BitBucket provider with API 2.0 [feeddcda] - Print ansi summary for exec > 60 secs [53c94270] - Remove deprecated countText operator #983 - Demote warmup into to debug level [c7d08337] - Demote barrier logging to trace level [5b7234a1] 19.05.0-edge - 20 May 2019 - Add Aws Batch maxParallelTransfers config #1107 [26d37556] - Add NXF_ANSI_SUMMARY var to disable log summary [d4b9cc44] - Add support for AWS user volumes and jobRoleArn [651eeadd] - Add Support for LSF per task resource reserve mode #1071 - Fix Env variable with blanks is not resolved correctly in containers #1146 - Fix method isDynamic visibility [f241781b] - Fix WebLogObserver data leak on completion #1010 - Fix unit test execution [622d97d4] - Fix Quiet cli option is not honoured [e656e4b0] - Fix Log messages don't show in the console #1129 [95f4dd7b] - Fix nextflow build timestamp json rendering [af6584c9] - Fix Launcher should return non-zero exit when fail to step env #1126 - Update get started docs [68f53367] - Update aws sdk to version 1.11.542 - Update created label in timestamp [e8945e8b] - Update readme IDE version - Refactor AWS cli path option [ad9af0dd] - Improve Dsl-2 error reporting [4e2621ff] - Improve CI tests scripts [febeb530] - Improve docs for config profiles [8cf95a5d] - Syntax enhancement aka DSL-2 #984 [651af95a] - Print summary only the run takes > 3mins [cd459713] - Render last tag along with the process name #1144 [8cf8cc44] - Sync build scripts [a5689217] - Provide scm credentials when fetching information about remote branches #1135 [808847b5] - Code cleanup [2322fbcf] 19.04.0-edge - 24 Apr 2019 - Add Experimental support for gpu resources #997 - Fix LSF executor should use mem setting in lsf.config #1124 - Fix Unable to list S3 bucket content #1121 19.04.0 - 15 Apr 2019 - Added support for NCBI_API_KEY variable [e4d9b62c] - Added warning message when using untested Java version [35acd1cb] - Added parameter and workflow metadata to weblog payload #1077 - Added warning on publish with a null var [7d58bfb7] [95c219fb] - Fixed Echo directive when Ansi log is enabled #1112 #996 - Fixed Do not mount inputs when `stageInMode == copy` #1105 - Fixed `splitCsv` operator fails to parse values containing commas #1102 - Fixed missing return type for Date.format method - Fixed Channel operations `toList` followed by `merge` hang execution #1083 - Avoid printing execution summary when no processes are computed #996 - Improved error reporting for null publishDir [0b9b52f0] 19.03.0-edge - 14 Mar 2019 - Fix Nextflow hangs submitting jobs to AWS Batch #1024 - Fix process builder incomplete output [2fe1052c] - Fix Grid executor reports invalid queue status #1045 - Fix Script execute permission is lost in container #1060 - Fix K8s serviceAccount is not honoured #1049 - Fix K8s kuberun login path #1072 - Fix K8s imagePullSecret and imagePullPolicy #1062 - Fix Google Storage docs #1023 - Fix Env variable NXF_CONDA_CACHEDIR is ignored #1051 - Fix failing task due to legacy sleep command [3e150b56] - Fix SplitText operator should accept a closure parameter #1021 - Add Channel.fromSRA factory method #1070 - Add voluntary/involuntary context switches to metrics #1047 - Add noHttps option to singularity config #1041) - Add docker-daemon Singularity support #1043 [dfef1391] - Use peak_vmem and peak_rss as default output in the trace file instead of rss and vmem #1020 - Improve ansi log rendering #996 [33038a18] 19.02.0-edge - 6 Feb 2019 - Added foreign files caching ability #686 - Added Ansi logging as default console output - Added Gitea source code provider [ae04fc37] - Fixed Join operator returns invalid remainder values #1015 - Fixed Invalid trigger of integration tests [7aa5908a] - Fixed memory allocation for SGE executor [29353c90] - Fixed properties access for TaskConfig and LazyMap [09b74a52] - Fixed Invalid decimal separator in mem unit string #999 - Fixed tail error on launcher script [38afea6c] - Improved Execution and Timeline memory reporting #980 #986 #1012 #1014 #1016 #1018 [01426097] [7d6c29f0] - Improved Google pipelines file copy strategy [678405b2] - Improved output file stage out behaviour docs #961 #1013 - Upgraded Groovy runtime to version 2.5.6 19.01.0 - 22 Jan 2019 - Added Google Cloud Platform integration - Added support for K8s nodeSelector #955 - Added new AWS regions #935 - Added json/yaml output to info command #657 - Added More duration and memory unit syntax sugar #921 - Added NO_PROXY env variable should be honoured #864 - Added keepHeader option to splitText operator #912 - Added countLines, countFasta and countFastq methods #972 - Added an env variable to define default cloud driver #973 - Fixed Unable to find JVM 1.8 err message #1000 - Fixed Memory unit should contain thousand separator [e6ec4c84] #989 - Fixed LSF long user names breaks jobs status parsing [b4306151] #988 - Fixed Move output files to storeDir instead of copying them #745 - Fixed Interpolated strings in a from statement are misinterpreted #978 - Fixed ConcurrentModificationException when publishing output files #971 - Fixed Launcher fails with Java 10 or later #953 - Fixed remote bin directory when using bucketDir option [6d796783] - Fixed foreign file system detection [1489cc72] - Fixed Ansi logger division by zero [ae2b1380] - Fixed Unparsable Data format on http file #962 - Fixed Log command history #405 - Fixed Too long process tag name can cause SLURM failure #941 - Fixed LSF can return an inconsistent jobs status #927 - Fixed dump last queue status on failure [36e80242] - Fixed Allow the usage of a custom docker image for K8s driver pod #877 - Fixed K8s executor when the cluster has no available cpus #824 - Fixed Prevent duplicate process definitions #920 - Fixed Update queue statuses used by PBS Pro #908 - Fixed K8s launcher fails to set pod work directory [dc8bfead] - Fixed cmd cloud error message [14d603b9] - Fixed RejectedExecutionException on successive Console executions #906 - Fixed Invalid config rendering #801 - Fixed Invalid warning message for config selector #905 - Fixed Queue status command fail on LSF version 8 #910 - Fixed Use `bash` instead of `sh` to fetch queue status - Improved script runner api [da4a6c17] - Improved file hashing logging [0d35b2b4] - Refactored ScriptRunner class [15ee2f1c] - Refactored DSL code visitor [67904c1f] - Revert "Apache Ignite to version 2.6" #909 - Better report warning when grid status command fails [3ac8b972] 19.01.0-edge - 10 Jan 2019 - Enhanced timeline and execution reports #985 #986 [fb00c3a6] [092f0b9e] - Enhanced BashWrapperBuilder using template file [7d7e116a] [c62b9dff] - Fixed CPU usage accounting #982 [7d7e116a] [c62b9dff] - Fixed Move output files to storeDir instead of copying them #745 - Fixed Interpolated strings in a from statement are misinterpreted #978 - Fixed Launcher fails with Java 10 or later #953 - Fixed LSF long user names breaks jobs status parsing [b4306151] #988 - Fixed Memory unit should contain thousand separator [e6ec4c84] #989 - Fixed Allows fromFilePairs to handle non globs #946 - Added an env variable to define default cloud driver #973 - Added countLines, countFasta and countFastq methods #972 - Added NXF_DIST launcher variable #954 - Added NXF_SMOKE var to disable long running tests - Deprecated groupBy and route operators [b7ca53d2] - Updated S3 storage classes #977 - Updated groovy to version 2.5.5 - Updated copyright disclaimer - Refactored project structure [516294e7] - Speed-up CI tests [3320dcec] 18.12.0-edge - 18 Dic 2018 - Add Google Cloud Platform integration - Added support for K8s nodeSelector #955 - Added new AWS regions #935 - Added json/yaml output to info command #657 - Fixed remote bin directory when using buckerDir option [6d796783] - Fixed foreign file system detection [1489cc72] - Fixed Ansi logger division by zero [ae2b1380] - Fixed Unparsable Data format on http file #962 - Fixed Log command history #405 - Fixed Too long process tag name can cause SLURM failure #941 - Fixed LSF can return an inconsistent jobs status #927 - Fixed dump last queue status on failure [36e80242] - Fixed Allow the usage of a custom docker image for K8s driver pod #877 - Fixed K8s executor when the cluster has no available cpus #824 - Fixed Prevent duplicate process definitions #920 - Fixed Update queue statuses used by PBS Pro #908 - Fixed K8s launcher fails to set pod work directory [dc8bfead] - Fixed cmd cloud error message [14d603b9] - Improved script runner api [da4a6c17] - Revert "Apache Ignite to version 2.6" #909 - Fixed Invalid config rendering #801 - Improved file hashing logging [0d35b2b4] - Refactored ScriptRunner class [15ee2f1c] - Refactored DSL code visitor [67904c1f] 18.11.0-edge - 12 Nov 2018 - Added More duration and memory unit syntax sugar #921 - Added NO_PROXY env variable should be honoured #864 - Added keepHeader option to splitText operator #912 - Fixed Invalid warning message for config selector #905 - Fixed Queue status command fail on LSF version 8 #910 - Fixed Use `bash` instead of `sh` to fetch queue status - Better report warning when grid status command fails [3ac8b972] - Fixed RejectedExecutionException on successive Console executions #906 18.10.1 - 24 Oct 2018 - Fixed test [011e8e23] - Fixed version number check [fb780347] 18.10.0 - 24 Oct 2018 - Added lenient cache mode #828 [ba907a2f] - Added support for java 11 [60da50b5] - Added support for Singularity 3.0 library #898 - Added support for AWS Batch hybrid executions #744 - Added weblog JSON format docs #882 - Added weblog example documentation #891 - Added PbsPro executor [33ae1104] - Added support for ANSI console logging [9c14a947] - Fixed License prevents scientific use #788 - Fixed process submitter slow-down [495e900a] - Fixed Comparing duration and memory units with null throws an exception #872 - Fixed Html format dag fails when 'each' qualifier is used #887 - Fixed Collate/Buffer hangs with one emission after Collect operator #868 - Fixed Option checkIfExists should be applied when a glob pattern does not match any file #874 - Fixed Add name to manifest and reject other attributes #871 - Fixed warning message grammar when resuming on new project #885 - Fixed Missing DSL Xform transformation in console execution [9621f8c6] - Fixed Enum declared in nextflow script causes error #878 - Fixed Report a warning message when queue status fetch fails [39aae6a2] - Fixed Pbs executor may return nonzero exit code when checking queue status #904 - Renamed weblog `runStatus` to `event` #892 - Renamed K8s config attribute userDir to launchDir #895 - Merged tests as subtree [a03eb59a] - Refactored service discovery - Removed FastXxxYyyyStream - Demoted igfs subsystem - Upgraded Groovy to version 2.5.3 [119300b3] - Upgrade Gradle to version 4.10 - Updated AWS batch docs 0.32.0 - 8 Aug 2018 - Fixed CPU usage metrics can be wrongly reported #858 - Fixed Allow a process to access input file metadata #731 - Fixed Completed jobs are detected with a big delay #799 - Fixed Misleading message is shown when pulling a project with a invalid config #863 - Fixed Allow groupTuple operator to handle multi-size tuples #796 - Fixed Ignite executor fills up logs when node is disconnected #810 - Fixed Log filter option is misinterpreted when enclosed in double quotes #846 - Fixed Metrics collector process may cause the main process to report a false non-zero exit status #836 - Fixed K8s imagePullPolicy is not included in the pod spec #815 - Fixed Splitter caching is too eager when caching path is specified #835 - Fixed Improve error message for missing git provider configuration #847 - Fixed Byte hashing is never reached in CacheHelper class 9ac81153 - Fixed K8s launcher should not delete pod when `login` command fails (5175942a) - Fixed Dump operator should nicely print ArrayBag content (91e371ba) - Added manifest data in workflow metadata object #841 - Added support for K8s imagePullSecrets pod attribute #800 - Added option "checkIfExists" to Channel.fromPath method #666 - Upgraded Apache Groovy to version 2.5.1 - Upgraded Apache Ignite to version 2.6 - Upgraded Slf4j to version 1.7.25 - Upgraded Logback to version 1.1.11 - Upgraded Grengine to version 1.3.0 - Upgraded LevelDB to version 0.10 - Upgraded Guava to version 21.0 - Upgraded Spock to version 1.2 - Using javax.activation:activation:1.1.1 (from com.sun.activation:javax.activation:1.2.0) 0.31.1 - 7 Aug 2018 - Fixed AWS Batch execution hangs when running on 1 cpu machine #825 - Fixed AWS Batch fails if process tag length is too long #822 - Fixed AWS Batch executor creates timeline report with missing time data #816 - Added Ignite failure detection timeout configuration parameters #820 - Added VersionNumber class to CacheHelper handler [90fb69fa] - Added CONTRIBUTING file #564 0.31.0 - 25 Jul 2018 - Fixed CLI parameter value starting with a `-` is misinterpreted #808 - Added keep-logs option to clean command #775 0.31.0-RC1 - 19 Jul 2018 - Fixed K8s pod request should include resources spec when 1 cpu is specified #806 - Fixed PBS executor should fail when submit response contains invalid data #753 - Fixed SLURM executor fail to submit jobs when cluster option is specified #805 - Fixed Allow the use relative paths for symlinks process input files #296 - Fixed AWS batch jobs are not properly stopped when execution is interrupted #782 - Fixed splitCsv is not properly handling blank lines #795 - Fixed K8s pod runAsUser definition #707 - Fixed Prevent NPE when K8s reports an empty pod state [dcc7ec5f] - Fixed Allow list of patterns for fromPath and fromFilePairs channel factories #732 - Fixed K8s execution hangs if an invalid pod secret file is specified #754 - Fixed Correctly shutdown executor service #732 - Fixed bug in dot rendering due to unquoted graph name when DOT language keyword used #783 - Fixed Execution hangs if one or more inputs evaluate to null #764 - Fixed Method `file` should thrown an error null is given as input #765 - Fixed invalid relative link resolution with `readlink` - Added AWS batch requests throttling handling #710 #709 - Added AWS Batch parallel downloads/uploads [codefest] [8ba1716b,ba5ad7a8] - Added K8s pod config and security context definition #707 - Added Container env variables whitelist #803 - Added support for K8s pod labels #762 - Added support for K8s volume mount subPath #758 - Added Nextflow required version in the config manifest #752 - Added disk resource requirement in LSF executor #747 - Added GA4GH TES executor [experimental] #794 - Added System info to workflow metadata object #759 - Added weblog feature #681 - Deprecated process.$name syntax to define process specific settings #713 - Upgrade to Gradle 4.9 0.30.2 - 16 Jun 2018 - Fixed Output declarations with a glob pattern fail when AWS Batch executor is used #748 - Fixed Scratch directive not working for AWS Batch executor #740 - Fixed K8s launcher does not parse remote config files #738 - Minor refactoring to enable Groovy 2.5 compilation 20b6d933 a8b994f1 0.30.1 - 11 Jun 2018 - Use a daemon thread for watchPath method #735 - Fixed Gitlab API v3 has been deprecated and does not work any more #734 - Fixed Unable to access params defined in the top scope from a nested profile #733 - Fixed Process config selectors do not work when the config is included #729 - Fixed Improve the error message when a missing property is used in the config file #730 - Added Travis build support for jdk10 - Added documentation for `until` operator #736 - Added mailer recipients check - Increased Singularity pull timeout to 20 minutes - Updated build to Gradle 4.8 0.30.0 - 5 Jun 2018 - Added the support for Bioconda #493 - Added support for AWS Batch job timeout #648 - Added jobs submit rate limit #198 - Added offline option #665 - Enabling Java 9/10 support for build and launcher scripts #674 - Fixed Expose Kubernetes Secrets to worker pods #651 - Fixed K8s execution hangs when a non-existing docker image is specified #697 - Fixed K8s execution terminates abruptly if a pod requires more resources than available ones #676 - Fixed K8s executor does not report command log when a task fail #699 - Fixed Configuration profile is not handled properly by the kuberun command #696 - Fixed Enhance process metrics to avoid usage of ps tool #499 - Fixed PublishDir should use copy mode by default when the target is a S3 path #718 - Fixed Unbounded variable breaks task launcher script #722 - Fixed Escape filenames when copying from S3 #717 - Fixed AWS executor should use putObject API to upload job scripts to S3 #712 - Fixed Exception is thrown when an output folder contains a circular symlink path #701 0.29.1 - 10 May 2018 - Fixed Default ext property are not included in process context #673 - Fixed Operator concat throws a ConcurrentModificationException #675 - Fixed Output file is not recognised when it's created into a subdir and the name matches an input #688 - Fixed Empty container definition being ignored when default one is specified #691 - Fixed K8s client fails to connect the cluster when client key nor certificate is specified #692 - Fixed K8s executor hang on pod creation failure - Added select in -R for memory for LSF executor #683 0.29.0 - 24 Apr 2018 - Fixed Buffer operator fails to recognise optional parameter when a closing condition is specified #652 - Fixed PublishDir mode "copyNoFollow" does not work for directories #658 - Update NameGenerator adjectives #656 0.29.0-RC1 - 8 Apr 2018 - Added `containerOptions` directive #415 - Added support for multiple `publishDir` directives for process #256 - Added cleanup feature to delete workflow work dir on completion #649 - Added label directive and process configuration selectors `withLabel` and `withName` #623 - Fixed Invalid process cache when using a different environment module #627 - Upgrading groovy runtime to version 2.4.15 0.28.2 - 6 Apr 2018 - Fixed Class FtpURLConnection is not accessible when using Java 9 #646 - Fixed Lengthen mktemp TEMPLATE so works on BusyBox #647 - Fixed Report HTML/CSS tweaks to make progress bar text overflow work properly #645 - Fixed typo in the nextflow launcher #643 0.28.1 - 27 Mar 2018 - Fixed A HTTP access error is raised when the URL contains a ? character #634 - Fixed Creation of temp files in the /dev/shm directory can result in a permission error in some Linux installations #638 - Make process echo safer 0.28.0 - 10 Mar 2018 - Fixed Singularity pull is executed even when container execution is disabled #628 - Fixed issue when setting container attribute to `false` [9de636c5] - Added MemoryUnit getters [f99d2dc9] - Added default NXF_TEMP variable [d36ac4dd] - Added progress stacked bars to workflow report #534 [455fcb4f] - Added namespace option to `kuberun` command [50154ec5] - Improved workflow stats and warn report [e795b134] - Improved K8s error reporting [86f172eb] 0.28.0-RC1 - 27 Feb 2018 - Added support for directory wildcards in input file declarations #568 - Added ability to access task existStatus value as an output value #577 - Added ability to use property syntax in the declaration of output values #578 - Added NXF_JAVA_HOME variable to specify nextflow nextflow JVM #607 - Added support for docker mount flags #572 - Added ability to select multiple configuration profiles #370 - Added ability to copy symlinks to publishDir directive #592 - Added missing native_id TraceRecord field to K8s and AWS Batch task handlers - Enhanced support for Kubernetes #468 - Fixed Launcher breaks when JAVA_HOME path contains a blank char #616 - Fixed Operator toList hangs when applied to a value channel #612 - Workflow report should warn if some task executions were ignored #534 - Enable support for large execution reports #547 - Replaced the use of named pipes with anonymous pipes #606 - Enhance the config command show dynamic attributes #604 - Fixed bin path is not recognised when contains a blank char #603 - Fixed A NPE exception is thrown when a env variable is assigned to an null value #593 - Fixed summary stats when for empty series #547 - Removed support for Extrae #588 - Removed support for DRMAA #587 0.27.6 - 19 Feb 2018 - Fixed Operator toList hangs when applied to a value channel #612 - Allow launcher to track installation verb 0.27.5 - 15 Feb 2018 - Fixed dir/* input file pattern invalidate cached processes #610 - Fixed Mail attachment are not correctly recognised by the email client #609 - Fixed Workflow metadata container attribute is not resolved when it's defined dynamically #602 0.27.4 - 5 Feb 2018 - Fixed Resume does not work for tasks successfully executed in a re-submit attempt #591 - Fixed An error is reported when a NF script contains a class definition #594 - Fixed Launcher error when download target path contains a blank character 0.27.3 - 29 Jan 2018 - Fixed publishDir directive fails on S3 when attempting to copy objects larger than 5 GB #585 - Process name does not reflect dynamic tag declaration when a task execution is retried #586 - Fixed examples in the documentation - Update to Gradle 4.5 0.27.2 - 23 Jan 2018 - Fixed Config property keys may contain invalid characters - Fixed Local process kill signal is not propagated to children processes #581 - Fixed Operator join throws a stack overflow exception when an invalid argument type is specified #582 0.27.1 - 18 Jan 2018 - Fixed Invalid cast exception when cpus value is missing #575 - Fixed Kill the tee commands when the launcher script exit #574 - Fixed Splitter `limit` option is not honored when splitting more than one file #573 - Fixed AWS CLI operations with S3 should use the --only-show-errors options #567 - Fixed Splitter by option is not honored when splitting more than one file #570 - Documentation editing/improvement 0.27.0 - 9 Jan 2018 - Fixed Log command prints true instead of actual message #561 - Fixed NXF_TEMP definition when instanceStorageMount is set - Improved S3 exitfile logging - Improved cloud config canonical formatting 0.27.0-RC2 - 29 Dic 2017 - Fixed Ignore Windows instances from AWS cloud price listing - Fixed AWS price reader catching unexpected errors - Fixed sendMail access to owner variables - Fixed NPE when creating task with ignite executor - Fixed null exit status in notification template #554 - Added XPath serialiser - Added mail smtp proxy configuration #375 - Added built-in notification documentation #554 - Added built-in mail documentation #375 - Added support for Syslog logging #330 #557 - Improved support for AWS EC2 instance storage #558 - Improved documentation #558 - Improved config command adding `-flat` and `-properties` formats and using canonical curly brackets format as default - Update copyright info 0.27.0-RC1 - 20 Dic 2017 - AWS Batch increased queue to 1000 tasks and poll interval to 10 secs - AWS Batch improved executor scalability caching recurrent API call and batching similar requests together - Added notification message on workflow completion #554 - Added Built `sendMail` function #375 - Added Warning message when a local version on a GH repo is different from remote #376 - Added keepHeader option to collectFile #479 - Added Dump operator to enable easier debugging #517 - Fixed Report an error message when a config file contains an unresolved attribute #525 - Fixed Session working file system not defined when staging input files with Ignite executor #555 - Fixed storeDir writes output files even when process fails #227 - Fixed storeDir does not work with S3 targets #247 - Fixed Config file available in introspection #264 - Fixed Enhance container interoperability between Docker and Singularity #503 - Fixed Process environment is not exported in the container context when a process uses an interpreter other than BASH #495 - Deprecated support for executable containers #529 - Deprecated DRMAA executor #488 - Deprecated Extrae profiling #543 - Renamed .command.run.1 to .command.stub #523 0.26.4 - 11 Dec 2017 - Fixed GitLab auth token is not applied when user credentials are not provided #542 0.26.3 - 30 Nov 2017 - Fixed AWS Batch S3 upload function does not work if output is a directory #539 - Fixed AWS Batch S3 uploaded function does not resolve glob patterns containing curly brackets #535 - Added author field in the config manifest scope #537 - Upgrading s3fs library to 1.0.2 version supporting `signerOverride` S3 config property. 0.26.2 - 27 Nov 2017 - Fixed readlink illegal option when installing in macOS #527 - Fixed Getting not descriptive error when using a when condition and script statement is not explicit #528 - Fixed Function nxf_module_load matches partial names #530 0.26.1 - 17 Nov 2017 - Execution report enhancements #521 - Fixed Add AWS_DEFAULT_REGION environment variable to bash wrapper scripts #512 #513 - Fixed New launcher script does not allow the execution of legacy version with Java 7 #519 - Fixed Error message reporting file name collision is misleading #516 0.26.0 - 8 Nov 2017 - Fixed file method does not interpret correctly S3 path with globs #509 - Fixed Execution hangs when the amount of requested resources exceed the available ones #502 - Minor change in the execution report #507 #508 - Make AWS clustering compliant with billing by seconds - Refactored `nf-token` AWS job definition parameter #475 - Run Batch task in a scratch directory to avoid undefined execution folder #475 - Renamed `iamProfile` to `instanceRole` #422 - Renamed ProcessNotRecoverableException to ProcessUnrecoverableException 0.26.0-RC2 - 30 Oct 2107 - Fixed TMP and TMPDIR variables are not passed in Singularity environment #496 - Fixed Dynamic resources directive when defined both in a process and the config file cause an error #497 - Added Experimental support for Shifter containers #500 #501 - Improved AWS Batch task logging and task attempts - Improved Execution report showing task realtime instead of task duration on time box plot 0.26.0-RC1 - 24 Oct 2017 - Added support for AWS Batch #475 - Added support for AWS IAM role #422 - Added Experimental support for Java 9 #462 - Added transpose operator #440 - Added join operator #460 - Added html report (-with-report option) - Added Gzip compression support to splitXxx operators #484 - Added Support PE Fastq files splitting #436 - Added Operator splitFasta should allow the creation of chunk having the same size #472 - Added HTML execution report #490 #491 - Added New scientist names #485 - Improved merge operator #458 - Improved value channel handling for reduce, filter, first, take and randomSample operators - Prints a warning message when the config file defines setting not matching any process definition - Fixed HEAD is detached error #389 - Fixed Include container name when calculating cache key #443 - Fixed Invalidate process cache when a referenced external script is modified #413 - Fixed Execution failure is not reported in the trace file when retry error strategy is used #404 - Fixed "when" directive should not allow staging of input files for a process, if the criteria are not met #424 - Fixed Failure during foreign files download cause execution to stop abruptly #295 - Fixed The parameter groupName cannot be used with the parameter subnet #465 - Fixed unable to download from gitlab.com public repository #457 - Fixed Print work directory when a task fails #445 - Fixed Misleading command line parameter type conversion #434 - Fixed Nextflow should not stage files that have the same name #470 - Fixed SplitCsv returns array objects instead of Lists #487 - Fixed Cannot cast object FtpURLConnection error #482 - Fixed Nested Environment Module names are not loaded properly #489 - Removed support support for Java 7 #385 - Removed deprecated Cirrus/ClusterK executor - Removed deprecated support for DNAnexus #386 0.25.7 - 6 Sep 2017 - Fixed Unable to parse the AWS price list API #444 - Added seed parameter to `randomSample` operator #410 0.25.6 - 13 Aug 2017 - Fixed Empty channel waiting forever when viewed and mixed #428 - Fixed Error Channels cannot be used as input in more than one process or operator #429 - Fixed Script body is resolved even if the `when` guard evaluate to false - Added queue process directive as option for trace file 0.25.5 - 4 Aug 2017 - Fixed NF fails to pull images hosted in the Singularity Hub #414 - Added `-y` to cloud create command to skip confirmation request 0.25.4 - 31 Jul 2017 - Removed invalid debug information 0.25.3 - 31 Jul 2017 - Fixed NPE when parsing AWS price file #408 - Fixed Grid queue status return wrong data when a process change the submission queue dynamically #412 - Fixed MPI-like execution for SLURM batch scheduler - Fixed NPE when log params key is not defined - Fixed Optional parameter for set #399 - Added automatic pull for Singularity remote images #356 - Added London and Canada AWS regions - Merged Pass NXF_OPTS to JVM during the java version check to allow memory definition on memory-restricted environments #411 - Improved error message in launcher file 0.25.2 - 3 Jul 2017 - Fixed Execution hangs if a job submission fail #396 - Fixed stdout can not be sent into multiple channels #388 - Fixed Pipeline execution hangs when a process exceed the time limit and retry error strategy is used #387 - Added scientists and adjectives to run name generator - Deprecated `route` operator 0.25.1 - 27 Jun 2017 - Duplicate mount point docker error #384 - Disable Docker read-only mounts by default 0.25.0 - 26 Jun 2017 - Fixed Dataflow threads pool get exhausted with a large number of tasks #92 - Fixed Custom function cannot be invoked in the workflow completion handler #374 - Fixed Runtime errors are not reported in the `workflow.errorMessage` property #369 - Fixed Warn if params.something is defined twice in a NF script #372 - Fixed Map.Entry values deserialization process fail #373 - Fixed List active operators that may hang the script execution #315 - Fixed launcher error message #366 - Fixed AWS spot instance bootStorageSize property is ignored #368 - Fixed Implicit variable `task` is not accessible in cached processes #363 - Fixed Do not export user environment when submitting job to SGE-like batch scheduler #362 - Fixed Process termination can throw a ConcurrentModificationException hiding the error cause message #359 - Fixed GroovyRuntimeException during foreign file copy process #360 - Fixed Helper function to compare version numbers #319 - Fixed Docker input file mounts should be read-only for enforce container security #346 - Fixed Extend `each` repeater syntax to support file collections #355 - Fixed Modified task properties are not accessible in the command script during task retry #345 - Fixed PublishDir warning message - Fixed Spread operator mishandles Iterable values provided as a dataflow variable #353 - Fixed UUID cli options are wrongly interpreted as Duration objects #349 - New toInteger and toLong converter operators - New randomSample operator #344 - New `simpleName` extension method to Path/File objects #354 - New warning message when input tuple cardinality does not match declared length #348 - Improved use example into ext directive documentation #327 - Improved error handing when parsing trace file #371 - Improved error reporting for process missing input definition - Improved launcher script to support https protocol by default #379 - Change `maxErrors` default to -1 - Deprecated identifier `channel` as variable name 0.24.4 - 19 May 2017 - Fixed PublishDir creates nested directory structures when a folder already exists #342 - Fixed NoSuchFileException is thrown when trace file path does not exist #334 - Fixed watchPath glob directory not working #335 - Fixed Channel.fromFilePairs does not handle properly multiple star wildcards #337 - Added executor for NQSII, queuing system used on NEC clusters. - Added `relative` option to `fromPath` channel factory 0.24.3 - 24 Apr 2017 - Fixed Process execution fails with not GNU version of sleep and date tools #321 - Fixed Pending processes are not cleaned up properly #322 - Fixed NPE is thrown when Singularity is enabled and a process uses no container #324 - Fixed Cached processes are not included in the timeline report #325 - Added MD5 digest file upload - Updated docs 0.24.2 - 5 Apr 2017 - Fixed Tuple array object deserialisation fails #317 - Use SLURM squeue —-noheader instead -h command line option to support not standard implementation #316 - Fixed Execution time is incorrect for the local executor #313 0.24.1 - 24 Mar 2017 - Fixed Improve explanation of cache DB IOException #303 - Fixed Operator ifEmpty results in a error when applied to a dataflow variable #308 - Fixed Process execution fails when the work path contains a parenthesis character #310 - Fixed Installer script fails when current path contains a blank character #311 - Fixed Include SLURM partition when checking job status #312 - Allow the usage of `close` operator on unbounded dataflow variable 0.24.0 - 20 Mar 2017 - Added new `combine` operator #298 - Added new `collect` operator #297 - Added new CLI option `-params-file` to load parameters from a json/yaml file #208 - Fixed SCM user name is not set accessing private repository #300 - Fixed Infer singleton process outputs from inputs declaration #301 - Fixed Use exit status 1 for all NF errors #304 - Fixed Invalid SGE job name as defined in `sge_types` #299 - Added `skip` parameter to collectFile operator #306 - Added experimental `fs` command - Improved file staging error reports #295 - Upgraded Groovy to version 2.4.10 0.23.4 - 24 Feb 2017 - Fixed Show a warning message when accessing undefined parameters #293 - Fixed Staging input files in a subfolder changes their names when they are symlinks #292 - Fixed NPE accessing foreign files - Added column char to list of path escaped chars - Fixed Boothook script fails on Ubuntu 16.04 0.23.3 - 9 Feb 2017 - Fixed Job termination is not recognised if the starter file is not created #268 - Fixed Allow NF console to resume process executions (second take) #280 - Fixed PublishDir may throw a FileAlreadyExistsException #283 - Increased logger file appender buffer size to 64kb - Updated Logback to version 1.1.10 - Updated copyright info - Fixed NXF_DEBUG level 0.23.2 - 2 Feb 2017 - Improved history lock error message - Fixed typo in warning message - Added `cleanup` to list of accepted directives - Added NXF_OWNER to kubernetes executor - Fixed Function nxf_kill is not invoked properly on a containerised process #275 - Fixed Pending grid jobs are not cancelled upon pipeline interruption - Documented that the toSortedList operator can accept a comparator closure #277 0.23.1 - 23 Jan 2017 - Fixed FixOwnership flag break non BASH scripts/templates #270 - Fixed Fixed PBS Executor should not have parenthesis #271 - Fixed Function nxf_kill is not invoked properly on process termination #275 - Fixed Timeline.html is not working on IE11 #272 - Fixed Merge process specific extended properties with the ones defined in the default scope #273 - Fixed Using storeDir and publishDir in the same process yields unexpected results #266 0.23.0 - 13 Dec 2016 - Added support for Singularity containers #252 - Added support for HTTP/S and FTP files (read-only) - Fixed stream close leak while copy foreign file to local file system - Fixed Task scheduling may hang while checking for job completion #261 - Fixed Specifying the keyFile cloud config attribute result in an error #263 - Added support for multiple target channels in `tap` operator #255 - Added `uri` property to Path and File objects - Made NXF_SCRATCH variable accessible to `beforeScript` handler 0.22.6 - 4 Dec 2016 - Fixed Script execution terminates before all operators complete #259 - Fixed A script variable with the same name of a global variable invalidate process resume #254 - Fixed `when` is not recognised when used before an `input` and `script` is not declared - Fixed count operator hung when applied to a dataflow variable - Added warning message when an input/output `set` defines only one component #216 #251 - Reduced log verbosity of Ignite Scheduler classes 0.22.5 - 17 Nov 2016 - Fixed QueueSize=1 doesn't handle multi-cpu processes #246 - Fixed Accessing to a not defined script params should raise an error #243 - Fixed An input channel evaluating to null results in a misleading error message #242 - Fixed Use of publicDnsName should failover to IP if no name is available #240 - Fixed Use of yum in cloud boothook may cause problems #239 - Fixed Execution hang when an operator invokes the `exit` function and no processes have run - Fixed fromFilePairs does not match patterns containing curly brackets w/o a star wild character - Added `-dump-hashes` command line option to print task key hash keys #211 - Improved logging 0.22.4 - 4 Nov 2016 - Added `—no-requeue` flag to SLURM job submission - Report log content when a wrapper script execution fail #213 - Improved error message when cache DB cannot be created - Logging error track trace on task re-submit failure - Fixed Channel.fromPath throws an exception when the argument is a S3 path - Modified `make_temp` so that uses `NXF_TEMP` when defined 0.22.3 - 12 Oct 2016 - Fixed PBS qsub fails when the job name is longer than 15 chars #228 - Fixed Spread operator doesn't connect channels in DAG #231 - Fixed amazon prices file format parser - Added Cleanup scratch dir upon process completion #230 - Added `optional` flag to output file declaration - Added `region` option to `cloud` command - Added Check for missing instance type description 0.22.2 - 3 Oct 2016 - Fixed Copy input files to scratch directory #197 - Fixed PBS qsub fails when the job name starts with a dot #228 - Fixed issue when staging-out a symlink output file - Fixed log warning when running a script in the console 0.22.1 - 26 Sep 2016 - Fixed Nested symlinks are not resolved by Docker container mounts #222 - Fixed Nextflow execution log fail to get field starting with '%' #223 - Fixed Nextflow console launcher - Added `ContainerCreation` status to K8S executor - Expand `=` to `==` in filter expressions to avoid misleading results 0.22.0 - 19 Sep 2016 - Fixed queue-size attribute for local executor - Fixed Kubernetes pod id parse issue - Move `.nextflow.history` and `.cache` files under `.nextflow` directory 0.22.0.RC2 - 12 Sep 2016 - Fixed File name containing glob wildcards cannot be captured in the process output #219 - Fixed Work dir containing glob wildcards are not supported #194 - Added `revision id` to execution log - Added `scriptId`, `scriptFile` and `scriptName` attributes to workflow metadata object - Added time delay penalty on error burst to prevent failing node to drain all pending jobs - Load classes without creating an instance of each cloud driver - Improved AWS driver missing credentials error report - Merged experimental Kubernetes support - Improved clean and log command - Added EFS default mount path - Refactored daemon shutdown 0.22.0.RC1 - 1 Sep 2016 - Fixed Implement clean up command #19 - Fixed Trace file should include cached tasks #114 - Added ability to log each command run #108 - Added new `cloud` command - Added AWS EFS support - Added AWS Spot instance error fail-over - Added support cloud auto scaling - Added Ignite job-stealing distributed scheduler 0.21.3 - 26 Aug 2016 - Fixed Spaces in work directory path stops slurm from accepting the job #218 0.21.2 - 12 Aug 2016 - Fixed PBS professional batch scheduler submission error #209 - Fixed Reference to a collection of files is not resolved properly in the output section #214 - Improved failed and ignored processes reporting - Fixed null workflow.projectDir when launching a script file - Do no output link file when `followLinks` option is disabled 0.21.1 - 29 July 2016 - Fixed NFS work dir is not detected correctly #206 - Fixed `splitFasta` operator with the file parameter will not split into single fasta files #181 - Enable log file for commands when debug or trace option is specified - Added validation checks to `fromPath` and `fromFilePairs` methods 0.21.0 - 20 July 2016 - Fixed Command line params do not override params defined in the nextflow.config file #202 0.21.0-RC1 - 14 Jul 2016 - Fixed Ability to customize job name submitted to the scheduler #140 - Fixed Duplicate output error when no channel specified #182 - Fixed File paths containing a timestamp are parsed as a Duration object #185 - Fixed ClosedByInterruptException is thrown randomly #188 - Fixed Pipeline hangs when `Channel.from` argument is an empty list #189 - Fixed Handle customised sbatch returning the jobid by itself #190 - Fixed LocalExecutor can randomly hang with no running task #191 - Fixed Missing flag in SLURM `squeue` call #193 - Fixed Process script declaring a regexp expression results in a IllegalAccessException #199 - Merged Silence mkdir error if NXF_HOME not writable #187 - Refactored ParallelTaskProcessor and TaskProcessor classes to a single class - Added `ST` and `BF` queue statuses to SLURM executor - Improved logging information - Upgrade to Gradle 2.14 0.20.1 - 18 Jun 2016 - Fixed Directives do not accept a negative numeric value #180 - Fixed Dynamic errorStrategy is not evaluated correctly #183 - Fixed Pipeline hangs when error strategy is used and an upstream process fail - Added environment to ContainerBuilder and implement environment export for Shifter containers - Updated Groovy runtime to version 2.4.7 0.20.0 - 8 Jun 2016 - Added fromFilePairs channel factory method - Added `finish` error strategy #158 - Added ability to change the name and the save path of published files #178 - Added a syntax validation check for process blocks keywords #177 - Fixed It's not possible to specify environment modules w/o a version number #174 - Fixed Local process kill signal is not propagated to children processes #172 - Fixed scratchDir is overwritten by TMPDIR #171 - Removed deprecated `Channel.path` methods - Ignore missing COUT and CERR variables 0.19.4 - 3 Jun 2016 - Fixed Exception is thrown while reporting an invalid output declaration #170 0.19.3 - 31 May 2016 - Fixed Local executor does not run an job when host cpus == 1 #166 0.19.2 - 26 May 2016 - Fixed Module load problem #161 - Fixed PublishDir does not overwrite symlinks #163 - Fixed Implement resource accounting for local executor #162 - Fixed PublishDir fail to move the output directory when the target is a S3 path #160 0.19.1 - 19 May 2016 - Fixed Spread operator is using deprecated `just` operator #159 - Fixed Invalid call to `notifyError` method - Fixed Invalid URL in citoscape.js DAG template - Improved documentation 0.19.0 - 18 May 2016 - Added Pipeline execution DAG #147 - Added support for OpenLava batch scheduler #152 - Added `-revision` option to `pull` command #110 - Set `UTF-8` as default file encoding #149 - Fixed Extend support for empty curly glob pattern #154 - Fixed Add process directives validation #153 - Fixed Calculation of freePhysicalMemorySize does not currently take disk cache into account #150 - Fixed Improve error message when pulling a non-existing branch could be more explicit #156 - Updated JGit to version 4.3.1 0.18.3 - 9 May 2016 - Fixed Timeline report no longer works in Safari #143 - Fixed Invalid or corrupt jarfile if your CTRL-C initial run of nextflow #145 - Fixed Pipeline execution hangs when the into declaration is not provided #146 0.18.2 - 3 May 2016 - Fixed Variable task.exitStatus throws an exception when comparing it to an integer value #142 - Fixed PublishDir does not handle hard linking of directories #126 - Added `index` implicit variable to the `task` execution context #139 - Improved installer messages - Updated Gradle runtime to version 2.13 0.18.1 - 26 Apr 2016 - Fixed Input files containing a parenthesis in the path are not staged properly #133. - Fixed Process execution hangs when using Ignite executor with a foreign work path #136. - Fixed Sort output files in lexicographical order #137. - Added `false` as `sort` option in the `collectFile` operator. 0.18.0 - 11 Apr 2016 - Added `legacy` option to docker configuration properties. Added support for `--cpuset-cpus` Docker command line option. See #115 - Added `region` option to AWS S3 config properties #116 - Added support for AWS S3 multipart uploads #112 - Added `NXF_TRACE` to enable application trace logging - Added experimental support for Shifter containers - Added experimental support for HTCondor scheduler - Fixed Input file names staged into a subdirectory are not expanded properly #111 - Fixed Main script class name collides with variable names in global scope #113 - Fixed config file having a name as a top level config options raise a MissingPropertyException #117 - Fixed Process script errors should not be ignored #119 - Fixed timeline margin for long labels - fix #120 - Fixed Process `start` time is not reported correctly when using the Ignite executor #122 - Fixed Allow for a per-job memory limit for LSF executor #123 - Fixed Memory reservation should not be divided by the number of cpus #124 - Fixed Mixed content errors if timeline.html served over HTTPS #127 - Fixed Nextflow won't start if a proxy URL env variable contains a trailing slash #109 - Set poolSize as the number of avail cpus - Set `java.io.tmpdir` to the same path as `NXF_TEMP` - Updated Apache Ignite to version 1.5.0 - Updated Logback to version 1.1.6 - Updated Slf4j to version 1.7.21 - Updated JGit to version 4.3.0.201604071810-r 0.17.3 - 18 Feb 2016 - Fixed task status in the trace file when execution is retried #107 - Improved Ignite scheduling and node resources allocation - Upgraded Logback to version 1.1.5 - Upgraded Slf4j to version 1.7.16 0.17.2 - 2 Feb 2016 - Fixed Channel.subscribe is invoked after the Workflow.onComplete handler #105 - Changed default trace file name to `trace.txt` #106 - Changed launcher classpath cache file under user home - Added JobStealingFailoverSpi to Ignite executor - Update JGit to version 4.2.0 0.17.1 - 21 Jan 2016 - Fixed splitText performance issue #102 - Fixed execution hang when a process script block report and error and retry error strategy is set - Added support for partition to SLURM executor #101 - Use a dedicated reentrant lock to handle task completion event 0.17.0 - 7 Jan 2016 - Fixed PBS/Torque executor does not parse correctly job IDs #96 - Fixed issue when `TraceFileObserver` tries to access task context metadata on task completion #98 - Fixed support for Git local bare repositories #95 - Fixed single quotes in file names result in script error #99 - Added workflow.sessionId and workflow.resume attributes #94 - Added output into multiple channels #97 - Added `attempt` field to execution tracing - Do not allow output clause to reference files outside the process working directory (see #91) 0.16.5 - 18 Dec 2015 - Fixed race condition when creating cached launcher class path file - Fixed `run` for local repositories - Enhanced output file handling #91 - Set thread pool size to avail cpus +1 - Removed config object from remote session that was causing a serialization issue - Upgraded Slf4j to version 1.7.13 0.16.4 - 6 Dec 2015 - Use batch strategy to kill pending cluster jobs on termination #93 - Added support for Git Large File Storage (LFS) extension #82 - Added configurable thread pool factory #92 0.16.3 - 30 Nov 2015 - Fixed #90. System `user.dir` property is cached causing unexpected behaviour. - Allow directories in a process input file name declaration. See #91. - Improved build script for local snapshot deployment. - Updated cli-args test. 0.16.2 - 14 Nov 2015 - Fixed #87. Include current configuration profile option in the workflow metadata. - Fixed #86. Failure if work dir contains one or more blank characters. - Fixed #76. Include process name and tag information in process wrapper script. 0.16.1 - 7 Nov 2015 - Fixed issue #85. Directive `publishDir` can't access process local variables. - Fixed wrong error message when trying to run a project sticked on a specific revision. - Fixed `IllegalArgumentException: other must be an instance of nextflow.cloud.aws.nio.S3Path` exception when publishing to a S3 path. - Fixed indentation in repo info command. 0.16.0 - 4 Nov 2015 - Added ability to resubmit task executions changing resource requirements. See #70 - Added support for private SCM servers and private Gitlab repositories. See #38 - Added `workflow` metadata and execution `onComplete` notification handler. See #79. - Added `publishDir` directive. See #81. - Added extension method `mklink` to create file system links. - Added Apache Ignite based executor. - Removed deprecated GridGain executor. - Updated Capsule to version 1.0.1. 0.15.6 - 7 Oct 2015 - Fixed #78. Command line parsing of parameters does not handle some strings properly. - Fixed #80. Command line argument containing a glob pattern is expanded even when escaped or enclosed in quote characters. 0.15.5 - 28 Sep 2015 - Fixed #74. Operator "spread" hangs when it is applied to a singleton channel. 0.15.4 - 22 Sep 2015 - Fixed #72. Adding cache support for `collectFile` operator. - Added experimental operator `until` - Added `self-update` in the command usage help - Updated Capsule to version 1.0 - Updated to Gradle 2.7 0.15.3 - 26 Aug 2015 - Merged #68. Add `engineOptions` setting to Docker configuration. 0.15.2 - 19 Aug 2015 - Improved `groupTuple` operator adding the support of `size` and `remainder` parameters. - Fixed issue #47. Creation of scratch folder on Mac OS-X. - Fixed issue #64. `Channel.fromPath` throws an exception when curly brackets glob pattern is used with a S3 path. - Fixed issue #65. An input file that is staged from a foreign file system lost it's original name. - Fixed issue #66. Git submodules are not cloned/updated when a pipeline project is pulled from a remote repository. - Fixed minor issue when evaluating config lazy property with no binding object. - Updated Capsule to latest version () fixing an issue that was preventing to add a custom path to the application classpath. - Added Path matches extension method [experimental]. - Added support for `into` parameter to `splitXxx` operators. - Changed signature of `close` operator so that it returns the channel to which it is applied. 0.15.1 - 4 Aug 2015 - Added feature #60 - Implements support for Gitlab source code management platform. - Added support for `disk` directive to `crg` executor. - Fixed issue #57 - Creation folder lock must be a singleton instance. - Fixed issue #62 - Operator hangs for negative values or when it is greater or equals to the total number of emitted items. - Fixed an exception when output file is specified with variable identifier e.g. output: file(x) into channel 0.15.0 - 27 Jul 2015 - Issue #56 - Added method `all()` to params object - Issue #57 - Processes having identical commands and inputs are given the same hash key - Issue #59 - Enhanced output `val` declaration adding support for value literals and value expressions - Fixed minor issue when deleting pipeline repo with `drop` command - Removed deprecated `share` process clause - Updated JGit to version 4.0.1 0.14.4 - 20 Jul 2015 - Fixed issue #54 - Nextflow installer does not work when running behind a proxy server - Upgraded Capsule package manager to version 1.0-rc2 0.14.3 - 3 Jul 2015 - Fixed issue #53 - Cannot access files list entry by using square bracket syntax 0.14.2 - 25 Jun 2015 - Fixed issue #48 - IncludeConfig does not support dot properties syntax - Fixed issue #49 - GridGain executor raises a NPE exception when launching a native process - Fixed issue #52 - Method `moveTo` should not throw a `FileAlreadyExistsException` when target file already exists 0.14.1 - 8 Jun 2015 - Strip colon character from grid task name - Fixed synchronisation issue that caused pipeline hung when execution was aborted - Fixed an issue raising a MissingPropertyException when a script global variable was referenced in a process `shell` block 0.14.0 - 4 Jun 2015 - Added support for file templates in process definition - Added process `when` guard for conditional execution - Added process `shell` block that allows both BASH and Groovy variables in the same script block - Added support for includes in configuration files - Added support for profiles in configuration files - Added channel operator `set { }` - Added channel operator `into { }` - Added channel operator `tap { }` - Added channel method `close()` - Added channel factory `value()` - Added `fixOwnership` docker config option - Added `unstageStrategy` process config option - Added minlog-slf4j kryo logging redirection - Added `ext` directive for user defined configuration properties - Added support for multi-indices grouping key to `groupTuple` operator - Fixed issue that caused task attribute to be lost when resuming execution - Fixed pipeline hangs when `map` operator is applied to a dataflow variables - Issue #44 - Fixed pipeline hangs when `into` operator is applied to a dataflow variable - Improved dynamic code compilation with `Grengine` module - Increased default queue size to 100 tasks when using a grid executor - Refactored `Session` to remove dependency with `CmdRun` object Added ability to set `workDir` in the config file - New implicit lazy Gstring in process parameter and directive definitions - Changed file unstage strategy using `cp` command instead of `rsync` I - Removed `workDir` variable from config file - Updated JGit to version 3.7.1 - Updated Slf4j to version 1.7.12 0.13.5 - 7 May 2015 - Fixed issue #44 - Pipeline hangs when `map` operator is applied to a dataflow variable 0.13.4 - 4 May 2015 - Added html processes execution time report - Added support for Docker executable containers - Feature #33 - Added support for missing number types to CacheHelper - Added warning message when using a deprecated input/output shared parameter - Fixed issue causing process hangs when stdout+stderr is bigger than 64K when using local executor - Fixed process stdout/stderr synchronisation issue - Fixed race condition when accessing `processor` attribute - Issue #41 - Fixed race condition on processes registration/termination - See issue #43 - Fixed `echo` synchronisation strategy when writing to stdout - Use a fixed thread pool for tasks execution and keep it separated from Gpars thread pool - Do not set Gpars thread pool size along with nextflow pool size - Improved resolution to tenths of a second when converting a `Duration` to string - Removed unnecessary local scope map argument from `getTaskGlobalVars` method - Read trace file w/o checking existence in order to reduce round-trip on remote storage - Workaround for Groovy compiler issue GROOVY-7409 0.13.3 - 19 Apr 2015 - Fixed issue when staging file when using a non local pipeline workdir - Fixed invalid values in the trace file returned by `awk` - Removed unnecessary `S3Path` serialiser registration on DnaNexus executor initialisation - Updated S3 file system client to version 0.2.8g 0.13.2 - 16 Apr 2015 - Handle staging in the local process directory of files on remote/foreign file systems - Fixed issue in resources stats tracing script -- awk uses scientific notation for numbers instead of decimal format. - Fixed external links to Groovy docs - Fixed issue #40 -- Cannot find java binary on Mac OSX - Fixed missing `DynamicParameter` in usage string - Fixed docker run `—-cpuset` command line option when using `crg` executor 0.13.1 - 10 Apr 2015 - Fixed IllegalStateException when executing a script in Nextflow console 0.13.0 - 8 Apr 2015 - Added support for AWS S3 storage - Added support for ClusterK Cirrus cloud scheduler - Added multiple debugging level in command scripts by using `NXF_DEBUG` variable - Added ability to disable docker kill command - Added explicit `entrypoint` definition in docker run command - Added `uge` executor as alias of SgeExecutor class - Added `-D` JVM properties command line option - Added `.command.log` to grid executors - Separated `stdout` and `stderr` outputs - Refactored DRMAA executor to a separate sub-project - Refactored application packaging based on Capsule modes - Refactored application installer downloading dependencies at runtime - Optimised file attributes access usage - Increased log and trace files rolling max index to 9 - Print revision and commit ID on pipeline startup - Improved handling of docker cpuset for `crg` executor - Improved TraceFileObserver to flush written content - Improved `info ` command with `-d` option that shows git revision commit IDs - Fixed issue #39 - Per process containers not working with -with-docker option - Upgraded Groovy runtime to version 2.3.11 - Upgraded Logback library to version 1.1.3 0.12.5 - 18 Mar 2015 - Fixed regression preventing jobs cleanup when nextflow process is killed - Fixed issue when command line flag has not value making it to consume following option - Added `uge` executor as alias of SgeExecutor class - Improved log messages - Upgraded Spock testing library to version 1.0 0.12.4 - 4 Mar 2015 - Added suspended job status handling to SLURM executor -- Issue #36 - Added `print` and `println` operators plus tests and updated docs - Fixed issue on `view` operator when specifying a closure - Fixed Docker image resource request in CRG executor - Fixed typo in documentation - Improved task hash key generation and task variables handling - Compute `baseDir` and `workDir` as string values when creating task unique hash - Improved `sum` operator to allows it to handle lists with varying size - Upgrading Groovy runtime to version 2.3.10 0.12.3 - 16 Feb 2015 - Added support for `module` and `container` fields in execution trace log - Fixed a small inconsistency on polling monitor queue size for local executor when using single core or two-cores cpu - Enhanced process key generation including global variables referenced in the process scope - Enhanced `sum` operator and added `mean` operator 0.12.2 - 12 Feb 2015 - Fixed issue on some SGE implementation where `-terse` directive in job script is not working - Downgrade Capsule to 0.9.0 due to an issue in version 0.10.0 - https://github.com/puniverse/capsule/issues/56 0.12.1 - 8 Feb 2015 - Fixed NoSuchMethodException issue on Java 1.7.0_01 due to missing private constructor - Fixed logging issue on Nextflow console - Fixed issue `view` operator which hung when used on a dataflow variable - Upgrade SLF4J to version 1.7.10 - Upgrade Capsule to version 0.10.0 - Removed dependency on jsr166y module - Removed `synchronized` declaration on Session cleanUp method 0.12.0 - 5 Jan 2015 - Added afterScript/beforeScript directives - Added tag directive to label task executions with a custom identifier - Added dynamic directives evaluation - Added support for dynamic input/output file names with closures - Added `ifEmpty` operator - Added `view` operator - Added `remainder` optional parameter to `phase` operator - Removed 'undef' directive - Refactored grid executors so that jobs directives are added on top of script wrapper - Renamed ContextMap to TaskContext - Renamed TaskConfig to ProcessConfig - Renamed LocalConfig to TaskConfig - Print pid/hostname in the status log - Upgraded to Groovy 2.3.9 and Slf4j 1.7.8 0.11.4 - 3 Dec 2014 - Fixed issue in TextFileCollector empty condition that was creating an empty split file when the split size was equals to the number or records - Fixed bug that prevents a job is added to the polling queue when submit operation fails - Added more strict checks on $JAVA_CMD executable and $JAVA_HOME folder - Refactored 'sge' and 'crg' executors so that qsub directives are provided on top of job wrapper script - Added BSC specific executor - Upgraded to Groovy 2.3.8 0.11.3 - 27 Nov 2014 - Added to splitters ability to save chunks to files - Fixed a bug that prevented an error message to be reported when using a missing variable in the process script - Improved info command showing local and remote branches - Improved error report when failing to delete pipeline directory - Removed gpars methods implicit imports - Fixed unit for 'syscr' and 'syscw' fields in trace report - Upgraded JGit library version to 3.5.2.201411120430-r 0.11.2 - 19 Nov 2014 - Added 'groupTuple' operator - Added NXF_WORK variable to define default scratch path - Added Gzip un-compress ability to splitter operators - Added 'limit' parameter to splitter operators - Added 'meta' parameter to splitter operators - Field 'walltime' has been renamed to 'realtime' in tracing file - Fixed issue on 'collectFile' operator when no 'name' parameter is specified - Removed dependency on Picard library - Improved error reporting 0.11.1 - 11 Nov 2014 - Fixed serialisation issue on pipeline resume - Fixed issue on command line parameters with no arg (flag) - Refactored class HubOptions to a trait 0.11.0 - 5 Nov 2014 - Added sorting ability to collectFile operator - Added new 'cpus', 'memory', 'time', 'penv' process directives - Added cpu, memory and I/O resources in execution tracing report - Upgraded to groovy 2.3.7 - Relaxed validation check of -resume option - Fixed symlink support to Github and BitBucket shared repositories - Fixed Channel.fromPath with S3 path - Enhanced error reporting - Removed blanks from jobs name - Added NXF_ASSEST environment variable - Added NXF_TEMP environment variable to define local temporary path 0.10.3 - 3 Oct 2014 - Fixed bug when composing SLURM 'squeue' command line which was containing unnecessary quote characters thus invalidating the jobs status check mechanism 0.10.2 - 1 Oct 2014 - Fixed bug while submitting a job to SLURM scheduler due to special characters in job name - Fixed bug in TaskConfig#toBool() method - Fixed bug resolving configuration file when pipeline script is a symlink - Fixed bug while setting 'workDir' attribute on PBS job executor - Improved error message when the name of a process is missing - Removed TaskConfig#getMerge() method - Updated method Channel.fromPath(String) so that it returns normalised absolute paths - Updated Capsule to version 0.9.0 stable - Fixed typos in documentation 0.10.1 - 15 Sept 2014 - Added ability to 'run' implicitly a script when it's specified as the very first parameter (for backward compatibility) - Added 'workDir' and 'baseDir' implicit variables in configuration files - Fixed docker remove issue by executing as an external command - Fixed an issue when finding the longest common path used by docker mounts - Fixed issue #13 - Show a detailed error message when hitting GitHub rate limits 0.10.0 - 8 Sep 2014 - Added DRMAA executor - Added PBS/Torque executor - Added processes execution report - Added Extrae tracing support - Added support for GitHub private repositories - Added integration for BitBucket hosted repositories (Git vcs only) - Added native integration AWS S3 file system - Improved Docker support and configuration - Improved GridGain cluster integration - Removed Hazelcast integration - Added Capsule based application packaging - Added commands view: that prints the content a pipeline repository config: shows pipeline configuration - Fixed issue #12 - Error resuming process with command defined on multiple lines 0.9.0 - 11 Aug 2014 - Added GitHub/Git support. It allows one to pull and run pipelines published on a remote GitHub repository - Changed command line structure. Since this version it is organised in sub-commands. The following sub-commands are available: ls: list all downloaded pipelines; run: launch a pipeline execution; pull: download or update a pipeline hosted on GitHub; info: show pipeline information; drop: remote a locally stored pipeline; clone: copy a pipeline to a directory specified; history: list all pipeline runs; help: show program help. - Added 'baseDir' and 'workDir' script variables - Removed Merge processor 0.8.5 - 3 Aug 2014 - Upgraded to Groovy 2.3.6 - Added '-noverify' to JVM launcher options as workaround for Java bug JDK-8051012 0.8.4 - 20 Jul 2014 - Upgrade to Groovy 2.3.4 - Fixed method Path.list() - Added '-notify' option to SGE qsub command to handle killed jobs correctly 0.8.3 - 27 Jun 2014 - Added support for Modules package maages - Fixed issue #1 - process hung when only a parameter of type 'each' is defined - Fixed issue #6 -- exception while resuming a process that declares a parametric file output name - Fixed support for curly brackets glob path matching in Channel.fromPath - Updated Groovy runtime to 2.3.3 - Updated to Groovy-nio module in place of 'native' implementation 0.8.2 - 18 Jun 2014 - Fixed issue #7 - NoClassDefFoundError HashMap$Entry exception with Java 8 - Enhanced launch script: removed '-Xms' Java option; verify the Java version coherent with JAVA_HOME definition; improved error messages. 0.8.1 - 26 May 2014 - Fixed a ConcurrentModificationException issue on splitXxx method due to a misused @Memoized annotation 0.8.0 - 24 May 2014 - Added support for Java 8 - Upgraded to Groovy 2.3.0 - Upgraded to Kryo 2.24.0 - New splitter operators: 'splitText', 'splitFasta', 'splitFastq', 'splitCsv' - New operator 'collectFile' to gather file chunks - New operator Channel.fromPath which allows fine control on paths traversal - Operator Channel.from has been deprecated in favor of Channel.fromPath - Operator Channel.watch has been deprecated in favor of Channel.watchPath - Clean-up API for operators: 'into', 'choice', 'separate', 'filter' - Operator 'grep' has been removed and features included in 'filter' operator - Deprecated 'chopXxx' operators - Deprecated 'chunkXxx' operators - Deprecated 'each' operator in favor of 'subscribe' - Deprecated process 'merge' directive - Executor service now uses a fixed thread pool - Fixed issue on 'maxForks' process directive - Added 'info' cli parameter - Improved documentation 0.7.3 - 16 May 2014 - Enhanced stability and errors reporting 0.7.2 - 5 May 2014 - Enhanced support for Docker containers: Now the current user id is added on the Docker command line and /tmp folder in the container is mounted on a temporary path in the host disk 0.7.1 - 14 Apr 2014 - Fixed an issue with 'scratch' directive i.e. Fixed issue when copying a symlink - Added 'Retry' error handling strategy and 'maxRetries' and 'maxErrors' process directives - Added GridGain cluster sub-module - Added TaskDispatcher submit, start, complete and error listeners - Added new ServiceDiscovery to handle sub-modules executors - Added Map#getOrCreate() extension method - Using @CompileStatic for AST transformation - Removing unused APP_TMP_DIR const - Renamed class 'AbstractExecutor' to 'Executor' - Added ProcessFactory class - Refactored sub-modules directory structure - Define the default 'lib' path relative to the pipeline 'baseDir' i.e. relative to the main script location - Save the history entry just before launch the execution 0.7.0 - 24 Mar 2014 - New self-downloadable and self-updatable script launcher - New cluster mode, Nextflow can run as a daemon node by using Hazelcast cluster (incubating) - New support for Docker containers. Any process can be executed through Docker adding 'container = name' in the process definition (incubating) - New native processes (groovy closure) can executed in the cluster. - Enhanced task polling monitor - Use 'rsync' to upstage task result files to target directory - Pipeline execution can be launched in background by adding the option '-bg- to the command line - Updated documentation 0.6.2 - 20 Feb 2014 - Added 'concat' operator to concatenate two or more channels - Added 'into(ch1,ch2...)' operator which maps tuple elements into the corresponding target channel - Implemented queue status check for SLURM grid executor - Implemented queue status check for LSF grid executor - Improved grid executors stability - Fixed a bug when setting setting the monitor queue size 0.6.1 - 16 Feb 2014 - Added operator 'cross()' - Added operator 'collate()' - Added options 'remainder' to 'buffer()' operator - Added 'deep' option to cache directive in order to index file content. - Added Kryo based serialization - Added 'storeDir' process directive to cache process results permanently - Added 'watch' channel factory method that watches for files changes - Added parametric input/output file names - Renaming "mapMany" to "flatMap" - Enhanced stability for grid executors - SGE executor periodically invokes the 'qstat' command to fetch the queue jobs status - Processes and executors can be configured separately in the configuration file by using the $name special scope - Completed Path methods extension equivalent to legacy File - Reporting a random tip when a process fail 0.6.0 - 16 Jan 2014 - New channel factory methods - New reactive operators on channel objects (similar to RxJava) - New shared parameters - New input/output set parameters - New conditional scripts using - New groovy native processes 0.5.4 - 10 Dec 2013 - Fixed an issue while checking an - empty - process exit file - Fixed a race condition while resuming cached tasks 0.5.3 - 9 Dec 2013 - Fixed file close leaks - Fixed DirectoryStream close leaks - Enhanced process executor, supporting multiple executors in the same pipeline 0.5.2 - 28 Nov 2013 - Changed caching hash function to murmur3_128 to avoid cache collision - Fixed issue on process termination when resuming pipeline execution 0.5.1 - 24 Oct 2013 - Major executors refactoring - Featuring new single-thread tasks scheduler - New enhanced DSL syntax with extended semantic - Switched file handling to new NIO.2 file system - Introducing support for DNAnexus cloud platform - Removed unnecessary library dependencies - Slim self-contained executable package 0.3.4 - 24 Aug 2012 - Extending semantic for method File.copyTo(source,target) so that when 'target' argument is a directory, it copies the 'source' file to that folder, with the same name as the original file. - Bug: Fixed a ClassCastEx exception when the 'bin' folder is added to the PATH - Bug: Fixed an issue that raised an error "error=26 Text file busy" on some platforms (CentOS) 0.3.3 - 8 Aug 2013 - Added optional parameters to 'chunkLines' and 'chunkFasta' methods - Added '-lib' command line parameter specify external libraries (.jar files) or extension scripts - Folder 'lib' in the launch directory is added by as default libraries path - Added 'tempFile()' and 'tempDir()' methods to BaseScript class - The 'bin' directory in the script folder is added to the task PATH environment by default - Upgraded to Groovy 2.1.6 - Upgraded to Slf4j 1.7.5 - Upgraded to Logback 1.0.13 0.3.2 - 22 Jul 2013 - New command line option '-log' to specify the application log file - New command line options '-task.xxx' to task default parameters (overriding the ones in the configuration file) - Fixed a bug which was preventing the caching mechanism to work properly - Fixed synchronization issue caused by a miss-used CountDownLatch, replaced with a Phaser - Fixed a bug by which cached tasks didn't print out any result when 'echo' was set - Fixed a bug in the timezone handling in the build timestamp 0.3.1 - 18 Jul 2013 - Added command line parameter 'echo' to enable default tasks output - Fixed an issue on merge task, when it doesn't collect any data the execution is skipped 0.3.0 - 11 Jul 2013 - Decoupled the processing policy by the execution strategy classes - Normalised script level arguments so that a blank char may be used in place of the equals char - Added a new configuration option named 'clusterOptions' where specify grid native configuration parameters - Added a new configuration option named 'scratch' which enable/disable usage of scratch temporary folder when using cluster executors - Enhanced implementation of LSF executor 0.2.11 - 28 May 2013 - Added 'lefTrim' and 'rightTrim' extension methods to String class - The task script interprets correctly the 'shebang' header declaration - The task save the command environment to a separated file, in order to simply task reproducibility and debugging 0.2.10 - Adding '-pool-size' cli option and config parameter to define size of executor threads - Removed SGE output file - Initial SLURM support 0.2.9 - Adding 'test' feature 0.2.8 - 30 Apr 2013 - Improved scheduling of 'merge', there are executed like a single job - Fixed caching for 'merge' task - Refactored class 'TaskDef' to 'TaskRun' 0.2.7 - 25 Apr 2013 - Added 'eachWithIndex' iterator like method on dataflow channel - Make the SGE task processor to write the output file in the job execution directory - Renaming the CLI option -continue to -resume - Adding File extension methods: getBaseName(), getExtension() 0.2.6 - 22 Apr 2013 - Fixed a bug on errors handling - Added default parameters in config file - Added Channel type - Added cacheableDir and cacheableFile - Upgraded to Groovy 2.1.3 0.2.5 - 19 Apr 2013 - Added LSF executor (experimental) - Added command line option '-history' - Added command line option '-continue' to resume the execution of an interrupted execution - Using Non-daemon threads by default - Refactored SGE task processor 0.2.4 - Using minimal Groovy dependencies - SGE/OGE processor works in the scratch folder and un-stage result files when complete - SGE/OGE handles stdin transparently 0.2.3 - Renamed 'queue' to 'channel' - Adding a basic tasks cache mechanism - Supporting 'shell' parameters 0.2.2 - 9 Apr 2013 - Fixed file/stream close leaks, that caused 'Too many open files' error on big pipeline execution - Rolling log file '.nextflow.log' on startup - CLI option 'quiet' suppress all 'info' messages - Added 'maxDuration' and 'maxMemory' attributes to OgeTaskProcessor - Added 'maxDuration' attribute to LocalTaskProcessor 0.2.1 - 3 Apr 2013 - Initial support for SGE/OGE grid engine 0.2.0 - 2 Apr 2013 - General improvement - Enhanced parameters handling - 'chunkLines' and 'chunkFasta' API extension - 'each' iterator over dataflow queue API extension 0.1 - 25 Mar 2013 - Initial release