Version 22.10.6

• backport: Add refresh token to wave request [47a7408]
• backport:Add tower endpoint to wave [fe24b42]
• backport:Fix Wave layer invalid checksum due to not closed stream [20df640]
• Bump [email protected] [c1ec759]

Version 23.01.0-edge

• Add support for rclone as stageOutMode option [fde2ac2]
• Add queueGlobalStatus config setting [ci fast] [f333954]
• Add support for bearer token to GithubRepositoryProvider [c4d3938] [a2d2cbf]
• Add -with-fusion cli option [d22337c]
• Add support for Fusion container custom options [56e29d3]
• Add schedulingPriority option to AWS Batch (use with shareIdentifier) (#3505) [06960bb]
• Fix support for AWS ACL for Batch #2671 [a964491]
• Fix Java options.release in Gradle build [b362d6f]
• Fix nf-httpfs module name in build file [568e47f]
• Fix GitHub creds in CI build [4c4d3f8]
• Fix FilePorter concurrency issue (#3511) [11ccfa2]
• Fix watchPath hang shutdown execution [bac0ced]
• Fix "no such file" error message to "no such file or directory" [ci fast] (#3547) [c292d84]
• Improve local exec workdir validation [4a3a272]
• Improve container native executor configuration [0312637]
• Improve AWS batch exit code reporting [d1bb2fe]
• Improve channel factories error message [0215b9f]
• Improve Google Batch executor [c0a25fc]
• Improve Fusion config [902e5b3] [52f4c5d]
• Improve redirection on Wave client [124cfb3]
• Remove unnecessary Fusion env var [ci fast] [dfa4755]
• Remove deprecated method 'just' [d17b3c4]
• Remove deprecated methods [75e6503]
• Remove DSL1 deprecated code [5d290a4]
• Cleanup build from tmp manifests [326b383]
• Minor compilation improvements [4188a6a]
• Migrate all tests to DSL2 [14257d4]
• Bump 23.01.0-edge version [9ec3144]
• Bump groovy 3.0.14 [7c20423] [6f3ed6e]
• Bump Grengine 3.0 [c0b1a7a]
• Bump [email protected] [45d274e]
• Bump [email protected] [db0ebe7]
• Bump [email protected] [a663fe1]
• Bump [email protected] [45fd53a]
• Bump [email protected] [cf39ef8]
• Bump [email protected] [7a6a78a]
• Bump [email protected] [41fdcc7]

Version 22.10.5

• Fix FilePorter concurrency issue (#3511) [0f75715]
• Fix watchPath hang shutdown execution [e03d9ca]
• Add schedulingPriority option to AWS Batch (use with shareIdentifier) (#3505) [543ee7b]

Version 22.12.0-edge

• Add fair process directive [60d34cf]
• Add support for singularity registry setting [37c1aeb]
• Add AWS profile config setting [66f4669]
• Add support for AWS profile when resolving region [d894770]
• Add support for Sarus container engine (#3470) [54673f1]
• Add support for Fusion ARM64 client [d073c53]
• Add allowedLocations option to google batch (#3453) [c619eb8]
• Add support for AWS config profile in NF config [3711267]
• Add warning on Google Logs failure [bdbcdde]
• Add possible values of status in trace.txt to the documentation (#3451) [2425fcf]
• Add support for AWS Glacier restore [b611076]
• Add support for S3 storageClass to publishDir [066f920]
• Add MathHelper utility class [7eecb26]
• Fix Wave layer invalid checksum due to not closed stream [e188bbf]
• Fix Fusion test [2245a1c]
• Fix Run fails when home is a symlink [9ff820f]
• Fix math overflow when copying large AWS S3 files [f32ea0b]
• Fix Quote the logName in the Cloud Logging filter (#3464) [b397506]
• Fix Google Batch cloud logging (#3443) [e2bbcf1]
• Fix Tower plugin min nextflow requirement [1713a1c]
• Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [46af18e]
• Error & info messages, code comments language fixes (#3475) [29ae36c]
• Replace egrep with grep -E (#3485) [ac0c303]
• Gradle build optimizations (#3483) [19182a5]
• Refactor virtual FS schemes to XPath class [fd59b94]
• Update concat operator description (#3426) [e8d8c3b]
• Clarify usage of additional options for path qualifier (#3405) [0b70acb]
• Clarify limitation of -with-docker in the docs (#3408) [79afc85]
• Expose process queue as K8s pod label [4df8c8d]
• Prefix nextflow K8s labels with nextflow.io prefix [9951fcd]
• Remove deprecated code [c0b164f]
• Rewrite fetchIamRole and fetchRegion to use AWS SDK (#3425) [e350f31]
• Improve Wave config error reporting [ae50266]
• Improve K8s retry on transient failures [d86ddc3]
• Remove DSL1 output mode [fa400d5]
• Remove support for DSL1 multi into [f664af4]
• Bump [email protected] [ccaab71]
• Bump [email protected] [c07dcec]
• Bump [email protected]
• Bump [email protected] [652d088]
• Bump fusion version URLs 0.6 [a160a8b]
• Bump AWS sdk version 1.12.351 [4dd82b6]

Version 22.10.4

• Fix math overflow when copying large AWS S3 files [07f7cb7]
• Bump [email protected] [d96ca4c]

Version 22.11.1-edge

• Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [53e6348]
• Fix tower plugin min nextflow requirement [103dbf7]
• Fix typos in the documentation [ci skip] (#3441) [ae95d90]
• Add support for Java 19 [811e7ca]
• Add support for custom Conda channels (#3435) [ci fast] [0884e80]
• Add time directive to AWS Batch, clean language (#3436) [ci skip] [1ed2640]
• Update err message [ci fast] [ab5bd81]
• Fix Flux executor config (#3432) [ci fast] [68b45c9]
• Bump [email protected] [fe66915]
• Bump [email protected] [2dbf990]

Version 22.11.0-edge

• Add support for Apptainer container engine (#3345) [29f9897]
• Add Flux executor to nextflow (#3412) [cc9fc3f] [3711cef]
• Add support for Wave containerPlatform [10d56ca]
• Add CSI ephemeral volume for K8s (#2988) [f18f6e8]
• Add support for disk directive and emptyDir to K8s (#2998) [b548e1c]
• Add Fusion support for custom S3 endpoints [fba9b64]
• Add support for Tower refresh token for dataset (#3366) [a19e055]
• Prevent infinite loop while fetching git tags and branches [aa974d4]
• Improve file porter logging [626420b]
• Improve script err logging [2714770]
• Extend onFilePublish notification adding source path (#3284) [81acc3e]
• Remove cpu limits from K8s pod spec builder (#3338) [dc7f78b]
• Improve task name logging [5ddb7e3]
• Add tower endpoint to wave [ci fast] [b725ddc]
• Add Azure SAS token validation [e2244b4]
• Use cpus-shares for container resources (#3383) [b38c388]
• Report full path scheme on error [4089ba6]
• Allow identity based authentication on Azure Batch (#3132) [a08611b]
• Fix support for remote file mail attachment (#3384) [6b496bb]
• Fix task cache logging [ed37c4f]
• Fix unexpected error on task resume [1c3f468]
• Fix stripIndent failure with java 17 (#3377) [2b115c5]
• Fix -dockerized execution #3137 (#3148) [64a81a5]
• Improve default value in cli help of nextflow log -s (#3371) [2141f96]
• upgrade jsoup and snakeyaml version (#3374) [6e2ca45]
• Bump Java 17 lang version + Java 11 as target [34f133e]
• Bump [email protected] [e307912]
• Bump [email protected] [07391d96]
• Bump [email protected] [4d787561]

Version 22.10.3

• Prevent infinite loop while fetching git tags/branches [73a59d3]
• Bump [email protected] [f9b54ce]
• Improve S3 thread pool config [01541b0]

Version 22.10.2

• Fix initialize the plugin once it's defined (#3360) [dd150b9]
• Fix tags typo in docs (#3355) [b82df4e]
• Fix unexpected error on task resume [e02e8c2]
• Fix template script in trace record [cf828a6]
• Fix ip v6 support for K8s executor [53af5a7]
• Fix refresh token for tower served resources [9dec2b6] #3366
• Fix full path scheme on error [1399f45]
• Add note to some process implicit variables (#3373) [0374f63]
• Add retry policy on plugin download failure [e8dbec3]
• Add examples of when dynamic output filenames are important (#3275) [72a1730]
• Update google batch java sdk, add serviceAccountEmail and installGpuDrivers (#3324) [7f7007a]
• Update github actions to v3 (#3376) [d3b4a83]
• Update error messages and docs with new report filename behavior [f572548]
• Bump [email protected] [164edf7]
• Bump [email protected] [30cb118]

Version 22.10.1

• Fix mount pwd in the container when work dir is a symlink [ca39718] [b5b7d3c]
• Fix secrets command name in the CLI (#3320) [ci fast] [321486d]
• Fix ver num rendering [ci fast] #3226 [5312a25]
• Fix K8s config namespace is not applied [b3d33e3]
• Fix log fetching from remote storage [be35693] [3efa1a2]
• Update docs about default mail ssl protocol [ci skip] (#3299) [15ffffc]
• Update docs repeated words from documentation (#3311) [ci skip] [d59ea18]
• Update docs to clarify the difference between collect and toList (#3276) [7ee2b00]
• Update docs [516a744]
• Update docs adding Fusion [11eac70]