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changelog.txt
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NEXTFLOW CHANGE-LOG
===================
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 [ci skip] [5627c69a]
- Security fixes [83e8fd6a]
- Bump [email protected] [d8cb763c]
- Bump [email protected] [b2354380]
- Bump [email protected] [22a68cfe]
- Bump gson:2.10.1 [83ca1e32]
- Bump [email protected] [b40b5165]
- Bump [email protected] [98a89154]
- Bump aws-java-sdk-s3:1.12.429 [b71ee0a3]
- Bump [email protected] [a5da54d3]
- Bump [email protected] [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 [ci fast] [e6c60a6c]
- Bump [email protected] [26b01b83]
- Bump [email protected] [2a886fe0]
- Bump [email protected] [b8769f1a]
- Bump [email protected] [89d902ec]
- Bump [email protected] [9b0f4bfb]
- Bump [email protected] [f7aaddc6]
- Bump [email protected] [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 [email protected] [0f98b245]
- Bump [email protected] [e1732be9]
- Bump [email protected] [99477f79]
- Bump [email protected] [939195b5]
- Bump [email protected] [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 [email protected] [aa1b065d]
- Bump [email protected] [2aaaf2a7]
- Bump [email protected] [f358b008]
- Bump [email protected] [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 [email protected] [1c697ab5]
- Bump amazoncorretto:17.0.6 [a33a6f47]
23.02.0-edge - 21 Feb 2023
- Add Fusion support for Google Batch (#3577) [d5fbab4f]
- Add Header provider to Google Batch client [20979929]
- Add Wave integration tests [c5faf971]
- Add errorStrategy validation [954cd921]
- Add Java install recommendations to docs (#3617) [7e9bee1e]
- Add nextflow tags to AWS Batch job def [b465ac52] [BREAKING]
- Add readOnlyInputs option for CharliecloudBuilder (#3590) [8ae001fc]
- Add refresh token to Wave request [41510e87]
- Add requirements for container images to run with Nextflow (#3586) [7af1cb66]
- Add support for Fusion to Slurm and LSF executors (#3516) [fbc95e6b]
- Add support for Fusion tags (#3609) [8385ec22] [BREAKING]
- Add support for the Spack package manager (#3580) [a5df62f6]
- Add the fcp tool option to file copy strategy (#3556) [2a224258]
- Add Fusion integration test
- Add Wave + Fusion test with Google Batch [b541c061]
- Add support for entryless Fusion configuration and Singularity support (#3584) [34a27733]
- Improve Fusion config [a1d08463]
- Ignore resource directives if -l option is specified in PBS executor (#3015) [28a67969]
- Improve K8s securityContext support [3f76240b]
- Improve AWS Batch error logging [8f4884c1]
- Improve secrets docs [9a3b4214]
- Improve Wave debug-task plugin command [cf3fd747]
- Improve Wave logging [fced3761]
- Increase Wave token duration to 30 mins [e1a712c2]
- Fix -with-apptainer cli option (#3621) [8c9588fe]
- Fix GH action tests step [bb890d9a]
- Fix Spack failing test [868374d3]
- Fix Tower doc links, fix typos (#3647) [1278e1a5]
- Fix Wave cli messages [10cf414b]
- Fix collectFile cache over remote storage [762ba19c]
- Fix output env var tokenize [40d56735]
- Fix plugin install version [59e9a91b]
- Fix race condition on Wave requests [f57fae2c]
- Fix serialization of S3 paths with spaces (#3565) [ce487624]
- Fix string literal method names with parens (#3604) [8278078a]
- Fix submit command in error message for grid executors that pipe wrapper script (#3548) [40ebd308]
- Fix typos in the documentation [skip ci] (#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 [email protected] [b797fac2]
- Bump [email protected] [dd2f69dd]
- Bump [email protected] [8cb9fa35]
- Bump [email protected] [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 [email protected] [f466b266]
- Bump [email protected] [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 [email protected] [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 [email protected] [45d274e3]
- Bump [email protected] [db0ebe72]
- Bump [email protected] [a663fe16]
- Bump [email protected] [45fd53ad]
- Bump [email protected] [cf39ef8f]
- Bump [email protected] [7a6a78aa]
- Bump [email protected] [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 [email protected] [ccaab713]
- Bump [email protected] [c07dcec2]
- Bump [email protected]
- Bump [email protected] [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 [email protected] [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 [email protected] [fe669152]
- Bump [email protected] [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 [email protected] [e307912e]
- Bump [email protected] [07391d96]
- Bump [email protected] [4d787561]
22.10.3 - 21 Nov 2022
- Prevent infinite loop while fetching git tags/branches [73a59d33]
- Bump [email protected] [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 [email protected] [164edf7c]
- Bump [email protected] [30cb118d]
22.10.1 - 27 Oct 2022
- Fix mount pwd in the container when work dir is a symlink [ca397181] [b5b7d3cd] <Paolo Di Tommaso>
- Fix secrets command name in the CLI (#3320) [321486df] <Marcel Ribeiro Dantas>
- Fix ver num rendering #3226 [5312a25e] <Paolo Di Tommaso>
- Fix K8s config namespace is not applied [b3d33e3b] <Paolo Di Tommaso>
- Fix log fetching from remote storage [be356939] [3efa1a20] <Paolo Di Tommaso>
- Update docs about default mail ssl protocol (#3299) [15ffffc1] <Ben Sherman>
- Update docs repeated words from documentation (#3311) [d59ea186] <Marcel Ribeiro Dantas>
- Update docs to clarify the difference between collect and toList (#3276) [7ee2b008] <Marcel Ribeiro Dantas>
- Update docs [516a7441] <Paolo Di Tommaso>
- Update docs adding Fusion [11eac707] <Paolo Di Tommaso>
22.10.0 - 13 Oct 2022
- Fix timestamp encoding [47a3a3c4]
- Minor type change in Bridge executor [1f446ee1]
- Bump [email protected] [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 [email protected] [a2b44c4d]
- Update docs
22.10.0-RC1 - 3 Oct 2022
- Add module binaries enabling flag + docs [c50e178f] <Paolo Di Tommaso>
- Add timestamp and fingerprint to wave request [a5a7e138] <Paolo Di Tommaso>
- Add missing inputs to the incremental task "test" (#1442) [f85d59a6] <Thodoris Sotiropoulos>
- Add support for refresh token to Wave [ed9f25f1] <Paolo Di Tommaso>
- Add pretty option to dump operator [4218b299] <Paolo Di Tommaso>
- Add support for custom S3 content type [02afa332] <Paolo Di Tommaso>
- Get rid of file name rolling for report files [a762ed59] <Paolo Di Tommaso>
- Ignore JGit warning when missing git tool [a94fa9c1] <Paolo Di Tommaso>
- Remove jobname limit to HyperQueue executor (#3251) [99604ccb] <Henrik Nortamo>
- Rename baseImage to mambaImage [50086028] <Paolo Di Tommaso>
- Fix failing test [e6790003] <Paolo Di Tommaso>
- Fix K8s cluster token when using serviceAccount [c3364d0f] <Paolo Di Tommaso>
- Fix hanging test [44c04874] <Paolo Di Tommaso>
- Improve docs (#3212) [5d80388c] <Marcel Ribeiro Dantas>
- Bump fusion snapshot [8e03f655] <Paolo Di Tommaso>
- Bump wave endpoint [a044cc6a] <Paolo Di Tommaso>
- Bump [email protected] [7424dc4b] <Paolo Di Tommaso>
- Bump fusion config v0.5.1 [4dbdf112] <Paolo Di Tommaso>
- Bump [email protected]
- Bump [email protected]
- Bump [email protected]
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] <Abhinav Sharma>
- Bump [email protected] [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] <Kibubu>
- Apply GCP resourceLabels to the VirtualMachine (#3234) [2275c03c] <Doug Daniels>
- 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] <Vishwas>
- Add support for module custom bin dirs [77f55262]
- Add support for tower token to wave client [928d5b04]
- Update CLI docs (#3200) [8acebee6] <Marcel Ribeiro Dantas>
- 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] <Abhinav Sharma>
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] <Jorge Aguilera>
- Fix fusion enable detection [3ef91512]
- Add before-afterScript warning to docs (#3167) [09464590] <Kibubu>
- 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] <Paolo Di Tommaso>
- Update Azure vm types [80f5fbe4]
- Update docs logos (#3174) [529bad81] <Phil Ewels>
22.09.1-edge - 1 Sep 2022
- Add support for Charliecloud v0.28 (#3116) [84f43a33] <Patrick Hüther>
- Add Support for EC-encrypted keys for K8s client [fd759d09]
- Add support for Bridge batch scheduler (#3106) [343c17e6] <Eric Bonnet>
- 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] <Paolo Di Tommaso>
- 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] <Mike Lee>
- 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] <Ben Sherman>
- Wave improve conda settings [6f087fec]
- Improve secrets cmd (#3158) [115b2f3d] <Jorge Aguilera>
- Improve Wave resolution strategy [2eb700c6]
- Improve Az Batch err handling and testing [85d31e8d] <Paolo Di Tommaso>
- 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] <Ben Sherman>
- 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] <Jorge Aguilera>
- Add support for AWS Batch logs group (#3092) [4ef043ac] <Ben Sherman>
- Add share identifier to Aws Batch (#3089) [c0253aba] <Ben Sherman>
- Improve Tower cache manager [0091afc5]
- Improve S3 copy via xfer manager [02d2beae]
- Reports a warning when using NXF vars in the config [009ec256] <Marcel Ribeiro Dantas>
- 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] <Ben Sherman>
- Fix queueSize setting is not honoured by AWS Batch executor (#3093) [d07bb52b] <Ben Sherman>
- Fix Allow disabling scratch with Google Batch [e8e5c721]
- Fix Emit relative path when relative parameter is set (#3072) [39797759] <Jorge Aguilera>
- Bump [email protected] [e46d341d]
- Bump [email protected] [cdc2be53]
- Bump [email protected] [c39935a5]
- Bump [email protected] [ccdf62d0]
22.08.0-edge - 1 Aug 2022
- Add warning to env config docs (#3083) [ca933c16] <Ben Sherman>
- 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] <Ben Sherman>
- Add support for GPU accelerator to Google Batch (#3056) [f34ad7f6] <Ben Sherman>
- Add support for archive dir to tower plugin [c234681a]
- Add support tower cache backup/restore [bc2f9d13]
- Add disk directive to google batch (#3057) [ec6e290c] <Ben Sherman>
- Add retry when Azure submit fails with OperationTimedOut [6a3f9742]
- Add warning when Google Batch quota is exceeded (#3066) [6b9c52ad] <Ben Sherman>
- Allow fully disabling history file [0a45f858]
- Allow the support function overloading and default parameters (#3011) [042d3857] <Jorge Aguilera>
- Improve S3 file upload/download via Transfer manager [7e8d2a5a] <Jorge Aguilera>
- 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] <Ben Sherman>
- Fix Unable to disable scratch attribute with AWS Batch [1770f73a]
- Fix unit test setting explicit permissions for test files [1c821139] <Jorge Aguilera>
- Fix Default plugins are overridden by config plugins [46cf3bfa] <Paolo Di Tommaso>
- Fix S3 transfer download directory [b7bf9fe5]
- Fix NPE while setting S3 ObjectMetada #3031 [d6163431] <Jorge Aguilera>
- 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] <Ben Sherman>
- 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 [email protected] [12f17176]
- Bump [email protected]
- Bump [email protected]
- Bump [email protected]
- Bump [email protected]
- Bump [email protected]
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] <romanaduraciova>
- Add docs aws.client.s3PathStyleAccess config (#3000) [20005500] <Abhinav Sharma>
- Allow to override lsf.conf settings with nextflow config #2862 [dae191a1] <Paolo Di Tommaso>
- Allow hybrid containers execution [0af1bcb3]
- Improve error msg when script file cannot be read [52c2780e]
- Improve error reporting for custom function [877c7931] <Jorge Aguilera>
- Improve error message for missing plugin extension [4a43db84]
- Improve test #3019 [7c37e0be] <Paolo Di Tommaso>
- Rename kuberun -pod-image to -head-image [2576ba62] <Ben Sherman>
- Externalise sqldb plugin source code [17e80b4f] <Paolo Di Tommaso>
- Fix escape unstage outputs with double quotes #2912 #2904 #2790 [49ff02a6] <Ben Sherman>
- Fix Exception when settings AWS Batch containerOptions #3019 [89312ad8] <Paolo Di Tommaso>
- Fix Missing query param in http file (#2918) [43cc8511] <Paolo Di Tommaso>
- Fix Publish copy mode for S3 based path [085f6b2b]
- Fix Fail fast uploads to S3 (#2969) [7fd1a6e1] <Jorge Aguilera>
- Fix null script name in launch info [7118849f]
- Bump [email protected] [a06b4442]
- Bump [email protected] [3331826f]
- Bump [email protected] [de62fd3f]
- Bump [email protected] [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 + [email protected] [70fc0745]
- Fix typo in log message [a8f8529d]
- Add more scientists to the list of random names [8d5b36a2] <Marcel Ribeiro Dantas>
22.06.0-edge - 9 Jun 2022
- Add AWS CodeCommit initial support [80fba6e9]
- Add support for 307 and 308 HTTP redirection [92382012]
- Add DirWatcher v2 [209c82cd]
- Add Moriondo in the list of random names [e0abca58]
- Add preview CLI option (#2914) [aa8f1aa4]
- Fix Git config resultion error [64436697]
- Fix StackOverflowError when dump all profiles (#2922) [28cd11a2] <Jorge Aguilera>
- Fix gradle warning message in nf-sqldb (#2921) [b09ceabe] <Jorge Aguilera>
- Fix log for LsfExecutror perTaskReserve attribute [7c3ec874] <Prete>
- Fix external pod deletion for jobs (#2915) [4dd1af7a] <xhejtman>
- Prevent function overloading in module definition [c0b522ab]
- Improve error message of non sensical include (#2623) [285fe49c] <Jorge Aguilera>
- Mount PWD path only when scratch is used [9b3c6e31]
- Stripe sensitive data into strings (#2908) [7fa4c86c] <Jorge Aguilera>
- Dump scm content when trace is enabled [c3117ada]
22.05.0-edge 25 May 2022
- Add Hyperqueue executor (#2896) [ffa5712e] <Henrik Nortamo>
- Add support for K8s Job resource [c70eb12d] <xhejtman>
- Add support for time process directive in GLS executor (#2880) [1402e183] <Florian De Temmerman>
- Add support for priviledge option for K8s containers [7ffe3a02]
- Add DSL1 option to docs (#2836) [d30841a5] <Jose Espinosa-Carrasco>
- 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] <Fabian Lehmann>
- Add support for AWS S3 encyption using a custom KMS key [c1e45aa9] <Paolo Di Tommaso>
- Add support for Micromamba [383e023f]
- Add jaxb-api dependecy 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] <Jorge Aguilera>
- Fix AthenaJdbc into distribution zip [853a1f2a] [4b3579d5] [70ef7ee3] <Jorge Aguilera>
- Fix Inconsistent bool parsing #2881 [40bf2b2a]
- Fix Unable to pull pipeline if config file is not in default branch (#2876) [4ee5b04f] <Jorge Aguilera>
- Fix Prevent crash when scratch dir does not exist (#2888) [9ef44ae5] <Fabian Lehmann>
- Fix DSL1 detection to invalid workflow keyword matching [fe0700b0] (#2879) <Jose Espinosa-Carrasco>
- Fix Aws Batch retry policy on spot reclaim [6e029b79]
- Fix 'false' string in config interpreted as true (#2865) [079a18ce] <Fabian Lehmann>
- 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] <Jorge Aguilera>
- 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] <Abhinav Sharma>]
- Update dependencies [405d9545]
- Refactoring to prevent name conflict [aba2671b]
- Few DSL syntax to explicit declaration of plugin extensions (#2820) [bfc4a067] <Jorge Aguilera>
- Sanitize k8s label and annotation keys, don't sanitize annotation value (#2843) [5287a984] <Ben Sherman>
- Docs improvement (#2835) [09e5bca3] <Ben Sherman>
- 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] <Jose Espinosa-Carrasco
22.04.2 - 16 May 2022
- Fix stackoverflow error when probe dsl [a05fcbea]
22.04.1 - 15 May 2022
- Improve dsl detection [739b959f]
- Improve missing workflow err message [f3fc081b] (#2871)
- Fix Aws Batch retry policy on spot reclaim [d855f0d9]
- Update default SKU for Azure Batch (#2868) [be60fc14]
- Bump nf-amazon 1.7.2
- Bump nf-azure 0.13.2
22.04.0 - 23 Apr 2022
- Improve error reporting (#2658) [e6ef017d] <Jorge Aguilera>
- Document params-file and improve self-update (#2673) [1e008f47] <Abhinav Sharma>
- Add support for AWS S3 anonymous credentials (#2810) [ae7ba35a]
- Add tolerations K8s pod option (#2763) [7f7cdadc] <Ben Sherman>
- 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] <Fabian Lehmann>
- Document params-file and improve self-update (#2673) [1e008f47] <Abhinav Sharma>
- Improve deprecation message (#2788) [720a84d7] <Fabian Lehmann>
- General docs improvements (#2800) [88acd26b] <Ben Sherman>
- Decrease Aws upload chunk size to 20 MB [086138fb]
- Improve error reporting (#2658) [e6ef017d] <Jorge Aguilera>
- Improve err reporting for Azure Batch [798bae1f]
- Rename echo directive to debug (#2776) [8f906aa5] <Ben Sherman>
- Remove embedded Read The Docs theme [728d545f] <Paolo Di Tommaso>
- Use a remote config in kuberun (#2781) [5485b699] <Fabian Lehmann>
- Start Github Actions also for edited PRs (#2796) [78f5c10f] <Fabian Lehmann>
- Deprecate isDsl2Final method [0f63f1a7]
- Document task object [1c83e21e] <Ben Sherman>
- Bump [email protected] [a137e93a]
- Bump [email protected] [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] <xhejtman>
- Honour background option for kuberun command [b1b0ddd9] <kfrancisdev>
- 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] <xhejtman>
- Add retry policy Azure create job [792820a2]
- Fix log message in nf-azure [80a0e937] <Manuele Simi>
- 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] <Jorge Aguilera>
- Fix Allow comments after nextflow.enable.dsl (#2746) [6988638b] <Jorge Aguilera>
- Fix allow blank spaces in java path (#2690) [a966020e] <Jorge Aguilera>
- 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]
- Decrese log verbosity [9237d587] [d1a5e5a8]
- Throw an error if a required secret is missing [8e5129d6]
- Wait for pod to stop running before shutdown (#2667) [505c5ad6]) <kfrancisdev>
- 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 isse 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] <Jorge Aguilera>
- Feature: Abort session if publish fails (#2643) [79b3836b] <Jorge Aguilera>
- Fix report overwrite cannot be disabled [202b5c9c] #2647
- Fix match bash interpreter irrespective the path [c2d2b9b2]
- Fix build warning + plugins assemble (#2634) [00dd143a] <Jorge Aguilera>
- Fix CITATION.cff and add automatic validation of your citation metadata [15698a45] <Faruk D>
- Bump [email protected] [a4496bb2]
- Bump [email protected] [e51139bb]
22.01.0-edge - 7 Feb 2022
- Add support for Tower reports (#2523) [de3d76349] <Jordi Deu-Pons>
- 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] <Ben Sherman>
- Add securityContext pod option to docs (#2584) [19f16f0da] <Ben Sherman>
- Add automountServiceAccountToken option for k8s executor (#2562) [1b5908e4c] <xhejtman>
- Add warn about AWS CLI grandparent path in container (#2565) [67073b0c5] <Simon Li>
- Add affinity option to pod directive (#2522) [640cbed48](3 weeks ago) <Ben Sherman>
- Add ability to specify memory/cpu resources for the control pod (#2559) [13f3e036d] <xhejtman>
- Add `-entry` parameter to pass in k8s executor (#2525) [a96233af6] <xhejtman>
- Add AWS Athena JDBC driver for nf-sqldb plugin (#2500) [462575f05] <Abhinav Sharma>
- Fix process output 'env' as array (#2624) [0a246dc2c] <Jorge Aguilera>
- Fix make date format to change independent from system locale [d1e5f6e76] <Jorge Aguilera>
- Fix double access of params file [459ebab7b] <Paolo Di Tommaso>
- Fix Use account SAS token instead of service SAS token (#2576) [d5125975d] <Florian De Temmerman>
- Fix upload of nested directory outputs on azure (#2578) [85ad55225] [744447155] <Florian De Temmerman>
- Fix Docs Typo (#2556) [942be46f6] <Kibubu>
- Fix NXF_PARAMS_FILE is not recognised #2549 [62f5fe1d9]
- Fix failing tests (4 weeks ago) <Paolo Di Tommaso>
- Fix Unable to use output path with nested properties [ceceb0784]
- Fix Nextflow couldn't parse generated nextflow.config under some circumstances (#2496) [2dfbbc63c] <Fabian Lehmann>
- Fix invalid use of `var` keyword [8418cc8d6]
- Improve k8s executor throwing NodeTerminationException on node shutdown (#2590) [084c8d6ca] <Patrick Hüther>
- Improve docs on `include` statements (#2520) [9c140cee3] <Alexander Toenges>
- Improve core plugins info & logging [dfa544ac9]
- Improve Secrets handling [1c0ad4679] [329502d19] [[26b4be906]]
- Improve DSL2 documentation [048b026f2] [e2e8b5557] <Manuele Simi>
- Improve documentation (#2600) [787a1fd84] <Ben Sherman>
- 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] <Ben Sherman>
- Update the azure docs for registry [96baf288e] <Abhinav Sharma>
- Update copyright info [807a816a5]
- Remove gradle logs about tasks dependencies (#2618) [cae44e00b] <Jorge Aguilera>
- Remove Tika deps for nf-amazon module [95620d42b]
- Remove deprecated validExitStatuas directive [b3117e789] [2188d51a0]
- Remove support for Apache Ignite [d4dc1cfe1] [64d2773fd]
- Bump [email protected] as default plugin
- Bump Gradle 7.3.3 [f00bfb0d3]
- Bump [email protected] [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] <Manuele Simi>
- 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] <Jose Espinosa-Carrasco>
- 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] <Jay Carey>
- Fix race condition on plugin autoload status [ab00a50f5]
- Fix failing test with Java 17 [1c6183c92] [4daf8d0a1]
- Note on Azure Batch inactive pools #2483 [7fc116067] <Manuele Simi>
- Remove drip launcher [909f95279]
- Update azure test image [de9d5ee8c]
- Update logging library [a957db646]
- Bump [email protected] [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] <Abhinav Sharma>
- Improve plugins dev root detection [b095bee15]
- Change Azure test pool vmType [ad5ad97ab]
- Downgrade Google NIO library to version 0.121.2 [896ec3abd]
- Bump [email protected] - bump [email protected] (6 days ago)
- Bump gradle 7.3.1 [2c34a3a27]
21.10.4 - 30 Nov 2021
- Fix include no longer works for custom functions #2469 [e17f6155d]
- Bump [email protected] - bump [email protected] [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] <mmatthews06>
21.10.1 - 18 Nov 2021
- Fix Azure batch NPE when missing pool spec [84b2983f4]
- Fix Docker bin in image PATH #2445 [d30da377a] <Josh Chorlton>
- 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 [email protected] [eb1e6fbd2]
- Bump [email protected] - bump [email protected] [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] <Mike Smoot>
- 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] <Lukas Jelonek>
- Fix implict 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 <Ben Shealy>
- Add K8s env fieldPath option to pod directive #2363 <Ben Shealy>
- Improve AWS Batch error report fetching CloudWatch logs [b9f9578f1] [e229700ef]
- Improve docs about IAM policies for AWS Batch #2391 <Manuele Simi>
- Accommodate token in password field for Gitlab #2389 [ee32b7726] <Abhinav Sharma>
- Report a warning when main workflow is not defined [83aec6e8b]
- Bump nf-amazon 1.3.0
- Bump [email protected]
- Bump [email protected]
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 [email protected]
- Bump [email protected]
- Bump [email protected]
- Bump [email protected]
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 groupping [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]