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NEXTFLOW CHANGE-LOG
===================
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]
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]
22.10.4 - 9 Dec 2022
- Fix math overflow when copying large AWS S3 files [07f7cb72]
- Bump [email protected] [d96ca4c3]
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) [ci skip] [b82df4e0]
- Fix unexpected error on task resume [ci fast] [e02e8c27]
- Fix template script in trace record [cf828a68]
- Fix ip v6 support for K8s executor [ci fast] [53af5a7c]
- Fix refresh token for tower served resources [9dec2b66] #3366
- Fix full path scheme on error [1399f451]
- Add note to some process implicit variables [ci skip] (#3373) [0374f63a]
- Add retry policy on plugin download failure [e8dbec3f]
- Add examples of when dynamic output filenames are important (#3275) [ci skip] [72a17306]
- Update google batch java sdk, add serviceAccountEmail and installGpuDrivers (#3324) [7f7007a8]
- Update github actions to v3 (#3376) [ci fast] [d3b4a837]
- Update error messages and docs with new report filename behavior [ci fast] [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) [ci fast] [321486df] <Marcel Ribeiro Dantas>
- Fix ver num rendering [ci fast] #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 [ci skip] (#3299) [15ffffc1] <Ben Sherman>
- Update docs repeated words from documentation (#3311) [ci skip] [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) [ci fast] [f85d59a6] <Thodoris Sotiropoulos>
- Add support for refresh token to Wave [ed9f25f1] <Paolo Di Tommaso>
- Add pretty option to dump operator [ci fast] [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 [ci fast] [50086028] <Paolo Di Tommaso>
- Fix failing test [ci fast] [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) [ci skip] [5d80388c] <Marcel Ribeiro Dantas>
- Bump fusion snapshot [ci skip] [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 custon 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]
- 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 overriden 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 [ci fast] [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] (3 days ago) <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]
- 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 [email protected] [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 suppor 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 dependant 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 [email protected] + [email protected] [aff1d355]
- Bump [email protected] - [email protected] - solve #1830 [b3b221c1]
- Bump [email protected] [29fdd9f7]
- Bump [email protected] + [email protected] [c638af80]
- Bump [email protected] [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) <Paolo Di Tommaso>
- 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) <Paolo Di Tommaso>
- 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 containes 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 suscribe{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 defintions 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