nextflow-io/nextflow v22.10.0

Version 22.10.0

on GitHub

• Fix timestamp encoding [47a3a3c]
• Minor type change in Bridge executor [1f446ee]
• Bump nf-wave@0.5.2 [326803f]

Included in previous RC and edge releases:

22.10.0-RC3 - 7 Oct 2022

• Fix K8s context selection [58b354e]

22.10.0-RC2 - 7 Oct 2022

• Improve K8s labels/annotation validation [a569afd]
• Bump fusion final url [8039888]
• Bump nf-wave@0.5.1 [a2b44c4]
• Update docs

22.10.0-RC1 - 3 Oct 2022

• Add module binaries enabling flag + docs [c50e178]
• Add timestamp and fingerprint to wave request [a5a7e13]
• Add missing inputs to the incremental task "test" (#1442) [ci fast] [f85d59a]
• Add support for refresh token to Wave [ed9f25f]
• Add pretty option to dump operator [ci fast] [4218b29]
• Add support for custom S3 content type [02afa33]
• Get rid of file name rolling for report files [a762ed5]
• Ignore JGit warning when missing git tool [a94fa9c]
• Remove jobname limit to HyperQueue executor (#3251) [99604cc]
• Rename baseImage to mambaImage [ci fast] [5008602]
• Fix failing test [ci fast] [e679000]
• Fix K8s cluster token when using serviceAccount [c3364d0]
• Fix hanging test [44c0487]
• Improve docs (#3212) [ci skip] [5d80388]
• Bump fusion snapshot [ci skip] [8e03f65]
• Bump wave endpoint [a044cc6]
• Bump nf-wave@0.4.5 [7424dc4]
• Bump fusion config v0.5.1 [4dbdf11]
• Bump nf-wave@0.5.0
• Bump nf-tower@1.5.5
• Bump nf-amazon@1.11.0

22.09.7-edge - 28 Sep 2022

• Fix Issue copying file bigger than 5gb to S3 [18fd9a4]
• Fix chmod command to accommodate hidden files in bindir (or empty bindir) (#3247) [a0fcc7b]
• Bump nf-amazon@1.10.7 [f7f96e6]

22.09.6-edge - 26 Sep 2022

• Add SocketTimeoutException to k8s client request retry [527e0d5]
• Add MaxErrorRetry to K8s config [58be212]
• Add tags propagation to AWS Batch [d64eeff]
• Fix task resume when updating fusion layer [f38fd2d]
• Fix Channel merge still deprecated for DSL2 (#3220) [d27384d]
• Apply GCP resourceLabels to the VirtualMachine (#3234) [2275c03]
• Update Google Batch mount point with the requirements [5aec28a]
• Improve wave error reporting [7384221]
• Bump fusion 0.4.x [26f1f89]

22.09.5-edge - 21 Sep 2022

• Use default wave strategy [abbfa7f]
• Handle errors reported by tower report writer [0e81464]
• Fix AWS S3 copy object [b3b90d2]

22.09.4-edge - 19 Sep 2022

• Add Fusion display name [f789d45]
• Add container cleanup [cd2ae7d]
• Add Wave interactive debug session [ce7fa65]
• Add support for wave build and cache repositories[692043f]
• Add shutdown to Google Batch client [8f413cf]
• Add native_id to Google Batch handler [352b423]
• Add java sts library to enable use of IRSA in k8s (#3207) [62df42c]
• Add support for module custon bin dirs [77f5526]
• Add support for tower token to wave client [928d5b0]
• Update CLI docs (#3200) [8acebee]
• Fix issue with empty report file [9cc4f07]
• Do not return resource bundle for root module [775c7ed]
• Improve tower config [ee03c24]
• Bump groovy 3.0.13 [4a17e19]

22.09.3-edge - 10 Sep 2022

• Add fusion support to K8s executor (#3142) [6bb27b3]
• Fix shutdown/cleanup hooks invocation [f418507]
• Fix Use smaller buffer size for S3 stream uploader [8c64307] [9926d15]
• Fix Azure NPE on missing pool opts [d5c0aab]
• Fix handling of targetDir when using Fusion fs [2091b27]
• Document aws.batch.retryMode config (#3195) [56f75e0]

22.09.2-edge - 7 Sep 2022

• Fix thread pool race condition on shutdown [8d2b058]
• Fix Intermediate multipart upload requires a minimum size (#3193) [0b66aed]
• Fix fusion enable detection [3ef9151]
• Add before-afterScript warning to docs (#3167) [0946459]
• Add httpReadTimeout and httpConnectTimeout config to K8s client [064f9bc]
• Add support for Wave build & cache repos [98a275b]
• Finalise secrets feature (#3161) [49021b8]
• Update executor retry config docs (#3001) [aed6c23]
• Change Azure test pool name [0c72450]
• Improve Wave error reporting [b11d0f1]
• Remove unneeded launcher file remapping [a255118]
• Update Azure vm types [80f5fbe]
• Update docs logos (#3174) [529bad8]

22.09.1-edge - 1 Sep 2022

• Add support for Charliecloud v0.28 (#3116) [84f43a3] <Patrick Hüther>
• Add Support for EC-encrypted keys for K8s client [fd759d0]
• Add support for Bridge batch scheduler (#3106) [343c17e]
• Add fusion support to local executor [17160bb] [6cfb51e]
• Add getTags and getBranches to BitBucketServer [53bd89c]
• Add retry strategy to httpfs client [55f9c87]
• Add support for project resources [c2ad656]
• Add mamba build options [987a13c]
• Fix Do not override tower endpoint in the config [41fb1ad]
• Fix Hyperqueue job names must be less than 40 chars #3151 [8e43670]
• Fix typo in ConfigBuilder.groovy (#3143) [659e610]
• Fix Resume for dynamic resolved containers [13483ff]
• Improve fusion env handling [10f35b6]
• Improve foreign file(s) cache detection logic [3a9352c]
• Rename ModuleBundle to ResourcesBundle [0e51dc0]
• Use quiet output mode for hyperqueue executor (#3103) [70a91fd]
• Wave improve conda settings [6f087fe]
• Improve secrets cmd (#3158) [115b2f3]
• Improve Wave resolution strategy [2eb700c]
• Improve Az Batch err handling and testing [85d31e8]
• Bump google-cloud-batch 0.2.2
• Bump spock 2.2

22.08.2-edge - 16 Aug 2022

• Fix queueSize setting is not honoured by AWS Batch executor (again) #3117 [1733bb2]
• Add files() method to docs (#3123) [00bb889]
• Refactor wave packing [bc87698]
• Improve logging [aa380d5]
• Update dockerfile [e632928]

22.08.1-edge - 11 Aug 2022

• Add support for disabling config include [e0859a1]
• Add experimental fusion support [1854f1f]
• Add support for plugin provided function extension (#3079) [16230c2]
• Add support for AWS Batch logs group (#3092) [4ef043a]
• Add share identifier to Aws Batch (#3089) [c0253ab]
• Improve Tower cache manager [0091afc]
• Improve S3 copy via xfer manager [02d2bea]
• Reports a warning when using NXF vars in the config [009ec25]
• Make wake token cache duration config [5f955fc]
• Patch unable to start non-core plugin [a55f58f]
• Increase S3 upload chunk size to 100 MB [9c94a08]
• Change Google Batch disk directive to override boot disk size (#3097) [7e1c068]
• Fix queueSize setting is not honoured by AWS Batch executor (#3093) [d07bb52]
• Fix Allow disabling scratch with Google Batch [e8e5c72]
• Fix Emit relative path when relative parameter is set (#3072) [3979775]
• Bump nf-wave@0.3.0 [e46d341]
• Bump nf-tower@1.5.1 [cdc2be5]
• Bump nf-google@1.4.1 [c39935a]
• Bump nf-amazon@1.10.0 [ccdf62d]

22.08.0-edge - 1 Aug 2022

• Add warning to env config docs (#3083) [ca933c1]
• Add -with-conda CLI option (#3073) [98b2ac8]
• Add simple wave plugin cli commands [8888b86]
• Add default wave plugin [7793a0e]
• Add boot disk, cpu platform to google batch (#3058) [17a8483]
• Add support for GPU accelerator to Google Batch (#3056) [f34ad7f]
• Add support for archive dir to tower plugin [c234681]
• Add support tower cache backup/restore [bc2f9d1]
• Add disk directive to google batch (#3057) [ec6e290]
• Add retry when Azure submit fails with OperationTimedOut [6a3f974]
• Add warning when Google Batch quota is exceeded (#3066) [6b9c52a]
• Allow fully disabling history file [0a45f85]
• Allow the support function overloading and default parameters (#3011) [042d385]
• Improve S3 file upload/download via Transfer manager [7e8d2a5]
• Prevent overriding container entrypoint [b3a4bf8]
• Update FileTransfer pool settings [503aafc]
• Remove deprecated commands [93228b4]
• Prevent nextflow config to break tower launch [e059a72]
• Refactor Google Batch executor to use Java API (#3044) [31a6e85]
• Fix Unable to disable scratch attribute with AWS Batch [1770f73]
• Fix unit test setting explicit permissions for test files [1c82113]
• Fix Default plugins are overriden by config plugins [46cf3bf]
• Fix S3 transfer download directory [b7bf9fe]
• Fix NPE while setting S3 ObjectMetada #3031 [d616343]
• Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3]
• Fix AWS Batch job definition conflict (#3048) [e508441]
• Fix JAVA_TOOL_OPTIONS breaking launch #1716 [0e7b416]
• Fix add ps shared objects to Dockerfile (#3033) [1c23b40]
• Parallelize build integration tests [807800a]
• Bump google-cloud-nio:0.124.8 [dfaa9d1]
• Bump groovy 3.0.12 [5c900b9]
• Bump Moment.js 2.29.4 [a9ced86]
• Bump gson@2.9.0 [12f1717]
• Bump nf-azure@0.13.4
• Bump nf-google@1.4.0
• Bump nf-tower@1.5.0
• Bump nf-wave@0.2.1
• Bump nf-amazon@1.9.0

22.07.1-edge - 13 Jul 2022

• Add support for Google Batch API v1 [4c116d5] [e85d87e]
• Add time directive support for K8s executor (#2948) [2b6f70a]
• Add docs aws.client.s3PathStyleAccess config (#3000) [2000550]
• Allow to override lsf.conf settings with nextflow config #2862 [dae191a]
• Allow hybrid containers execution [0af1bcb]
• Improve error msg when script file cannot be read [52c2780]
• Improve error reporting for custom function [877c793]
• Improve error message for missing plugin extension [4a43db8]
• Improve test #3019 [7c37e0b]
• Rename kuberun -pod-image to -head-image [2576ba6]
• Externalise sqldb plugin source code [17e80b4]
• Fix escape unstage outputs with double quotes #2912 #2904 #2790 [49ff02a]
• Fix Exception when settings AWS Batch containerOptions #3019 [89312ad]
• Fix Missing query param in http file (#2918) [43cc851]
• Fix Publish copy mode for S3 based path [085f6b2]
• Fix Fail fast uploads to S3 (#2969) [7fd1a6e]
• Fix null script name in launch info [7118849]
• Bump commons-code@1.15 [a06b444]
• Bump jgit@6.2.0 [3331826]
• Bump snakeyaml@1.30 [de62fd3]
• Bump gson@2.8.9 [3234ddd]

22.07.0-edge - [SKIPPED]

22.06.1-edge - 17 Jun 2022

• Fix CodeCommit creds handling + nf-codecommit@0.1.2 [70fc0745]
• Fix typo in log message [a8f8529d]
• Add more scientists to the list of random names [8d5b36a]

22.06.0-edge - 9 Jun 2022

• Add AWS CodeCommit initial support [80fba6e]
• Add support for 307 and 308 HTTP redirection [9238201]
• Add DirWatcher v2 [209c82c]
• Add Moriondo in the list of random names [e0abca5]
• Add preview CLI option (#2914) [aa8f1aa]
• Fix Git config resultion error [6443669]
• Fix StackOverflowError when dump all profiles (#2922) [28cd11a]
• Fix gradle warning message in nf-sqldb (#2921) [b09ceab]
• Fix log for LsfExecutror perTaskReserve attribute [7c3ec87]
• Fix external pod deletion for jobs (#2915) [4dd1af7]
• Prevent function overloading in module definition [c0b522a]
• Improve error message of non sensical include (#2623) [285fe49]
• Mount PWD path only when scratch is used [9b3c6e3]
• Stripe sensitive data into strings (#2908) [7fa4c86]
• Dump scm content when trace is enabled [c3117ad]

22.05.0-edge 25 May 2022

• Add Hyperqueue executor (#2896) [ffa5712]
• Add support for K8s Job resource [c70eb12]
• Add support for time process directive in GLS executor (#2880) [1402e18]
• Add support for priviledge option for K8s containers [7ffe3a0]
• Add DSL1 option to docs (#2836) [d30841a]
• Add support for container options to Azure Batch [3f4f00f]
• Add support for move operation to AWS S3 [8c0ddfd]
• Add K8s execution hostname in the trace file (#2828) [ebaef92]
• Add support for AWS S3 encyption using a custom KMS key [c1e45aa]
• Add support for Micromamba [383e023]
• Add jaxb-api dependecy to nf-amazon [c1a09f8]
• Add strict mode config setting [ci fast] [696e70b]
• Add -head-prescript option to kuberun (#2830) [9e38705]
• Fix missing err message on submit failure [233e67f] (#2899)
• Fix resolve azure devops repositories when projectId is present [2500ff0]
• Fix AthenaJdbc into distribution zip [853a1f2] [4b3579d] [70ef7ee]
• Fix Inconsistent bool parsing #2881 [40bf2b2]
• Fix Unable to pull pipeline if config file is not in default branch (#2876) [4ee5b04]
• Fix Prevent crash when scratch dir does not exist (#2888) [9ef44ae]
• Fix DSL1 detection to invalid workflow keyword matching [fe0700b] (#2879)
• Fix Aws Batch retry policy on spot reclaim [6e029b7]
• Fix 'false' string in config interpreted as true (#2865) [079a18c]
• Improve Git Provider config logging [d7dbca8]
• Improve K8s task handler [1822b2c]
• Improve missing workflow err message [da101e8] (#2871)
• Include revision in the Azure Repos provider when specified (#2861) [3342c76]
• Remove unnecessary change dir echo [372d1f4]
• Abort execution when accessing undefined params with strict mode [9383608]
• Update docker base image [50cd795]
• Update default SKU for Azure Batch (#2868) [9ea09db] ]
• Update dependencies [405d954]
• Refactoring to prevent name conflict [aba2671]
• Few DSL syntax to explicit declaration of plugin extensions (#2820) [bfc4a06]
• Sanitize k8s label and annotation keys, don't sanitize annotation value (#2843) [5287a98]
• Docs improvement (#2835) [09e5bca]
• Bump Jgit 6.1 [7186348]
• Bump Spock 2.1 [51100d1]
• Bump capsule 1.1.1 [20ec169]