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Version 22.08.2-edge

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Version 22.08.1-edge

  • 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]
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Version 22.08.0-edge


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

Breaking changes

  • The container entrypoint is not overridden anymore with /bin/bash by Nextflow when using Local, Kubernetes and batch scheduler executors. This has been made for consistency with the AWS, Google and Azure Batch executors that do not set it either. Make sure the containers used in your pipeline use sh or bash as the default entry point. If you want to continue to use the old behaviour set the variable NXF_CONTAINER_ENTRYPOINT_OVERRIDE=true in the launch environment
  • The use of Conda environment defined in the process definition via the conda directive needs to be enabled in an explicit manner using either the CLI option -with-conda or using the config setting conda.enabled=true or setting environment variable NXF_CONDA_ENABLED=true. See #3073 for details.
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  • Allow fully disabling history file [1a36c9b]
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Version 22.07.1-edge

  • 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]
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  • Fix Publish copy mode for s3 based path [bb510ce]
  • Add strict mode config setting [b0567e6]
  • Update docker base image [b00c141]
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Version 22.06.1-edge


Tagging version 22.06.1-edge [release]
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Version 22.06.0-edge

  • 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]
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Version 22.05.0-edge

  • 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]
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