nextflow-io/nextflow v22.08.0-edge

Version 22.08.0-edge

on GitHub

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.