nextflow-io/nextflow v23.05.0-edge

Version 23.05.0-edge

on GitHub

23.05.0-edge - 15 May 2023

• Add support for custom custom root directory to resolve relative paths (#3942) [f06bb1f]
• Add arch directive support for Spack (#3786) [62dfc48]
• Add clone deep option to run and pull commands [b44b645]
• Add fusion.exportStorageCredentials option [acb6aed]
• Add groovy-yaml to core runtime [003e1f7]
• Add missing test env variables to CI build [a0e501b]
• Add splitJson Operator (#3830) [4f58f69]
• Add support for Java 20 [3788a68]
• Add support for time directive in Azure Batch (#3869) [5c11a0d]
• Add support for the Spack recipes to Wave build (#3636) [b03cbe7]
• Add Preview support for virtual threads (#3871) [5c42904]
• Convert docs to Markdown (#3196) [3cad402]
• Deprecate DSL1 syntax for tap operator (#3004) [2be0edf]
• Enable static compilation to missing classes (#3906) [c3c4b2f]
• Fix -with-conda option in the docs (#3867) [9b350ba]
• Fix AWS SSE env propagation to Fusion [e24608c]
• Fix Apptainer rendering by removing superflous space [36607ed]
• Fix Azure jobs correctly deleted after completion (#3927) [b173a98]
• Fix Azure pool creation when using scaling formula (#3868) [79984a8]
• Fix DSL2 support in nextflow console (#3864) [0253f8d]
• Fix K8s handling PodUnschedulableException (#3938) [5b756c6]
• Fix interval channel factory (#3848) [d001e4c]
• Fix invalid warning on func import (#3807) [bb83696]
• Fix minor typo in nextflow subcommand (#3853) [dd3be3d]
• Fix misleading error message on NoSuchFileException [f3dceba]
• Fix missing SAS token fusion env for Azure [4301502]
• Fix problem args were not correctly represented in debug yaml (#3904) [eeb4b5c]
• Fix string comparison in S3 client (#3875) [9344d29]
• Fix use of remote dir with local exec statement [850bc3d]
• Fix Quote Singularity/Apptainer env values [586417a]
• Improve handling default out param [9147197]
• Improve plugin test detection [29794bf]
• Improve plugin updater err handling [f3d72f2]
• Improve task out redirect remove the use of mkfifo (#3863) [efedec7]
• Improve Use Docker stop instead of docker kill [32e6fd8]
• Improve Use separate script for long stage/unstage commands (#3851) [4343e33]
• Increase Azure default maxRetries to 10 [a017139]
• Keep plugins-info content sorted [d5552ee]
• Minor change on Docker-spack templates [e0e24bd]
• Refactor the AWS configuration (#3498) [a74e42d]
• Remove Channel.from in favor of Channel.of from tests and docs (#3670) [aa8b72f]
• Rename AmazonS3Client to S3Client [cc59596]
• Rename com.upplication.s3fs package to nextflow.cloud.aws.nio [a2f3bb2]
• Run build CI tests on push to branches starting with test* or dev* (#3852) [7032e17]
• Security fixes [973b7be]
• Support enums in cache helper (#3901) [e4b977a]
• Bump slf4j 2.0.7 and logback 1.4.6 [d7eae86]
• Bump JGit 6.5 and use depth 1 when cloning repos [eda0845]
• Bump aws-java-sdk-s3:1.12.429 [465171f]
• Bump fusion 2.2 [f1ebe29]
• Bump groovy 3.0.17 [cfe4ba5]
• Bump gson:2.10.1 [be55568]
• Bump micromamba:1.4.2 [334df1e]
• Bump nf-wave@0.9.0 [7d6d010]
• Bump nf-tower@1.5.13 [b06ffd0]
• Bump nf-google@1.7.4 [2e0a15c]
• Bump nf-ga4gh@1.0.6 [0c8fd7d]
• Bump nf-console@1.0.6 [a733b81]
• Bump nf-codecommit@0.1.5 [12edf0e]
• Bump nf-amazon@2.0.0 [69b6edd]
• Bump nf-azure@1.1.0 [d05d51b]