nextflow-io/nextflow v23.02.0-edge

Version 23.02.0-edge

on GitHub

• Add Fusion support for Google Batch (#3577) [d5fbab4]
• Add Header provider to Google Batch client [2097992]
• Add Wave integration tests [c5faf97]
• Add errorStrategy validation [954cd92]
• Add Java install recommendations to docs (#3617) [7e9bee1]
• Add nextflow tags to AWS Batch job def [b465ac5] [BREAKING]
• Add readOnlyInputs option for CharliecloudBuilder (#3590) [8ae001f]
• Add refresh token to Wave request [41510e8]
• Add requirements for container images to run with Nextflow (#3586) [7af1cb6]
• Add support for Fusion to Slurm and LSF executors (#3516) [fbc95e6]
• Add support for Fusion tags (#3609) [8385ec2]
• Add support for the Spack package manager (#3580) [a5df62f]
• Add the fcp tool option to file copy strategy (#3556) [2a22425]
• Add Fusion integration test
• Add Wave + Fusion test with Google Batch [b541c06]
• Add support for entryless Fusion configuration and Singularity support (#3584) [34a2773]
• Improve Fusion config [a1d0846]
• Ignore resource directives if -l option is specified in PBS executor (#3015) [28a6796]
• Improve K8s securityContext support [3f76240]
• Improve AWS Batch error logging [8f4884c]
• Improve secrets docs [9a3b421]
• Improve Wave debug-task plugin command [cf3fd74]
• Improve Wave logging [fced376]
• Increase Wave token duration to 30 mins [e1a712c]
• Fix -with-apptainer cli option (#3621) [8c9588f]
• Fix GH action tests step [bb890d9]
• Fix Spack failing test [868374d]
• Fix Tower doc links, fix typos (#3647) [1278e1a]
• Fix Wave cli messages [10cf414]
• Fix collectFile cache over remote storage [762ba19]
• Fix output env var tokenize [40d5673]
• Fix plugin install version [59e9a91]
• Fix race condition on Wave requests [f57fae2]
• Fix serialization of S3 paths with spaces (#3565) [ce48762]
• Fix string literal method names with parens (#3604) [8278078]
• Fix submit command in error message for grid executors that pipe wrapper script (#3548) [40ebd30]
• Fix typos in the documentation [skip ci] (#3640) [eccc113]
• Fix unique fingerprint for Wave bundle resources [b59fa72]
• Log exception when an unexpected occurs (#3603) [9aeca99]
• Minor change on container resolution [23d47de]
• Refactor httpfs configuration [445218a]
• Remove deprecated buckets field [0a355ac]
• Remove leading/trailing special chars from tag [7d3cc70]
• Remove unused -with-k8s CLI option (#3624) [85b6e7d]
• Update config.rst (#3655) [1555e18]
• Update Fusion docs [12782ee]
• Bump Fusion 2.1 [f48ef5b]
• Bump Groovy 3.0.15 [7a3ebc7]
• Bump Micromamba 1.3.1 [aa2bf37]
• Bump Spock 2.3 [9f0dac3]
• Bump nf-wave@0.7.1 [b797fac]
• Bump nf-tower@1.5.10 [dd2f69d]
• Bump nf-google@1.7.0 [8cb9fa3]
• Bump nf-amazon@1.15.0 [7ccca43]

Breaking changes

• Using the AWS Batch executor, Nextflow requires the permission batch:TagResource when creating Batch job permissions
• Using the AWS Batch executor with Fusion file system, Nextflow requires s3:PutObjectTagging permission on the S3 objects created by job executions