nextflow-io/nextflow v23.04.0

Version 23.04.0

on GitHub

• Add several names to the name generator feat:(#3790) [dfa2f6c]
• Add support for Fusion to Azure Batch executor (#3209) [3d3cbfa]
• Add support for testing custom plugin uri [227910a]
• Add warnings for Azure named pools (#3819) [a2c71ac]
• Enable new pid namespace with Singularity & Apptainer [3601b01]
• Fix NoSuchMethodError String.stripIndent with Java 11 [308eafe]
• Fix issue checking Google Batch script launcher type [39c3a51]
• Fix resolution of module resources [2c5a687]
• Fix Relax caching across task retries [840e843]
• Fix Java version for tests [7ce05c1]
• Remove extra context from workflow error message [38c8bd3]
• Revert "Enable Fusion on Google Batch tests" [2ba7ea5]
• Bump micromamba 1.4.1 [ec1439e]
• Bump nf-amazon@1.16.1 [0f98b24]
• Bump nf-azure@1.0.0 [e1732be]
• Bump nf-google@1.7.2 [99477f7]
• Bump nf-wave@0.8.1 [939195b]
• Bump nf-tower@1.5.11 [b7b5d4c]

From previous edge releases

23.03.0-edge - 19 Mar 2023

• Add Azure batch pool virtualNetwork option (#3723) [e3917b8]
• Add basePackages option to Wave config [7e82781]
• Add error message for missing container image with Google Batch (#3747) [6419e68]
• Add notifyFilePublish optional source argument (#3737) [a65a9ff]
• Add retry strategy on Bash wrapper write logic [1e38274]
• Add support for AWS S3 Glacier Retrieval Tier (#3680) [fab6bd5]
• Add sync invocation on job completion (#3678) [e29c4e4]
• Add workflowId to Wave request [025ff9d]
• Add Clone result list objects before output binding [3876208]
• Add plugins option to kuberun command (#3766) [6515294]
• Fix Google Batch logging exception [d7e38e9]
• Fix Java Matcher serialization [6aecc4e]
• Fix Logger failure type detection [f1b89c1]
• Fix Orphaned processes when using Singularity [7236f83]
• Fix groupTuple with mismatching tuple cardinality [1d32e2c]
• Fix special chars escaping in container env [b93634e]
• Fix commit revision type for Azure DevOps repos (#3721) [fb71767]
• Improve DAG API (#3703) [21afb35]
• Improve Wave docs [7299dac]
• Improve fair directive docs (#3677) [7ca7520]
• Improve transpose and groupTuple examples in the docs (#3685) [7870dfc]
• Increase pwd obfuscation min length [ba23d03]
• Make GroupKey cloneable (#3738) [0760b0f]
• Prepare Nextflow for the CWS Plugin (#3727) [fd8bf70]
• Remove DNAnexus page from docs (#3695) [fa58c18]
• Remove outdated FAQ page from docs (#3683) [e59c7fb]
• Remove unused classes [9fa8d75]
• Update Azure VM sizes (#3751) [1d06e9a]
• Enable Fusion on Google Batch tests [2f1b109]
• Bump groovy 3.0.16 [d3ff5dc]
• Bump nf-wave@0.8.0 [aa1b065]
• Bump nf-google@1.7.1 [2aaaf2a]
• Bump nf-azure@0.16.0 [f358b00]
• Bump nf-amazon@1.16.0 [2395187]

23.02.1-edge - 26 Feb 2023

• Add Fusion logs and tags config [0919207]
• Add support for NXF_DEBUG to K8s task handler [828583d]
• Add support for Mamba HTTP based lock files [7fe88c8]
• Add container name validation [c3b6d9a]
• Add Fusion for Google storage docs [34fcfe0]
• Improve K8s auth token discovery [44f8cc0]
• Bump nf-wave@0.7.2 [1c697ab]
• Bump amazoncorretto:17.0.6 [a33a6f4]

23.02.0-edge - 21 Feb 2023

• 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] [BREAKING]
• 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]

23.01.0-edge - 14 Jan 2023

• Add support for rclone as stageOutMode option [fde2ac2]
• Add queueGlobalStatus config setting [f333954]
• Add support for bearer token to GithubRepositoryProvider [c4d3938] [a2d2cbf]
• Add -with-fusion cli option [d22337c]
• Add support for Fusion container custom options [56e29d3]
• Add schedulingPriority option to AWS Batch (use with shareIdentifier) (#3505) [06960bb]
• Fix support for AWS ACL for Batch #2671 [a964491]
• Fix Java options.release in Gradle build [b362d6f]
• Fix nf-httpfs module name in build file [568e47f]
• Fix GitHub creds in CI build [4c4d3f8]
• Fix FilePorter concurrency issue (#3511) [11ccfa2]
• Fix watchPath hang shutdown execution [bac0ced]
• Fix "no such file" error message to "no such file or directory" (#3547) [c292d84]
• Improve local exec workdir validation [4a3a272]
• Improve container native executor configuration [0312637]
• Improve AWS batch exit code reporting [d1bb2fe]
• Improve channel factories error message [0215b9f]
• Improve Google Batch executor [c0a25fc]
• Improve Fusion config [902e5b3] [52f4c5d]
• Improve redirection on Wave client [124cfb3]
• Remove unnecessary Fusion env var [dfa4755]
• Remove deprecated method 'just' [d17b3c4]
• Remove deprecated methods [75e6503]
• Remove DSL1 deprecated code [5d290a4]
• Cleanup build from tmp manifests [326b383]
• Minor compilation improvements [4188a6a]
• Migrate all tests to DSL2 [14257d4]
• Bump 23.01.0-edge version [9ec3144]
• Bump groovy 3.0.14 [7c20423] [6f3ed6e]
• Bump Grengine 3.0 [c0b1a7a]
• Bump nf-wave@0.7.0 [45d274e]
• Bump nf-tower@1.5.9 [db0ebe7]
• Bump nf-google@1.6.0 [a663fe1]
• Bump nf-console@1.0.5 [45fd53a]
• Bump nf-codecommit@0.1.3 [cf39ef8]
• Bump nf-azure@0.15.1 [7a6a78a]
• Bump nf-amazon@1.14.0 [41fdcc7]

22.12.0-edge - 13 Dec 2022

• Add fair process directive [60d34cf]
• Add support for singularity registry setting [37c1aeb]
• Add AWS profile config setting [66f4669]
• Add support for AWS profile when resolving region [d894770]
• Add support for Sarus container engine (#3470) [54673f1]
• Add support for Fusion ARM64 client [d073c53]
• Add allowedLocations option to google batch (#3453) [c619eb8]
• Add support for AWS config profile in NF config [3711267]
• Add warning on Google Logs failure [bdbcdde]
• Add possible values of status in trace.txt to the documentation (#3451) [2425fcf]
• Add support for AWS Glacier restore [b611076]
• Add support for S3 storageClass to publishDir [066f920]
• Add MathHelper utility class [7eecb26]
• Fix Wave layer invalid checksum due to not closed stream [e188bbf]
• Fix Fusion test [2245a1c]
• Fix Run fails when home is a symlink [9ff820f]
• Fix math overflow when copying large AWS S3 files [f32ea0b]
• Fix Quote the logName in the Cloud Logging filter (#3464) [b397506]
• Fix Google Batch cloud logging (#3443) [e2bbcf1]
• Fix Tower plugin min nextflow requirement [1713a1c]
• Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [46af18e]
• Error & info messages, code comments language fixes (#3475) [29ae36c]
• Replace egrep with grep -E (#3485) [ac0c303]
• Gradle build optimizations (#3483) [19182a5]
• Refactor virtual FS schemes to XPath class [fd59b94]
• Update concat operator description (#3426) [e8d8c3b]
• Clarify usage of additional options for path qualifier (#3405) [0b70acb]
• Clarify limitation of -with-docker in the docs (#3408) [79afc85]
• Expose process queue as K8s pod label [4df8c8d]
• Prefix nextflow K8s labels with nextflow.io prefix [9951fcd]
• Remove deprecated code [c0b164f]
• Rewrite fetchIamRole and fetchRegion to use AWS SDK (#3425) [e350f31]
• Improve Wave config error reporting [ae50266]
• Improve K8s retry on transient failures [d86ddc3]
• Remove DSL1 output mode [fa400d5]
• Remove support for DSL1 multi into [f664af4]
• Bump nf-amazon@1.13.0 [ccaab71]
• Bump nf-google@1.5.0 [c07dcec]
• Bump nf-wave@0.6.3
• Bump nf-tower@1.5.8 [652d088]
• Bump fusion version URLs 0.6 [a160a8b]
• Bump AWS sdk version 1.12.351 [4dd82b6]

22.11.1-edge - 29 Nov 2022

• Fix TowerArchiver resolve envar paths relative to baseDir (#3438) [53e6348]
• Fix tower plugin min nextflow requirement [103dbf7]
• Fix typos in the documentation (#3441) [ae95d90]
• Add support for Java 19 [811e7ca]
• Add support for custom conda channels (#3435) [0884e80]
• Add time directive to AWS Batch, clean language (#3436) [1ed2640]
• Update err message [ab5bd81]
• Fix Flux executor config (#3432) [68b45c9]
• Bump nf-wave@0.6.1 [fe66915]
• Bump nf-tower@1.5.7 [2dbf990]

22.11.0-edge - 23 Nov 2022

• Add support for Apptainer container engine (#3345) [29f9897]
• Add Flux executor to nextflow (#3412) [cc9fc3f] [3711cef]
• Add support for Wave containerPlatform [10d56ca]
• Add CSI ephemeral volume for K8s (#2988) [f18f6e8]
• Add support for disk directive and emptyDir to K8s (#2998) [b548e1c]
• Add Fusion support for custom S3 endpoints [fba9b64]
• Add support for Tower refresh token for dataset (#3366) [a19e055]
• Prevent infinite loop while fetching git tags and branches [aa974d4]
• Improve file porter logging [626420b]
• Improve script err logging [2714770]
• Extend onFilePublish notification adding source path (#3284) [81acc3e]
• Remove cpu limits from K8s pod spec builder (#3338) [dc7f78b]
• Improve task name logging [5ddb7e3]
• Add tower endpoint to wave [b725ddc]
• Add Azure SAS token validation [e2244b4]
• Use cpus-shares for container resources (#3383) [b38c388]
• Report full path scheme on error [4089ba6]
• Allow identity based authentication on Azure Batch (#3132) [a08611b]
• Fix support for remote file mail attachment (#3384) [6b496bb]
• Fix task cache logging [ed37c4f]
• Fix unexpected error on task resume [1c3f468]
• Fix stripIndent failure with java 17 (#3377) [2b115c5]
• Fix -dockerized execution #3137 (#3148) [64a81a5]
• Improve default value in cli help of nextflow log -s (#3371) [2141f96]
• upgrade jsoup and snakeyaml version (#3374) [6e2ca45]
• Bump Java 17 lang version + Java 11 as target [34f133e]
• Bump nf-amazon@1.12.0 [e307912]
• Bump nf-azure@0.15.0 [07391d96]
• Bump nf-wave@0.6.0 [4d787561]