Nextflow

- Fix non-deterministic null container engine error [f93221ab]
- Add retry policy to Wave client [2f1532f6]
- Fix wave build docs [34a73022]
- Bump nf-wave0.8.3 [350201b5]

23.05.0-edge - 15 May 2023
- Add support for custom custom root directory to resolve relative paths (3942) [f06bb1f7]
- Add `arch` directive support for Spack (3786) [62dfc482]
- Add clone deep option to run and pull commands [b44b6453]
- Add fusion.exportStorageCredentials option [acb6aedf]
- Add groovy-yaml to core runtime [003e1f70]
- Add missing test env variables to CI build [a0e501bf]
- Add splitJson Operator (3830) [4f58f695]
- Add support for Java 20 [3788a689]
- Add support for `time` directive in Azure Batch (3869) [5c11a0d4]
- Add support for the Spack recipes to Wave build (3636) [b03cbe70]
- Add Preview support for virtual threads (3871) [5c429046]
- Convert docs to Markdown (3196) [3cad402f]
- Deprecate DSL1 syntax for tap operator (3004) [2be0edfe]
- Enable static compilation to missing classes (3906) [c3c4b2f0]
- Fix -with-conda option in the docs (3867) [9b350ba8]
- Fix AWS SSE env propagation to Fusion [e24608c3]
- Fix Apptainer rendering by removing superfluous space [36607ed1]
- Fix Azure jobs correctly deleted after completion (3927) [b173a983]
- Fix Azure pool creation when using scaling formula (3868) [79984a87]
- Fix DSL2 support in nextflow console (3864) [0253f8d7]
- Fix K8s handling PodUnschedulableException (3938) [5b756c63]
- Fix `interval` channel factory (3848) [d001e4c7]
- Fix invalid warning on func import (3807) [bb836960]
- Fix minor typo in nextflow subcommand (3853) [dd3be3d1]
- Fix misleading error message on NoSuchFileException [f3dceba6]
- Fix missing SAS token fusion env for Azure [43015029]
- Fix problem args were not correctly represented in debug yaml (3904) [eeb4b5c8]
- Fix string comparison in S3 client (3875) [9344d294]
- Fix use of remote dir with local exec statement [850bc3d9]
- Fix Quote Singularity/Apptainer env values [586417ac]
- Improve handling default out param [91471970]
- Improve plugin test detection [29794bf4]
- Improve plugin updater err handling [f3d72f22]
- Improve task out redirect remove the use of mkfifo (3863) [efedec74]
- Improve Use Docker stop instead of docker kill [32e6fd85]
- Improve Use separate script for long stage/unstage commands (3851) [4343e333]
- Increase Azure default maxRetries to 10 [a017139f]
- Keep plugins-info content sorted [d5552ee6]
- Minor change on Docker-spack templates [e0e24bda]
- Refactor the AWS configuration (3498) [a74e42d9]
- Remove `Channel.from` in favor of `Channel.of` from tests and docs (3670) [aa8b72fa]
- Rename AmazonS3Client to S3Client [cc59596a]
- Rename com.upplication.s3fs package to nextflow.cloud.aws.nio [a2f3bb24]
- Run build CI tests on push to branches starting with `test*` or `dev*` (3852) [7032e17c]
- Security fixes [973b7bea]
- Support enums in cache helper (3901) [e4b977a4]
- Bump slf4j 2.0.7 and logback 1.4.6 [d7eae86e]
- Bump JGit 6.5 and use depth 1 when cloning repos [eda0845c]
- Bump aws-java-sdk-s3:1.12.429 [465171f5]
- Bump fusion 2.2 [f1ebe29a]
- Bump groovy 3.0.17 [cfe4ba56]
- Bump gson:2.10.1 [be555683]
- Bump micromamba:1.4.2 [334df1e0]
- Bump nf-wave0.9.0 [7d6d0108]
- Bump nf-tower1.5.13 [b06ffd0c]
- Bump nf-google1.7.4 [2e0a15cd]
- Bump nf-ga4gh1.0.6 [0c8fd7df]
- Bump nf-console1.0.6 [a733b818]
- Bump nf-codecommit0.1.5 [12edf0e6]
- Bump nf-amazon2.0.0 [69b6edde]
- Bump nf-azure1.1.0 [d05d51b4]

- Add support for Java 20 [f6933db7]
- Fix use of remote dir with local exec statement [6ea1f68c]
- Fix Azure pool creation when using scaling formula (3868) [84a808a5]
- Fix interval channel factory (3848) [82ccf6ad]
- Fix invalid warning on func import (3807) [4678ffe3]
- Improve plugin test detection [57cfb0d9]
- Improve plugin updater err handling [5627c69a]
- Security fixes [83e8fd6a]
- Bump nf-wave0.8.2 [d8cb763c]
- Bump nf-tower1.5.12 [b2354380]
- Bump nf-google1.7.3 [22a68cfe]
- Bump gson:2.10.1 [83ca1e32]
- Bump nf-ga4gh1.0.5 [b40b5165]
- Bump nf-codecommit0.1.4 [98a89154]
- Bump aws-java-sdk-s3:1.12.429 [b71ee0a3]
- Bump nf-azure1.0.1 [a5da54d3]
- Bump nf-amazon1.16.2 [c90553c9]

- Add several names to the name generator feat:(3790) [dfa2f6ca]
- Add support for Fusion to Azure Batch executor (3209) [3d3cbfa2]
- Add support for testing custom plugin uri [227910ab]
- Add warnings for Azure named pools (3819) [a2c71acf]
- Enable new pid namespace with Singularity & Apptainer [3601b014]
- Fix NoSuchMethodError String.stripIndent with Java 11 [308eafe6]
- Fix issue checking Google Batch script launcher type [39c3a517]
- Fix resolution of module resources [2c5a6878]
- Fix Relax caching across task retries [840e8432]
- Fix Java version for tests [7ce05c15]
- Remove extra context from workflow error message [38c8bd33]
- Revert "Enable Fusion on Google Batch tests" [2ba7ea54]
- Bump micromamba 1.4.1 [ec1439e6]
- Bump nf-amazon1.16.1 [0f98b245]
- Bump nf-azure1.0.0 [e1732be9]
- Bump nf-google1.7.2 [99477f79]
- Bump nf-wave0.8.1 [939195b5]
- Bump nf-tower1.5.11 [b7b5d4c9]

23.03.0-edge - 19 Mar 2023
- Add Azure batch pool virtualNetwork option (3723) [e3917b8e]
- Add basePackages option to Wave config [7e827810]
- Add error message for missing container image with Google Batch (3747) [6419e68f]
- Add notifyFilePublish optional source argument (3737) [a65a9ff7]
- Add retry strategy on Bash wrapper write logic [1e38274a]
- Add support for AWS S3 Glacier Retrieval Tier (3680) [fab6bd5e]
- Add sync invocation on job completion (3678) [e29c4e4b]
- Add workflowId to Wave request [025ff9d0]
- Add Clone result list objects before output binding [38762080]
- Add plugins option to kuberun command (3766) [6515294f]
- Fix Google Batch logging exception [d7e38e9e]
- Fix Java Matcher serialization [6aecc4ed]
- Fix Logger failure type detection [f1b89c1f]
- Fix Orphaned processes when using Singularity [7236f830]
- Fix groupTuple with mismatching tuple cardinality [1d32e2c2]
- Fix special chars escaping in container env [b93634e9]
- Fix commit revision type for Azure DevOps repos (3721) [fb71767e]
- Improve DAG API (3703) [21afb358]
- Improve Wave docs [7299dac9]
- Improve `fair` directive docs (3677) [7ca7520f]
- Improve transpose and groupTuple examples in the docs (3685) [7870dfc8]
- Increase pwd obfuscation min length [ba23d036]
- Make GroupKey cloneable (3738) [0760b0fd]
- Prepare Nextflow for the CWS Plugin (3727) [fd8bf709]
- Remove DNAnexus page from docs (3695) [fa58c18c]
- Remove outdated FAQ page from docs (3683) [e59c7fbb]
- Remove unused classes [9fa8d75b]
- Update Azure VM sizes (3751) [1d06e9a6]
- Enable Fusion on Google Batch tests [2f1b1094]
- Bump groovy 3.0.16 [d3ff5dcb]
- Bump nf-wave0.8.0 [aa1b065d]
- Bump nf-google1.7.1 [2aaaf2a7]
- Bump nf-azure0.16.0 [f358b008]
- Bump nf-amazon1.16.0 [2395187d]

23.02.1-edge - 26 Feb 2023
- Add Fusion logs and tags config [09192078]
- Add support for NXF_DEBUG to K8s task handler [828583dc]
- Add support for Mamba HTTP based lock files [7fe88c84]
- Add container name validation [c3b6d9ab]
- Add Fusion for Google storage docs [34fcfe06]
- Improve K8s auth token discovery [44f8cc07]
- Bump nf-wave0.7.2 [1c697ab5]
- Bump amazoncorretto:17.0.6 [a33a6f47]

23.02.0-edge - 21 Feb 2023
- Add Fusion support for Google Batch (3577) [d5fbab4f]
- Add Header provider to Google Batch client [20979929]
- Add Wave integration tests [c5faf971]
- Add errorStrategy validation [954cd921]
- Add Java install recommendations to docs (3617) [7e9bee1e]
- Add nextflow tags to AWS Batch job def [b465ac52] [BREAKING]
- Add readOnlyInputs option for CharliecloudBuilder (3590) [8ae001fc]
- Add refresh token to Wave request [41510e87]
- Add requirements for container images to run with Nextflow (3586) [7af1cb66]
- Add support for Fusion to Slurm and LSF executors (3516) [fbc95e6b]
- Add support for Fusion tags (3609) [8385ec22] [BREAKING]
- Add support for the Spack package manager (3580) [a5df62f6]
- Add the fcp tool option to file copy strategy (3556) [2a224258]
- Add Fusion integration test
- Add Wave + Fusion test with Google Batch [b541c061]
- Add support for entryless Fusion configuration and Singularity support (3584) [34a27733]
- Improve Fusion config [a1d08463]
- Ignore resource directives if -l option is specified in PBS executor (3015) [28a67969]
- Improve K8s securityContext support [3f76240b]
- Improve AWS Batch error logging [8f4884c1]
- Improve secrets docs [9a3b4214]
- Improve Wave debug-task plugin command [cf3fd747]
- Improve Wave logging [fced3761]
- Increase Wave token duration to 30 mins [e1a712c2]
- Fix -with-apptainer cli option (3621) [8c9588fe]
- Fix GH action tests step [bb890d9a]
- Fix Spack failing test [868374d3]
- Fix Tower doc links, fix typos (3647) [1278e1a5]
- Fix Wave cli messages [10cf414b]
- Fix collectFile cache over remote storage [762ba19c]
- Fix output env var tokenize [40d56735]
- Fix plugin install version [59e9a91b]
- Fix race condition on Wave requests [f57fae2c]
- Fix serialization of S3 paths with spaces (3565) [ce487624]
- Fix string literal method names with parens (3604) [8278078a]
- Fix submit command in error message for grid executors that pipe wrapper script (3548) [40ebd308]
- Fix typos in the documentation (3640) [eccc1130]
- Fix unique fingerprint for Wave bundle resources [b59fa728]
- Log exception when an unexpected occurs (3603) [9aeca99f]
- Minor change on container resolution [23d47ded]
- Refactor httpfs configuration [445218a8]
- Remove deprecated buckets field [0a355ac3]
- Remove leading/trailing special chars from tag [7d3cc707]
- Remove unused `-with-k8s` CLI option (3624) [85b6e7d3]
- Update config.rst (3655) [1555e188]
- Update Fusion docs [12782eeb]
- Bump Fusion 2.1 [f48ef5b3]
- Bump Groovy 3.0.15 [7a3ebc7d]
- Bump Micromamba 1.3.1 [aa2bf37e]
- Bump Spock 2.3 [9f0dac31]
- Bump nf-wave0.7.1 [b797fac2]
- Bump nf-tower1.5.10 [dd2f69dd]
- Bump nf-google1.7.0 [8cb9fa35]
- Bump nf-amazon1.15.0 [7ccca430]

- Security fixes [fc2627bb]
- Add support for testing custom plugin uri [718d4562]
- Improve plugin updater err handling [84042082]
- Improve plugin test detection [e6c60a6c]
- Bump nf-google1.4.6 [26b01b83]
- Bump nf-wave0.5.5 [2a886fe0]
- Bump nf-ga4gh1.0.5 [b8769f1a]
- Bump nf-tower1.5.7-patch0 [89d902ec]
- Bump nf-azure0.14.3 [9b0f4bfb]
- Bump nf-amazon1.11.5 [f7aaddc6]
- Bump amazoncorretto17.0.6 [7898cc04]

- Fix plugin install version [895e4f34]
- Fix unique fingerprint for wave bundle resources [7c55aa37]
- Fix race condition on wave requests [7f76d19b]
- Fix serialization of S3 paths with spaces (3565) [935df949]
- Improve aws batch error logging [1eddeea7]
- Improve wave logging [94415914]
- Increase Wave token duration to 30 mins [8d5fbefe]
- Update fusion docs [b24ee138]
- Bump nf-wave0.5.4 [f466b266]
- Bump nf-amazon1.11.4 [d5f6c125]

- backport: Add refresh token to wave request [47a7408b]
- backport:Add tower endpoint to wave [fe24b422]
- backport:Fix Wave layer invalid checksum due to not closed stream [20df6400]
- Bump nf-wave0.5.3 [c1ec759f]

23.01.0-edge - 14 Jan 2023
- Add support for rclone as stageOutMode option [fde2ac27]
- Add queueGlobalStatus config setting [f3339541]
- Add support for bearer token to GithubRepositoryProvider [c4d39384] [a2d2cbf60]
- Add -with-fusion cli option [d22337cd]
- Add support for Fusion container custom options [56e29d35]
- Add `schedulingPriority` option to AWS Batch (use with `shareIdentifier`) (3505) [06960bb2]
- Fix support for AWS ACL for Batch 2671 [a9644919]
- Fix Java options.release in Gradle build [b362d6f6]
- Fix nf-httpfs module name in build file [568e47f6]
- Fix GitHub creds in CI build [4c4d3f81]
- Fix FilePorter concurrency issue (3511) [11ccfa26]
- Fix watchPath hang shutdown execution [bac0cedf]
- Fix "no such file" error message to "no such file or directory" (3547) [c292d84e]
- Improve local exec workdir validation [4a3a2720]
- Improve container native executor configuration [03126371]
- Improve AWS batch exit code reporting [d1bb2fe2]
- Improve channel factories error message [0215b9fc]
- Improve Google Batch executor [c0a25fc2]
- Improve Fusion config [902e5b34] [52f4c5d5]
- Improve redirection on Wave client [124cfb3e]
- Remove unnecessary Fusion env var [dfa47556]
- Remove deprecated method 'just' [d17b3c46]
- Remove deprecated methods [75e65035]
- Remove DSL1 deprecated code [5d290a47]
- Cleanup build from tmp manifests [326b3839]
- Minor compilation improvements [4188a6ac]
- Migrate all tests to DSL2 [14257d49]
- Bump 23.01.0-edge version [9ec31444]
- Bump groovy 3.0.14 [7c204236] [6f3ed6e8]
- Bump Grengine 3.0 [c0b1a7a6]
- Bump nf-wave0.7.0 [45d274e3]
- Bump nf-tower1.5.9 [db0ebe72]
- Bump nf-google1.6.0 [a663fe16]
- Bump nf-console1.0.5 [45fd53ad]
- Bump nf-codecommit0.1.3 [cf39ef8f]
- Bump nf-azure0.15.1 [7a6a78aa]
- Bump nf-amazon1.14.0 [41fdcc72]