Nextflow

- Fix FilePorter concurrency issue (3511) [0f757156]
- Fix watchPath hang shutdown execution [e03d9ca6]
- Add `schedulingPriority` option to AWS Batch (use with `shareIdentifier`) (3505) [543ee7b1]

22.12.0-edge - 13 Dec 2022
- Add `fair` process directive [60d34cfd]
- Add support for singularity registry setting [37c1aeb9]
- Add AWS profile config setting [66f4669f]
- Add support for AWS profile when resolving region [d8947707]
- Add support for Sarus container engine (3470) [54673f18]
- Add support for Fusion ARM64 client [d073c538]
- Add allowedLocations option to google batch (3453) [c619eb81]
- Add support for AWS config profile in NF config [37112672]
- Add warning on Google Logs failure [bdbcdde9]
- Add possible values of `status` in `trace.txt` to the documentation (3451) [2425fcfb]
- Add support for AWS Glacier restore [b6110766]
- Add support for S3 storageClass to publishDir [066f9203]
- Add MathHelper utility class [7eecb266]
- Fix Wave layer invalid checksum due to not closed stream [e188bbf9]
- Fix Fusion test [2245a1c7]
- Fix Run fails when home is a symlink [9ff820f4]
- Fix math overflow when copying large AWS S3 files [f32ea0ba]
- Fix Quote the logName in the Cloud Logging filter (3464) [b3975063]
- Fix Google Batch cloud logging (3443) [e2bbcf15]
- Fix Tower plugin min nextflow requirement [1713a1cd]
- Fix TowerArchiver resolve envar paths relative to baseDir (3438) [46af18e5]
- Error & info messages, code comments language fixes (3475) [29ae36ca]
- Replace `egrep` with `grep -E` (3485) [ac0c3035]
- Gradle build optimizations (3483) [19182a57]
- Refactor virtual FS schemes to XPath class [fd59b943]
- Update concat operator description (3426) [e8d8c3b5]
- Clarify usage of additional options for path qualifier (3405) [0b70acb1]
- Clarify limitation of `-with-docker` in the docs (3408) [79afc85d]
- Expose process queue as K8s pod label [4df8c8d2]
- Prefix nextflow K8s labels with `nextflow.io` prefix [9951fcd9]
- Remove deprecated code [c0b164f2]
- Rewrite fetchIamRole and fetchRegion to use AWS SDK (3425) [e350f319]
- Improve Wave config error reporting [ae502668]
- Improve K8s retry on transient failures [d86ddc36]
- Remove DSL1 output mode [fa400d5f]
- Remove support for DSL1 multi into [f664af45]
- Bump nf-amazon1.13.0 [ccaab713]
- Bump nf-google1.5.0 [c07dcec2]
- Bump nf-wave0.6.3
- Bump nf-tower1.5.8 [652d0880]
- Bump fusion version URLs 0.6 [a160a8b1]
- Bump AWS sdk version 1.12.351 [4dd82b66]

- Fix math overflow when copying large AWS S3 files [07f7cb72]
- Bump nf-amazon1.11.2 [d96ca4c3]

22.11.1-edge - 29 Nov 2022
- Fix TowerArchiver resolve envar paths relative to baseDir (3438) [53e6348c]
- Fix tower plugin min nextflow requirement [103dbf74]
- Fix typos in the documentation (3441) [ae95d90d]
- Add support for Java 19 [811e7ca8]
- Add support for custom conda channels (3435) [0884e80e]
- Add time directive to AWS Batch, clean language (3436) [1ed2640a]
- Update err message [ab5bd81b]
- Fix Flux executor config (3432) [68b45c92]
- Bump nf-wave0.6.1 [fe669152]
- Bump nf-tower1.5.7 [2dbf9906]

22.11.0-edge - 23 Nov 2022
- Add support for Apptainer container engine (3345) [29f98975]
- Add Flux executor to nextflow (3412) [cc9fc3f0] [3711cef0]
- Add support for Wave containerPlatform [10d56ca1]
- Add CSI ephemeral volume for K8s (2988) [f18f6e81]
- Add support for disk directive and emptyDir to K8s (2998) [b548e1c7]
- Add Fusion support for custom S3 endpoints [fba9b649]
- Add support for Tower refresh token for dataset (3366) [a19e055a]
- Prevent infinite loop while fetching git tags and branches [aa974d44]
- Improve file porter logging [626420b6]
- Improve script err logging [2714770e]
- Extend onFilePublish notification adding source path (3284) [81acc3ef]
- Remove cpu limits from K8s pod spec builder (3338) [dc7f78bf]
- Improve task name logging [5ddb7e3f]
- Add tower endpoint to wave [b725ddc4]
- Add Azure SAS token validation [e2244b48]
- Use cpus-shares for container resources (3383) [b38c3880]
- Report full path scheme on error [4089ba65]
- Allow identity based authentication on Azure Batch (3132) [a08611be]
- Fix support for remote file mail attachment (3384) [6b496bb9]
- Fix task cache logging [ed37c4fd]
- Fix unexpected error on task resume [1c3f4685]
- Fix stripIndent failure with java 17 (3377) [2b115c50]
- Fix -dockerized execution 3137 (3148) [64a81a58]
- Improve default value in cli help of `nextflow log -s` (3371) [2141f96e]
- upgrade jsoup and snakeyaml version (3374) [6e2ca454]
- Bump Java 17 lang version + Java 11 as target [34f133e2]
- Bump nf-amazon1.12.0 [e307912e]
- Bump nf-azure0.15.0 [07391d96]
- Bump nf-wave0.6.0 [4d787561]

- Prevent infinite loop while fetching git tags/branches [73a59d33]
- Bump nf-amazon1.11.1 [f9b54ce3]
- Improve S3 thread pool config [01541b0a]

- Fix initialize the plugin once it's defined (3360) [dd150b92]
- Fix tags typo in docs (3355) [b82df4e0]
- Fix unexpected error on task resume [e02e8c27]
- Fix template script in trace record [cf828a68]
- Fix ip v6 support for K8s executor [53af5a7c]
- Fix refresh token for tower served resources [9dec2b66] 3366
- Fix full path scheme on error [1399f451]
- Add note to some process implicit variables (3373) [0374f63a]
- Add retry policy on plugin download failure [e8dbec3f]
- Add examples of when dynamic output filenames are important (3275) [72a17306]
- Update google batch java sdk, add serviceAccountEmail and installGpuDrivers (3324) [7f7007a8]
- Update github actions to v3 (3376) [d3b4a837]
- Update error messages and docs with new report filename behavior [f5725480]
- Bump nf-tower1.5.6 [164edf7c]
- Bump nf-google1.4.5 [30cb118d]

- Fix mount pwd in the container when work dir is a symlink [ca397181] [b5b7d3cd] <Paolo Di Tommaso>
- Fix secrets command name in the CLI (3320) [321486df] <Marcel Ribeiro Dantas>
- Fix ver num rendering 3226 [5312a25e] <Paolo Di Tommaso>
- Fix K8s config namespace is not applied [b3d33e3b] <Paolo Di Tommaso>
- Fix log fetching from remote storage [be356939] [3efa1a20] <Paolo Di Tommaso>
- Update docs about default mail ssl protocol (3299) [15ffffc1] <Ben Sherman>
- Update docs repeated words from documentation (3311) [d59ea186] <Marcel Ribeiro Dantas>
- Update docs to clarify the difference between collect and toList (3276) [7ee2b008] <Marcel Ribeiro Dantas>
- Update docs [516a7441] <Paolo Di Tommaso>
- Update docs adding Fusion [11eac707] <Paolo Di Tommaso>

- Fix timestamp encoding [47a3a3c4]
- Minor type change in Bridge executor [1f446ee1]
- Bump nf-wave0.5.2 [326803ff]