changelog.txt

NEXTFLOW CHANGE-LOG
===================
23.06.0-edge - 14 Jun 2023
- Add AWS Kms integration test [19449bf4]
- Add Wave containers reports (preview) [9d9e2758]
- Add disk resource with type option for google batch (#3861) [166b3638]
- Add httpConnectTimeout and httpReadTimeout to Google options (#3974) [49fa15f7]
- Add plugin cmd help descrption [d3788f9f]
- Add retry policy on Az blob operations [295bc1ff]
- Add retry policy to Wave http client [1daebeef]
- Add support for AWS SES as mail sending provider [df85d443]
- Add support for arch auto-detection to Wave [7b5fdaf0]
- Add wave.httpClient.connectTimeout config option [dd999a3c]
- Clarify tip about groupTuple size and groupKey (#3949) [e60d327f]
- Consolidate Wave retryPolicy options [7d7464fe]
- Enhanced support for Spack + Wave (#3998) [63ac03b3]
- Fix Google Batch default instance family types (#3960) [b5257cd7]
- Fix S3 path normalization [b75ec444]
- Fix access to public S3 bucket when no creds are provided (#3992) [cf8ba466] [680f0a90]
- Fix containerOptions when using Fusion [dcde7b7f]
- Fix dump pretty print to not modify input (#3955) [46c17ee3]
- Fix invalid machine type setting when no valid machine type is found (#3961) [5eb93971]
- Fix matching symlink files [d63af784]
- Fix missing options for JsonSplitter creation (#3958) [f991fe9e]
- Fix non-deterministic null container engine error [f227f2e5]
- Fix packing all including Wave [735b8d9c]
- Fix static compiler errors [f48a473c]
- Improve documentation on Nextflow scripts (#3953) [80050c03]
- Improve description of channels and channel types (#4120) [8975734d]
- Improve "Unexpected input: '{'" error message (#4122) [ci fast] [ef9d3cf0]
- Minor change in Wave config [4da0442a]
- Prevent null exit code when Google batch is unable to acces exit status [f68a39ec]
- Refactor Conda and Spack support for Wave to Java [36b9e226]
- Remove `--no-home` default option from charliecloud builder (#3956) [915074a4]
- Update workflow.revision max length to match the one in Tower (#4010) [1433a903]
- Bump amazocorretto:17.0.7 [c8aa1214]
- Bump azure-storage-blob:12.22.1 [2a36fa77]
- Bump nf-wave@0.11.0 [2998db5d]
- Bump nf-tower@1.5.15 [3278d798]
- Bump nf-google@1.8.1 [6aede7c0]
- Bump nf-ga4gh@1.1.0 [f98feb77]
- Bump nf-azure@1.1.4 [1895efc4]
- Bump nf-amazon@2.1.0 [57464746]
- Bump nf-cloudcache@0.1.0 [cb6242c4]

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 superflous 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-wave@0.9.0 [7d6d0108]
- Bump nf-tower@1.5.13 [b06ffd0c]
- Bump nf-google@1.7.4 [2e0a15cd]
- Bump nf-ga4gh@1.0.6 [0c8fd7df]
- Bump nf-console@1.0.6 [a733b818]
- Bump nf-codecommit@0.1.5 [12edf0e6]
- Bump nf-amazon@2.0.0 [69b6edde]
- Bump nf-azure@1.1.0 [d05d51b4]

23.04.1 - 15 Apr 2023
- 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-wave@0.8.2 [d8cb763c]
- Bump nf-tower@1.5.12 [b2354380]
- Bump nf-google@1.7.3 [22a68cfe]
- Bump gson:2.10.1 [83ca1e32]
- Bump nf-ga4gh@1.0.5 [b40b5165]
- Bump nf-codecommit@0.1.4 [98a89154]
- Bump aws-java-sdk-s3:1.12.429 [b71ee0a3]
- Bump nf-azure@1.0.1 [a5da54d3]
- Bump nf-amazon@1.16.2 [c90553c9]

22.10.8 - 15 Apr 2023
- Security fixes [fc2627bb]
- Add support for testing custom plugin uri [718d4562]
- Improve plugin updater err handling [84042082]
- Improve plugin test detection [e6c60a6c]
- Bump nf-google@1.4.6 [26b01b83]
- Bump nf-wave@0.5.5 [2a886fe0]
- Bump nf-ga4gh@1.0.5 [b8769f1a]
- Bump nf-tower@1.5.7-patch0 [89d902ec]
- Bump nf-azure@0.14.3 [9b0f4bfb]
- Bump nf-amazon@1.11.5 [f7aaddc6]
- Bump amazoncorretto@17.0.6 [7898cc04]

23.04.0 - 1 Apr 2023
- 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-amazon@1.16.1 [0f98b245]
- Bump nf-azure@1.0.0 [e1732be9]
- Bump nf-google@1.7.2 [99477f79]
- Bump nf-wave@0.8.1 [939195b5]
- Bump nf-tower@1.5.11 [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-wave@0.8.0 [aa1b065d]
- Bump nf-google@1.7.1 [2aaaf2a7]
- Bump nf-azure@0.16.0 [f358b008]
- Bump nf-amazon@1.16.0 [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-wave@0.7.2 [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 [skip ci] (#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-wave@0.7.1 [b797fac2]
- Bump nf-tower@1.5.10 [dd2f69dd]
- Bump nf-google@1.7.0 [8cb9fa35]
- Bump nf-amazon@1.15.0 [7ccca430]

22.10.7 - 18 Feb 2023
- 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-wave@0.5.4 [f466b266]
- Bump nf-amazon@1.11.4 [d5f6c125]

22.10.6 - 24 Jan 2023
- 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-wave@0.5.3 [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-wave@0.7.0 [45d274e3]
- Bump nf-tower@1.5.9 [db0ebe72]
- Bump nf-google@1.6.0 [a663fe16]
- Bump nf-console@1.0.5 [45fd53ad]
- Bump nf-codecommit@0.1.3 [cf39ef8f]
- Bump nf-azure@0.15.1 [7a6a78aa]
- Bump nf-amazon@1.14.0 [41fdcc72]

22.10.5 - 14 Jan 2023
- 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-amazon@1.13.0 [ccaab713]
- Bump nf-google@1.5.0 [c07dcec2]
- Bump nf-wave@0.6.3
- Bump nf-tower@1.5.8 [652d0880]
- Bump fusion version URLs 0.6 [a160a8b1]
- Bump AWS sdk version 1.12.351 [4dd82b66]

22.10.4 - 9 Dec 2022
- Fix math overflow when copying large AWS S3 files [07f7cb72]
- Bump nf-amazon@1.11.2 [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-wave@0.6.1 [fe669152]
- Bump nf-tower@1.5.7 [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-amazon@1.12.0 [e307912e]
- Bump nf-azure@0.15.0 [07391d96]
- Bump nf-wave@0.6.0 [4d787561]

22.10.3 - 21 Nov 2022
- Prevent infinite loop while fetching git tags/branches [73a59d33]
- Bump nf-amazon@1.11.1 [f9b54ce3]
- Improve S3 thread pool config [01541b0a]

22.10.2 - 13 Nov 2022
- 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-tower@1.5.6 [164edf7c]
- Bump nf-google@1.4.5 [30cb118d]

22.10.1 - 27 Oct 2022
- 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>

22.10.0 - 13 Oct 2022
- Fix timestamp encoding [47a3a3c4]
- Minor type change in Bridge executor [1f446ee1]
- Bump nf-wave@0.5.2 [326803ff]

22.10.0-RC3 - 7 Oct 2022 
- Fix K8s context selection [58b354e6]

22.10.0-RC2 - 7 Oct 2022 
- Improve K8s labels/annotation validation [a569afdf]
- Bump fusion final url [80398880]
- Bump nf-wave@0.5.1 [a2b44c4d]
- Update docs 

22.10.0-RC1 - 3 Oct 2022
- Add module binaries enabling flag + docs [c50e178f] <Paolo Di Tommaso>
- Add timestamp and fingerprint to wave request [a5a7e138] <Paolo Di Tommaso>
- Add missing inputs to the incremental task "test" (#1442) [f85d59a6] <Thodoris Sotiropoulos>
- Add support for refresh token to Wave [ed9f25f1] <Paolo Di Tommaso>
- Add pretty option to dump operator [4218b299] <Paolo Di Tommaso>
- Add support for custom S3 content type [02afa332] <Paolo Di Tommaso>
- Get rid of file name rolling for report files [a762ed59] <Paolo Di Tommaso>
- Ignore JGit warning when missing git tool [a94fa9c1] <Paolo Di Tommaso>
- Remove jobname limit to HyperQueue executor (#3251) [99604ccb] <Henrik Nortamo>
- Rename baseImage to mambaImage [50086028] <Paolo Di Tommaso>
- Fix failing test [e6790003] <Paolo Di Tommaso>
- Fix K8s cluster token when using serviceAccount [c3364d0f] <Paolo Di Tommaso>
- Fix hanging test [44c04874] <Paolo Di Tommaso>
- Improve docs (#3212) [5d80388c] <Marcel Ribeiro Dantas>
- Bump fusion snapshot [8e03f655] <Paolo Di Tommaso>
- Bump wave endpoint [a044cc6a] <Paolo Di Tommaso>
- Bump nf-wave@0.4.5 [7424dc4b] <Paolo Di Tommaso>
- Bump fusion config v0.5.1 [4dbdf112] <Paolo Di Tommaso>
- Bump nf-wave@0.5.0
- Bump nf-tower@1.5.5
- Bump nf-amazon@1.11.0

22.09.7-edge - 28 Sep 2022
- Fix Issue copying file bigger than 5gb to S3 [18fd9a44]
- Fix chmod command to accommodate hidden files in bindir (or empty bindir) (#3247) [a0fcc7b0] <Abhinav Sharma>
- Bump nf-amazon@1.10.7 [f7f96e6f] 

22.09.6-edge - 26 Sep 2022
- Add SocketTimeoutException to k8s client request retry [527e0d5d]
- Add MaxErrorRetry to K8s config [58be2128]
- Add tags propagation to AWS Batch [d64eeffc]
- Fix task resume when updating fusion layer [f38fd2db]
- Fix Channel merge still deprecated for DSL2 (#3220) [d27384d2] <Kibubu>
- Apply GCP resourceLabels to the VirtualMachine (#3234) [2275c03c] <Doug Daniels>
- Update Google Batch mount point with the requirements [5aec28ac]
- Improve wave error reporting [73842215]
- Bump fusion 0.4.x [26f1f896]

22.09.5-edge - 21 Sep 2022
- Use default wave strategy [abbfa7f4]
- Handle errors reported by tower report writer [0e814647]
- Fix AWS S3 copy object [b3b90d23]

22.09.4-edge - 19 Sep 2022
- Add Fusion display name [f789d457]
- Add container cleanup [cd2ae7dc]
- Add Wave interactive debug session [ce7fa651]
- Add support for wave build and cache repositories[692043ff]
- Add shutdown to Google Batch client [8f413cf7]
- Add native_id to Google Batch handler [352b4239]
- Add java sts library to enable use of IRSA in k8s (#3207) [62df42c3] <Vishwas>
- Add support for module custom bin dirs [77f55262]
- Add support for tower token to wave client [928d5b04]
- Update CLI docs (#3200) [8acebee6] <Marcel Ribeiro Dantas>
- Fix issue with empty report file [9cc4f079]
- Do not return resource bundle for root module [775c7ed9]
- Improve tower config [ee03c243]
- Bump groovy 3.0.13 [4a17e198]

22.09.3-edge - 10 Sep 2022
- Add fusion support to K8s executor (#3142) [6bb27b32]
- Fix shutdown/cleanup hooks invocation [f4185070]
- Fix Use smaller buffer size for S3 stream uploader [8c643074] [9926d15d]
- Fix Azure NPE on missing pool opts [d5c0aabd]
- Fix handling of targetDir when using Fusion fs [2091b272]
- Document aws.batch.retryMode config (#3195) [56f75e0c] <Abhinav Sharma>

22.09.2-edge - 7 Sep 2022
- Fix thread pool race condition on shutdown [8d2b0587]
- Fix Intermediate multipart upload requires a minimum size (#3193) [0b66aed6] <Jorge Aguilera>
- Fix fusion enable detection [3ef91512]
- Add before-afterScript warning to docs (#3167) [09464590] <Kibubu>
- Add httpReadTimeout and httpConnectTimeout config to K8s client [064f9bc4]
- Add support for Wave build & cache repos [98a275ba]
- Finalise secrets feature (#3161) [49021b82]
- Update executor retry config docs (#3001) [aed6c234]
- Change Azure test pool name [0c724504]
- Improve Wave error reporting [b11d0f11]
- Remove unneeded launcher file remapping [a255118d] <Paolo Di Tommaso>
- Update Azure vm types [80f5fbe4]
- Update docs logos (#3174) [529bad81] <Phil Ewels>

22.09.1-edge - 1 Sep 2022 
- Add support for Charliecloud v0.28 (#3116) [84f43a33] <Patrick Hüther>
- Add Support for EC-encrypted keys for K8s client [fd759d09]
- Add support for Bridge batch scheduler (#3106) [343c17e6] <Eric Bonnet>
- Add fusion support to local executor [17160bb0] [6cfb51e7]
- Add getTags and getBranches to BitBucketServer [53bd89cd]
- Add retry strategy to httpfs client [55f9c87b]
- Add support for project resources [c2ad6566]
- Add mamba build options [987a13cb] <Paolo Di Tommaso>
- Fix Do not override tower endpoint in the config [41fb1ad0]
- Fix Hyperqueue job names must be less than 40 chars #3151 [8e43670b]
- Fix typo in ConfigBuilder.groovy (#3143) [659e6108] <Mike Lee>
- Fix Resume for dynamic resolved containers [13483ff2]
- Improve fusion env handling [10f35b60]
- Improve foreign file(s) cache detection logic [3a9352c8]
- Rename ModuleBundle to ResourcesBundle [0e51dc0f]
- Use quiet output mode for hyperqueue executor (#3103) [70a91fdf] <Ben Sherman>
- Wave improve conda settings [6f087fec]
- Improve secrets cmd (#3158) [115b2f3d] <Jorge Aguilera>
- Improve Wave resolution strategy [2eb700c6]
- Improve Az Batch err handling and testing [85d31e8d] <Paolo Di Tommaso>
- Bump google-cloud-batch 0.2.2 
- Bump spock 2.2 

22.09.0-edge - [SKIPPED]

22.08.2-edge - 16 Aug 2022
- Fix queueSize setting is not honoured by AWS Batch executor (again) #3117 [1733bb2e]
- Add `files()` method to docs (#3123) [00bb8896] <Ben Sherman>
- Refactor wave packing [bc876986]
- Improve logging [aa380d5f]
- Update dockerfile [e6329282]

22.08.1-edge - 11 Aug 2022
- Add support for disabling config include [e0859a12]
- Add experimental fusion support [1854f1f2]
- Add support for plugin provided function extension (#3079) [16230c2b] <Jorge Aguilera>
- Add support for AWS Batch logs group (#3092) [4ef043ac] <Ben Sherman>
- Add share identifier to Aws Batch (#3089) [c0253aba] <Ben Sherman>
- Improve Tower cache manager [0091afc5]
- Improve S3 copy via xfer manager [02d2beae]
- Reports a warning when using NXF vars in the config [009ec256] <Marcel Ribeiro Dantas>
- Make wake token cache duration config [5f955fc9]
- Patch unable to start non-core plugin [a55f58ff]
- Increase S3 upload chunk size to 100 MB [9c94a080]
- Change Google Batch disk directive to override boot disk size (#3097) [7e1c0686] <Ben Sherman>
- Fix queueSize setting is not honoured by AWS Batch executor (#3093) [d07bb52b] <Ben Sherman>
- Fix Allow disabling scratch with Google Batch [e8e5c721]
- Fix Emit relative path when relative parameter is set (#3072) [39797759] <Jorge Aguilera>
- Bump nf-wave@0.3.0 [e46d341d]
- Bump nf-tower@1.5.1 [cdc2be53]
- Bump nf-google@1.4.1 [c39935a5]
- Bump nf-amazon@1.10.0 [ccdf62d0]

22.08.0-edge - 1 Aug 2022
- Add warning to env config docs (#3083) [ca933c16] <Ben Sherman>
- Add -with-conda CLI option (#3073) [98b2ac80]
- Add simple wave plugin cli commands [8888b866]
- Add default wave plugin [7793a0ec]
- Add boot disk, cpu platform to google batch (#3058) [17a8483d] <Ben Sherman>
- Add support for GPU accelerator to Google Batch (#3056) [f34ad7f6] <Ben Sherman>
- Add support for archive dir to tower plugin [c234681a]
- Add support tower cache backup/restore [bc2f9d13]
- Add disk directive to google batch (#3057) [ec6e290c] <Ben Sherman>
- Add retry when Azure submit fails with OperationTimedOut [6a3f9742]
- Add warning when Google Batch quota is exceeded (#3066) [6b9c52ad] <Ben Sherman>
- Allow fully disabling history file [0a45f858]
- Allow the support function overloading and default parameters (#3011) [042d3857] <Jorge Aguilera>
- Improve S3 file upload/download via Transfer manager [7e8d2a5a] <Jorge Aguilera>
- Prevent overriding container entrypoint [b3a4bf85]
- Update FileTransfer pool settings [503aafce]
- Remove deprecated commands [93228b4b]
- Prevent nextflow config to break tower launch [e059a724]
- Refactor Google Batch executor to use Java API (#3044) [31a6e85c] <Ben Sherman>
- Fix Unable to disable scratch attribute with AWS Batch [1770f73a]
- Fix unit test setting explicit permissions for test files [1c821139] <Jorge Aguilera>
- Fix Default plugins are overridden by config plugins [46cf3bfa] <Paolo Di Tommaso>
- Fix S3 transfer download directory [b7bf9fe5]
- Fix NPE while setting S3 ObjectMetada #3031 [d6163431] <Jorge Aguilera>
- Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b]
- Fix AWS Batch job definition conflict (#3048) [e5084418]
- Fix JAVA_TOOL_OPTIONS breaking launch #1716 [0e7b416d]
- Fix add ps shared objects to Dockerfile (#3033) [1c23b40a] <Ben Sherman>
- Parallelize build integration tests [807800a3]
- Bump google-cloud-nio:0.124.8 [dfaa9d19]
- Bump groovy 3.0.12 [5c900b91]
- Bump Moment.js 2.29.4 [a9ced868]
- Bump gson@2.9.0 [12f17176]
- Bump nf-azure@0.13.4 
- Bump nf-google@1.4.0
- Bump nf-tower@1.5.0
- Bump nf-wave@0.2.1
- Bump nf-amazon@1.9.0

22.04.5 - 15 Jul 2022
- Allow fully disabling history file [1a36c9bc]

22.07.1-edge - 13 Jul 2022
- Add support for Google Batch API v1 [4c116d58] [e85d87ee]
- Add time directive support for K8s executor (#2948) [2b6f70a8] <romanaduraciova>
- Add docs aws.client.s3PathStyleAccess config (#3000) [20005500] <Abhinav Sharma>
- Allow to override lsf.conf settings with nextflow config #2862 [dae191a1] <Paolo Di Tommaso>
- Allow hybrid containers execution [0af1bcb3]
- Improve error msg when script file cannot be read [52c2780e]
- Improve error reporting for custom function [877c7931] <Jorge Aguilera>
- Improve error message for missing plugin extension [4a43db84]
- Improve test #3019 [7c37e0be] <Paolo Di Tommaso>
- Rename kuberun -pod-image to -head-image [2576ba62] <Ben Sherman>
- Externalise sqldb plugin source code [17e80b4f] <Paolo Di Tommaso>
- Fix escape unstage outputs with double quotes #2912 #2904 #2790 [49ff02a6] <Ben Sherman>
- Fix Exception when settings AWS Batch containerOptions #3019 [89312ad8] <Paolo Di Tommaso>
- Fix Missing query param in http file (#2918) [43cc8511] <Paolo Di Tommaso>
- Fix Publish copy mode for S3 based path [085f6b2b]
- Fix Fail fast uploads to S3 (#2969) [7fd1a6e1] <Jorge Aguilera>
- Fix null script name in launch info [7118849f]
- Bump commons-code@1.15 [a06b4442]
- Bump jgit@6.2.0 [3331826f]
- Bump snakeyaml@1.30 [de62fd3f]
- Bump gson@2.8.9 [3234ddd5]

22.07.0-edge - [SKIPPED]

22.04.4 - 19 Jun 2022
- Fix Publish copy mode for s3 based path [bb510ce6]
- Add strict mode config setting [b0567e62]
- Update docker base image [b00c1418]

22.06.1-edge - 17 Jun 2022
- Fix CodeCommit creds handling + nf-codecommit@0.1.2 [70fc0745]
- Fix typo in log message [a8f8529d]
- Add more scientists to the list of random names [8d5b36a2] <Marcel Ribeiro Dantas>

22.06.0-edge - 9 Jun 2022
- Add AWS CodeCommit initial support [80fba6e9]
- Add support for 307 and 308 HTTP redirection [92382012]
- Add DirWatcher v2 [209c82cd]
- Add Moriondo in the list of random names [e0abca58]
- Add preview CLI option (#2914) [aa8f1aa4]
- Fix Git config resultion error [64436697]
- Fix StackOverflowError when dump all profiles (#2922) [28cd11a2] <Jorge Aguilera>
- Fix gradle warning message in nf-sqldb (#2921) [b09ceabe] <Jorge Aguilera>
- Fix log for LsfExecutror perTaskReserve attribute [7c3ec874] <Prete>
- Fix external pod deletion for jobs (#2915) [4dd1af7a] <xhejtman>
- Prevent function overloading in module definition [c0b522ab]
- Improve error message of non sensical include (#2623) [285fe49c] <Jorge Aguilera>
- Mount PWD path only when scratch is used [9b3c6e31] 
- Stripe sensitive data into strings (#2908) [7fa4c86c] <Jorge Aguilera>
- Dump scm content when trace is enabled [c3117ada]

22.05.0-edge 25 May 2022
- Add Hyperqueue executor (#2896) [ffa5712e] <Henrik Nortamo>
- Add support for K8s Job resource [c70eb12d] <xhejtman>
- Add support for time process directive in GLS executor (#2880) [1402e183] <Florian De Temmerman>
- Add support for priviledge option for K8s containers [7ffe3a02]
- Add DSL1 option to docs (#2836) [d30841a5] <Jose Espinosa-Carrasco>
- Add support for container options to Azure Batch [3f4f00f9] 
- Add support for move operation to AWS S3 [8c0ddfd5] 
- Add K8s execution hostname in the trace file (#2828) [ebaef92a] <Fabian Lehmann>
- Add support for AWS S3 encyption using a custom KMS key [c1e45aa9] <Paolo Di Tommaso>
- Add support for Micromamba [383e023f]
- Add jaxb-api dependecy to nf-amazon [c1a09f87]
- Add strict mode config setting [696e70b5]
- Add -head-prescript option to kuberun (#2830) [9e387055] 
- Fix missing err message on submit failure [233e67f0] (#2899)
- Fix resolve azure devops repositories when projectId is present [2500ff01] <Jorge Aguilera>
- Fix AthenaJdbc into distribution zip [853a1f2a] [4b3579d5] [70ef7ee3] <Jorge Aguilera>
- Fix Inconsistent bool parsing #2881 [40bf2b2a]
- Fix Unable to pull pipeline if config file is not in default branch (#2876) [4ee5b04f] <Jorge Aguilera>
- Fix Prevent crash when scratch dir does not exist (#2888) [9ef44ae5] <Fabian Lehmann>
- Fix DSL1 detection to invalid workflow keyword matching [fe0700b0] (#2879) <Jose Espinosa-Carrasco>
- Fix Aws Batch retry policy on spot reclaim [6e029b79]
- Fix 'false' string in config interpreted as true (#2865) [079a18ce] <Fabian Lehmann>
- Improve Git Provider config logging [d7dbca8ec]
- Improve K8s task handler [1822b2ca]
- Improve missing workflow err message [da101e8f] (#2871)
- Include revision in the Azure Repos provider when specified (#2861) [3342c767] <Jorge Aguilera>
- Remove unnecessary change dir echo [372d1f47]
- Abort execution when accessing undefined params with strict mode [93836081]
- Update docker base image [50cd7956]
- Update default SKU for Azure Batch (#2868) [9ea09dba] <Abhinav Sharma>]
- Update dependencies [405d9545]
- Refactoring to prevent name conflict [aba2671b]
- Few DSL syntax to explicit declaration of plugin extensions (#2820) [bfc4a067] <Jorge Aguilera>
- Sanitize k8s label and annotation keys, don't sanitize annotation value (#2843) [5287a984] <Ben Sherman>
- Docs improvement (#2835) [09e5bca3] <Ben Sherman>
- Bump Jgit 6.1 [7186348c]
- Bump Spock 2.1 [51100d16]
- Bump capsule 1.1.1 [20ec1697]

22.04.3 - 18 May 2022
- Fix dsl1 detection (#2879) [1a7ea0d1] <Jose Espinosa-Carrasco

22.04.2 - 16 May 2022
- Fix stackoverflow error when probe dsl [a05fcbea]

22.04.1 - 15 May 2022
- Improve dsl detection [739b959f]
- Improve missing workflow err message [f3fc081b] (#2871)
- Fix Aws Batch retry policy on spot reclaim [d855f0d9]
- Update default SKU for Azure Batch (#2868) [be60fc14]
- Bump nf-amazon 1.7.2
- Bump nf-azure 0.13.2

22.04.0 - 23 Apr 2022
- Improve error reporting (#2658) [e6ef017d] <Jorge Aguilera>
- Document params-file and improve self-update (#2673) [1e008f47] <Abhinav Sharma>
- Add support for AWS S3 anonymous credentials (#2810) [ae7ba35a]
- Add tolerations K8s pod option (#2763) [7f7cdadc] <Ben Sherman>
- Add support for batched queries to nf-sqldb plugin [3a9dad8b]
- Add `emitColumns` option fromQuery operator [6a6a6eac]
- Add mermaid DAG renderer [653f1e57]
- Fix missing SSE flag on AWS Batch job submit (#2809) [4b3e946d]
- Fix Task execution is not evicted on unexpected execution error (#2787) [05ea0c86] <Fabian Lehmann>
- Document params-file and improve self-update (#2673) [1e008f47] <Abhinav Sharma>
- Improve deprecation message (#2788) [720a84d7] <Fabian Lehmann>
- General docs improvements (#2800) [88acd26b] <Ben Sherman>
- Decrease Aws upload chunk size to 20 MB [086138fb]
- Improve error reporting (#2658) [e6ef017d] <Jorge Aguilera>
- Improve err reporting for Azure Batch [798bae1f]
- Rename echo directive to debug (#2776) [8f906aa5] <Ben Sherman>
- Remove embedded Read The Docs theme [728d545f] <Paolo Di Tommaso>
- Use a remote config in kuberun (#2781) [5485b699] <Fabian Lehmann>
- Start Github Actions also for edited PRs (#2796) [78f5c10f] <Fabian Lehmann>
- Deprecate isDsl2Final method [0f63f1a7]
- Document task object [1c83e21e] <Ben Sherman>
- Bump nf-sqldb@0.4.0 [a137e93a]
- Bump nf-amazon@1.7.1 [912b9bb2]
- Bump moment.js version2.29.2 [a229c1ed]

22.03.1-edge - 6 Apr 2022 
- Fix default dsl env detection [b9a09bf6]
- Handle K8s timeout error - 500 status code (#2756) [89a1a46b] <xhejtman>
- Honour background option for kuberun command [b1b0ddd9] <kfrancisdev>
- Add Aws Batch native retry on spot reclaim [cd95e297]
- Improve Aws Batch error reporting [00443510]
- Add missing workflow err report [fa687789]
- Use local nextflow when packing docker image (#2757) [40271b08] <xhejtman>
- Add retry policy Azure create job [792820a2]
- Fix log message in nf-azure [80a0e937] <Manuele Simi>
- Prevent build on tag [5b660c73]
- Fix missing linux/amd64 platform on docker build [05f117d7]

22.03.0-edge - 27 Mar 2022
- Add experimental proxy reg [b3836691]
- Add api to access config raw value [977f6305]
- Add warning for invalid emit names [0045834c]
- Add retry policy on grid submit failure #2696 [673f560c]
- Add config tests #2422 [885993b1]
- Add ability to disable config names check [814a2605]
- Add azcopy fine grain config settings [3998a56b]
- Add binary compatibility with Java 8 [763ec999]
- Add retry policy to Az Batch operations [991c6175]
- Make DSL2 default syntax [4e9189ac] [0c80784a]
- Fix Reduce task command runner script size [6930408b]
- Fix K8s task retry strategy on node termination [bd093081]
- Fix use first config in stack when is into profile #2701 [44bdde8d] <Jorge Aguilera>
- Fix Allow comments after nextflow.enable.dsl (#2746) [6988638b] <Jorge Aguilera>
- Fix allow blank spaces in java path (#2690) [a966020e] <Jorge Aguilera>
- Improve AWS Batch job retry on spot termination [bd8f2e26] [72fbda848]
- Improve error reporting [55466be7]
- Undeprecate merge operation [1649944b]
- Bump support for Java 18 [f3a11e4c]
- Prevent invalid use of large maxForks values [5de0c200]
- Prevent race condition on thread pool creation [3e707a1d]
- Refactor AWS batch job unique token generation [d64f5a21]
- Decrese log verbosity [9237d587] [d1a5e5a8]
- Throw an error if a required secret is missing [8e5129d6]
- Wait for pod to stop running before shutdown (#2667) [505c5ad6]) <kfrancisdev>
- Restore AZ tests [858a4568]

22.02.1-edge - 3 Mar 2022
- Prevent multiple parsing of params file [38bb1f71]

22.02.0-edge - 25 Feb 2022
- Fix Prevent S3 tagging with empty list [ae7db466]
- Fix Azure repos tests [856aacf0]
- Fix isse on includeConfig resolution #2675 [6591a9e1]
- Fix NPE when accessing not existing Git file [6c79f8fd]
- Fix Batch Job name exceed max allowed size [e8b70ca3]
- Fix detect and skip bom mark in files (#2645) [02b06ba3] <Jorge Aguilera>
- Feature: Abort session if publish fails (#2643) [79b3836b] <Jorge Aguilera>
- Fix report overwrite cannot be disabled [202b5c9c] #2647 
- Fix match bash interpreter irrespective the path [c2d2b9b2]
- Fix build warning + plugins assemble (#2634) [00dd143a] <Jorge Aguilera>
- Fix CITATION.cff and add automatic validation of your citation metadata [15698a45] <Faruk D>
- Bump nf-amazon@1.5.1 [a4496bb2]
- Bump nf-amazon@1.5.2 [e51139bb]

22.01.0-edge - 7 Feb 2022
- Add support for Tower reports (#2523) [de3d76349] <Jordi Deu-Pons>
- Add RateLimitExceededException when GitHub api limit is reached [ff123c605]
- Add fetch tags and branches to local git provider [e1de8e0ac]
- Add K8s priorityClassName pod option, updated tests (#2585) [51650f8c4] <Ben Sherman>
- Add securityContext pod option to docs (#2584) [19f16f0da] <Ben Sherman>
- Add automountServiceAccountToken option for k8s executor (#2562) [1b5908e4c] <xhejtman>
- Add warn about AWS CLI grandparent path in container (#2565) [67073b0c5] <Simon Li>
- Add affinity option to pod directive (#2522) [640cbed48](3 weeks ago) <Ben Sherman>
- Add ability to specify memory/cpu resources for the control pod (#2559) [13f3e036d] <xhejtman>
- Add `-entry` parameter to pass in k8s executor (#2525) [a96233af6] <xhejtman>
- Add AWS Athena JDBC driver for nf-sqldb plugin (#2500) [462575f05] <Abhinav Sharma>
- Fix process output 'env' as array (#2624) [0a246dc2c] <Jorge Aguilera>
- Fix make date format to change independent from system locale [d1e5f6e76] <Jorge Aguilera>
- Fix double access of params file [459ebab7b] <Paolo Di Tommaso>
- Fix Use account SAS token instead of service SAS token (#2576) [d5125975d] <Florian De Temmerman>
- Fix upload of nested directory outputs on azure (#2578) [85ad55225] [744447155] <Florian De Temmerman>
- Fix Docs Typo (#2556) [942be46f6] <Kibubu>
- Fix NXF_PARAMS_FILE is not recognised #2549 [62f5fe1d9]
- Fix failing tests (4 weeks ago) <Paolo Di Tommaso>
- Fix Unable to use output path with nested properties [ceceb0784]
- Fix Nextflow couldn't parse generated nextflow.config under some circumstances (#2496) [2dfbbc63c] <Fabian Lehmann>
- Fix invalid use of `var` keyword [8418cc8d6]
- Improve k8s executor throwing NodeTerminationException on node shutdown (#2590) [084c8d6ca] <Patrick Hüther>
- Improve docs on `include` statements (#2520) [9c140cee3] <Alexander Toenges>
- Improve core plugins info & logging [dfa544ac9]
- Improve Secrets handling [1c0ad4679] [329502d19] [[26b4be906]]
- Improve DSL2 documentation [048b026f2] [e2e8b5557] <Manuele Simi>
- Improve documentation (#2600) [787a1fd84] <Ben Sherman>
- Allow disabling history file unique check [c3677c311]
- Make S3 parallel download as default [b490f146d] [03dae9d6e]
- Run Azure integration tests only with Java 11 [0890ceeb3]
- Prepare for Java >= 11 build [8c0566fc3] [5ba16dd18] [405b67365]
- Use Standard_A3 instance type for Azure tests [67e7d3ab3] [b97b0010c]
- Refactor cache store using plugins [54bf7a61d]
- Update google cloud docs (#2594) [dfa867953] <Ben Sherman>
- Update the azure docs for registry [96baf288e] <Abhinav Sharma>
- Update copyright info [807a816a5]
- Remove gradle logs about tasks dependencies (#2618) [cae44e00b] <Jorge Aguilera>
- Remove Tika deps for nf-amazon module [95620d42b]
- Remove deprecated validExitStatuas directive [b3117e789] [2188d51a0]
- Remove support for Apache Ignite [d4dc1cfe1] [64d2773fd]
- Bump nf-amazon@1.5.0 as default plugin
- Bump Gradle 7.3.3 [f00bfb0d3]
- Bump nf-amazon@1.5.0 [40f90aa92] [[2bc16732e]]

21.12.1-edge - 22 Dec 2021
- Add tags attribute to publishDir directive [e78a997b5]
- Add ability to disable running jobs cancellation [a13af9a3c]
- Add ability to define containerProperties with using AWS Batch #2471 [ac7f1e71e] <Manuele Simi>
- Add NXF_JVM_ARGS env variable [7afb2deed]
- Improve paths validation [0849d583f]
- Include S3FS provider into nf-amazon plugin [3a7bf8c7a]
- Fix error reporting on missing script file #1951 [e1a0b240a]
- Fix singularity docs #2493 [c66cb3ba7] <Jose Espinosa-Carrasco>
- Fix cross compilation error cause by ByteBuffer [74916100f]
- Fix File staging race condition + beta AWS parallel downloader [b7c262de3]
- Fix enableAIAcaIssuers launcher flag [cd780aabd]
- Fix task index sequence generation [3447e735b]
- Fix Changes process directives invalidates tasks cache [967c1adff]
- Fix Interrupted download of staged files cause execution to fail #1552 [847789fad]
- Fix plugins start/stop for fs command [88d8be1f4]
- Fix for nested params with the same name #2485 [02de4147c] <Jay Carey>
- Fix race condition on plugin autoload status [ab00a50f5]
- Fix failing test with Java 17 [1c6183c92] [4daf8d0a1]
- Note on Azure Batch inactive pools #2483 [7fc116067] <Manuele Simi>
- Remove drip launcher [909f95279]
- Update azure test image [de9d5ee8c]
- Update logging library [a957db646]
- Bump nf-google@1.1.4 [93193a3f3]
- Bump version 21.12.0-edge [9cb7ee81f]
- Bump AWS sdk 1.12.129 [bd7ba1706]
- Bump logback 1.2.9 [29f260717]
- Bump Jsoup 1.14.3 [5776c0391]
- Bump corretto:17.0.1 [f7e047ea4]

21.12.0-edge - 22 Dec 2021 [SKIPPED]

21.10.6 - 21 Dec 2021 
- Bump Slf4j 1.7.32
- Bump Logback 1.2.9

21.10.5 - 8 Dec 2021
- Fix race condition on plugin autoload status [73a0893ce]

21.11.0-edge - 5 Dec 2021
- Add process and workflow recursion (PREVIEW) [9f51155e9]
- Fix include no longer works for custom methods [6adfce099]
- Fix Azure executor fail to cleanup jobs on completion [533448be4]
- Fix Missing AWS SSE encryption for begin and exit task files #2452 [2c6665ef9]
- Fix false positive detection of publishDir conflict [6ea54eaea]
- Fix execution hang when reading empty error file [414240a1a]
- Test with java-17 LTS [c2141e826] <Abhinav Sharma>
- Improve plugins dev root detection [b095bee15]
- Change Azure test pool vmType [ad5ad97ab]
- Downgrade Google NIO library to version 0.121.2 [896ec3abd]
- Bump nf-amazon@1.3.4 - bump nxf-s3fs@1.1.3 (6 days ago)
- Bump nf-amazon@1.3.3 nf-google@1.1.3 nf-azure@0.11.2 [92f94bfeb]
- Bump gradle 7.3.1 [2c34a3a27]

21.10.4 - 30 Nov 2021
- Fix include no longer works for custom functions #2469 [e17f6155d]
- Bump nf-amazon@1.3.4 - bump nxf-s3fs@1.1.3 [be893dcb1]

21.10.3 - 23 Nov 2021
- Fix execution hang when reading empty error file [414240a1a]

21.10.2 - 22 Nov 2021 
- Fix Azure executor fail to cleanup jobs on completion [4d5b71370]
- Fix Missing AWS SSE encryption for begin and exit task files #2452 [841e6101b]
- Fix Azure integration test [a8051bc01]
- Fix false positive detection of publishDir conflict [292b439ad]
- Make Azure executor logging less verbose [7452e386d]
- Change Azure test pool vmType [85682be7d]
- Downgrade Google NIO library to version 0.121.2 [66ae98820]
- Add java 16 and 17 to the launch.sh for debugging #2457 [3ff0a248e] <mmatthews06>

21.10.1 - 18 Nov 2021 
- Fix Azure batch NPE when missing pool spec [84b2983f4]
- Fix Docker bin in image PATH #2445 [d30da377a] <Josh Chorlton>
- Fix failing test with Java 16 [f2d01888d] 
- Fix AWS_RETRY_MODE var definition in Batch job [f1a58600d]
- Add docs for AWS endpoints for China region [e96c56d1e] 
- Correct description of cross #2446 [e4c7f3d98]
- Dump resolved config when log trace is enabled [2580fb108]
- Bump nf-azure@0.11.1 [eb1e6fbd2]
- Bump nf-amazon@1.3.2 - bump nxf-s3fs@1.1.2 [ae9e885a8]

21.10.0 - 11 Nov 2021
- Add support for Java 17 [cb207cd64]
- Allow override Bash wrapper template files [e6e25ed7c]
- Fix issue with plugins local root sync [1d974a4eb]
- Fix Nextflow does not recognised Failed pod (#2430) [9c80cdea0] <Mike Smoot>
- Fix Error reporting on Bash launcher creation failure [63e01c324]
- Fix Channel.fromSRA error one some project ids #2156 [dbcbac139]
- Fix Task completion percentage #2440
- Display no workflow warn if no main is defined [0f1295694]
- Invalidate task cache on directive change (EXPERIMENTAL) [62ded3421]
- Upgrade XmlParser used by SraExplorer [543b582b5]
- Use AWS Batch resources requirement for CPUs and memory [1cf2c379c]
- Bump Gradle 7.3 stable + GHA cache [4eaa4f25f]

21.09.1-edge - 28 Oct 2021
- Fix issue with config selectors and DSL2 [4d7d3e972]
- Fix issue evaluating dynamic errorStrategy with AWS Batch [8c6a5a6e2] [ce4d491b1]
- Fix verbose logging [92b113134]
- Fix docker image url [ed24a475d]
- Fix Temporary directories not deleted in on_exit #2406 [181bdf528] <Lukas Jelonek>
- Fix implict authentication for resources served by Tower [e30310b4f]
- Fix No more of 255 channels can be defined into a workflow context #2417 [7f91ecb39]
- Add tip about escaping variables in env scope #2366 <Ben Shealy>
- Add K8s env fieldPath option to pod directive #2363 <Ben Shealy>
- Improve AWS Batch error report fetching CloudWatch logs [b9f9578f1] [e229700ef]
- Improve docs about IAM policies for AWS Batch #2391 <Manuele Simi>
- Accommodate token in password field for Gitlab #2389 [ee32b7726] <Abhinav Sharma>
- Report a warning when main workflow is not defined [83aec6e8b]
- Bump nf-amazon 1.3.0
- Bump nf-tower@1.3.0
- Bump nf-google@1.1.2

21.09.0-edge - 12 Oct 2021 
- Add secrets manager (preview) [da2a5ff1a] [2d66f83ca]
- Add Built-in support for Azure File Shares #2285 [a4c3e0ad5]
- Add Azure pool node SKU selection #2360 [9afcac756]
- Add support for protocol option to fromSRA #2087 [371f858ab]
- Add retry on AWS Job definition not-found error [452cae5d8]
- Add ability to define templates library at module level #2332 [7e7d52573]
- Add missing information for pulling images from private registry in Azure Batch #2355 [040e190bd]
- Add $NXF_CLI_OPTS env variable [7d57acca5]
- Add NXF_CACHE_MODE env variable [1c345c497]
- Fix asset directory consistent hashing via sha256 checksum [4c5c0ef41]
- Fix issue invoking extension method with GString params [570e5299c]
- Fix Prevent pipeline stopping when K8s pod is evicted [f9db9cc77]
- Fix clean command for Google storage [dc9625eb9]
- Fix plugins detection in local repo [6441a3882]
- Fix S3 canned ACL documentation #2334 [69216e292]
- Fix docker image build with recent docker [2aad36897] [1e485b32b]
- Fix amazon plugin is not used when using bucketDir option [6a8c50ad4]
- Fix Plugin dependency requirement overrides core plugin #2303 [4d1762fb3]
- Fix Make K8s ImagePullBackOff and ErrImagePull recoverable #2302 [766ffde40]
- Improve cache resume strategy [0b0eae225]
- Improve GH action build compressing integration tests [ab9d747d4]
- Prevent NPE if session is not set [83bb46d94]
- Remove deprecated attribute [50d63b6fb]
- Find newest matching plugin #2303 [e6cf79ff3]
- Documents noproxy variable #2325 [bc769b1b4]
- Bump Groovy 3.0.9 [dee2d6c99]
- Bump nf-sqldb@0.2.0
- Bump nf-amazon@1.2.1
- Bump nf-azure@0.11.0
- Bump nf-google@1.1.1

21.08.0-edge - 30 Aug 2021
- Fix plugin updater version logging [d162eb8b4]
- Fix Nextflow launcher breaks when java path contains blanks #2265 [8097a2a90]
- Fix docker build [efb2f449b]
- Fix NPE in AnsiLogObserver #2283 [cffc683df]
- Fix run script when fixing ownership in aws batch #2262
- Improve plugins auto start [283144474]
- Improve log error reporting [401863085]
- Improve handling of K8s node shutdown [67250c041]
- Update GitHub docs [4532b8e1e]
- Merge nf-sqldb 0.1.0

21.07.0-edge - 6 Aug 2021
- Add support for AWS_MAX_ATTEMPTS variable [3cc543589]
- Add app plugin to gradle build [007bc1cb4]
- Add self pid to tower client [d2e54ea22]
- Add support for head job operationId + log/out files [a7a76cf91]
- Add enable CA Issuers option to NF launcher [8f51dc787]
- Fix Clean cmd fails removing foreign files [8bf8ab720]
- Fix Prevent script var names conflicting with private names #2246 [82bbc180e]
- Fix ENA download URL #2239 [befbabbc8]
- Fix Tower client is not activated launching all packaging #2145 [c507518c2]
- Fix orphaned AWS Batch jobs after pipeline interruption #2169 [65e2a4d05]
- Fix Process error report on target exception #1896 [1bac3f17b]
- Fix Unexpected bool conversion on publishDir enable/overwrite attributes #2220 [651835d2d]
- Fix BatchCleanup toString method [ec9bb5648]
- Improve error reporting [49ac01dbb]
- Improve Unknown host error message [ad41d1e98]
- Improve AWS Batch task handler [eb1aff275]
- Use AWS cli standard retry mode by default [f2f1fdea4]
- Report warn on cache hashing failures [7bf93de06] [3b579c954]

21.04.3 [stable] - 21 Jl 2021
- Fix Tower client is not activated launching all packaging

21.04.2 [stable] - 12 Jul 2021
- Fix Plugin install lock file is not deleted #2103 [29c3e516c]
- Fix Default plugin version lookup [d340a221f]
- Fix BatchCleanup toString method [3c67fa3ae]
- Implicit variable projectDir breaks caching #2186 [7a4d1f1a2]

21.06.0-edge - 3 Jul 2021
- Add Keep alive option to Google LS executor [994222074]
- Add support for FTP proxy and proxy servers authentication [8ec33b04d]
- Add support for plugins groupping [aa5bc7d34]
- Add More details about the reason why a AWS Batch job has failed #2146 [27a4e88b2]
- Add support for extensions priority [ae083f1aa]
- Add stubRun attribute to workflow metadata #2164 [86cfc66fd]
- Add Run tasks under user accounts in Azure Batch #2157 [1c9fc4a40]
- Refactor GLS executor [2c86b79a4] [97fc49c09]
- Refactor AWS batch job def creation [89ce364c9] [986894287]
- Fix Default plugin version lookup [e0c8151d9]
- Fix Negative labels do not work as expected #2155 [491191811]
- Fix PublishDir overwriting task output files [190aa4eaf]
- Fix directory deletion strategy [b96fcedc8]
- Fix Implicit variable projectDir breaks caching #2186 [76417d273]
- Fix Prevent empty download array [9492cde5d]
- Fix output unstage with glob pattern [2d4c3dfcf]
- Fix Connection-reset crashes the workflow [3ee4fd0eb] [1400ded6d] [61bbc240a] [175c66584]
- Fix Slurm does not send soft kill message #2163 [f0ccfc7e8]
- Fix storeDir directive does not work with S3 #2141 [2e95a6a76]
- Fix maven local publish [05cfb7cf7]
- Fix GLS transfer attempts opts [f7c705db5]
- Fix build exportClasspath task [88d27f0c8]
- Fix PbsPro clusterOptions directive priority #2036 [75e3f225e]
- Disallow include nested within a workflow block [7dbf64bea]
- Upgrade AWS SDK minor version #2167 [296afaa8f]
- Improve gsutil transfer throughput [2da120b91]
- Improve config error reporting [6aa102430]

21.05.0-edge - 28 May 2021
- Add support for using mamba with conda (#2030) [10c8385b]
- Add AWS cli native error fail-over [fd7670ef]
- Add support for Container Registry to Az Batch executor (#2078) [12bf2da6]
- Add support for Tower workspace (#2097) [8a4dd3ab]
- Add support custom service account email in Google Cloud LifeSciences executor (#2044) [a642c9ea]
- Add support for Java 16 + Gradle 7 [caace1c5] [e2dd4510] [74e466e0] [1245ab1c] [bfc69fb6]
- Improve tower client error reporting [4efb6bf6]
- Fix Plugin install lock file is not deleted #2103 [b7fdffac]
- Fix Use caller runs policy of default thread pool #2021 [48b4e8ee]
- Fix Error reporting for malformed config [68e5ca18]
- Decrease max par transfers to 4 [c7ea816a]
- Prevent fetching aws instance type when missing container id [f5f96049]
- Use default opts for trace file creation [d8ae94bf]
- Improve Azure Batch executor error code and messages for failed Tasks (#2099) [1d5fa5d5]
- Bump groovy 3.0.8 [aa695e12]
- Bump snakeyaml@1.28 [8d361954]

21.04.1 [stable] - 14 May 2021
- Fix nested params file parse #2091
- Fix Malformed config error reporting #2105
- Fix Use default opts for trace file creation [09e6c6ac]

21.04.0 [stable] - 2 May 2021
- Fix NPE when AWS Batch job container is not returned [412b6fde]
- Fix execution hang when native task fail to submit #2060 [1253485d]
- Update preview message [e1eebdcd]
- Fix nf-ignite all packaging [72b6a428]
- Fix GS failing tests [be4f91e9]
- Fix AWS batch executor fails when using self-contained distribution #2058 [2e344c18]
- Fix groupTuple sort criteria with closure #2020 [28a579a9]
- Patch invalid double number cli parsing #2039 [4de4670c] [dcadaaeb]
- Update sphinx_rtd_theme 0.5.2 [4a165f43]
- Disable cpus option when running docker with legacy opt [1a7854a5]

21.04.0-edge - 8 Apr 2021
- Add readOnly flag to k8s volume mounts (#2013) [33bd24ac]
- Add Start default plugins on-demand #1964 [cf2a9d73]
- Add support for tower workspaceId [e2977688]
- Improve suppor for BitBucket server repos [eb946e27]
- Fix toInt/Long/Float/Double operator hangs with value channel [7c35d985]
- Fix regression caused by nested params handling #1923 [b25af49b]
- Fix Cache invalidation when repo is cloned between runs #1989 [ac526f38]
- Fix Invalid setting of TMP var with singularity #1997 [23f80121] [472cfbdd]
- Fix issue overriding nested params from cli #1923 [cfe6b1d1]
- Fix az path handling curly brackets globs #1969 [c78a1bbf]
- Fix Missing git credentials when checking last commit id [f101308e]
- Fix plugins version check against local installation [535c2bb5]
- Fix local dependant formatting #1962 [2a5cbac1]
- Fix Encode path parameter at GitLab getContentUrl [6f80f651]
- Fix Only use sudo rm with docker #1956 [f9490423]
- Prevent AZ NPE when missing vmtype + better logging #1992 [711362ca]
- Refactor params file var binding #1860 #1972 [330f044a]
- Prevent jobs names longer than 100 chars OAR exec [6daa21b9]
- Bump nf-azure@0.9.6 + nf-amazon@1.0.3 [aff1d355]
- Bump nf-amazon@1.0.3 - s3fs@1.0.9 - solve #1830 [b3b221c1]
- Bump nf-tower@1.1.0 [29fdd9f7]
- Bump nf-amazon@1.0.4 + nxf-s3fs@1.1.0 [c638af80]
- Bump nf-azure@0.9.7 [07c59946]

21.03.0-edge - 5 Mar 2021
- Add support for serializable ValueObject [8dfaadf3]
- Add abilitity to fetch revisioned git assets 
- Add support for FixOwnership to AWS batch [24f83741]
- Add support for custom network to GLS #1810 [171f4aa8]
- Add ability to handle list of az vm types [00ced0b3]
- Add tower config scope to docs #1890 f2bd96fa
- Add charliecloud container environment from file (#1909) 4553648b
- Add azcopy tool install mode opts [9e9337d3]
- Update Az default vm type to Standard_D4_v3 [4c6e76b6]
- Update NF console dependency [a2d06e15]
- Remove CDN from timeline reports and make them offline readable #1927 [c0e5a941]
- Fix plugins install failing in some file systems #1882 [8cc43391]
- Fix catch failing commands in nxf_parallel #1884 [dd56f6c1]
- Fix missing error on empty process script [3607f84e]
- Fix GSL path de-serialization issue [c6cf784f]
- Fix Memory unit cannot be a negative number #1902 [abd1c9d9]
- Fix pod spec labels to start with numbers in addition to alphas [79740edf]
- Fix OAR executor log files #1761 [6f2ff4e4]
- Fix issue cause by sleep with subsecond argument [c4be8d00] [63974ac6]
- Fix az blob storage SAS permissions [18a33213]
- Fix sort human-readable tasks in report [6d68f28d]

21.02.0-edge - 1 Feb 2021
- Fix Issue when merging nested cli params #1856 [275e54c4] [fe37da6d]
- Fix job status detection on PBS pro #1840 [c1598908]
- Fix Issue when merging nested cli params #1856 (19 hours ago) <Paolo Di Tommaso>
- Revert the CPU/memory options being passed to singularity VM instead of singularity container [0d04e0f9]
- Add ability to specify plugins with cli [de91218f]
- Decrease upload/download process polling to 0.2secs [6ca2d6ca]
- Remove nf-amazon as default [e6810e90]
- Make plugin services singleton [cacd9328] [5787be6d]
- Make repository provider accessible to subclasses [988bccc6]
- Fix error on plugin downloading #1859 [77cabb3c]

21.01.1-edge - 15 Jan 2021
- Plugins stability improvements [8d849ec9] [bf093826]
- Charliecloud improvements [2242411a]
- Fix issue of FS discovery with dyn plugin loading [bf5e86df]
- Fix crash on startup when mem reported < 0 [095236b8]
- Fix and stability [e4b8afb5]
- Fix launcher on Java11 [c6b78034]
- Add plugins custom version manager (4 days ago) <Paolo Di Tommaso>
- Improve NF version checking [d33ea642]
- Bump plugins minor upgrade [f91bc21e]

21.01.0-edge - 04 Jan 2021
- Merge plugins feature [d959bfdb]
- Prevent twice access remote scm file [b2798556]
- Fix DAG edges not connected correctly #1486 [cece1161]
- Fix k8s executor must provide cpu resource requests #1570 [6896e923]
- Fix http/ftp read buffer size [a2886baf]
- Add support for OAuth Bearer auth [5823c280]
- Add support for basic auth for http/s file provider [6027fcba]
- Add User-Agent info to httpfs requests [222637de]
- Update CPU and RAM for containers (#1833) [ccf5c8ba]
- Move test containes to quay.io [7db053eb] [773be707] [c10a7f53]

20.12.0-edge - 12 Dec 2020 
- Add support for charliecloud container engine #1809
- Fix glitch on K8s task progress update [668434f6]
- Upgrade to groovy 3.0.7 [27056035]

20.11.0-edge - 16 Nov 2020
- Fix Allow nextflow to handle http protocol for Singularity images #1791
- Fix params-file overrides config parameters [b03efcac]
- Fix println failing test #1621 [8c6f0f97] [9d2e5850]
- Let output env variables be optional (#1740) [3fca3655]
- Add stub-run feature #1774 [3de45c22] [e2d6d55b]
- Add overwrite option to trace/time/report/dag features #813 [a0615474]
- Allow nested CLI params #1182 [19ab8a8f] [df6204e3] 
- Allow setting google projectId in nextflow config [223b5d6c]
- Make binDir accessible from the executor scope [1405a28f]

20.10.0 - 1 Nov 2020
- Add warning for AWS Batch mem request lower than 4 GB [e9240fc9]
- Fix issue with docker images tagged by SHA #1777
- Add support for Bitbucket tags and branches retrivial [5083066e]
- Add support for Tower client bearer authentication [532282ae]
- Fix Skip FS lock when Conda dir exist #1771
- Add support for Java 15 [b1f48884]
- Fix build with Gradle 6.7 [8d7227f0] 

20.09.1-edge - 15 Oct Sep 2020 
- Prevent USR1 signal to stop jobs #1753
- Add -main-script cli option [702ff64c]
- Improve Singularity image file caching #1706 [dd92772b]
- Fix unexpected default GLS action flags #1749
- Patch unpexpected error on tower serialization [f922324a]

20.09.0-edge - 23 Sep 2020 
- Fix invalid error message on missing process #1719 [fc607f11]
- Deduplicate GS file + parallel up/downloads [29d37083]
- Deduplicate S3 file uploads [0b65d61f]
- Fix issue on GS path composition [276f0ed3]
- Add NXF_PARAMS_FILE env var [2e3c9232]
- Allow configurable container mounts [8dc0adf4]
- Refactor common Bash helper functions [22a0ff34] [502309b7]
- Fix race condition creating FTP file system #1725 
- Fix invalid checkWarn method invocation [ba052a02]
- Move makeDigest into build.gradle file [a2b5de8f]
- Add variable NXF_CONFIG_FILE [83365aa3]
- Patch use of GString for fromSra apiKey option [a8b81ada]
- Use repository URL instead of Git clone URL [75a04d90]
- Fix Invalid exception capture for missing config [ce427924]
- Fix podman issue on duplicate mounts [661a40e9]
- Fix FromSra illegal character error [5a86d180]
- Fix Allow custom SCM file location #1657 [a90e66e3]

20.08.1-edge - 2 Sep 2020 
- Add variable NXF_CONFIG_FILE [d15edcb8]

20.08.0-edge - 24 Aug 2020
- Merge Groovy3 runtime and support for Java 12/13/14
- Use repository URL instead of Git clone URL [102f8b01]
- Fix Invalid exception capture for missing config [8c7accca]
- Fix podman issue on duplicate mounts #1710 [d0cc38de]
- Fix FromSra illegal character error #1700 [a45decfb]
- Fix Allow custom SCM file location #1657 [7c27f895]
- Fix dynamic executors loading [7b9ce82f]
- Fix missing newline on cmd log stdout/err #1705 [1416a388]
- Fix k8s timeline start #1687 [24dff871]
- Remove unneeded parentheses from stdout declaration [dc029c04]
- Merge execution logs command docs [577ec744]
- Passing exact memory to TES executor in GiB #1696 [c8a15545]
- Improve docs replacing suscribe{println it} with view() [f84ccb6f] [cb2d607d]
- Use current environment Bash #1598 #1614 [e70ef87a]
- Include GA4GH support into the standalone binary (make pack) #1666 [e2175d45]
- Update Bitbucket docs [b9b57f83]
- Clone/Pull submodules recursively #1615 [5f20ab6a]
- Bump nf-ignite to version 1.1.0

20.07.1 - 24 Jul 2020
- see 20.07.0 and 20.07.0-RC1

20.07.0 - (skipped)
- Allow unqualified stdin/stdout defintions with DSL2 [bcdcaab6]

20.07.0-RC1 - 21 Jul 2020 
- Add Dsl2 enable flag [08238109]
- Add check on invalid scope syntax definition [23c92021]
- Add channel as alias for Channel [05c358c9]
- Add DSL2 deprecation + clean up syntax [1b4b1307]
- Add DOI field to NF manifest #1676 [ec6ee223]
- Improve join duplicate detection [33eb9ef5]
- Improve mix operator error message [8074d714]
- Remove invalid log message [48b1b9f1]
- Fix hidden error message on fail fast run [3b4b377c]
- Disallow upwrapped includes + hard deprecation [19130f87]
- Suppress trap for SIGUSR1 signal #1656 [ca5bcf46]
- Improve error reporting on invalid task id [3921de1a]

20.06.0-edge - 5 Jul 2020 
- Add more debug logging for AWS helper [2a62fdf7]
- Add join options failOnDuplicate and failOnMismatch [387366aa]
- Add strict mode flag [4ba5ac18]
- Add support for selecting minimum CPU platform on GCP (#1633) [afc4375d]
- Add missing trace fields to docs [bf2e1637]
- Fix Invalid GLS path composition in staging directories #1654 [e33fff98]
- Fix for feature 1647 that allows non gpu k8s accelerator resources. (#1649) [c1efa29d]
- Fix Issue accessing S3 bucket #1596 [ffc6f843]
- Fix Update getDomain method in ProviderConfig to support local repositories - #1492 (#1624) [651501ac]

20.05.0-edge - 31 May 2020
- Add support for NXF_LOG_NAME env var [cf496615]
- Add exception specialiation for ambiguous repo [a34b1d2a]
- Add support for tower_workflow_id env var [53188126]
- Add config profile names accessor [2784cdb8]
- Add support for Google Cloud buckets with Requester Pays set #1466 [bc9db8d8]
- Add Git tag and branch retrieval [7c97f23f]
- Fix PublishDir error caused by duplicates output files [5f3b69c1]
- Fix weird issue on config resolution [0d0fef4b]
- Fix resolution of malformed configs [fe213e41]
- Fix K8s labels and annotation normalization [6434b9d] #1577 #1584 
- Fix minor git path provider ending slash [9888be29]
- Fix bugs in GA4GH TES support (#1589) [26708335]

20.04.1-edge - 19 Apr 2020
- Fix AWS auth with temporary security token [6a7b11b8]

20.04.0-edge - 13 Apr 2020
- Add SGE hr status handling (#1558) [f4db0049]
- Add moduleDir, projectDir and launchDir vars [7832a697] [576a5694]
- Add executor display name rendering [74c90ca9]
- Add ability to pipe custom fun [DSL2] [80bb6485]
- Add Aws Batch container image validation [e73951fa]
- Recognizes more UGE states (#1536) [4dacebbf]
- Prevent invalid process tag values [f2da1357]
- Report Tower backend error cause on failure [da8ac8f5]
- Fix Config cmd should resolve remote projects #889 [c2e0ac0b]
- Fix issue applying branch/multiMap to value channel [e69f39fa]
- Fix Kill signal is not propagated for Singularity container #1561
- Fix docs typos [d7261d2e]
- Fix Minor docs update #1545 
- Revert "Bump jline 2.14.9" [ef7040cb]
- Deprecate validExitStatus directive #1564
- Improve error message [DSL2] [f8a0ee1c]
- Add sluper parse method for Path [a54fd03d]
- Report error message when accessing invalid out #1553 [83bd009c]
- Remove deprecated $ config syntax [0a31f9df]
- Remove deprecated workflow publish [DSL2] [1bd7b4a4]
- Remove support for workflow 'get' [d9b91149]
- Remove deprecated process output getter [013a323b]
- Remove deprecated out cardinal getters [414fae94]
- Remove deprecated gpu directive [f48b2c24]
- Minor executor logging [7f94299b]
- Minor improvement createDirIfNotExists API [34211675]
- Bump groovy 2.5.11 

20.03.0-edge - 28 Mar 2020
- Add support for GLS private addr #1545 [a481b42b]
- Add AWS batch job def normalise function [79239f05]
- Fix Escape Singularity env variables #1535 [b651a371]
- Add Local executor file system check [ffc92926]
- Add Launch Id to Tower client [d768d2d1]
- Add workflow progress on completion [aea41f37]
- Remove deprecated onFlowStart method [14f12b5f]
- Minor method visibility change [43bc9697]
- Minor log change [130a963b]
- Fix docs broken link [0a1ec9a9]
- Fix typo CVS -> CSV #1500 [d89281c3]

20.02.0-edge - 29 Feb 2020
- Fix Unable to create AWS helper class warn #1504
- Fix Ansi log flickers when variable-length tags are used #1288
- Fix Directive maxForks may cause execution to hang #1432
- Fix Missing tag in ansi log #1503
- Fix PBSPRO res req should always include cpus #1510 
- Deprecate workflow publish 7f315a63

20.01.0 - 12 Feb 2020
- Fix ansi logging and line count [4f5c7187]
- Fix Division by 0 in launcher script with Biocontainers #1488
- Fix Run name validation to 80 chars max #1491
- Add GitHub badge to README
- Add Bash version to issue template [78928546]
- Bump jline 2.14.9 [5df2b27e]

20.01.0-rc1 - 6 Feb 2020
- Add ability to extend module params #1484 [17c6acca]
- Add dsl2 command line opt [1cf544d5]
- Add GLS executor docs [574f2098] [7ce2597a]
- Add HTCondor detail on data sharing #1473 [f0af66de]
- Allow aliased process to inherit config settings [DSL2] [1c447e85]
- Allow module inclusion to inherit context params #1484 
- Allow multiple inclusion from the same module [DSL2] [a9ae36f9]
- Fix Script template fails to render list of files #1478 [2e97bbbc]
- Fix process name validation when using legacy script [1543365c]
- Fix Early detection Dsl2 declaration #1468 [93a642aa]
- Fix Missing script validation checks #1468 [5d0cf145]
- Revert "Disable ansi log on non-tty env #1417" [98e6758b]
- Minor changes gradle build [619385f1]
- Minor AWS Batch api refactor [c20abc11]
- Improve foreign file detection [50508684]
- Improve GLS location validation [5b89ab50]
- Removed unused module flag [cf19cc9c]
- Update dsl2 docs [5c57c3a8]

20.01.0-edge - 20 Jan 2020 
- Add Prevent negative progress stats [87cdddc6]
- Add More cloud tests [7a5dd828]
- Add support for UGE throttled jobs (Tr) #1461 [20408e4b]
- Add progress stats to tower client [781116a4] [138cf0b0]
- Add experimental Podman containers support (#1451) 026866cd
- Add support for Gexf format for DAG rendering [28bfe0ee]
- Improve ansi logging for multilines output [1ce978c3] [004e23eb]
- Improve progress stats and ansi log [0212ba16]
- Improve api to enable wr executor #1148 [21088ad3]
- Update tower trace client requests [138cf0b0]
- Enhance progress execution stats & tracking [a30e2b9a]
- Unexpected output when using Google Storage as work dir #1452
- Fix typos and minor changes [fb2f954f]
- Fix Operator splitFastq fails with PE option and DSL2 enabled #1390
- Fix Container entrypoint when using GLS executor #1291
- Fix GLS file unstaging #1406 [e67ef3be]
- Fix GLS unstage for file patterns #1406 
- Fix Scratch directive does not work #1280 [644e9ac7] [6c7291fa]
- Fix Resume fails due to LevelDB exception #1358 [28fa3a6c]
- Fix Conda env activation #1195 [e3919275]
- Fix java command in launch script #1436 [f28b015f]
- Rename variable java to JAVA_BIN [086377d8]
- Removed unused compile deps [686bcd98]
- Bump capsule-maven 1.0.3.2 and fix broken env [004684e3]
- Bump capsule-maven 1.0.3.1 and seqera repo [62964eed]

19.12.0-edge - 20 Dec 2019 
- Add GLS assigned zone discovery #1406
- Add Google Life sciences (GLS) executor improvements #1406 [ead29c11] [8228e9b4]
- Add GLS bootDiskSize support #1331 [f118798c] [af8fe16d]
- Add GLS job debugging #1351
- Fix NPE when file pattern is missing [1cbb6e49]
- Fix AWS cloud parsing for NVEe storage and tests
- Fix Disable ansi log on non-tty env #1417
- Fix Allow Singularity image path with blank #1368
- Fix Shell template invalid caching #1422
- Fix Task vars ordering may invalidate cache #1408 
- Fix Join operator not matching gstrings #1394 
- Fix sigpipe error caused by runner script #1332 
- Fix Google Storage bucket with underscore is not recognized #1069 [85cd0cde]
- Fix fromFilePairs can't take list of paths #1405 [c00f5669]
- Refactor onFlowInit to onFlowCreate event [c477eeaf]
- Improve err msg when input files are remove from output [5d5744a8]
- Upgrade to Gradle 6.0.1 [e0c1a3ac]

19.11.0-edge - 2 Dec 2019 
- Increase tasks.module to 255 [7332c606]
- Fix Allow the output of process env variables #69 [1c1befc7]
- Fix docs rounding issue #1350 [af824fc7]
- Fix Join operation incorrectly represented in DAG #1346 [9d83ed51]
- Fix Tiny typo in docs #1361
- Fix lost trace/report/timeline file name
- Fix invalid class exception [4308d6a4]
- Fix Invalid dynamic resolution of stageIn/OutMode directive #1374
- Fix No such property stackTraceDepth error #1387 [49450f67] [f5342e71]
- Fix Singularity env variables are not accessible #1386 [036af4a6]
- Fix PublishDir should not create dir when disabled #1381
- Fix Process hangs for non zero exit status #1344
- Fix Output stdout does not support emit attribute #1373
- Fix False positive warning when importing module #1349
- Fix HTCondor queue status command #1353 [a1addc8f]
- Fix Escape file names with blanks #1392
- Fix broken docs tutorial #1366
- Patch Duration unit cannot be a negative number #1384
- Handle ProviderMismatchException in CacheHelper (#1382) [cc584368] [3523f174]
- Introduce workflow take in place of get [DSL2] [e8cbbf08]
- Disable ansi log when using dockerized run [86bc2ada]
- Minor logging change [238b0e6c] [f5342e71] [b707882f] [ce97f073]
- Add multiMap in place of fork operator [afd671c8]
- Add Show Tower init response message as warning 
- Add output path includeInputs docs [2ce7e861]
- Add metrics fields check #1360 [5b7f42e9] [caf9f137]
- Add console command to cli help #1347
- Add OAR executor #1343
- Add graphiviz to Docker image #1370
- Removed unused property [9c65426a]

19.10.0 - 21 Oct 2019
- Merge Use a delete function that doesn't follow symlinks #1337
- Merge Allow multiple mounts for the same K8s claim name [1d288a3d] #1284
- Make Google Pipelines logging less verbose [6edd9954]
- Merge Shifterimg workaround for ensuring image pulls #1327
- Merge Add ENDPOINT support for China regions #1323 [636cbfb5]
- Add limit on max field lengths sent by Tower [4d5cabc2]
- Add retry ability to Tower client for 500 class errors [c7f70fc5]
- Add support for Java 12 #1082 [b86b2da0]
- Add BitBucket Server provider [6af6a902] #1297 #1309
- Add support for AWS temporary security credentials #934
- Fix Broken container environment when enabling metrics #1289
- Improve resource not found error message [02cf0a55]
- Remove route operator #991

19.09.0-edge - 16 Sep 2019
- Add `of` and `fromList` channel factories [cc60b305]
- Add nf-tower init request [120ed8ba]
- Add support for accelerator directive #997 [624c8e83]
- Add support for native shifterimg for shifter engine (#1292) [a106712e]
- Add nf-tower subproject [285e09ce]
- Add sticky log marker [f9a3c9da]
- Add support for config resolution [4754abc6]
- Add enable option to publishDir [7b9c2d2f]
- Fix race condition on task workdir creation [5bc323a0]
- Fix issue when fetching aws profile from env #1248 [ba30b97c]
- Fix minor issue when reporting invalid entry error msg [814d6728]
- Fix non determinist test failure [a9289e9e]
- Throw error cause on InovationTargetException [9e1467d0]
- Remove verbos logs on readExitFile check [a5a6a1fc]
- Revert "Patch capsule error message" [ac4ac073]
- Patch for inconsistent cached task id #1301 [7bfd0008]
- Improve flow execution events [335b76d1]

19.08.1-edge - 26 Aug 2019
- Add Process named output channels #1290 [DSL] [6a756fd2]
- Add workflow publish directive [DSL2] [287a095e]
- Add stageAs option to input path [DSL2] [9b5f55f6]
- Add workflow entry option [DSL2] [f29e3e04]
- Add extension to module file name instead of simpleName [DSL2] [71a60365]
- Add support AWS temporary session token support [15ac3938]
- Add support for GCP disk resource [72bb9c41]
- Add fork operator #1281 [DSL2] [6f89833a]
- Add branch operator #1202 [706a182a] [DSL2]
- Add workflow definition and composition #1276 [13f43291] [DSL2]
- Add projectName to workflow metadata [55be0762]
- Add support for tower [1255f702]
- Add support for timezoned timestamp to metadata [6f4a2e28]
- Add task pending event [d2d66698]]
- Add support for path in/out qualifier [DSL2] #1201 [5552b38a]
- Add set chainable operator #1262 [2651a099]
- Fix name generator uniq check [0bbf7015]
- Fix execution report nested processes aggregation [e4fad827]
- Fix nested process names config resolution [ccd8e833]
- Fix missing deprecation [8af85189]
- Fix broken div structure in html report [3e055a7a]
- Fix set operator for multi-channel #1262 [eab39378] [DSL2]
- Fix typo in the `delete` file docs [38fa2dca]
- Fix test #1276 [cc03d76b]
- Fix classpath resolving when launched from foreign path [04024fe6]
- Fix console cmd throws runtime exception #1273 [2f78d943]
- Fix process names validation fails for included modules #1175 [75b96aa8] [DSL2]
- Fix issue with `set` as operator #1262
- Fix misleading name when throwing multiple in/out channel [e7c8cdb9]
- Fix Combine operation incorrectly represented in DAG #1268 [6e86e28a]
- Fix docs collectFile `size` vs `skip` option [8cfb5a64]
- Fix K8s TaskHandler updates its status correctly to 'RUNNING' (#1256) [a1457a1c]
- Remove potential sensitive environment vars #1075 [a413b967]
- Enable use AWS profiles other than `default` (#1248) [d7434773]
- Relax deprecation messages #1269 [454e78f1] [fd11f8d8]
- Defer process start and channel emission [DSL2] [f5eef256]
- Rename ChannelFactory helper to CH [4b5b3c7e]
- Improve modules error checking and reporting [aa650b9e] [DSL2]
- Increase build test max heap size [daca896e]
- Upgrade Gradle to version 5.5.1 [027cb16b]
- Enforce process execution in `workflow` scope` [DSL2] [bca15a91] [0a582240]
- Replace InterruptedException with TimeoutException in GCP test [a6d3c24c]
- Explicitly check whether module path does not end with .nf (#1254) [8253608a]
- Minor improvement AWS Batch docs [bd56ea44]
- Upgrade Groovy to version 2.5.8 [36dffa18]
- Enhance execution report [ab5f8d98]
- Enhance simple http client [2e0f5c2b]
- Refactor resource metrics collector [fec86ed2]
- Refactor observers plugin system [9dab8f08]
- Replace input/output set type with tuple [DSL2] #1207 [5e19f72f]
- Convert any simple object to a value channel [DSL2] [86b0469d]
- Improve logging [5adc2c09]

19.07.0 - 27 Jul 2019
- Add support for K8s annotations #1240 [8eeb7f9f]
- Add support for Moab resource manager #1224 [3ba51a19]
- Add Pbs Pro execution documentation [1d39ab31]
- Add code of conduct document
- Fix missing LFS executor register invocation #1234 [b1b7ab1]
- Fix "invalid pod status" when running scrips with the kubernetes executor #1242 [11caac68]
- Revert Fix Environment activation fails with recent versions of Conda #1195 [98c0d1f8]
- (includes changes from `19.07.0-edge`, `19.05.0-edge` and `19.05.0-edge`)

19.07.0-edge - 9 Jul 2019
- Fix Remote input file download slowdown submission rate #1206 [b710e21e]
- Fix serial publishDir uploads #856 [14774854]
- Fix Trace file option is not honoured #1217 
- Fix Custom lib path is not added to the classpath #1213 
- Fix Discovery executor tracing error [3e26c146]
- Add megabyte unit to Slurm memory requirement #1216 [efabdd2f]
- Add support for GCP dynamic machine type #1198 [5c2c7665]
- Add setCredentialsProvider for submodules #1205 [e2460414]
- Improve google pipelines docs [aed407ed]
- Improve FileTransfer await termination log #1206 [cb968da7]
- Allow trace logging for `com.upplication.s3fs` package [d71b94e1]
- Upgrade s3fs lib to version 1.0.6 #856 

19.06.0-edge - 21 Jun 2019
- Fix Nextflow indefinitely waiting for killed jobs #981
- Fix Suppress Unknown hashing type logging message #1178 [a005b1b0]
- Fix a typo in AWS docs (#1171)
- Fix Invalid response cause Google pipelines exec to crash #1163
- Fix kuberun doesn't delete config maps #1165
- Fix Disable ansi logging when using kuberun command #1161
- Fix comparable test with groovy 2.5.8 [3d1c0833]
- Fix Unexpected config selector warning #1167 [52e70e31]
- Fix Kuberun should honour `-bg` (background) option #1159 [4b160b7b]
- Add S3 download retry (#1164)
- Upgrade BitBucket provider with API 2.0 [feeddcda]
- Print ansi summary for exec > 60 secs [53c94270]
- Remove deprecated countText operator #983
- Demote warmup into to debug level [c7d08337]
- Demote barrier logging to trace level [5b7234a1]

19.05.0-edge - 20 May 2019
- Add Aws Batch maxParallelTransfers config #1107 [26d37556]
- Add NXF_ANSI_SUMMARY var to disable log summary [d4b9cc44]
- Add support for AWS user volumes and jobRoleArn [651eeadd]
- Add Support for LSF per task resource reserve mode #1071
- Fix Env variable with blanks is not resolved correctly in containers #1146
- Fix method isDynamic visibility [f241781b]
- Fix WebLogObserver data leak on completion #1010
- Fix unit test execution [622d97d4]
- Fix Quiet cli option is not honoured [e656e4b0]
- Fix Log messages don't show in the console #1129 [95f4dd7b]
- Fix nextflow build timestamp json rendering [af6584c9]
- Fix Launcher should return non-zero exit when fail to step env #1126
- Update get started docs [68f53367]
- Update aws sdk to version 1.11.542
- Update created label in timestamp [e8945e8b]
- Update readme IDE version
- Refactor AWS cli path option [ad9af0dd]
- Improve Dsl-2 error reporting [4e2621ff]
- Improve CI tests scripts [febeb530]
- Improve docs for config profiles [8cf95a5d]
- Syntax enhancement aka DSL-2 #984 [651af95a]
- Print summary only the run takes > 3mins [cd459713]
- Render last tag along with the process name #1144 [8cf8cc44]
- Sync build scripts [a5689217]
- Provide scm credentials when fetching information about remote branches #1135 [808847b5]
- Code cleanup [2322fbcf]

19.04.0-edge - 24 Apr 2019
- Add Experimental support for gpu resources #997
- Fix LSF executor should use mem setting in lsf.config #1124
- Fix Unable to list S3 bucket content #1121

19.04.0 - 15 Apr 2019
- Added support for NCBI_API_KEY variable [e4d9b62c]
- Added warning message when using untested Java version [35acd1cb]
- Added parameter and workflow metadata to weblog payload #1077
- Added warning on publish with a null var [7d58bfb7] [95c219fb]
- Fixed Echo directive when Ansi log is enabled #1112 #996
- Fixed Do not mount inputs when `stageInMode == copy` #1105
- Fixed `splitCsv` operator fails to parse values containing commas #1102 
- Fixed missing return type for Date.format method
- Fixed Channel operations `toList` followed by `merge` hang execution #1083
- Avoid printing execution summary when no processes are computed #996
- Improved error reporting for null publishDir [0b9b52f0]

19.03.0-edge - 14 Mar 2019
- Fix Nextflow hangs submitting jobs to AWS Batch #1024
- Fix process builder incomplete output [2fe1052c]
- Fix Grid executor reports invalid queue status #1045
- Fix Script execute permission is lost in container #1060
- Fix K8s serviceAccount is not honoured #1049
- Fix K8s kuberun login path #1072
- Fix K8s imagePullSecret and imagePullPolicy #1062
- Fix Google Storage docs #1023
- Fix Env variable NXF_CONDA_CACHEDIR is ignored #1051
- Fix failing task due to legacy sleep command [3e150b56]
- Fix SplitText operator should accept a closure parameter #1021
- Add Channel.fromSRA factory method #1070
- Add voluntary/involuntary context switches to metrics #1047
- Add noHttps option to singularity config #1041)
- Add docker-daemon Singularity support #1043 [dfef1391]
- Use peak_vmem and peak_rss as default output in the trace file instead of rss and vmem #1020
- Improve ansi log rendering #996 [33038a18]

19.02.0-edge - 6 Feb 2019
- Added foreign files caching ability #686
- Added Ansi logging as default console output
- Added Gitea source code provider [ae04fc37]
- Fixed Join operator returns invalid remainder values #1015
- Fixed Invalid trigger of integration tests [7aa5908a]
- Fixed memory allocation for SGE executor [29353c90]
- Fixed properties access for TaskConfig and LazyMap [09b74a52]
- Fixed Invalid decimal separator in mem unit string #999
- Fixed tail error on launcher script [38afea6c]
- Improved Execution and Timeline memory reporting #980 #986 #1012 #1014 #1016 #1018 [01426097] [7d6c29f0]
- Improved Google pipelines file copy strategy [678405b2]
- Improved output file stage out behaviour docs #961 #1013
- Upgraded Groovy runtime to version 2.5.6

19.01.0 - 22 Jan 2019
- Added Google Cloud Platform integration
- Added support for K8s nodeSelector #955
- Added new AWS regions #935
- Added json/yaml output to info command #657
- Added More duration and memory unit syntax sugar #921
- Added NO_PROXY env variable should be honoured #864
- Added keepHeader option to splitText operator #912
- Added countLines, countFasta and countFastq methods #972
- Added an env variable to define default cloud driver #973
- Fixed Unable to find JVM 1.8 err message #1000
- Fixed Memory unit should contain thousand separator [e6ec4c84] #989
- Fixed LSF long user names breaks jobs status parsing [b4306151] #988
- Fixed Move output files to storeDir instead of copying them #745
- Fixed Interpolated strings in a from statement are misinterpreted #978
- Fixed ConcurrentModificationException when publishing output files #971
- Fixed Launcher fails with Java 10 or later #953
- Fixed remote bin directory when using bucketDir option [6d796783]
- Fixed foreign file system detection [1489cc72]
- Fixed Ansi logger division by zero [ae2b1380]
- Fixed Unparseable Data format on http file #962
- Fixed Log command history #405
- Fixed Too long process tag name can cause SLURM failure #941
- Fixed LSF can return an inconsistent jobs status #927
- Fixed dump last queue status on failure [36e80242]
- Fixed Allow the usage of a custom docker image for K8s driver pod #877
- Fixed K8s executor when the cluster has no available cpus #824
- Fixed Prevent duplicate process definitions #920
- Fixed Update queue statuses used by PBS Pro #908
- Fixed K8s launcher fails to set pod work directory [dc8bfead]
- Fixed cmd cloud error message [14d603b9]
- Fixed RejectedExecutionException on successive Console executions #906
- Fixed Invalid config rendering #801
- Fixed Invalid warning message for config selector #905
- Fixed Queue status command fail on LSF version 8 #910
- Fixed Use `bash` instead of `sh` to fetch queue status
- Improved script runner api [da4a6c17]
- Improved file hashing logging [0d35b2b4]
- Refactored ScriptRunner class [15ee2f1c]
- Refactored DSL code visitor [67904c1f]
- Revert "Apache Ignite to version 2.6" #909
- Better report warning when grid status command fails [3ac8b972]

19.01.0-edge - 10 Jan 2019
- Enhanced timeline and execution reports #985 #986 [fb00c3a6] [092f0b9e]
- Enhanced BashWrapperBuilder using template file [7d7e116a] [c62b9dff]
- Fixed CPU usage accounting #982 [7d7e116a] [c62b9dff]
- Fixed Move output files to storeDir instead of copying them #745
- Fixed Interpolated strings in a from statement are misinterpreted #978
- Fixed Launcher fails with Java 10 or later #953
- Fixed LSF long user names breaks jobs status parsing [b4306151] #988
- Fixed Memory unit should contain thousand separator [e6ec4c84] #989
- Fixed Allows fromFilePairs to handle non globs #946
- Added an env variable to define default cloud driver #973
- Added countLines, countFasta and countFastq methods #972
- Added NXF_DIST launcher variable #954
- Added NXF_SMOKE var to disable long running tests
- Deprecated groupBy and route operators [b7ca53d2]
- Updated S3 storage classes #977
- Updated groovy to version 2.5.5
- Updated copyright disclaimer
- Refactored project structure [516294e7]
- Speed-up CI tests [3320dcec]

18.12.0-edge - 18 Dic 2018
- Add Google Cloud Platform integration
- Added support for K8s nodeSelector #955
- Added new AWS regions #935
- Added json/yaml output to info command #657
- Fixed remote bin directory when using buckerDir option [6d796783]
- Fixed foreign file system detection [1489cc72]
- Fixed Ansi logger division by zero [ae2b1380]
- Fixed Unparseable Data format on http file #962
- Fixed Log command history #405
- Fixed Too long process tag name can cause SLURM failure #941
- Fixed LSF can return an inconsistent jobs status #927
- Fixed dump last queue status on failure [36e80242]
- Fixed Allow the usage of a custom docker image for K8s driver pod #877
- Fixed K8s executor when the cluster has no available cpus #824
- Fixed Prevent duplicate process definitions #920
- Fixed Update queue statuses used by PBS Pro #908
- Fixed K8s launcher fails to set pod work directory [dc8bfead]
- Fixed cmd cloud error message [14d603b9]
- Improved script runner api [da4a6c17]
- Revert "Apache Ignite to version 2.6" #909
- Fixed Invalid config rendering #801
- Improved file hashing logging [0d35b2b4]
- Refactored ScriptRunner class [15ee2f1c]
- Refactored DSL code visitor [67904c1f]

18.11.0-edge - 12 Nov 2018
- Added More duration and memory unit syntax sugar #921
- Added NO_PROXY env variable should be honoured #864
- Added keepHeader option to splitText operator #912
- Fixed Invalid warning message for config selector #905
- Fixed Queue status command fail on LSF version 8 #910
- Fixed Use `bash` instead of `sh` to fetch queue status
- Better report warning when grid status command fails [3ac8b972]
- Fixed RejectedExecutionException on successive Console executions #906

18.10.1 - 24 Oct 2018
- Fixed test [011e8e23]
- Fixed version number check [fb780347]

18.10.0 - 24 Oct 2018
- Added lenient cache mode #828 [ba907a2f]
- Added support for java 11 [60da50b5]
- Added support for Singularity 3.0 library #898
- Added support for AWS Batch hybrid executions #744
- Added weblog JSON format docs #882
- Added weblog example documentation #891
- Added PbsPro executor [33ae1104]
- Added support for ANSI console logging [9c14a947]
- Fixed License prevents scientific use #788
- Fixed process submitter slow-down [495e900a]
- Fixed Comparing duration and memory units with null throws an exception #872
- Fixed Html format dag fails when 'each' qualifier is used #887
- Fixed Collate/Buffer hangs with one emission after Collect operator #868
- Fixed Option checkIfExists should be applied when a glob pattern does not match any file #874
- Fixed Add name to manifest and reject other attributes #871
- Fixed warning message grammar when resuming on new project #885
- Fixed Missing DSL Xform transformation in console execution [9621f8c6]
- Fixed Enum declared in nextflow script causes error #878
- Fixed Report a warning message when queue status fetch fails [39aae6a2]
- Fixed Pbs executor may return nonzero exit code when checking queue status #904
- Renamed weblog `runStatus` to `event` #892
- Renamed K8s config attribute userDir to launchDir #895
- Merged tests as subtree [a03eb59a]
- Refactored service discovery
- Removed FastXxxYyyyStream
- Demoted igfs subsystem
- Upgraded Groovy to version 2.5.3 [119300b3]
- Upgrade Gradle to version 4.10
- Updated AWS batch docs

0.32.0 - 8 Aug 2018
- Fixed CPU usage metrics can be wrongly reported #858
- Fixed Allow a process to access input file metadata #731
- Fixed Completed jobs are detected with a big delay #799
- Fixed Misleading message is shown when pulling a project with a invalid config #863
- Fixed Allow groupTuple operator to handle multi-size tuples #796
- Fixed Ignite executor fills up logs when node is disconnected #810
- Fixed Log filter option is misinterpreted when enclosed in double quotes #846
- Fixed Metrics collector process may cause the main process to report a false non-zero exit status #836
- Fixed K8s imagePullPolicy is not included in the pod spec #815
- Fixed Splitter caching is too eager when caching path is specified #835
- Fixed Improve error message for missing git provider configuration #847
- Fixed Byte hashing is never reached in CacheHelper class 9ac81153
- Fixed K8s launcher should not delete pod when `login` command fails (5175942a)
- Fixed Dump operator should nicely print ArrayBag content (91e371ba)
- Added manifest data in workflow metadata object #841
- Added support for K8s imagePullSecrets pod attribute #800
- Added option "checkIfExists" to Channel.fromPath method #666
- Upgraded Apache Groovy to version 2.5.1
- Upgraded Apache Ignite to version 2.6
- Upgraded Slf4j to version 1.7.25
- Upgraded Logback to version 1.1.11
- Upgraded Grengine to version 1.3.0
- Upgraded LevelDB to version 0.10
- Upgraded Guava to version 21.0
- Upgraded Spock to version 1.2 
- Using javax.activation:activation:1.1.1 (from com.sun.activation:javax.activation:1.2.0)

0.31.1 - 7 Aug 2018
- Fixed AWS Batch execution hangs when running on 1 cpu machine #825 
- Fixed AWS Batch fails if process tag length is too long #822
- Fixed AWS Batch executor creates timeline report with missing time data #816
- Added Ignite failure detection timeout configuration parameters #820
- Added VersionNumber class to CacheHelper handler [90fb69fa]
- Added CONTRIBUTING file #564

0.31.0 - 25 Jul 2018
- Fixed CLI parameter value starting with a `-` is misinterpreted #808
- Added keep-logs option to clean command #775

0.31.0-RC1 - 19 Jul 2018
- Fixed K8s pod request should include resources spec when 1 cpu is specified #806
- Fixed PBS executor should fail when submit response contains invalid data #753
- Fixed SLURM executor fail to submit jobs when cluster option is specified #805
- Fixed Allow the use relative paths for symlinks process input files #296
- Fixed AWS batch jobs are not properly stopped when execution is interrupted #782
- Fixed splitCsv is not properly handling blank lines #795
- Fixed K8s pod runAsUser definition #707
- Fixed Prevent NPE when K8s reports an empty pod state [dcc7ec5f]
- Fixed Allow list of patterns for fromPath and fromFilePairs channel factories #732
- Fixed K8s execution hangs if an invalid pod secret file is specified #754
- Fixed Correctly shutdown executor service #732
- Fixed bug in dot rendering due to unquoted graph name when DOT language keyword used #783
- Fixed Execution hangs if one or more inputs evaluate to null #764
- Fixed Method `file` should thrown an error null is given as input #765
- Fixed invalid relative link resolution with `readlink`
- Added AWS batch requests throttling handling #710 #709
- Added AWS Batch parallel downloads/uploads [codefest] [8ba1716b,ba5ad7a8]
- Added K8s pod config and security context definition #707
- Added Container env variables whitelist #803
- Added support for K8s pod labels #762
- Added support for K8s volume mount subPath #758
- Added Nextflow required version in the config manifest #752
- Added disk resource requirement in LSF executor #747
- Added GA4GH TES executor [experimental] #794
- Added System info to workflow metadata object #759
- Added weblog feature #681
- Deprecated process.$name syntax to define process specific settings #713
- Upgrade to Gradle 4.9

0.30.2 - 16 Jun 2018
- Fixed Output declarations with a glob pattern fail when AWS Batch executor is used #748
- Fixed Scratch directive not working for AWS Batch executor #740
- Fixed K8s launcher does not parse remote config files #738
- Minor refactoring to enable Groovy 2.5 compilation 20b6d933 a8b994f1

0.30.1 - 11 Jun 2018
- Use a daemon thread for watchPath method #735
- Fixed Gitlab API v3 has been deprecated and does not work any more #734
- Fixed Unable to access params defined in the top scope from a nested profile #733
- Fixed Process config selectors do not work when the config is included #729
- Fixed Improve the error message when a missing property is used in the config file #730
- Added Travis build support for jdk10
- Added documentation for `until` operator #736
- Added mailer recipients check
- Increased Singularity pull timeout to 20 minutes
- Updated build to Gradle 4.8

0.30.0 - 5 Jun 2018
- Added the support for Bioconda #493
- Added support for AWS Batch job timeout #648
- Added jobs submit rate limit #198
- Added offline option #665
- Enabling Java 9/10 support for build and launcher scripts #674
- Fixed Expose Kubernetes Secrets to worker pods #651
- Fixed K8s execution hangs when a non-existing docker image is specified #697
- Fixed K8s execution terminates abruptly if a pod requires more resources than available ones #676
- Fixed K8s executor does not report command log when a task fail #699
- Fixed Configuration profile is not handled properly by the kuberun command #696
- Fixed Enhance process metrics to avoid usage of ps tool #499
- Fixed PublishDir should use copy mode by default when the target is a S3 path #718
- Fixed Unbounded variable breaks task launcher script #722
- Fixed Escape filenames when copying from S3 #717
- Fixed AWS executor should use putObject API to upload job scripts to S3 #712
- Fixed Exception is thrown when an output folder contains a circular symlink path #701

0.29.1 - 10 May 2018
- Fixed Default ext property are not included in process context #673
- Fixed Operator concat throws a ConcurrentModificationException #675
- Fixed Output file is not recognised when it's created into a subdir and the name matches an input #688 
- Fixed Empty container definition being ignored when default one is specified #691
- Fixed K8s client fails to connect the cluster when client key nor certificate is specified #692
- Fixed K8s executor hang on pod creation failure
- Added select in -R for memory for LSF executor #683

0.29.0 - 24 Apr 2018
- Fixed Buffer operator fails to recognise optional parameter when a closing condition is specified #652
- Fixed PublishDir mode "copyNoFollow" does not work for directories #658
- Update NameGenerator adjectives #656

0.29.0-RC1 - 8 Apr 2018
- Added `containerOptions` directive #415
- Added support for multiple `publishDir` directives for process #256
- Added cleanup feature to delete workflow work dir on completion #649
- Added label directive and process configuration selectors `withLabel` and `withName` #623
- Fixed Invalid process cache when using a different environment module #627
- Upgrading groovy runtime to version 2.4.15

0.28.2 - 6 Apr 2018
- Fixed Class FtpURLConnection is not accessible when using Java 9 #646
- Fixed Lengthen mktemp TEMPLATE so works on BusyBox #647
- Fixed Report HTML/CSS tweaks to make progress bar text overflow work properly #645
- Fixed typo in the nextflow launcher #643

0.28.1 - 27 Mar 2018
- Fixed A HTTP access error is raised when the URL contains a ? character #634
- Fixed Creation of temp files in the /dev/shm directory can result in a permission
  error in some Linux installations #638
- Make process echo safer

0.28.0 - 10 Mar 2018
- Fixed Singularity pull is executed even when container execution is disabled #628
- Fixed issue when setting container attribute to `false` [9de636c5]
- Added MemoryUnit getters [f99d2dc9]
- Added default NXF_TEMP variable [d36ac4dd]
- Added progress stacked bars to workflow report #534 [455fcb4f]
- Added namespace option to `kuberun` command [50154ec5]
- Improved workflow stats and warn report [e795b134]
- Improved K8s error reporting [86f172eb]

0.28.0-RC1 - 27 Feb 2018
- Added support for directory wildcards in input file declarations #568
- Added ability to access task existStatus value as an output value #577
- Added ability to use property syntax in the declaration of output values #578
- Added NXF_JAVA_HOME variable to specify nextflow nextflow JVM #607
- Added support for docker mount flags #572
- Added ability to select multiple configuration profiles #370
- Added ability to copy symlinks to publishDir directive #592
- Added missing native_id TraceRecord field to K8s and AWS Batch task handlers
- Enhanced support for Kubernetes #468
- Fixed Launcher breaks when JAVA_HOME path contains a blank char #616
- Fixed Operator toList hangs when applied to a value channel #612
- Workflow report should warn if some task executions were ignored #534 
- Enable support for large execution reports #547
- Replaced the use of named pipes with anonymous pipes #606
- Enhance the config command show dynamic attributes #604
- Fixed bin path is not recognised when contains a blank char #603 
- Fixed A NPE exception is thrown when a env variable is assigned to an null value #593
- Fixed summary stats when for empty series #547
- Removed support for Extrae #588 
- Removed support for DRMAA #587

0.27.6 - 19 Feb 2018
- Fixed Operator toList hangs when applied to a value channel #612
- Allow launcher to track installation verb

0.27.5 - 15 Feb 2018
- Fixed dir/* input file pattern invalidate cached processes #610
- Fixed Mail attachment are not correctly recognised by the email client #609
- Fixed Workflow metadata container attribute is not resolved when it's defined dynamically #602

0.27.4 - 5 Feb 2018
- Fixed Resume does not work for tasks successfully executed in a re-submit attempt #591
- Fixed An error is reported when a NF script contains a class definition #594
- Fixed Launcher error when download target path contains a blank character

0.27.3 - 29 Jan 2018
- Fixed publishDir directive fails on S3 when attempting to copy objects larger than 5 GB #585
- Process name does not reflect dynamic tag declaration when a task execution is retried #586
- Fixed examples in the documentation
- Update to Gradle 4.5

0.27.2 - 23 Jan 2018
- Fixed Config property keys may contain invalid characters
- Fixed Local process kill signal is not propagated to children processes #581
- Fixed Operator join throws a stack overflow exception when an invalid argument type is specified #582

0.27.1 - 18 Jan 2018
- Fixed Invalid cast exception when cpus value is missing #575
- Fixed Kill the tee commands when the launcher script exit #574
- Fixed Splitter `limit` option is not honored when splitting more than one file #573
- Fixed AWS CLI operations with S3 should use the --only-show-errors options #567
- Fixed Splitter by option is not honored when splitting more than one file #570
- Documentation editing/improvement

0.27.0 - 9 Jan 2018
- Fixed Log command prints true instead of actual message #561
- Fixed NXF_TEMP definition when instanceStorageMount is set
- Improved S3 exitfile logging
- Improved cloud config canonical formatting

0.27.0-RC2 - 29 Dic 2017
- Fixed Ignore Windows instances from AWS cloud price listing
- Fixed AWS price reader catching unexpected errors
- Fixed sendMail access to owner variables
- Fixed NPE when creating task with ignite executor
- Fixed null exit status in notification template #554
- Added XPath serialiser
- Added mail smtp proxy configuration #375
- Added built-in notification documentation #554
- Added built-in mail documentation #375
- Added support for Syslog logging #330 #557
- Improved support for AWS EC2 instance storage #558
- Improved documentation #558
- Improved config command adding `-flat` and `-properties` formats and using canonical curly brackets format as default
- Update copyright info

0.27.0-RC1 - 20 Dic 2017
- AWS Batch increased queue to 1000 tasks and poll interval to 10 secs
- AWS Batch improved executor scalability caching recurrent API call and batching similar requests together
- Added notification message on workflow completion #554
- Added Built `sendMail` function #375
- Added Warning message when a local version on a GH repo is different from remote #376
- Added keepHeader option to collectFile #479
- Added Dump operator to enable easier debugging #517
- Fixed Report an error message when a config file contains an unresolved attribute #525
- Fixed Session working file system not defined when staging input files with Ignite executor #555
- Fixed storeDir writes output files even when process fails #227
- Fixed storeDir does not work with S3 targets #247
- Fixed Config file available in introspection #264
- Fixed Enhance container interoperability between Docker and Singularity #503
- Fixed Process environment is not exported in the container context when a process uses an interpreter other than BASH #495
- Deprecated support for executable containers #529
- Deprecated DRMAA executor #488
- Deprecated Extrae profiling #543
- Renamed .command.run.1 to .command.stub #523

0.26.4 - 11 Dec 2017
- Fixed GitLab auth token is not applied when user credentials are not provided #542

0.26.3 - 30 Nov 2017
- Fixed AWS Batch S3 upload function does not work if output is a directory #539
- Fixed AWS Batch S3 uploaded function does not resolve glob patterns containing curly brackets #535
- Added author field in the config manifest scope #537
- Upgrading s3fs library to 1.0.2 version supporting `signerOverride` S3 config property.

0.26.2 - 27 Nov 2017
- Fixed readlink illegal option when installing in macOS #527
- Fixed Getting not descriptive error when using a when condition and script statement is not explicit #528
- Fixed Function nxf_module_load matches partial names #530

0.26.1 - 17 Nov 2017
- Execution report enhancements #521
- Fixed Add AWS_DEFAULT_REGION environment variable to bash wrapper scripts #512 #513
- Fixed New launcher script does not allow the execution of legacy version with Java 7 #519
- Fixed Error message reporting file name collision is misleading #516

0.26.0 - 8 Nov 2017
- Fixed file method does not interpret correctly S3 path with globs #509
- Fixed Execution hangs when the amount of requested resources exceed the available ones #502
- Minor change in the execution report #507 #508
- Make AWS clustering compliant with billing by seconds
- Refactored `nf-token` AWS job definition parameter #475
- Run Batch task in a scratch directory to avoid undefined execution folder #475
- Renamed `iamProfile` to `instanceRole` #422
- Renamed ProcessNotRecoverableException to ProcessUnrecoverableException

0.26.0-RC2 - 30 Oct 2107
- Fixed TMP and TMPDIR variables are not passed in Singularity environment #496
- Fixed Dynamic resources directive when defined both in a process and the config file cause an error #497
- Added Experimental support for Shifter containers #500 #501
- Improved AWS Batch task logging and task attempts
- Improved Execution report showing task realtime instead of task duration on time box plot

0.26.0-RC1 - 24 Oct 2017
- Added support for AWS Batch #475
- Added support for AWS IAM role #422
- Added Experimental support for Java 9 #462
- Added transpose operator #440
- Added join operator #460
- Added html report (-with-report option)
- Added Gzip compression support to splitXxx operators #484
- Added Support PE Fastq files splitting #436
- Added Operator splitFasta should allow the creation of chunk having the same size #472
- Added HTML execution report #490 #491
- Added New scientist names #485
- Improved merge operator #458
- Improved value channel handling for reduce, filter, first, take and randomSample operators
- Prints a warning message when the config file defines setting not matching any process definition
- Fixed HEAD is detached error #389
- Fixed Include container name when calculating cache key #443
- Fixed Invalidate process cache when a referenced external script is modified #413
- Fixed Execution failure is not reported in the trace file when retry error strategy is used #404
- Fixed "when" directive should not allow staging of input files for a process, if the criteria are not met #424
- Fixed Failure during foreign files download cause execution to stop abruptly #295
- Fixed The parameter groupName cannot be used with the parameter subnet #465
- Fixed unable to download from gitlab.com public repository #457
- Fixed Print work directory when a task fails #445
- Fixed Misleading command line parameter type conversion #434
- Fixed Nextflow should not stage files that have the same name #470
- Fixed SplitCsv returns array objects instead of Lists #487
- Fixed Cannot cast object FtpURLConnection error #482
- Fixed Nested Environment Module names are not loaded properly #489
- Removed support support for Java 7 #385
- Removed deprecated Cirrus/ClusterK executor
- Removed deprecated support for DNAnexus #386

0.25.7 - 6 Sep 2017
- Fixed Unable to parse the AWS price list API #444
- Added seed parameter to `randomSample` operator #410

0.25.6 - 13 Aug 2017
- Fixed Empty channel waiting forever when viewed and mixed #428
- Fixed Error Channels cannot be used as input in more than one process or operator #429
- Fixed Script body is resolved even if the `when` guard evaluate to false
- Added queue process directive as option for trace file

0.25.5 - 4 Aug 2017
- Fixed NF fails to pull images hosted in the Singularity Hub #414
- Added `-y` to cloud create command to skip confirmation request

0.25.4 - 31 Jul 2017
- Removed invalid debug information

0.25.3 - 31 Jul 2017
- Fixed NPE when parsing AWS price file #408
- Fixed Grid queue status return wrong data when a process change the submission queue dynamically #412
- Fixed MPI-like execution for SLURM batch scheduler
- Fixed NPE when log params key is not defined
- Fixed Optional parameter for set #399
- Added automatic pull for Singularity remote images #356
- Added London and Canada AWS regions
- Merged Pass NXF_OPTS to JVM during the java version check to allow memory definition on memory-restricted environments #411
- Improved error message in launcher file

0.25.2 - 3 Jul 2017
- Fixed Execution hangs if a job submission fail #396
- Fixed stdout can not be sent into multiple channels #388
- Fixed Pipeline execution hangs when a process exceed the time limit and retry error strategy is used #387
- Added scientists and adjectives to run name generator
- Deprecated `route` operator

0.25.1 - 27 Jun 2017
- Duplicate mount point docker error #384
- Disable Docker read-only mounts by default

0.25.0 - 26 Jun 2017
- Fixed Dataflow threads pool get exhausted with a large number of tasks #92
- Fixed Custom function cannot be invoked in the workflow completion handler #374
- Fixed Runtime errors are not reported in the `workflow.errorMessage` property #369
- Fixed Warn if params.something is defined twice in a NF script #372
- Fixed Map.Entry values deserialization process fail #373
- Fixed List active operators that may hang the script execution #315
- Fixed launcher error message #366
- Fixed AWS spot instance bootStorageSize property is ignored #368
- Fixed Implicit variable `task` is not accessible in cached processes #363
- Fixed Do not export user environment when submitting job to SGE-like batch scheduler #362
- Fixed Process termination can throw a ConcurrentModificationException hiding the error cause message #359
- Fixed GroovyRuntimeException during foreign file copy process #360
- Fixed Helper function to compare version numbers #319
- Fixed Docker input file mounts should be read-only for enforce container security #346
- Fixed Extend `each` repeater syntax to support file collections #355
- Fixed Modified task properties are not accessible in the command script during task retry #345
- Fixed PublishDir warning message
- Fixed Spread operator mishandles Iterable values provided as a dataflow variable #353
- Fixed UUID cli options are wrongly interpreted as Duration objects #349
- New toInteger and toLong converter operators
- New randomSample operator #344
- New `simpleName` extension method to Path/File objects #354
- New warning message when input tuple cardinality does not match declared length #348
- Improved use example into ext directive documentation #327
- Improved error handing when parsing trace file #371
- Improved error reporting for process missing input definition
- Improved launcher script to support https protocol by default #379
- Change `maxErrors` default to -1
- Deprecated identifier `channel` as variable name

0.24.4 - 19 May 2017
- Fixed PublishDir creates nested directory structures when a folder already exists #342
- Fixed NoSuchFileException is thrown when trace file path does not exist #334
- Fixed watchPath glob directory not working #335
- Fixed Channel.fromFilePairs does not handle properly multiple star wildcards #337
- Added executor for NQSII, queuing system used on NEC clusters.
- Added `relative` option to `fromPath` channel factory

0.24.3 - 24 Apr 2017
- Fixed Process execution fails with not GNU version of sleep and date tools #321
- Fixed Pending processes are not cleaned up properly #322
- Fixed NPE is thrown when Singularity is enabled and a process uses no container #324
- Fixed Cached processes are not included in the timeline report #325
- Added MD5 digest file upload
- Updated docs

0.24.2 - 5 Apr 2017
- Fixed Tuple array object deserialisation fails #317
- Use SLURM squeue —-noheader instead -h command line option to support not standard implementation #316
- Fixed Execution time is incorrect for the local executor #313

0.24.1 - 24 Mar 2017
- Fixed Improve explanation of cache DB IOException #303
- Fixed Operator ifEmpty results in a error when applied to a dataflow variable #308
- Fixed Process execution fails when the work path contains a parenthesis character #310
- Fixed Installer script fails when current path contains a blank character #311
- Fixed Include SLURM partition when checking job status #312
- Allow the usage of `close` operator on unbounded dataflow variable

0.24.0 - 20 Mar 2017
- Added new `combine` operator #298
- Added new `collect` operator #297
- Added new CLI option `-params-file` to load parameters from a json/yaml file #208
- Fixed SCM user name is not set accessing private repository #300
- Fixed Infer singleton process outputs from inputs declaration #301
- Fixed Use exit status 1 for all NF errors #304
- Fixed Invalid SGE job name as defined in `sge_types` #299
- Added `skip` parameter to collectFile operator #306
- Added experimental `fs` command
- Improved file staging error reports #295
- Upgraded Groovy to version 2.4.10

0.23.4 - 24 Feb 2017
- Fixed Show a warning message when accessing undefined parameters #293
- Fixed Staging input files in a subfolder changes their names when they are symlinks #292
- Fixed NPE accessing foreign files
- Added column char to list of path escaped chars
- Fixed Boothook script fails on Ubuntu 16.04

0.23.3 - 9 Feb 2017
- Fixed Job termination is not recognised if the starter file is not created #268
- Fixed Allow NF console to resume process executions (second take) #280
- Fixed PublishDir may throw a FileAlredyExistsException #283
- Increased logger file appender buffer size to 64kb
- Updated Logback to version 1.1.10
- Updated copyright info
- Fixed NXF_DEBUG level

0.23.2 - 2 Feb 2017
- Improved history lock error message
- Fixed typo in warning message
- Added `cleanup` to list of accepted directives
- Added NXF_OWNER to kubernetes executor
- Fixed Function nxf_kill is not invoked properly on a containerised process #275
- Fixed Pending grid jobs are not cancelled upon pipeline interruption
- Documented that the toSortedList operator can accept a comparator closure #277

0.23.1 - 23 Jan 2017
- Fixed FixOwnership flag break non BASH scripts/templates #270
- Fixed Fixed PBS Executor should not have parenthesis #271
- Fixed Function nxf_kill is not invoked properly on process termination #275
- Fixed Timeline.html is not working on IE11 #272
- Fixed Merge process specific extended properties with the ones defined in the default scope #273
- Fixed Using storeDir and publishDir in the same process yields unexpected results #266

0.23.0 - 13 Dec 2016
- Added support for Singularity containers #252
- Added support for HTTP/S and FTP files (read-only)
- Fixed stream close leak while copy foreign file to local file system
- Fixed Task scheduling may hang while checking for job completion #261
- Fixed Specifying the keyFile cloud config attribute result in an error #263
- Added support for multiple target channels in `tap` operator #255
- Added `uri` property to Path and File objects
- Made NXF_SCRATCH variable accessible to `beforeScript` handler

0.22.6 - 4 Dec 2016
- Fixed Script execution terminates before all operators complete #259
- Fixed A script variable with the same name of a global variable invalidate process resume #254
- Fixed `when` is not recognised when used before an `input` and `script` is not declared
- Fixed count operator hung when applied to a dataflow variable
- Added warning message when an input/output `set` defines only one component #216 #251
- Reduced log verbosity of Ignite Scheduler classes

0.22.5 - 17 Nov 2016
- Fixed QueueSize=1 doesn't handle multi-cpu processes #246
- Fixed Accessing to a not defined script params should raise an error #243
- Fixed An input channel evaluating to null results in a misleading error message #242
- Fixed Use of publicDnsName should failover to IP if no name is available #240
- Fixed Use of yum in cloud boothook may cause problems #239
- Fixed Execution hang when an operator invokes the `exit` function and no processes have run
- Fixed fromFilePairs does not match patterns containing curly brackets w/o a star wild character
- Added `-dump-hashes` command line option to print task key hash keys #211
- Improved logging

0.22.4 - 4 Nov 2016
- Added `—no-requeue` flag to SLURM job submission
- Report log content when a wrapper script execution fail #213
- Improved error message when cache DB cannot be created
- Logging error track trace on task re-submit failure
- Fixed Channel.fromPath throws an exception when the argument is a S3 path
- Modified `make_temp` so that uses `NXF_TEMP` when defined

0.22.3 - 12 Oct 2016
- Fixed PBS qsub fails when the job name is longer than 15 chars #228
- Fixed Spread operator doesn't connect channels in DAG #231
- Fixed amazon prices file format parser
- Added Cleanup scratch dir upon process completion #230
- Added `optional` flag to output file declaration
- Added `region` option to `cloud` command
- Added Check for missing instance type description

0.22.2 - 3 Oct 2016
- Fixed Copy input files to scratch directory #197
- Fixed PBS qsub fails when the job name starts with a dot #228
- Fixed issue when staging-out a symlink output file
- Fixed log warning when running a script in the console

0.22.1 - 26 Sep 2016
- Fixed Nested symlinks are not resolved by Docker container mounts #222
- Fixed Nextflow execution log fail to get field starting with '%' #223
- Fixed Nextflow console launcher
- Added `ContainerCreation` status to K8S executor
- Expand `=` to `==` in filter expressions to avoid misleading results

0.22.0 - 19 Sep 2016
- Fixed queue-size attribute for local executor
- Fixed Kubernetes pod id parse issue
- Move `.nextflow.history` and `.cache` files under `.nextflow` directory

0.22.0.RC2 - 12 Sep 2016
- Fixed File name containing glob wildcards cannot be captured in the process output #219
- Fixed Work dir containing glob wildcards are not supported #194
- Added `revision id` to execution log
- Added `scriptId`, `scriptFile` and `scriptName` attributes to workflow metadata object
- Added time delay penalty on error burst to prevent failing node to drain all pending jobs
- Load classes without creating an instance of each cloud driver
- Improved AWS driver missing credentials error report
- Merged experimental Kubernetes support
- Improved clean and log command
- Added EFS default mount path
- Refactored daemon shutdown

0.22.0.RC1 - 1 Sep 2016
- Fixed Implement clean up command #19
- Fixed Trace file should include cached tasks #114
- Added ability to log each command run #108
- Added new `cloud` command
- Added AWS EFS support
- Added AWS Spot instance error fail-over
- Added support cloud auto scaling
- Added Ignite job-stealing distributed scheduler

0.21.3 - 26 Aug 2016
- Fixed Spaces in work directory path stops slurm from accepting the job #218

0.21.2 - 12 Aug 2016
- Fixed PBS professional batch scheduler submission error #209
- Fixed Reference to a collection of files is not resolved properly in the output section #214
- Improved failed and ignored processes reporting
- Fixed null workflow.projectDir when launching a script file
- Do no output link file when `followLinks` option is disabled

0.21.1 - 29 July 2016
- Fixed NFS work dir is not detected correctly #206
- Fixed `splitFasta` operator with the file parameter will not split into single fasta files #181
- Enable log file for commands when debug or trace option is specified
- Added validation checks to `fromPath` and `fromFilePairs` methods

0.21.0 - 20 July 2016
- Fixed Command line params do not override params defined in the nextflow.config file #202

0.21.0-RC1 - 14 Jul 2016
- Fixed Ability to customize job name submitted to the scheduler #140
- Fixed Duplicate output error when no channel specified #182
- Fixed File paths containing a timestamp are parsed as a Duration object #185
- Fixed ClosedByInterruptException is thrown randomly #188
- Fixed Pipeline hangs when `Channel.from` argument is an empty list #189
- Fixed Handle customised sbatch returning the jobid by itself #190
- Fixed LocalExecutor can randomly hang with no running task #191
- Fixed Missing flag in SLURM `squeue` call #193
- Fixed Process script declaring a regexp expression results in a IllegalAccessException #199
- Merged Silence mkdir error if NXF_HOME not writable #187
- Refactored ParallelTaskProcessor and TaskProcessor classes to a single class
- Added `ST` and `BF` queue statuses to SLURM executor
- Improved logging information
- Upgrade to Gradle 2.14

0.20.1 - 18 Jun 2016
- Fixed Directives do not accept a negative numeric value #180
- Fixed Dynamic errorStrategy is not evaluated correctly #183
- Fixed Pipeline hangs when error strategy is used and an upstream process fail
- Added environment to ContainerBuilder and implement environment export for Shifter containers
- Updated Groovy runtime to version 2.4.7

0.20.0 - 8 Jun 2016
- Added fromFilePairs channel factory method
- Added `finish` error strategy #158
- Added ability to change the name and the save path of published files #178
- Added a syntax validation check for process blocks keywords #177
- Fixed It's not possible to specify environment modules w/o a version number #174
- Fixed Local process kill signal is not propagated to children processes #172
- Fixed scratchDir is overwritten by TMPDIR #171
- Removed deprecated `Channel.path` methods
- Ignore missing COUT and CERR variables

0.19.4 - 3 Jun 2016
- Fixed Exception is thrown while reporting an invalid output declaration #170

0.19.3 - 31 May 2016
- Fixed Local executor does not run an job when host cpus == 1 #166

0.19.2 - 26 May 2016
- Fixed Module load problem #161
- Fixed PublishDir does not overwrite symlinks #163
- Fixed Implement resource accounting for local executor #162
- Fixed PublishDir fail to move the output directory when the target is a S3 path #160

0.19.1 - 19 May 2016
- Fixed Spread operator is using deprecated `just` operator #159
- Fixed Invalid call to `notifyError` method
- Fixed Invalid URL in citoscape.js DAG template
- Improved documentation

0.19.0 - 18 May 2016
- Added Pipeline execution DAG #147
- Added support for OpenLava batch scheduler #152
- Added `-revision` option to `pull` command #110
- Set `UTF-8` as default file encoding #149
- Fixed Extend support for empty curly glob pattern #154
- Fixed Add process directives validation #153
- Fixed Calculation of freePhysicalMemorySize does not currently take disk cache into account #150
- Fixed Improve error message when pulling a non-existing branch could be more explicit #156
- Updated JGit to version 4.3.1

0.18.3 - 9 May 2016
- Fixed Timeline report no longer works in Safari #143
- Fixed Invalid or corrupt jarfile if your CTRL-C initial run of nextflow #145
- Fixed Pipeline execution hangs when the into declaration is not provided #146

0.18.2 - 3 May 2016
- Fixed Variable task.exitStatus throws an exception when comparing it to an integer value #142
- Fixed PublishDir does not handle hard linking of directories #126
- Added `index` implicit variable to the `task` execution context #139
- Improved installer messages
- Updated Gradle runtime to version 2.13

0.18.1 - 26 Apr 2016
- Fixed Input files containing a parenthesis in the path are not staged properly #133.
- Fixed Process execution hangs when using Ignite executor with a foreign work path #136.
- Fixed Sort output files in lexicographical order #137.
- Added `false` as `sort` option in the `collectFile` operator.

0.18.0 - 11 Apr 2016
- Added `legacy` option to docker configuration properties.
  Added support for `--cpuset-cpus` Docker command line option. See #115
- Added `region` option to AWS S3 config properties #116
- Added support for AWS S3 multipart uploads #112
- Added `NXF_TRACE` to enable application trace logging
- Added experimental support for Shifter containers
- Added experimental support for HTCondor scheduler
- Fixed Input file names staged into a subdirectory are not expanded properly #111
- Fixed Main script class name collides with variable names in global scope #113
- Fixed config file having a name as a top level config options raise a MissingPropertyException #117
- Fixed Process script errors should not be ignored #119
- Fixed timeline margin for long labels - fix #120
- Fixed Process `start` time is not reported correctly when using the Ignite executor #122
- Fixed Allow for a per-job memory limit for LSF executor #123
- Fixed Memory reservation should not be divided by the number of cpus #124
- Fixed Mixed content errors if timeline.html served over HTTPS #127
- Fixed Nextflow won't start if a proxy URL env variable contains a trailing slash #109
- Set poolSize as the number of avail cpus
- Set `java.io.tmpdir` to the same path as `NXF_TEMP`
- Updated Apache Ignite to version 1.5.0
- Updated Logback to version 1.1.6
- Updated Slf4j to version 1.7.21
- Updated JGit to version 4.3.0.201604071810-r

0.17.3 - 18 Feb 2016
- Fixed task status in the trace file when execution is retried #107
- Improved Ignite scheduling and node resources allocation
- Upgraded Logback to version 1.1.5
- Upgraded Slf4j to version 1.7.16

0.17.2 - 2 Feb 2016
- Fixed Channel.subscribe is invoked after the Workflow.onComplete handler #105
- Changed default trace file name to `trace.txt` #106
- Changed launcher classpath cache file under user home
- Added JobStealingFailoverSpi to Ignite executor
- Update JGit to version 4.2.0

0.17.1 - 21 Jan 2016
- Fixed splitText performance issue #102
- Fixed execution hang when a process script block report and error and retry error strategy is set
- Added support for partition to SLURM executor #101
- Use a dedicated reentrant lock to handle task completion event

0.17.0 - 7 Jan 2016
- Fixed PBS/Torque executor does not parse correctly job IDs #96
- Fixed issue when `TraceFileObserver` tries to access task context metadata on task completion #98
- Fixed support for Git local bare repositories #95
- Fixed single quotes in file names result in script error #99
- Added workflow.sessionId and workflow.resume attributes #94
- Added output into multiple channels #97
- Added `attempt` field to execution tracing
- Do not allow output clause to reference files outside the process working directory (see #91)

0.16.5 - 18 Dec 2015
- Fixed race condition when creating cached launcher class path file
- Fixed `run` for local repositories
- Enhanced output file handling #91
- Set thread pool size to avail cpus +1
- Removed config object from remote session that was causing a serialization issue
- Upgraded Slf4j to version 1.7.13

0.16.4 - 6 Dec 2015
- Use batch strategy to kill pending cluster jobs on termination #93
- Added support for Git Large File Storage (LFS) extension #82
- Added configurable thread pool factory #92

0.16.3 - 30 Nov 2015
- Fixed #90. System `user.dir` property is cached causing unexpected behaviour.
- Allow directories in a process input file name declaration. See #91.
- Improved build script for local snapshot deployment.
- Updated cli-args test.

0.16.2 - 14 Nov 2015
- Fixed #87. Include current configuration profile option in the workflow metadata.
- Fixed #86. Failure if work dir contains one or more blank characters.
- Fixed #76. Include process name and tag information in process wrapper script.

0.16.1 - 7 Nov 2015
- Fixed issue #85. Directive `publishDir` can't access process local variables.
- Fixed wrong error message when trying to run a project sticked on a specific revision.
- Fixed `IllegalArgumentException: other must be an instance of nextflow.cloud.aws.nio.S3Path` exception when publishing to a S3 path.
- Fixed indentation in repo info command.

0.16.0 - 4 Nov 2015
- Added ability to resubmit task executions changing resource requirements. See #70
- Added support for private SCM servers and private Gitlab repositories. See #38
- Added `workflow` metadata and execution `onComplete` notification handler. See #79.
- Added `publishDir` directive. See #81.
- Added extension method `mklink` to create file system links.
- Added Apache Ignite based executor.
- Removed deprecated GridGain executor.
- Updated Capsule to version 1.0.1.

0.15.6 - 7 Oct 2015
- Fixed #78. Command line parsing of parameters does not handle some strings properly.
- Fixed #80. Command line argument containing a glob pattern is expanded even when escaped or enclosed in quote characters.

0.15.5 - 28 Sep 2015
- Fixed #74. Operator "spread" hangs when it is applied to a singleton channel.

0.15.4 - 22 Sep 2015
- Fixed #72. Adding cache support for `collectFile` operator.
- Added experimental operator `until`
- Added `self-update` in the command usage help
- Updated Capsule to version 1.0
- Updated to Gradle 2.7

0.15.3 - 26 Aug 2015
- Merged #68. Add `engineOptions` setting to Docker configuration.

0.15.2 - 19 Aug 2015
- Improved `groupTuple` operator adding the support of `size` and `remainder` parameters.
- Fixed issue #47. Creation of scratch folder on Mac OS-X.
- Fixed issue #64. `Channel.fromPath` throws an exception when curly brackets glob pattern is used with a S3 path.
- Fixed issue #65. An input file that is staged from a foreign file system lost it's original name.
- Fixed issue #66. Git submodules are not cloned/updated when a pipeline project is pulled from a remote repository.
- Fixed minor issue when evaluating config lazy property with no binding object.
- Updated Capsule to latest version () fixing an issue that was preventing to add a custom path to the application classpath.
- Added Path matches extension method [experimental].
- Added support for `into` parameter to `splitXxx` operators.
- Changed signature of `close` operator so that it returns the channel to which it is applied.

0.15.1 - 4 Aug 2015
- Added feature #60 - Implements support for Gitlab source code management platform.
- Added support for `disk` directive to `crg` executor.
- Fixed issue #57 - Creation folder lock must be a singleton instance.
- Fixed issue #62 - Operator hangs for negative values or when it is greater or equals to the total number of emitted items.
- Fixed an exception when output file is specified with variable identifier e.g. output: file(x) into channel

0.15.0 - 27 Jul 2015
- Issue #56 - Added method `all()` to params object
- Issue #57 - Processes having identical commands and inputs are given the same hash key
- Issue #59 - Enhanced output `val` declaration adding support for value literals and value expressions
- Fixed minor issue when deleting pipeline repo with `drop` command
- Removed deprecated `share` process clause
- Updated JGit to version 4.0.1

0.14.4 - 20 Jul 2015
- Fixed issue #54 - Nextflow installer does not work when running behind a proxy server
- Upgraded Capsule package manager to version 1.0-rc2

0.14.3 - 3 Jul 2015
- Fixed issue #53 - Cannot access files list entry by using square bracket syntax

0.14.2 - 25 Jun 2015
- Fixed issue #48 - IncludeConfig does not support dot properties syntax
- Fixed issue #49 - GridGain executor raises a NPE exception when launching a native process
- Fixed issue #52 - Method `moveTo` should not throw a `FileAlreadyExistsException` when target file already exists

0.14.1 - 8 Jun 2015
- Strip colon character from grid task name
- Fixed synchronisation issue that caused pipeline hung when execution was aborted
- Fixed an issue raising a MissingPropertyException when a script global variable was referenced in a process `shell` block

0.14.0 - 4 Jun 2015
- Added support for file templates in process definition
- Added process `when` guard for conditional execution
- Added process `shell` block that allows both BASH and Groovy variables in the same script block
- Added support for includes in configuration files
- Added support for profiles in configuration files
- Added channel operator `set { }`
- Added channel operator `into { }`
- Added channel operator `tap { }`
- Added channel method `close()`
- Added channel factory `value()`
- Added `fixOwnership` docker config option
- Added `unstageStrategy` process config option
- Added minlog-slf4j kryo logging redirection
- Added `ext` directive for user defined configuration properties
- Added support for multi-indices grouping key to `groupTuple` operator
- Fixed issue that caused task attribute to be lost when resuming execution
- Fixed pipeline hangs when `map` operator is applied to a dataflow variables - Issue #44
- Fixed pipeline hangs when `into` operator is applied to a dataflow variable
- Improved dynamic code compilation with `Grengine` module
- Increased default queue size to 100 tasks when using a grid executor
- Refactored `Session` to remove dependency with `CmdRun` object Added ability to set `workDir` in the config file
- New implicit lazy Gstring in process parameter and directive definitions
- Changed file unstage strategy using `cp` command instead of `rsync` I
- Removed `workDir` variable from config file
- Updated JGit to version 3.7.1
- Updated Slf4j to version 1.7.12

0.13.5 - 7 May 2015
- Fixed issue #44 - Pipeline hangs when `map` operator is applied to a dataflow variable

0.13.4 - 4 May 2015
- Added html processes execution time report
- Added support for Docker executable containers - Feature #33
- Added support for missing number types to CacheHelper
- Added warning message when using a deprecated input/output shared parameter
- Fixed issue causing process hangs when stdout+stderr is bigger than 64K when using local executor
- Fixed process stdout/stderr synchronisation issue
- Fixed race condition when accessing `processor` attribute - Issue #41
- Fixed race condition on processes registration/termination - See issue #43
- Fixed `echo` synchronisation strategy when writing to stdout
- Use a fixed thread pool for tasks execution and keep it separated from Gpars thread pool
- Do not set Gpars thread pool size along with nextflow pool size
- Improved resolution to tenths of a second when converting a `Duration` to string
- Removed unnecessary local scope map argument from `getTaskGlobalVars` method
- Read trace file w/o checking existence in order to reduce round-trip on remote storage
- Workaround for Groovy compiler issue GROOVY-7409

0.13.3 - 19 Apr 2015
- Fixed issue when staging file when using a non local pipeline workdir
- Fixed invalid values in the trace file returned by `awk`
- Removed unnecessary `S3Path` serialiser registration on DnaNexus executor initialisation
- Updated S3 file system client to version 0.2.8g

0.13.2 - 16 Apr 2015
- Handle staging in the local process directory of files on remote/foreign file systems
- Fixed issue in resources stats tracing script  -- awk uses scientific notation for numbers instead of decimal format.
- Fixed external links to Groovy docs
- Fixed issue #40 -- Cannot find java binary on Mac OSX
- Fixed missing `DynamicParameter` in usage string
- Fixed docker run `—-cpuset` command line option when using `crg` executor

0.13.1 - 10 Apr 2015
- Fixed IllegalStateException when executing a script in Nextflow console

0.13.0 - 8 Apr 2015
- Added support for AWS S3 storage
- Added support for ClusterK Cirrus cloud scheduler
- Added multiple debugging level in command scripts by using `NXF_DEBUG` variable
- Added ability to disable docker kill command
- Added explicit `entrypoint` definition in docker run command
- Added `uge` executor as alias of SgeExecutor class
- Added `-D` JVM properties command line option
- Added `.command.log` to grid executors
- Separated `stdout` and `stderr` outputs
- Refactored DRMAA executor to a separate sub-project
- Refactored application packaging based on Capsule modes
- Refactored application installer downloading dependencies at runtime
- Optimised file attributes access usage
- Increased log and trace files rolling max index to 9
- Print revision and commit ID on pipeline startup
- Improved handling of docker cpuset for `crg` executor
- Improved TraceFileObserver to flush written content
- Improved `info <pipeline>` command with `-d` option that shows git revision commit IDs
- Fixed issue #39 - Per process containers not working with -with-docker option
- Upgraded Groovy runtime to version 2.3.11
- Upgraded Logback library to version 1.1.3

0.12.5 - 18 Mar 2015
- Fixed regression preventing jobs cleanup when nextflow process is killed
- Fixed issue when command line flag has not value making it to consume following option
- Added `uge` executor as alias of SgeExecutor class
- Improved log messages
- Upgraded Spock testing library to version 1.0

0.12.4 - 4 Mar 2015
- Added suspended job status handling to SLURM executor -- Issue #36
- Added `print` and `println` operators plus tests and updated docs
- Fixed issue on `view` operator when specifying a closure
- Fixed Docker image resource request in CRG executor
- Fixed typo in documentation
- Improved task hash key generation and task variables handling
- Compute `baseDir` and `workDir` as string values when creating task unique hash
- Improved `sum` operator to allows it to handle lists with varying size
- Upgrading Groovy runtime to version 2.3.10

0.12.3 - 16 Feb 2015
- Added support for `module` and `container` fields in execution trace log
- Fixed a small inconsistency on polling monitor queue size for local executor when using single core or two-cores cpu
- Enhanced process key generation including global variables referenced in the process scope
- Enhanced `sum` operator and added `mean` operator

0.12.2 - 12 Feb 2015
- Fixed issue on some SGE implementation where `-terse` directive in job script is not working
- Downgrade Capsule to 0.9.0 due to an issue in version 0.10.0 - https://github.com/puniverse/capsule/issues/56

0.12.1 - 8 Feb 2015
- Fixed NoSuchMethodException issue on Java 1.7.0_01 due to missing private constructor
- Fixed logging issue on Nextflow console
- Fixed issue `view` operator which hung when used on a dataflow variable
- Upgrade SLF4J to version 1.7.10
- Upgrade Capsule to version 0.10.0
- Removed dependency on jsr166y module
- Removed `synchronized` declaration on Session cleanUp method

0.12.0 - 5 Jan 2015
- Added afterScript/beforeScript directives
- Added tag directive to label task executions with a custom identifier
- Added dynamic directives evaluation
- Added support for dynamic input/output file names with closures
- Added `ifEmpty` operator
- Added `view` operator
- Added `remainder` optional parameter to `phase` operator
- Removed 'undef' directive
- Refactored grid executors so that jobs directives are added on top of script wrapper
- Renamed ContextMap to TaskContext
- Renamed TaskConfig to ProcessConfig
- Renamed LocalConfig to TaskConfig
- Print pid/hostname in the status log
- Upgraded to Groovy 2.3.9 and Slf4j 1.7.8

0.11.4 - 3 Dec 2014
- Fixed issue in TextFileCollector empty condition that was creating an empty split file
  when the split size was equals to the number or records
- Fixed bug that prevents a job is added to the polling queue when submit operation fails
- Added more strict checks on $JAVA_CMD executable and $JAVA_HOME folder
- Refactored 'sge' and 'crg' executors so that qsub directives are provided on top of job wrapper script
- Added BSC specific executor
- Upgraded to Groovy 2.3.8

0.11.3 - 27 Nov 2014
- Added to splitters ability to save chunks to files
- Fixed a bug that prevented an error message to be reported when using a missing variable in the process script
- Improved info command showing local and remote branches
- Improved error report when failing to delete pipeline directory
- Removed gpars methods implicit imports
- Fixed unit for 'syscr' and 'syscw' fields in trace report
- Upgraded JGit library version to 3.5.2.201411120430-r

0.11.2 - 19 Nov 2014
- Added 'groupTuple' operator
- Added NXF_WORK variable to define default scratch path
- Added Gzip un-compress ability to splitter operators
- Added 'limit' parameter to splitter operators
- Added 'meta' parameter to splitter operators
- Field 'walltime' has been renamed to 'realtime' in tracing file
- Fixed issue on 'collectFile' operator when no 'name' parameter is specified
- Removed dependency on Picard library
- Improved error reporting

0.11.1 - 11 Nov 2014
- Fixed serialisation issue on pipeline resume
- Fixed issue on command line parameters with no arg (flag)
- Refactored class HubOptions to a trait

0.11.0 - 5 Nov 2014
- Added sorting ability to collectFile operator
- Added new 'cpus', 'memory', 'time', 'penv' process directives
- Added cpu, memory and I/O resources in execution tracing report
- Upgraded to groovy 2.3.7
- Relaxed validation check of -resume option
- Fixed symlink support to Github and BitBucket shared repositories
- Fixed Channel.fromPath with S3 path
- Enhanced error reporting
- Removed blanks from jobs name
- Added NXF_ASSEST environment variable
- Added NXF_TEMP environment variable to define local temporary path

0.10.3 - 3 Oct 2014
- Fixed bug when composing SLURM 'squeue' command line which was containing
  unnecessary quote characters thus invalidating the jobs status check mechanism

0.10.2 - 1 Oct 2014
- Fixed bug while submitting a job to SLURM scheduler due to special characters in job name
- Fixed bug in TaskConfig#toBool() method
- Fixed bug resolving configuration file when pipeline script is a symlink
- Fixed bug while setting 'workDir' attribute on PBS job executor
- Improved error message when the name of a process is missing
- Removed TaskConfig#getMerge() method
- Updated method Channel.fromPath(String) so that it returns normalised absolute paths
- Updated Capsule to version 0.9.0 stable
- Fixed typos in documentation

0.10.1 - 15 Sept 2014
- Added ability to 'run' implicitly a script when it's specified as the very first parameter (for backward compatibility)
- Added 'workDir' and 'baseDir' implicit variables in configuration files
- Fixed docker remove issue by executing as an external command
- Fixed an issue when finding the longest common path used by docker mounts
- Fixed issue #13 - Show a detailed error message when hitting GitHub rate limits

0.10.0 - 8 Sep 2014
- Added DRMAA executor
- Added PBS/Torque executor
- Added processes execution report
- Added Extrae tracing support
- Added support for GitHub private repositories
- Added integration for BitBucket hosted repositories (Git vcs only)
- Added native integration AWS S3 file system
- Improved Docker support and configuration
- Improved GridGain cluster integration
- Removed Hazelcast integration
- Added Capsule based application packaging
- Added commands
        view: that prints the content a pipeline repository
        config: shows pipeline configuration
- Fixed issue #12 - Error resuming process with command defined on multiple lines

0.9.0 - 11 Aug 2014
- Added GitHub/Git support. It allows one to pull and run pipelines published on a
  remote GitHub repository
- Changed command line structure. Since this version it is organised in sub-commands.
  The following sub-commands are available:
      ls: list all downloaded pipelines;
      run: launch a pipeline execution;
      pull: download or update a pipeline hosted on GitHub;
      info: show pipeline information;
      drop: remote a locally stored pipeline;
      clone: copy a pipeline to a directory specified;
      history: list all pipeline runs;
      help: show program help.
- Added 'baseDir' and 'workDir' script variables
- Removed Merge processor


0.8.5 - 3 Aug 2014
- Upgraded to Groovy 2.3.6
- Added '-noverify' to JVM launcher options as workaround for Java bug JDK-8051012

0.8.4 - 20 Jul 2014
- Upgrade to Groovy 2.3.4
- Fixed method Path.list()
- Added '-notify' option to SGE qsub command to handle killed jobs correctly

0.8.3 - 27 Jun 2014
- Added support for Modules package maages
- Fixed issue #1 - process hung when only a parameter of type 'each' is defined
- Fixed issue #6 -- exception while resuming a process that declares a parametric file output name
- Fixed support for curly brackets glob path matching in Channel.fromPath
- Updated Groovy runtime to 2.3.3
- Updated to Groovy-nio module in place of 'native' implementation

0.8.2 - 18 Jun 2014
- Fixed issue #7 - NoClassDefFoundError HashMap$Entry exception with Java 8
- Enhanced launch script: removed '-Xms' Java option; verify the Java version coherent with JAVA_HOME definition; improved error messages.

0.8.1 - 26 May 2014
- Fixed a ConcurrentModificationException issue on splitXxx method due to a misused @Memoized annotation

0.8.0 - 24 May 2014
- Added support for Java 8
- Upgraded to Groovy 2.3.0
- Upgraded to Kryo 2.24.0
- New splitter operators: 'splitText', 'splitFasta', 'splitFastq', 'splitCsv'
- New operator 'collectFile' to gather file chunks
- New operator Channel.fromPath which allows fine control on paths traversal
- Operator Channel.from has been deprecated in favor of Channel.fromPath
- Operator Channel.watch has been deprecated in favor of Channel.watchPath
- Clean-up API for operators: 'into', 'choice', 'separate', 'filter'
- Operator 'grep' has been removed and features included in 'filter' operator
- Deprecated 'chopXxx' operators
- Deprecated 'chunkXxx' operators
- Deprecated 'each' operator in favor of 'subscribe'
- Deprecated process 'merge' directive
- Executor service now uses a fixed thread pool
- Fixed issue on 'maxForks' process directive
- Added 'info' cli parameter
- Improved documentation

0.7.3 - 16 May 2014
- Enhanced stability and errors reporting

0.7.2 - 5 May 2014
- Enhanced support for Docker containers:
  Now the current user id is added on the Docker command line
  and /tmp folder in the container is mounted on a temporary path in the host disk

0.7.1 - 14 Apr 2014
- Fixed an issue with 'scratch' directive i.e. Fixed issue when copying a symlink
- Added 'Retry' error handling strategy and 'maxRetries' and 'maxErrors' process directives
- Added GridGain cluster sub-module
- Added TaskDispatcher submit, start, complete and error listeners
- Added new ServiceDiscovery to handle sub-modules executors
- Added Map#getOrCreate() extension method
- Using @CompileStatic for AST transformation
- Removing unused APP_TMP_DIR const
- Renamed class 'AbstractExecutor' to 'Executor'
- Added ProcessFactory class
- Refactored sub-modules directory structure
- Define the default 'lib' path relative to the pipeline 'baseDir' i.e. relative to the main script location
- Save the history entry just before launch the execution

0.7.0 - 24 Mar 2014
- New self-downloadable and self-updatable script launcher
- New cluster mode, Nextflow can run as a daemon node by using Hazelcast cluster (incubating)
- New support for Docker containers. Any process can be executed through Docker adding 'container = name' in the process definition (incubating)
- New native processes (groovy closure) can executed in the cluster.
- Enhanced task polling monitor
- Use 'rsync' to upstage task result files to target directory
- Pipeline execution can be launched in background by adding the option '-bg- to the command line
- Updated documentation

0.6.2 - 20 Feb 2014
- Added 'concat' operator to concatenate two or more channels
- Added 'into(ch1,ch2...)' operator which maps tuple elements into the corresponding target channel
- Implemented queue status check for SLURM grid executor
- Implemented queue status check for LSF grid executor
- Improved grid executors stability
- Fixed a bug when setting setting the monitor queue size

0.6.1 - 16 Feb 2014
- Added operator 'cross()'
- Added operator 'collate()'
- Added options 'remainder' to 'buffer()' operator
- Added 'deep' option to cache directive in order to index file content.
- Added Kryo based serialization
- Added 'storeDir' process directive to cache process results permanently
- Added 'watch' channel factory method that watches for files changes
- Added parametric input/output file names
- Renaming "mapMany" to "flatMap"
- Enhanced stability for grid executors
- SGE executor periodically invokes the 'qstat' command to fetch the queue jobs status
- Processes and executors can be configured separately in the configuration file by using the $name special scope
- Completed Path methods extension equivalent to legacy File
- Reporting a random tip when a process fail

0.6.0 - 16 Jan 2014
- New channel factory methods
- New reactive operators on channel objects (similar to RxJava)
- New shared parameters
- New input/output set parameters
- New conditional scripts using
- New groovy native processes

0.5.4 - 10 Dec 2013
- Fixed an issue while checking an - empty - process exit file
- Fixed a race condition while resuming cached tasks

0.5.3 - 9 Dec 2013
- Fixed file close leaks
- Fixed DirectoryStream close leaks
- Enhanced process executor, supporting multiple executors in the same pipeline

0.5.2 - 28 Nov 2013
- Changed caching hash function to murmur3_128 to avoid cache collision
- Fixed issue on process termination when resuming pipeline execution

0.5.1 - 24 Oct 2013
- Major executors refactoring
- Featuring new single-thread tasks scheduler
- New enhanced DSL syntax with extended semantic
- Switched file handling to new NIO.2 file system
- Introducing support for DNAnexus cloud platform
- Removed unnecessary library dependencies
- Slim self-contained executable package

0.3.4 - 24 Aug 2012
- Extending semantic for method File.copyTo(source,target) so that when 'target' argument
  is a directory, it copies the 'source' file to that folder, with the same name as the original file.
- Bug: Fixed a ClassCastEx exception when the 'bin' folder is added to the PATH
- Bug: Fixed an issue that raised an error "error=26 Text file busy" on some platforms (CentOS)

0.3.3 - 8 Aug 2013
- Added optional parameters to 'chunkLines' and 'chunkFasta' methods
- Added '-lib' command line parameter specify external libraries (.jar files) or extension scripts
- Folder 'lib' in the launch directory is added by as default libraries path
- Added 'tempFile()' and 'tempDir()' methods to BaseScript class
- The 'bin' directory in the script folder is added to the task PATH environment by default
- Upgraded to Groovy 2.1.6
- Upgraded to Slf4j 1.7.5
- Upgraded to Logback 1.0.13

0.3.2 - 22 Jul 2013
- New command line option '-log' to specify the application log file
- New command line options '-task.xxx' to task default parameters (overriding the ones in the configuration file)
- Fixed a bug which was preventing the caching mechanism to work properly
- Fixed synchronization issue caused by a miss-used CountDownLatch, replaced with a Phaser
- Fixed a bug by which cached tasks didn't print out any result when 'echo' was set
- Fixed a bug in the timezone handling in the build timestamp

0.3.1 - 18 Jul 2013
- Added command line parameter 'echo' to enable default tasks output
- Fixed an issue on merge task, when it doesn't collect any data the execution is skipped

0.3.0 - 11 Jul 2013
- Decoupled the processing policy by the execution strategy classes
- Normalised script level arguments so that a blank char may be used in place of the equals char
- Added a new configuration option named 'clusterOptions' where specify grid native configuration parameters
- Added a new configuration option named 'scratch' which enable/disable usage of scratch temporary folder when using cluster executors
- Enhanced implementation of LSF executor

0.2.11 - 28 May 2013
- Added 'lefTrim' and 'rightTrim' extension methods to String class
- The task script interprets correctly the 'shebang' header declaration
- The task save the command environment to a separated file, in order to simply task reproducibility and debugging

0.2.10
- Adding '-pool-size' cli option and config parameter to define size of executor threads
- Removed SGE output file
- Initial SLURM support

0.2.9
- Adding 'test' feature

0.2.8 - 30 Apr 2013
- Improved scheduling of 'merge', there are executed like a single job
- Fixed caching for 'merge' task
- Refactored class 'TaskDef' to 'TaskRun'

0.2.7 - 25 Apr 2013
- Added 'eachWithIndex' iterator like method on dataflow channel
- Make the SGE task processor to write the output file in the job execution directory
- Renaming the CLI option -continue to -resume
- Adding File extension methods: getBaseName(), getExtension()

0.2.6 - 22 Apr 2013
- Fixed a bug on errors handling
- Added default parameters in config file
- Added Channel type
- Added cacheableDir and cacheableFile
- Upgraded to Groovy 2.1.3

0.2.5 - 19 Apr 2013
- Added LSF executor (experimental)
- Added command line option '-history'
- Added command line option '-continue' to resume the execution of an interrupted execution
- Using Non-daemon threads by default
- Refactored SGE task processor

0.2.4
- Using minimal Groovy dependencies
- SGE/OGE processor works in the scratch folder and un-stage result files when complete
- SGE/OGE handles stdin transparently

0.2.3
- Renamed 'queue' to 'channel'
- Adding a basic tasks cache mechanism
- Supporting 'shell' parameters

0.2.2 - 9 Apr 2013
- Fixed file/stream close leaks, that caused 'Too many open files' error on big pipeline execution
- Rolling log file '.nextflow.log' on startup
- CLI option 'quiet' suppress all 'info' messages
- Added 'maxDuration' and 'maxMemory' attributes to OgeTaskProcessor
- Added 'maxDuration' attribute to LocalTaskProcessor

0.2.1 - 3 Apr 2013
- Initial support for SGE/OGE grid engine

0.2.0 - 2 Apr 2013
- General improvement
- Enhanced parameters handling
- 'chunkLines' and 'chunkFasta' API extension
- 'each' iterator over dataflow queue API extension

0.1 - 25 Mar 2013
- Initial release