Nextflow

- 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]

- 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 scripts 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

- 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

- 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 Unparsable 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 Unparsable 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

- Fixed test [011e8e23]
- Fixed version number check [fb780347]

- 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