Nextflow

- 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

- 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)

- 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

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

- 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