@pditommaso pditommaso released this Aug 7, 2018 · 5 commits to master since this release

Assets 4
  • 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 [90fb69f]
  • Added CONTRIBUTING file #564

@pditommaso pditommaso released this Jul 25, 2018 · 21 commits to master since this release

Assets 4
  • Fixed CLI parameter value starting with a - is misinterpreted #808
  • Added keep-logs option to clean command #775

Already included in 0.31.0-RC1

  • 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 [dcc7ec5]
  • 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] [8ba1716,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
Pre-release

@pditommaso pditommaso released this Jul 19, 2018 · 29 commits to master since this release

Assets 4
  • 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 [dcc7ec5]
  • 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] [8ba1716][ba5ad7a]
  • 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

@pditommaso pditommaso released this Jun 16, 2018 · 105 commits to master since this release

Assets 4
  • 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 20b6d93 a8b994f

@pditommaso pditommaso released this Jun 11, 2018 · 120 commits to master since this release

Assets 4
  • 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

@pditommaso pditommaso released this Jun 5, 2018 · 140 commits to master since this release

Assets 4
  • 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

@pditommaso pditommaso released this May 10, 2018 · 194 commits to master since this release

Assets 4
  • 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

@pditommaso pditommaso released this Apr 24, 2018 · 211 commits to master since this release

Assets 4

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

(already included in 0.29.0-RC1)

  • 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
Pre-release

@pditommaso pditommaso released this Apr 8, 2018 · 219 commits to master since this release

Assets 4
  • 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

@pditommaso pditommaso released this Apr 6, 2018 · 235 commits to master since this release

Assets 4
  • 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