nextflow

• 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 [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

• 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

• 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

• 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

• 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

(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

• 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

• 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
• Improved documentation

• 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]

from 0.28.0-RC1

• 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

• Fixed Operator toList hangs when applied to a value channel #612
• Allow launcher to track installation verb

• 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

• 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

• 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

• 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

• 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

• 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

(from 0.27.0-RC1/2 release)

• 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
• 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-in 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

Fixed GitLab auth token is not applied when user credentials are not provided #542

• 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.

• 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

• 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