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Releases: nextflow-io/nextflow

Version 0.14.4

20 Jul 15:09
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  • Fixed issue #54 - Nextflow installer does not work when running behind a proxy server
  • Upgraded Capsule package manager to version 1.0-rc2

Version 0.14.3

03 Jul 17:49
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  • Fixed issue #53 - Cannot access files list entry by using square bracket syntax

Version 0.14.2

25 Jun 12:19
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  • 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

Version 0.14.1

08 Jun 14:59
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  • 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

Version 0.14.0

04 Jun 15:24
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  • 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
  • Added support for unlimited maxErrors when set to -1 - Issue #46
  • 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
  • Removed workDir variable from config file
  • Updated JGit to version 3.7.1
  • Updated Slf4j to version 1.7.12

Version 0.13.5

07 May 12:42
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  • Fixed issue #44 - Pipeline hangs when map operator is applied to a dataflow variable

Version 0.13.4

04 May 09:27
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  • 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

Version 0.13.3

19 Apr 17:53
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  • 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 registation on DnaNexus executor initialisation
  • Updated S3 file system client to version 0.2.8g

Version 0.13.2

16 Apr 11:37
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  • 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

Version 0.13.1

11 Apr 10:00
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  • Fixed IllegalStateException when executing a script in Nextflow console