Releases: nextflow-io/nextflow
Releases · nextflow-io/nextflow
Version 0.14.4
- 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
- Fixed issue #53 - Cannot access files list entry by using square bracket syntax
Version 0.14.2
Version 0.14.1
- 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
- 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 withCmdRun
object Added ability to setworkDir
in the config file - New implicit lazy Gstring in process parameter and directive definitions
- Changed file unstage strategy using
cp
command instead ofrsync
- Removed
workDir
variable from config file - Updated JGit to version 3.7.1
- Updated Slf4j to version 1.7.12
Version 0.13.5
- Fixed issue #44 - Pipeline hangs when
map
operator is applied to a dataflow variable
Version 0.13.4
- 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
- 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
- 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 usingcrg
executor
Version 0.13.1
- Fixed
IllegalStateException
when executing a script in Nextflow console