nextflow

nextflow - Version 0.14.3

Published by pditommaso over 9 years ago

Fixed issue #53 - Cannot access files list entry by using square bracket syntax

nextflow - Version 0.14.2

Published by pditommaso over 9 years ago

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

nextflow - Version 0.14.1

Published by pditommaso over 9 years ago

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

nextflow - Version 0.14.0

Published by pditommaso over 9 years ago

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

nextflow - Version 0.13.5

Published by pditommaso over 9 years ago

Fixed issue #44 - Pipeline hangs when map operator is applied to a dataflow variable

nextflow - Version 0.13.4

Published by pditommaso over 9 years ago

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

nextflow - Version 0.13.3

Published by pditommaso over 9 years ago

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

nextflow - Version 0.13.2

Published by pditommaso over 9 years ago

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

nextflow - Version 0.13.1

Published by pditommaso over 9 years ago

Fixed IllegalStateException when executing a script in Nextflow console

nextflow - Version 0.13.0

Published by pditommaso over 9 years ago

Added support for AWS S3 storage
Added support for ClusterK Cirrus cloud scheduler
Added multiple debugging level in command scripts by using NXF_DEBUG variable
Added ability to disable docker kill command
Added explicit entrypoint definition in docker run command
Added uge executor as alias of SgeExecutor class
Added -D JVM properties command line option
Added .command.log to grid executors
Separated stdout and stderr outputs
Refactored DRMAA executor to a separate sub-project
Refactored application packaging based on Capsule modes
Refactored application installer downloading dependencies at runtime
Optimised file attributes access usage
Increased log and trace files rolling max index to 9
Print revision and commit ID on pipeline startup
Improved handling of docker cpuset for crg executor
Improved TraceFileObserver to flush written content
Improved info <pipeline> command with -d option that shows git revision commit IDs
Fixed issue #39 - Per process containers not working with -with-docker option
Upgraded Groovy runtime to version 2.3.11
Upgraded Logback library to version 1.1.3

nextflow - Version 0.12.5

Published by pditommaso over 9 years ago

Fixed regression preventing jobs cleanup when nextflow process is killed
Fixed issue when command line flag has not value making it to consume following option
Added uge executor as alias of SgeExecutor class
Upgraded Spock testing library to version 1.0
Improved log messages

nextflow - Version 0.12.4

Published by pditommaso over 9 years ago

Added suspended job status handling to SLURM executor -- Issue #36
Added print and println operators plus tests and updated docs
Fixed issue on view operator when specifying a closure
Fixed Docker image resource request in crg executor
Improved task hash key generation and task variables handling
Compute baseDir and workDir as string values when creating task unique hash
Improved sum operator to allows it to handle lists with varying size
Upgrading Groovy runtime to version 2.3.10

nextflow - Version 0.12.3

Published by pditommaso over 9 years ago

Added support for module and container fields in execution trace log
Fixed a small inconsistency on polling monitor queue size for local executor when using single core or two-cores cpu
Enhanced process key generation including global variables referenced in the process scope
Enhanced sum operator and added mean operator

nextflow - Version 0.12.2

Published by pditommaso over 9 years ago

Fixed issue on some SGE implementation where -terse directive in job script is not working
Downgrade Capsule to 0.9.0 due to an issue in version 0.10.0 - https://github.com/puniverse/capsule/issues/56

nextflow - Version 0.12.1

Published by pditommaso over 9 years ago

Fixed NoSuchMethodException issue on Java 1.7.0_01 due to missing private constructor
Fixed logging issue on Nextflow console
Fixed issue view operator which hung when used on a dataflow variable
Upgrade SLF4J to version 1.7.10
Upgrade Capsule to version 0.10.0
Removed dependency on jsr166y module
Removed synchronized declaration on Session cleanUp method

nextflow - Version 0.12.0

Published by pditommaso almost 10 years ago

Added afterScript/beforeScript directives
Added tag directive to label task executions with a custom identifier
Added dynamic directives evaluation
Added support for dynamic input/output file names with closures
Added ifEmpty operator
Added view operator
Added remainder optional parameter to phase operator
Removed 'undef' directive
Refactored grid executors so that jobs directives are added on top of script wrapper
Renamed ContextMap to TaskContext
Renamed TaskConfig to ProcessConfig
Renamed LocalConfig to TaskConfig
Shared process declaration has been deprecated
Print pid/hostname in the status log
Upgraded to Groovy 2.3.9 and Slf4j 1.7.8

nextflow - Version 0.11.4

Published by pditommaso almost 10 years ago

Fixed issue in TextFileCollector empty condition that was creating a empty split file
when the split size was equals to the number or records
Fixed bug that prevents a job is added to the polling queue when submit operation fails
Fixed issue #24 -- Http/s proxy environment variables are not used properly
Added more strict checks on $JAVA_CMD executable and $JAVA_HOME folder
Upgraded to Groovy 2.3.8

nextflow - Version 0.11.3

Published by pditommaso almost 10 years ago

Added to splitters ability to save chunks to files
Fixed a bug that prevented an error message to be reported when using a missing variable in the process script
Improved info command showing local and remote branches
Improved error report when failing to delete pipeline directory
Removed gpars methods implicit imports
Fixed unit for 'syscr' and 'syscw' fields in trace report
Upgraded JGit library version to 3.5.2.201411120430-r

nextflow - Version 0.11.2

Published by pditommaso almost 10 years ago

Added 'groupTuple' operator
Added NXF_WORK variable to define default scratch path
Added Gzip un-compress ability to splitter operators
Added 'limit' parameter to splitter operators
Added 'meta' parameter to splitter operators
Field 'walltime' has been renamed to 'realtime' in tracing file
Fixed issue on 'collectFile' operator when no 'name' parameter is specified
Removed dependency on Picard library
Improved error reporting

nextflow - Version 0.11.1

Published by pditommaso almost 10 years ago

Fixed serialisation issue on pipeline resume
Fixed issue on command line parameters with no arg (flag)
Refactored class HubOptions to a trait

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