nextflow

• Added sorting ability to collectFile operator
• Added new 'cpus', 'memory', 'time', 'penv' process directives
• Added cpu, memory and I/O resources in execution tracing report
• Upgraded to groovy 2.3.7
• Relaxed validation check of -resume option
• Fixed symlink support to Github and BitBucket shared repositories
• Fixed Channel.fromPath with S3 path
• Enhanced error reporting
• Removed blanks from jobs name
• Added NXF_ASSEST environment variable
• Added NXF_TEMP environment variable to define local temporary path

• Fixed bug when composing SLURM 'squeue' command line which was containing
  unnecessary quote characters thus invalidating the jobs status check mechanism

• Fixed bug while submitting a job to SLURM scheduler due to special characters in job name
• Fixed bug in TaskConfig#toBool() method
• Fixed bug resolving configuration file when pipeline script is a symlink
• Fixed bug while setting 'workDir' attribute on PBS job executor
• Improved error message when the name of a process is missing
• Removed TaskConfig#getMerge() method
• Updated method Channel.fromPath(String) so that it returns normalised absolute paths
• Updated Capsule to version 0.9.0 stable
• Fixed typos in documentation

• Added ability to 'run' implicitly a script when it's specified as the very first parameter (for backward compatibility)
• Added 'workDir' and 'baseDir' implicit variables in configuration files
• Fixed docker remove issue by executing as an external command
• Fixed an issue when finding the longest common path used by docker mounts
• Fixed issue #13 - Show a detailed error message when hitting GitHub rate limits

0.10.0 - 8 Sept 2014

• Added DRMAA executor
• Added PBS/Torque executor
• Added processes execution report
• Added Extrae tracing support
• Added support for GitHub private repositories
• Added integration for BitBucket hosted repositories (Git vcs only)
• Added native integration AWS S3 file system
• Improved Docker support and configuration
• Improved GridGain cluster integration
• Removed Hazelcast integration
• Added Capsule based application packaging
• Added commands
  view: that prints the content a pipeline repository
  config: shows pipeline configuration
• Fixed issue #12 - Error resuming process with command defined on multiple lines

• Added GitHub/Git support. It allows one to pull and run pipelines published on a
  remote GitHub repository
• Changed command line structure. Since this version it is organised in sub-commands.
  The following sub-commands are available:
  • ls: list all downloaded pipelines;
  • run: launch a pipeline execution;
  • pull: download or update a pipeline hosted on GitHub;
  • info: show pipeline information;
  • drop: remote a locally stored pipeline;
  • clone: copy a pipeline to a directory specified;
  • history: list all pipeline runs;
  • help: show program help.
• Added 'baseDir' and 'workDir' script variables
• Removed Merge processor

• Upgraded to Groovy 2.3.6
• Added '-noverify' to JVM launcher options as workaround for Java bug JDK-8051012

• Upgrade to Groovy 2.3.4
• Fixed method Path.list()
• Added '-notify' option to SGE qsub command to handle killed jobs correctly

• Added support for Modules package maages
• Fixed issue #1 -- process hung when only a parameter of type 'each' is defined
• Fixed issue #6 -- exception while resuming a process that declares a parametric file output name
• Fixed support for curly brackets glob path matching in Channel.fromPath
• Updated Groovy runtime to 2.3.3
• Updated to Groovy-nio module in place of 'native' implementation

• Fixed issue #7 - NoClassDefFoundError HashMap$Entry exception with Java 8
• Enhanced launch script: removed '-Xms' Java option; verify the Java version coherent with JAVA_HOME definition; improved error messages.

• Fixed a ConcurrentModificationException issue on splitXxx method due to a misused Memoized annotation

• Added support for Java 8
• Upgraded to Groovy 2.3.0
• Upgraded to Kryo 2.24.0
• New splitter operators: 'splitText', 'splitFasta', 'splitFastq', 'splitCsv'
• New operator 'collectFile' to gather file chunks
• New operator Channel.fromPath which allows fine control on paths traversal
• Operator Channel.from has been deprecated in favor of Channel.fromPath
• Operator Channel.watch has been deprecated in favor of Channel.watchPath
• Clean-up API for operators: 'into', 'choice', 'separate', 'filter'
• Operator 'grep' has been removed and features included in 'filter' operator
• Deprecated 'chopXxx' operators
• Deprecated 'chunkXxx' operators
• Deprecated 'each' operator in favor of 'subscribe'
• Deprecated process 'merge' directive
• Executor service now uses a fixed thread pool
• Fixed issue on 'maxForks' process directive
• Added 'info' cli parameter
• Improved documentation

Enhanced stability and errors reporting

• Enhanced support for Docker containers:
  Now the current user id is added on the Docker command line
  and /tmp folder in the container is mounted on a temporary path in the host disk

• Fixed an issue with 'scratch' directive i.e. Fixed issue when copying a symlink
• Added 'Retry' error handling strategy and 'maxRetries' and 'maxErrors' process directives
• Added GridGain cluster sub-module
• Added TaskDispatcher submit, start, complete and error listeners
• Added new ServiceDiscovery to handle sub-modules executors
• Added Map#getOrCreate() extension method
• Using @CompileStatic for AST transformation
• Removing unused APP_TMP_DIR const
• Renamed class 'AbstractExecutor' to 'Executor'
• Added ProcessFactory class
• Refactored sub-modules directory structure
• Define the default 'lib' path relative to the pipeline 'baseDir' i.e. relative to the main script location
• Save the history entry just before launch the execution

• New self-downloadable and self-updatable script launcher
• New cluster mode, Nextflow can run as a daemon node by using Hazelcast cluster (incubating)
• New support for Docker containers. Any process can be executed through Docker adding 'container = name' in the process definition (incubating)
• New cluster distributed execution for native processes (groovy closures)
• Enhanced task polling monitor
• Use 'rsync' to unstage task result files to target directory
• Pipeline execution can be launched in background by adding the option '-bg- to the command line
• Updated documentation

• Added 'concat' operator to concatenate two or more channels
• Added 'into(ch1,ch2...)' operator which maps items in a tuple into the corresponding target channels
• Implemented queue status check for SLURM grid executor
• Implemented queue status check for LSF grid executor
• Improved grid executors stability

• Added operator 'cross()'
• Added operator 'collate()'
• Added options 'remainder' to 'buffer()' operator
• Added 'deep' option to cache directive in order to index file content.
• Added Kryo based serialization
• Added 'storeDir' process directive to cache process results permanently
• Added 'watch' channel factory method that watches for files changes
• Added parametric input/output file names
• Renaming "mapMany" to "flatMap"
• Enhanced stability for grid executors
• SGE executor periodically invokes the 'qstat' command to fetch the queue jobs status
• Processes and executors can be configured separately in the configuration file by using the $name special scope
• Completed Path methods extension equivalent to legacy File
• Reporting a random tip when a process fail

• New channel factory methods
• New reactive operators on channel objects (similar to RxJava)
• New shared parameters
• New input/output set parameters
• New conditional scripts using
• New groovy native processes

• Fixed an issue while checking an - empty - process exit file
• Fixed a race condition while resuming cached tasks