nextflow

• Fixed QueueSize=1 doesn't handle multi-cpu processes #246
• Fixed Accessing to a not defined script params should raise an error #243
• Fixed An input channel evaluating to null results in a misleading error message #242
• Fixed Use of publicDnsName should failover to IP if no name is available #240
• Fixed Use of yum in cloud boothook may cause problems #239
• Fixed Execution hang when an operator invokes the exit function and no processes have run
• Fixed fromFilePairs does not match patterns containing curly brackets w/o a star wild character
• Added -dump-hashes command line option to print task key hash keys #211
• Improved logging

• Added --no-requeue flag to SLURM job submission
• Report log content when a wrapper script execution fail #213
• Improved error message when cache DB cannot be created
• Logging error track trace on task re-submit failure
• Fixed Channel.fromPath throws an exception when the argument is a S3 path
• Modified make_temp so that uses NXF_TEMP when defined

• Fixed PBS qsub fails when the job name is longer than 15 chars #228
• Fixed Spread operator doesn't connect channels in DAG #231
• Fixed amazon prices file format parser
• Added Cleanup scratch dir upon process completion #230
• Added optional flag to output file declaration
• Added region option to cloud command
• Added Check for missing instance type description

• Fixed Copy input files to scratch directory #197
• Fixed PBS qsub fails when the job name starts with a dot #228
• Fixed issue when staging-out a symlink output file
• Fixed log warning when running a script in the console

• Fixed Nested symlinks are not resolved by Docker container mounts #222
• Fixed Nextflow execution log fail to get field starting with '%' #223
• Fixed Nextflow console launcher
• Added ContainerCreation status to K8S executor
• Expand = to == in filter expressions to avoid misleading results

• Fixed queue-size attribute for local executor
• Fixed Kubernetes pod id parse issue
• Moved .nextflow.history and .cache files under .nextflow directory

[0.22.0.RC2]

• Fixed File name containing glob wildcards cannot be captured in the process output #219
• Fixed Work dir containing glob wildcards are not supported #194
• Added revision id to execution log
• Added scriptId, scriptFile and scriptName attributes to workflow metadata object
• Added time delay penalty on error burst to prevent failing node to drain all pending jobs
• Load classes without creating an instance of each cloud driver
• Improved AWS driver missing credentials error report
• Merged experimental Kubernetes support
• Improved clean and log command
• Added EFS default mount path
• Refactored daemon shutdown

[0.22.0.RC1]

• Fixed Implement clean up command #19
• Fixed Trace file should include cached tasks #114
• Added ability to log each command run #108
• Added new cloud command
• Added AWS EFS support
• Added AWS Spot instance error fail-over
• Added support cloud auto scaling
• Added Ignite job-stealing distributed scheduler

• Fixed Spaces in work directory path stops SLURM from accepting the job #218

• Fixed PBS professional batch scheduler submission error #209
• Fixed Reference to a collection of files is not resolved properly in the output section #214
• Improved failed and ignored processes reporting
• Fixed null workflow.projectDir when launching a script file
• Do no output link file when followLinks option is disabled

• Fixed NFS work dir is not detected correctly #206
• Fixed splitFasta operator with the file parameter will not split into single fasta files #181
• Enable log file for commands when debug or trace option is specified
• Added validation checks to fromPath and fromFilePairs methods

• Fixed Command line params do not override params defined in the nextflow.config file #202

(included in 0.21.0-RC1)

• Fixed Ability to customize job name submitted to the scheduler #140
• Fixed Duplicate output error when no channel specified #182
• Fixed File paths containing a timestamp are parsed as a Duration object #185
• Fixed ClosedByInterruptException is thrown randomly #188
• Fixed Pipeline hangs when Channel.from argument is an empty list #189
• Fixed Handle customised sbatch returning the jobid by itself #190
• Fixed LocalExecutor can randomly hang with no running task #191
• Fixed Missing flag in SLURM squeue call #193
• Fixed Process script declaring a regexp expression results in a IllegalAccessException #199
• Merged Silence mkdir error if NXF_HOME not writable #187
• Refactored ParallelTaskProcessor and TaskProcessor classes to a single class
• Added ST and BF queue statuses to SLURM executor
• Improved logging information
• Upgrade to Gradle 2.14

• Fixed Directives do not accept a negative numeric value #180
• Fixed Dynamic errorStrategy is not evaluated correctly #183
• Fixed Pipeline hangs when error strategy is used and an upstream process fail
• Added environment to ContainerBuilder and implement environment export for Shifter containers
• Updated Groovy runtime to version 2.4.7

• Added fromFilePairs channel factory method
• Added finish error strategy #158
• Added ability to change the name and the save path of published files #178
• Added a syntax validation check for process blocks keywords #177
• Fixed It's not possible to specify environment modules w/o a version number #174
• Fixed Local process kill signal is not propagated to children processes #172
• Fixed scratchDir is overwritten by TMPDIR #171
• Removed deprecated Channel.path methods
• Ignore missing COUT and CERR variables

• Fixed Exception is thrown while reporting an invalid output declaration #170

• Fixed Local executor does not run an job when host cpus == 1 #166

• Fixed Module load problem #161
• Fixed PublishDir does not overwrite symlinks #163
• Fixed Implement resource accounting for local executor #162
• Fixed PublishDir fail to move the output directory when the target is a S3 path #160

• Fixed Spread operator is using deprecated just operator #159
• Fixed Invalid call to notifyError method
• Fixed Invalid URL in citoscape.js DAG template
• Improved documentation

• Added Pipeline execution DAG #147
• Added support for OpenLava batch scheduler #152
• Added -revision option to pull command #110
• Set UTF-8 as default file encoding #149
• Fixed Extend support for empty curly glob pattern #154
• Fixed Add process directives validation #153
• Fixed Calculation of freePhysicalMemorySize does not currently take disk cache into account #150
• Fixed Improve error message when pulling a non-existing branch could be more explicit #156
• Updated JGit to version 4.3.1

• Fixed Timeline report no longer works in Safari #143
• Fixed Invalid or corrupt JAR file if your CTRL-C initial run of nextflow #145
• Fixed Pipeline execution hangs when the into declaration is not provided #146

• Fixed Variable task.exitStatus throws an exception when comparing it to an integer value #142
• Fixed PublishDir does not handle hard linking of directories #126
• Added index implicit variable to the task execution context #139
• Improved installer messages
• Updated Gradle runtime to version 2.13

• Fixed Input files containing a parenthesis in the path are not staged properly #133.
• Fixed Process execution hangs when using Ignite executor with a foreign work path #136.
• Fixed Sort output files in lexicographical order #137.
• Added false as sort option in the collectFile operator.