nextflow-io/nextflow v0.25.0

Version 0.25.0

on GitHub

Improvements and fixed issue

• Fixed Dataflow threads pool get exhausted with a large number of tasks #92
• Fixed Custom function cannot be invoked in the workflow completion handler #374
• Fixed Runtime errors are not reported in the workflow.errorMessage property #369
• Fixed Warn if params.something is defined twice in a NF script #372
• Fixed Map.Entry values deserialisation process fail #373
• Fixed List active operators that may hang the script execution #315
• Fixed launcher error message #366
• Fixed AWS spot instance bootStorageSize property is ignored #368
• Fixed Implicit variable task is not accessible in cached processes #363
• Fixed Do not export user environment when submitting job to SGE-like batch scheduler #362
• Fixed Process termination can throw a ConcurrentModificationException hiding the error cause message #359
• Fixed GroovyRuntimeException during foreign file copy process #360
• Fixed Helper function to compare version numbers #319
• Fixed Docker input file mounts should be read-only for enforce container security #346
• Fixed Extend each repeater syntax to support file collections #355
• Fixed Modified task properties are not accessible in the command script during task retry #345
• Fixed PublishDir warning message
• Fixed Spread operator mishandles Iterable values provided as a dataflow variable #353
• Fixed UUID cli options are wrongly interpreted as Duration objects #349
• New toInteger converter operator
• New randomSample operator #344
• New simpleName extension method to Path/File objects #354
• New warning message when input tuple cardinality does not match declared length #348
• Improved use example into ext directive documentation #327
• Improved error handing when parsing trace file #371
• Improved error reporting for process missing input definition
• Improved launcher script to support https protocol by default #379
• Change maxErrors default to -1
• Deprecated identifier channel as variable name

Special note

• Directive maxErrors new default is -1, this means that by default this value is ignored when a task execution is retried and only maxRetries value the is taken in consideration.
• Docker input mounts are now enforced as read-only. This has been done to mitigate possible security concerns when using Docker containers. It must noted that this is coherent with the idempotent nature of nextflow processes by which a task cannot have side-effects (and therefore modify the input files).
• SGE, PBS/Torque and NGSII executors do not specify any more the -V flag when submitting a job request. If you need to export the user environment in your task you will need to add it by using the clusterOptions directive.