nextflow-io/nextflow v0.26.0

Version 0.26.0

on GitHub

• Fixed file method does not interpret correctly S3 path with globs #509
• Fixed Execution hangs when the amount of requested resources exceed the available ones #502
• Minor change in the execution report #507 #508
• Make AWS clustering compliant with billing by seconds
• Refactored nf-token AWS job definition parameter #475
• Run Batch task in a scratch directory to avoid undefined execution folder #475
• Renamed iamProfile to instanceRole #422
• Renamed ProcessNotRecoverableException to ProcessUnrecoverableException

From 0.26.0-RC2

• Fixed TMP and TMPDIR variables are not passed in Singularity environment #496
• Fixed Dynamic resources directive when defined both in a process and the config file cause an error #497
• Added Experimental support for Shifter containers #500 #501
• Improved AWS Batch task logging and task attempts
• Improved Execution report showing task realtime instead of task duration on time box plot

From 0.26.0-RC1

• Added support for AWS Batch #475
• Added support for AWS IAM role #422
• Added Experimental support for Java 9 #462
• Added transpose operator #440
• Added join operator #460
• Added html report (-with-report option)
• Added Gzip compression support to splitXxx operators #484
• Added Support PE Fastq files splitting #436
• Added Operator splitFasta should allow the creation of chunk having the same size #472
• Added HTML execution report #490 #491
• Added New scientist names #485
• Improved merge operator #458
• Improved value channel handling for reduce, filter, first, take and randomSample operators
• Prints a warning message when the config file defines setting not matching any process definition
• Fixed HEAD is detached error #389
• Fixed Include container name when calculating cache key #443
• Fixed Invalidate process cache when a referenced external script is modified #413
• Fixed Execution failure is not reported in the trace file when retry error strategy is used #404
• Fixed "when" directive should not allow staging of input files for a process, if the criteria are not met #424
• Fixed Failure during foreign files download cause execution to stop abruptly #295
• Fixed The parameter groupName cannot be used with the parameter subnet #465
• Fixed unable to download from gitlab.com public repository #457
• Fixed Print work directory when a task fails #445
• Fixed Misleading command line parameter type conversion #434
• Fixed Nextflow should not stage files that have the same name #470
• Fixed SplitCsv returns array objects instead of Lists #487
• Fixed Cannot cast object FtpURLConnection error #482
• Fixed Nested Environment Module names are not loaded properly #489
• Removed support support for Java 7 #385
• Removed deprecated Cirrus/ClusterK executor
• Removed deprecated support for DNAnexus #386