nextflow-io/nextflow v19.04.0

Version 19.04.0

on GitHub

• Added support for NCBI_API_KEY variable [e4d9b62]
• Added warning message when using untested Java version [35acd1c]
• Added parameter and workflow metadata to weblog payload #1077
• Added warning on publish with a null var [7d58bfb] [95c219f]
• Fixed Echo directive when Ansi log is enabled #1112 #996
• Fixed Do not mount inputs when stageInMode == copy #1105
• Fixed splitCsv operator fails to parse values containing commas #1102
• Fixed missing return type for Date.format method
• Fixed Channel operations toList followed by merge hang execution #1083
• Avoid printing execution summary when no processes are computed #996
• Improved error reporting for null publishDir [0b9b52f]

(from 19.03.0-edge)

• Fix Nextflow hangs submitting jobs to AWS Batch #1024
• Fix process builder incomplete output [2fe1052]
• Fix Grid executor reports invalid queue status #1045
• Fix Script execute permission is lost in container #1060
• Fix K8s serviceAccount is not honoured #1049
• Fix K8s kuberun login path #1072
• Fix K8s imagePullSecret and imagePullPolicy #1062
• Fix Google Storage docs #1023
• Fix Env variable NXF_CONDA_CACHEDIR is ignored #1051
• Fix failing task due to legacy sleep command [3e150b5]
• Fix SplitText operator should accept a closure parameter #1021
• Add Channel.fromSRA factory method #1070
• Add voluntary/involuntary context switches to metrics #1047
• Add noHttps option to singularity config #1041)
• Add docker-daemon Singularity support #1043 [dfef139]
• Use peak_vmem and peak_rss as default output in the trace file instead of rss and vmem #1020
• Improve ansi log rendering #996 [33038a1]

(from 19.02.0-edge)

• Added foreign files caching ability #686
• Added Ansi logging as default console output
• Added Gitea source code provider [ae04fc3]
• Fixed Join operator returns invalid remainder values #1015
• Fixed Invalid trigger of integration tests [7aa5908]
• Fixed memory allocation for SGE executor [29353c9]
• Fixed properties access for TaskConfig and LazyMap [09b74a5]
• Fixed Invalid decimal separator in mem unit string #999
• Fixed tail error on launcher script [38afea6]
• Improved Execution and Timeline memory reporting #980 #986 #1012 #1014 #1016 #1018 [0142609] [7d6c29f]
• Improved Google pipelines file copy strategy [678405b]
• Improved output file stage out behaviour docs #961 #1013
• Upgraded Groovy runtime to version 2.5.6