forked from nextflow-io/nextflow
-
Notifications
You must be signed in to change notification settings - Fork 0
/
changelog.txt
1612 lines (1443 loc) · 77.9 KB
/
changelog.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
NEXTFLOW CHANGE-LOG
===================
19.09.0-edge - 16 Sep 2019
- Add `of` and `fromList` channel factories [cc60b305]
- Add nf-tower init request [120ed8ba]
- Add support for accelerator directive #997 [624c8e83]
- Add support for native shifterimg for shifter engine (#1292) [a106712e]
- Add nf-tower subproject [285e09ce]
- Add sticky log marker [f9a3c9da]
- Add support for config resolution [4754abc6]
- Add enable option to publishDir [7b9c2d2f]
- Fix race condition on task workdir creation [5bc323a0]
- Fix issue when fetching aws profile from env #1248 [ba30b97c]
- Fix minor issue when reporting invalid entry error msg [814d6728]
- Fix non determinist test failure [a9289e9e]
- Throw error cause on InovationTargetException [9e1467d0]
- Remove verbos logs on readExitFile check [a5a6a1fc]
- Revert "Patch capsule error message" [ac4ac073]
- Patch for inconsistent cached task id #1301 [7bfd0008]
- Improve flow execution events [335b76d1]
19.08.1-edge - 26 Aug 2019
- Add Process named output channels #1290 [DSL] [6a756fd2]
- Add workflow publish directive [DLS2] [287a095e]
- Add stageAs option to input path [DSL2] [9b5f55f6]
- Add workflow entry option [DSL2] [f29e3e04]
- Add extension to module file name instead of simpleName [DSL2] [71a60365]
- Add support AWS temporary session token support [15ac3938]
- Add support for GCP disk resource [72bb9c41]
- Add fork operator #1281 [DSL2] [6f89833a]
- Add branch operator #1202 [706a182a] [DSL2]
- Add workflow definition and composition #1276 [13f43291] [DSL2]
- Add projectName to workflow metadata [55be0762]
- Add support for tower [1255f702]
- Add support for timezoned timestamp to metadata [6f4a2e28]
- Add task pending event [d2d66698]]
- Add support for path in/out qualifier [DSL2] #1201 [5552b38a]
- Add set chainable operator #1262 [2651a099]
- Fix name generator uniq check [0bbf7015]
- Fix execution report nested processes aggregation [e4fad827]
- Fix nested process names config resolution [ccd8e833]
- Fix missing deprecation [8af85189]
- Fix broken div structure in html report [3e055a7a]
- Fix set operator for multi-channel #1262 [eab39378] [DSL2]
- Fix typo in the `delete` file docs [38fa2dca]
- Fix test #1276 [cc03d76b]
- Fix classpath resolving when launched from foreign path [04024fe6]
- Fix console cmd throws runtime exception #1273 [2f78d943]
- Fix process names validation fails for included modules #1175 [75b96aa8] [DSL2]
- Fix issue with `set` as operator #1262
- Fix misleading name when throwing multiple in/out channel [e7c8cdb9]
- Fix Combine operation incorrectly represented in DAG #1268 [6e86e28a]
- Fix docs collectFile `size` vs `skip` option [8cfb5a64]
- Fix K8s TaskHandler updates its status correctly to 'RUNNING' (#1256) [a1457a1c]
- Remove potential sensitive environment vars #1075 [a413b967]
- Enable use AWS profiles other than `default` (#1248) [d7434773]
- Relax deprecation messages #1269 [454e78f1] [fd11f8d8]
- Defer process start and channel emission [DSL2] [f5eef256]
- Rename ChannelFactory helper to CH [4b5b3c7e]
- Improve modules error checking and reporting [aa650b9e] [DSL2]
- Increase build test max heap size [daca896e]
- Upgrade Gradle to version 5.5.1 [027cb16b]
- Enforce process execution in `workflow` scope` [DSL2] [bca15a91] [0a582240]
- Replace InterruptedException with TimeoutException in GCP test [a6d3c24c]
- Explicitly check whether module path does not end with .nf (#1254) [8253608a]
- Minor improvement AWS Batch docs [bd56ea44]
- Upgrade Groovy to version 2.5.8 [36dffa18]
- Enhance execution report [ab5f8d98]
- Enhance simple http client [2e0f5c2b]
- Refactor resource metrics collector [fec86ed2]
- Refactor observers plugin system [9dab8f08]
- Replace input/output set type with tuple [DSL2] #1207 [5e19f72f]
- Convert any simple object to a value channel [DSL2] [86b0469d]
- Improve logging [5adc2c09]
19.07.0 - 27 Jul 2019
- Add support for K8s annotations #1240 [8eeb7f9f]
- Add support for Moab resource manager #1224 [3ba51a19]
- Add Pbs Pro execution documentation [1d39ab31]
- Add code of conduct document
- Fix missing LFS executor register invocation #1234 [b1b7ab1]
- Fix "invalid pod status" when running scrips with the kubernetes executor #1242 [11caac68]
- Revert Fix Environment activation fails with recent versions of Conda #1195 [98c0d1f8]
- (includes changes from `19.07.0-edge`, `19.05.0-edge` and `19.05.0-edge`)
19.07.0-edge - 9 Jul 2019
- Fix Remote input file download slowdown submission rate #1206 [b710e21e]
- Fix serial publishDir uploads #856 [14774854]
- Fix Trace file option is not honoured #1217
- Fix Custom lib path is not added to the classpath #1213
- Fix Discovery executor tracing error [3e26c146]
- Add megabyte unit to Slurm memory requirement #1216 [efabdd2f]
- Add support for GCP dynamic machine type #1198 [5c2c7665]
- Add setCredentialsProvider for submodules #1205 [e2460414]
- Improve google pipelines docs [aed407ed]
- Improve FileTransfer await termination log #1206 [cb968da7]
- Allow trace logging for `com.upplication.s3fs` package [d71b94e1]
- Upgrade s3fs lib to version 1.0.6 #856
19.06.0-edge - 21 Jun 2019
- Fix Nextflow indefinitely waiting for killed jobs #981
- Fix Suppress Unknown hashing type logging message #1178 [a005b1b0]
- Fix a typo in AWS docs (#1171)
- Fix Invalid response cause Google pipelines exec to crash #1163
- Fix kuberun doesn't delete config maps #1165
- Fix Disable ansi logging when using kuberun command #1161
- Fix comparable test with groovy 2.5.8 [3d1c0833]
- Fix Unexpected config selector warning #1167 [52e70e31]
- Fix Kuberun should honour `-bg` (background) option #1159 [4b160b7b]
- Add S3 download retry (#1164)
- Upgrade BitBucket provider with API 2.0 [feeddcda]
- Print ansi summary for exec > 60 secs [53c94270]
- Remove deprecated countText operator #983
- Demote warmup into to debug level [c7d08337]
- Demote barrier logging to trace level [5b7234a1]
19.05.0-edge - 20 May 2019
- Add Aws Batch maxParallelTransfers config #1107 [26d37556]
- Add NXF_ANSI_SUMMARY var to disable log summary [d4b9cc44]
- Add support for AWS user volumes and jobRoleArn [651eeadd]
- Add Support for LSF per task resource reserve mode #1071
- Fix Env variable with blanks is not resolved correctly in containers #1146
- Fix method isDynamic visibility [f241781b]
- Fix WebLogObserver data leak on completion #1010
- Fix unit test execution [622d97d4]
- Fix Quiet cli option is not honoured [e656e4b0]
- Fix Log messages don't show in the console #1129 [95f4dd7b]
- Fix nextflow build timestamp json rendering [af6584c9]
- Fix Launcher should return non-zero exit when fail to step env #1126
- Update get started docs [68f53367]
- Update aws sdk to version 1.11.542
- Update created label in timestamp [e8945e8b]
- Update readme IDE version
- Refactor AWS cli path option [ad9af0dd]
- Improve Dsl-2 error reporting [4e2621ff]
- Improve CI tests scripts [febeb530]
- Improve docs for config profiles [8cf95a5d]
- Syntax enhancement aka DLS-2 #984 [651af95a]
- Print summary only the run takes > 3mins [cd459713]
- Render last tag along with the process name #1144 [8cf8cc44]
- Sync build scripts [a5689217]
- Provide scm credentials when fetching information about remote branches #1135 [808847b5]
- Code cleanup [2322fbcf]
19.04.0-edge - 24 Apr 2019
- Add Experimental support for gpu resources #997
- Fix LSF executor should use mem setting in lsf.config #1124
- Fix Unable to list S3 bucket content #1121
19.04.0 - 15 Apr 2019
- Added support for NCBI_API_KEY variable [e4d9b62c]
- Added warning message when using untested Java version [35acd1cb]
- Added parameter and workflow metadata to weblog payload #1077
- Added warning on publish with a null var [7d58bfb7] [95c219fb]
- 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 [0b9b52f0]
19.03.0-edge - 14 Mar 2019
- Fix Nextflow hangs submitting jobs to AWS Batch #1024
- Fix process builder incomplete output [2fe1052c]
- 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 [3e150b56]
- 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 [dfef1391]
- Use peak_vmem and peak_rss as default output in the trace file instead of rss and vmem #1020
- Improve ansi log rendering #996 [33038a18]
19.02.0-edge - 6 Feb 2019
- Added foreign files caching ability #686
- Added Ansi logging as default console output
- Added Gitea source code provider [ae04fc37]
- Fixed Join operator returns invalid remainder values #1015
- Fixed Invalid trigger of integration tests [7aa5908a]
- Fixed memory allocation for SGE executor [29353c90]
- Fixed properties access for TaskConfig and LazyMap [09b74a52]
- Fixed Invalid decimal separator in mem unit string #999
- Fixed tail error on launcher script [38afea6c]
- Improved Execution and Timeline memory reporting #980 #986 #1012 #1014 #1016 #1018 [01426097] [7d6c29f0]
- Improved Google pipelines file copy strategy [678405b2]
- Improved output file stage out behaviour docs #961 #1013
- Upgraded Groovy runtime to version 2.5.6
19.01.0 - 22 Jan 2019
- Added Google Cloud Platform integration
- Added support for K8s nodeSelector #955
- Added new AWS regions #935
- Added json/yaml output to info command #657
- Added More duration and memory unit syntax sugar #921
- Added NO_PROXY env variable should be honoured #864
- Added keepHeader option to splitText operator #912
- Added countLines, countFasta and countFastq methods #972
- Added an env variable to define default cloud driver #973
- Fixed Unable to find JVM 1.8 err message #1000
- Fixed Memory unit should contain thousand separator [e6ec4c84] #989
- Fixed LSF long user names breaks jobs status parsing [b4306151] #988
- Fixed Move output files to storeDir instead of copying them #745
- Fixed Interpolated strings in a from statement are misinterpreted #978
- Fixed ConcurrentModificationException when publishing output files #971
- Fixed Launcher fails with Java 10 or later #953
- Fixed remote bin directory when using bucketDir option [6d796783]
- Fixed foreign file system detection [1489cc72]
- Fixed Ansi logger division by zero [ae2b1380]
- Fixed Unparseable Data format on http file #962
- Fixed Log command history #405
- Fixed Too long process tag name can cause SLURM failure #941
- Fixed LSF can return an inconsistent jobs status #927
- Fixed dump last queue status on failure [36e80242]
- Fixed Allow the usage of a custom docker image for K8s driver pod #877
- Fixed K8s executor when the cluster has no available cpus #824
- Fixed Prevent duplicate process definitions #920
- Fixed Update queue statuses used by PBS Pro #908
- Fixed K8s launcher fails to set pod work directory [dc8bfead]
- Fixed cmd cloud error message [14d603b9]
- Fixed RejectedExecutionException on successive Console executions #906
- Fixed Invalid config rendering #801
- Fixed Invalid warning message for config selector #905
- Fixed Queue status command fail on LSF version 8 #910
- Fixed Use `bash` instead of `sh` to fetch queue status
- Improved script runner api [da4a6c17]
- Improved file hashing logging [0d35b2b4]
- Refactored ScriptRunner class [15ee2f1c]
- Refactored DSL code visitor [67904c1f]
- Revert "Apache Ignite to version 2.6" #909
- Better report warning when grid status command fails [3ac8b972]
19.01.0-edge - 10 Jan 2019
- Enhanced timeline and execution reports #985 #986 [fb00c3a6] [092f0b9e]
- Enhanced BashWrapperBuilder using template file [7d7e116a] [c62b9dff]
- Fixed CPU usage accounting #982 [7d7e116a] [c62b9dff]
- Fixed Move output files to storeDir instead of copying them #745
- Fixed Interpolated strings in a from statement are misinterpreted #978
- Fixed Launcher fails with Java 10 or later #953
- Fixed LSF long user names breaks jobs status parsing [b4306151] #988
- Fixed Memory unit should contain thousand separator [e6ec4c84] #989
- Fixed Allows fromFilePairs to handle non globs #946
- Added an env variable to define default cloud driver #973
- Added countLines, countFasta and countFastq methods #972
- Added NXF_DIST launcher variable #954
- Added NXF_SMOKE var to disable long running tests
- Deprecated groupBy and route operators [b7ca53d2]
- Updated S3 storage classes #977
- Updated groovy to version 2.5.5
- Updated copyright disclaimer
- Refactored project structure [516294e7]
- Speed-up CI tests [3320dcec]
18.12.0-edge - 18 Dic 2018
- Add Google Cloud Platform integration
- Added support for K8s nodeSelector #955
- Added new AWS regions #935
- Added json/yaml output to info command #657
- Fixed remote bin directory when using buckerDir option [6d796783]
- Fixed foreign file system detection [1489cc72]
- Fixed Ansi logger division by zero [ae2b1380]
- Fixed Unparseable Data format on http file #962
- Fixed Log command history #405
- Fixed Too long process tag name can cause SLURM failure #941
- Fixed LSF can return an inconsistent jobs status #927
- Fixed dump last queue status on failure [36e80242]
- Fixed Allow the usage of a custom docker image for K8s driver pod #877
- Fixed K8s executor when the cluster has no available cpus #824
- Fixed Prevent duplicate process definitions #920
- Fixed Update queue statuses used by PBS Pro #908
- Fixed K8s launcher fails to set pod work directory [dc8bfead]
- Fixed cmd cloud error message [14d603b9]
- Improved script runner api [da4a6c17]
- Revert "Apache Ignite to version 2.6" #909
- Fixed Invalid config rendering #801
- Improved file hashing logging [0d35b2b4]
- Refactored ScriptRunner class [15ee2f1c]
- Refactored DSL code visitor [67904c1f]
18.11.0-edge - 12 Nov 2018
- Added More duration and memory unit syntax sugar #921
- Added NO_PROXY env variable should be honoured #864
- Added keepHeader option to splitText operator #912
- Fixed Invalid warning message for config selector #905
- Fixed Queue status command fail on LSF version 8 #910
- Fixed Use `bash` instead of `sh` to fetch queue status
- Better report warning when grid status command fails [3ac8b972]
- Fixed RejectedExecutionException on successive Console executions #906
18.10.1 - 24 Oct 2018
- Fixed test [011e8e23]
- Fixed version number check [fb780347]
18.10.0 - 24 Oct 2018
- Added lenient cache mode #828 [ba907a2f]
- Added support for java 11 [60da50b5]
- Added support for Singularity 3.0 library #898
- Added support for AWS Batch hybrid executions #744
- Added weblog JSON format docs #882
- Added weblog example documentation #891
- Added PbsPro executor [33ae1104]
- Added support for ANSI console logging [9c14a947]
- Fixed License prevents scientific use #788
- Fixed process submitter slow-down [495e900a]
- Fixed Comparing duration and memory units with null throws an exception #872
- Fixed Html format dag fails when 'each' qualifier is used #887
- Fixed Collate/Buffer hangs with one emission after Collect operator #868
- Fixed Option checkIfExists should be applied when a glob pattern does not match any file #874
- Fixed Add name to manifest and reject other attributes #871
- Fixed warning message grammar when resuming on new project #885
- Fixed Missing DSL Xform transformation in console execution [9621f8c6]
- Fixed Enum declared in nextflow script causes error #878
- Fixed Report a warning message when queue status fetch fails [39aae6a2]
- Fixed Pbs executor may return nonzero exit code when checking queue status #904
- Renamed weblog `runStatus` to `event` #892
- Renamed K8s config attribute userDir to launchDir #895
- Merged tests as subtree [a03eb59a]
- Refactored service discovery
- Removed FastXxxYyyyStream
- Demoted igfs subsystem
- Upgraded Groovy to version 2.5.3 [119300b3]
- Upgrade Gradle to version 4.10
- Updated AWS batch docs
0.32.0 - 8 Aug 2018
- Fixed CPU usage metrics can be wrongly reported #858
- Fixed Allow a process to access input file metadata #731
- Fixed Completed jobs are detected with a big delay #799
- Fixed Misleading message is shown when pulling a project with a invalid config #863
- Fixed Allow groupTuple operator to handle multi-size tuples #796
- Fixed Ignite executor fills up logs when node is disconnected #810
- Fixed Log filter option is misinterpreted when enclosed in double quotes #846
- Fixed Metrics collector process may cause the main process to report a false non-zero exit status #836
- Fixed K8s imagePullPolicy is not included in the pod spec #815
- Fixed Splitter caching is too eager when caching path is specified #835
- Fixed Improve error message for missing git provider configuration #847
- Fixed Byte hashing is never reached in CacheHelper class 9ac81153
- Fixed K8s launcher should not delete pod when `login` command fails (5175942a)
- Fixed Dump operator should nicely print ArrayBag content (91e371ba)
- Added manifest data in workflow metadata object #841
- Added support for K8s imagePullSecrets pod attribute #800
- Added option "checkIfExists" to Channel.fromPath method #666
- Upgraded Apache Groovy to version 2.5.1
- Upgraded Apache Ignite to version 2.6
- Upgraded Slf4j to version 1.7.25
- Upgraded Logback to version 1.1.11
- Upgraded Grengine to version 1.3.0
- Upgraded LevelDB to version 0.10
- Upgraded Guava to version 21.0
- Upgraded Spock to version 1.2
- Using javax.activation:activation:1.1.1 (from com.sun.activation:javax.activation:1.2.0)
0.31.1 - 7 Aug 2018
- Fixed AWS Batch execution hangs when running on 1 cpu machine #825
- Fixed AWS Batch fails if process tag length is too long #822
- Fixed AWS Batch executor creates timeline report with missing time data #816
- Added Ignite failure detection timeout configuration parameters #820
- Added VersionNumber class to CacheHelper handler [90fb69fa]
- Added CONTRIBUTING file #564
0.31.0 - 25 Jul 2018
- Fixed CLI parameter value starting with a `-` is misinterpreted #808
- Added keep-logs option to clean command #775
0.31.0-RC1 - 19 Jul 2018
- Fixed K8s pod request should include resources spec when 1 cpu is specified #806
- Fixed PBS executor should fail when submit response contains invalid data #753
- Fixed SLURM executor fail to submit jobs when cluster option is specified #805
- Fixed Allow the use relative paths for symlinks process input files #296
- Fixed AWS batch jobs are not properly stopped when execution is interrupted #782
- Fixed splitCsv is not properly handling blank lines #795
- Fixed K8s pod runAsUser definition #707
- Fixed Prevent NPE when K8s reports an empty pod state [dcc7ec5f]
- Fixed Allow list of patterns for fromPath and fromFilePairs channel factories #732
- Fixed K8s execution hangs if an invalid pod secret file is specified #754
- Fixed Correctly shutdown executor service #732
- Fixed bug in dot rendering due to unquoted graph name when DOT language keyword used #783
- Fixed Execution hangs if one or more inputs evaluate to null #764
- Fixed Method `file` should thrown an error null is given as input #765
- Fixed invalid relative link resolution with `readlink`
- Added AWS batch requests throttling handling #710 #709
- Added AWS Batch parallel downloads/uploads [codefest] [8ba1716b,ba5ad7a8]
- Added K8s pod config and security context definition #707
- Added Container env variables whitelist #803
- Added support for K8s pod labels #762
- Added support for K8s volume mount subPath #758
- Added Nextflow required version in the config manifest #752
- Added disk resource requirement in LSF executor #747
- Added GA4GH TES executor [experimental] #794
- Added System info to workflow metadata object #759
- Added weblog feature #681
- Deprecated process.$name syntax to define process specific settings #713
- Upgrade to Gradle 4.9
0.30.2 - 16 Jun 2018
- Fixed Output declarations with a glob pattern fail when AWS Batch executor is used #748
- Fixed Scratch directive not working for AWS Batch executor #740
- Fixed K8s launcher does not parse remote config files #738
- Minor refactoring to enable Groovy 2.5 compilation 20b6d933 a8b994f1
0.30.1 - 11 Jun 2018
- Use a daemon thread for watchPath method #735
- Fixed Gitlab API v3 has been deprecated and does not work any more #734
- Fixed Unable to access params defined in the top scope from a nested profile #733
- Fixed Process config selectors do not work when the config is included #729
- Fixed Improve the error message when a missing property is used in the config file #730
- Added Travis build support for jdk10
- Added documentation for `until` operator #736
- Added mailer recipients check
- Increased Singularity pull timeout to 20 minutes
- Updated build to Gradle 4.8
0.30.0 - 5 Jun 2018
- Added the support for Bioconda #493
- Added support for AWS Batch job timeout #648
- Added jobs submit rate limit #198
- Added offline option #665
- Enabling Java 9/10 support for build and launcher scripts #674
- Fixed Expose Kubernetes Secrets to worker pods #651
- Fixed K8s execution hangs when a non-existing docker image is specified #697
- Fixed K8s execution terminates abruptly if a pod requires more resources than available ones #676
- Fixed K8s executor does not report command log when a task fail #699
- Fixed Configuration profile is not handled properly by the kuberun command #696
- Fixed Enhance process metrics to avoid usage of ps tool #499
- Fixed PublishDir should use copy mode by default when the target is a S3 path #718
- Fixed Unbounded variable breaks task launcher script #722
- Fixed Escape filenames when copying from S3 #717
- Fixed AWS executor should use putObject API to upload job scripts to S3 #712
- Fixed Exception is thrown when an output folder contains a circular symlink path #701
0.29.1 - 10 May 2018
- Fixed Default ext property are not included in process context #673
- Fixed Operator concat throws a ConcurrentModificationException #675
- Fixed Output file is not recognised when it's created into a subdir and the name matches an input #688
- Fixed Empty container definition being ignored when default one is specified #691
- Fixed K8s client fails to connect the cluster when client key nor certificate is specified #692
- Fixed K8s executor hang on pod creation failure
- Added select in -R for memory for LSF executor #683
0.29.0 - 24 Apr 2018
- Fixed Buffer operator fails to recognise optional parameter when a closing condition is specified #652
- Fixed PublishDir mode "copyNoFollow" does not work for directories #658
- Update NameGenerator adjectives #656
0.29.0-RC1 - 8 Apr 2018
- Added `containerOptions` directive #415
- Added support for multiple `publishDir` directives for process #256
- Added cleanup feature to delete workflow work dir on completion #649
- Added label directive and process configuration selectors `withLabel` and `withName` #623
- Fixed Invalid process cache when using a different environment module #627
- Upgrading groovy runtime to version 2.4.15
0.28.2 - 6 Apr 2018
- Fixed Class FtpURLConnection is not accessible when using Java 9 #646
- Fixed Lengthen mktemp TEMPLATE so works on BusyBox #647
- Fixed Report HTML/CSS tweaks to make progress bar text overflow work properly #645
- Fixed typo in the nextflow launcher #643
0.28.1 - 27 Mar 2018
- Fixed A HTTP access error is raised when the URL contains a ? character #634
- Fixed Creation of temp files in the /dev/shm directory can result in a permission
error in some Linux installations #638
- Make process echo safer
0.28.0 - 10 Mar 2018
- Fixed Singularity pull is executed even when container execution is disabled #628
- Fixed issue when setting container attribute to `false` [9de636c5]
- Added MemoryUnit getters [f99d2dc9]
- Added default NXF_TEMP variable [d36ac4dd]
- Added progress stacked bars to workflow report #534 [455fcb4f]
- Added namespace option to `kuberun` command [50154ec5]
- Improved workflow stats and warn report [e795b134]
- Improved K8s error reporting [86f172eb]
0.28.0-RC1 - 27 Feb 2018
- Added support for directory wildcards in input file declarations #568
- Added ability to access task existStatus value as an output value #577
- Added ability to use property syntax in the declaration of output values #578
- Added NXF_JAVA_HOME variable to specify nextflow nextflow JVM #607
- Added support for docker mount flags #572
- Added ability to select multiple configuration profiles #370
- Added ability to copy symlinks to publishDir directive #592
- Added missing native_id TraceRecord field to K8s and AWS Batch task handlers
- Enhanced support for Kubernetes #468
- Fixed Launcher breaks when JAVA_HOME path contains a blank char #616
- Fixed Operator toList hangs when applied to a value channel #612
- Workflow report should warn if some task executions were ignored #534
- Enable support for large execution reports #547
- Replaced the use of named pipes with anonymous pipes #606
- Enhance the config command show dynamic attributes #604
- Fixed bin path is not recognised when contains a blank char #603
- Fixed A NPE exception is thrown when a env variable is assigned to an null value #593
- Fixed summary stats when for empty series #547
- Removed support for Extrae #588
- Removed support for DRMAA #587
0.27.6 - 19 Feb 2018
- Fixed Operator toList hangs when applied to a value channel #612
- Allow launcher to track installation verb
0.27.5 - 15 Feb 2018
- Fixed dir/* input file pattern invalidate cached processes #610
- Fixed Mail attachment are not correctly recognised by the email client #609
- Fixed Workflow metadata container attribute is not resolved when it's defined dynamically #602
0.27.4 - 5 Feb 2018
- Fixed Resume does not work for tasks successfully executed in a re-submit attempt #591
- Fixed An error is reported when a NF script contains a class definition #594
- Fixed Launcher error when download target path contains a blank character
0.27.3 - 29 Jan 2018
- Fixed publishDir directive fails on S3 when attempting to copy objects larger than 5 GB #585
- Process name does not reflect dynamic tag declaration when a task execution is retried #586
- Fixed examples in the documentation
- Update to Gradle 4.5
0.27.2 - 23 Jan 2018
- Fixed Config property keys may contain invalid characters
- Fixed Local process kill signal is not propagated to children processes #581
- Fixed Operator join throws a stack overflow exception when an invalid argument type is specified #582
0.27.1 - 18 Jan 2018
- Fixed Invalid cast exception when cpus value is missing #575
- Fixed Kill the tee commands when the launcher script exit #574
- Fixed Splitter `limit` option is not honored when splitting more than one file #573
- Fixed AWS CLI operations with S3 should use the --only-show-errors options #567
- Fixed Splitter by option is not honored when splitting more than one file #570
- Documentation editing/improvement
0.27.0 - 9 Jan 2018
- Fixed Log command prints true instead of actual message #561
- Fixed NXF_TEMP definition when instanceStorageMount is set
- Improved S3 exitfile logging
- Improved cloud config canonical formatting
0.27.0-RC2 - 29 Dic 2017
- Fixed Ignore Windows instances from AWS cloud price listing
- Fixed AWS price reader catching unexpected errors
- Fixed sendMail access to owner variables
- Fixed NPE when creating task with ignite executor
- Fixed null exit status in notification template #554
- Added XPath serialiser
- Added mail smtp proxy configuration #375
- Added built-in notification documentation #554
- Added built-in mail documentation #375
- Added support for Syslog logging #330 #557
- Improved support for AWS EC2 instance storage #558
- Improved documentation #558
- Improved config command adding `-flat` and `-properties` formats and using canonical curly brackets format as default
- Update copyright info
0.27.0-RC1 - 20 Dic 2017
- AWS Batch increased queue to 1000 tasks and poll interval to 10 secs
- AWS Batch improved executor scalability caching recurrent API call and batching similar requests together
- Added notification message on workflow completion #554
- Added Built `sendMail` function #375
- Added Warning message when a local version on a GH repo is different from remote #376
- Added keepHeader option to collectFile #479
- Added Dump operator to enable easier debugging #517
- Fixed Report an error message when a config file contains an unresolved attribute #525
- Fixed Session working file system not defined when staging input files with Ignite executor #555
- Fixed storeDir writes output files even when process fails #227
- Fixed storeDir does not work with S3 targets #247
- Fixed Config file available in introspection #264
- Fixed Enhance container interoperability between Docker and Singularity #503
- Fixed Process environment is not exported in the container context when a process uses an interpreter other than BASH #495
- Deprecated support for executable containers #529
- Deprecated DRMAA executor #488
- Deprecated Extrae profiling #543
- Renamed .command.run.1 to .command.stub #523
0.26.4 - 11 Dec 2017
- Fixed GitLab auth token is not applied when user credentials are not provided #542
0.26.3 - 30 Nov 2017
- Fixed AWS Batch S3 upload function does not work if output is a directory #539
- Fixed AWS Batch S3 uploaded function does not resolve glob patterns containing curly brackets #535
- Added author field in the config manifest scope #537
- Upgrading s3fs library to 1.0.2 version supporting `signerOverride` S3 config property.
0.26.2 - 27 Nov 2017
- Fixed readlink illegal option when installing in macOS #527
- Fixed Getting not descriptive error when using a when condition and script statement is not explicit #528
- Fixed Function nxf_module_load matches partial names #530
0.26.1 - 17 Nov 2017
- Execution report enhancements #521
- Fixed Add AWS_DEFAULT_REGION environment variable to bash wrapper scripts #512 #513
- Fixed New launcher script does not allow the execution of legacy version with Java 7 #519
- Fixed Error message reporting file name collision is misleading #516
0.26.0 - 8 Nov 2017
- 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
0.26.0-RC2 - 30 Oct 2107
- 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
0.26.0-RC1 - 24 Oct 2017
- 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
0.25.7 - 6 Sep 2017
- Fixed Unable to parse the AWS price list API #444
- Added seed parameter to `randomSample` operator #410
0.25.6 - 13 Aug 2017
- Fixed Empty channel waiting forever when viewed and mixed #428
- Fixed Error Channels cannot be used as input in more than one process or operator #429
- Fixed Script body is resolved even if the `when` guard evaluate to false
- Added queue process directive as option for trace file
0.25.5 - 4 Aug 2017
- Fixed NF fails to pull images hosted in the Singularity Hub #414
- Added `-y` to cloud create command to skip confirmation request
0.25.4 - 31 Jul 2017
- Removed invalid debug information
0.25.3 - 31 Jul 2017
- Fixed NPE when parsing AWS price file #408
- Fixed Grid queue status return wrong data when a process change the submission queue dynamically #412
- Fixed MPI-like execution for SLURM batch scheduler
- Fixed NPE when log params key is not defined
- Fixed Optional parameter for set #399
- Added automatic pull for Singularity remote images #356
- Added London and Canada AWS regions
- Merged Pass NXF_OPTS to JVM during the java version check to allow memory definition on memory-restricted environments #411
- Improved error message in launcher file
0.25.2 - 3 Jul 2017
- Fixed Execution hangs if a job submission fail #396
- Fixed stdout can not be sent into multiple channels #388
- Fixed Pipeline execution hangs when a process exceed the time limit and retry error strategy is used #387
- Added scientists and adjectives to run name generator
- Deprecated `route` operator
0.25.1 - 27 Jun 2017
- Duplicate mount point docker error #384
- Disable Docker read-only mounts by default
0.25.0 - 26 Jun 2017
- 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 deserialization 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 and toLong converter operators
- 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
0.24.4 - 19 May 2017
- Fixed PublishDir creates nested directory structures when a folder already exists #342
- Fixed NoSuchFileException is thrown when trace file path does not exist #334
- Fixed watchPath glob directory not working #335
- Fixed Channel.fromFilePairs does not handle properly multiple star wildcards #337
- Added executor for NQSII, queuing system used on NEC clusters.
- Added `relative` option to `fromPath` channel factory
0.24.3 - 24 Apr 2017
- Fixed Process execution fails with not GNU version of sleep and date tools #321
- Fixed Pending processes are not cleaned up properly #322
- Fixed NPE is thrown when Singularity is enabled and a process uses no container #324
- Fixed Cached processes are not included in the timeline report #325
- Added MD5 digest file upload
- Updated docs
0.24.2 - 5 Apr 2017
- Fixed Tuple array object deserialisation fails #317
- Use SLURM squeue —-noheader instead -h command line option to support not standard implementation #316
- Fixed Execution time is incorrect for the local executor #313
0.24.1 - 24 Mar 2017
- Fixed Improve explanation of cache DB IOException #303
- Fixed Operator ifEmpty results in a error when applied to a dataflow variable #308
- Fixed Process execution fails when the work path contains a parenthesis character #310
- Fixed Installer script fails when current path contains a blank character #311
- Fixed Include SLURM partition when checking job status #312
- Allow the usage of `close` operator on unbounded dataflow variable
0.24.0 - 20 Mar 2017
- Added new `combine` operator #298
- Added new `collect` operator #297
- Added new CLI option `-params-file` to load parameters from a json/yaml file #208
- Fixed SCM user name is not set accessing private repository #300
- Fixed Infer singleton process outputs from inputs declaration #301
- Fixed Use exit status 1 for all NF errors #304
- Fixed Invalid SGE job name as defined in `sge_types` #299
- Added `skip` parameter to collectFile operator #306
- Added experimental `fs` command
- Improved file staging error reports #295
- Upgraded Groovy to version 2.4.10
0.23.4 - 24 Feb 2017
- Fixed Show a warning message when accessing undefined parameters #293
- Fixed Staging input files in a subfolder changes their names when they are symlinks #292
- Fixed NPE accessing foreign files
- Added column char to list of path escaped chars
- Fixed Boothook script fails on Ubuntu 16.04
0.23.3 - 9 Feb 2017
- Fixed Job termination is not recognised if the starter file is not created #268
- Fixed Allow NF console to resume process executions (second take) #280
- Fixed PublishDir may throw a FileAlredyExistsException #283
- Increased logger file appender buffer size to 64kb
- Updated Logback to version 1.1.10
- Updated copyright info
- Fixed NXF_DEBUG level
0.23.2 - 2 Feb 2017
- Improved history lock error message
- Fixed typo in warning message
- Added `cleanup` to list of accepted directives
- Added NXF_OWNER to kubernetes executor
- Fixed Function nxf_kill is not invoked properly on a containerised process #275
- Fixed Pending grid jobs are not cancelled upon pipeline interruption
- Documented that the toSortedList operator can accept a comparator closure #277
0.23.1 - 23 Jan 2017
- Fixed FixOwnership flag break non BASH scripts/templates #270
- Fixed Fixed PBS Executor should not have parenthesis #271
- Fixed Function nxf_kill is not invoked properly on process termination #275
- Fixed Timeline.html is not working on IE11 #272
- Fixed Merge process specific extended properties with the ones defined in the default scope #273
- Fixed Using storeDir and publishDir in the same process yields unexpected results #266
0.23.0 - 13 Dec 2016
- Added support for Singularity containers #252
- Added support for HTTP/S and FTP files (read-only)
- Fixed stream close leak while copy foreign file to local file system
- Fixed Task scheduling may hang while checking for job completion #261
- Fixed Specifying the keyFile cloud config attribute result in an error #263
- Added support for multiple target channels in `tap` operator #255
- Added `uri` property to Path and File objects
- Made NXF_SCRATCH variable accessible to `beforeScript` handler
0.22.6 - 4 Dec 2016
- Fixed Script execution terminates before all operators complete #259
- Fixed A script variable with the same name of a global variable invalidate process resume #254
- Fixed `when` is not recognised when used before an `input` and `script` is not declared
- Fixed count operator hung when applied to a dataflow variable
- Added warning message when an input/output `set` defines only one component #216 #251
- Reduced log verbosity of Ignite Scheduler classes
0.22.5 - 17 Nov 2016
- 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
0.22.4 - 4 Nov 2016
- 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
0.22.3 - 12 Oct 2016
- 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
0.22.2 - 3 Oct 2016
- 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
0.22.1 - 26 Sep 2016
- 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
0.22.0 - 19 Sep 2016
- Fixed queue-size attribute for local executor
- Fixed Kubernetes pod id parse issue
- Move `.nextflow.history` and `.cache` files under `.nextflow` directory
0.22.0.RC2 - 12 Sep 2016
- 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 - 1 Sep 2016
- 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
0.21.3 - 26 Aug 2016
- Fixed Spaces in work directory path stops slurm from accepting the job #218
0.21.2 - 12 Aug 2016
- 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
0.21.1 - 29 July 2016
- 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
0.21.0 - 20 July 2016
- Fixed Command line params do not override params defined in the nextflow.config file #202
0.21.0-RC1 - 14 Jul 2016
- 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
0.20.1 - 18 Jun 2016
- 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
0.20.0 - 8 Jun 2016
- 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
0.19.4 - 3 Jun 2016
- Fixed Exception is thrown while reporting an invalid output declaration #170
0.19.3 - 31 May 2016
- Fixed Local executor does not run an job when host cpus == 1 #166
0.19.2 - 26 May 2016
- 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
0.19.1 - 19 May 2016
- 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
0.19.0 - 18 May 2016
- 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
0.18.3 - 9 May 2016
- Fixed Timeline report no longer works in Safari #143
- Fixed Invalid or corrupt jarfile if your CTRL-C initial run of nextflow #145
- Fixed Pipeline execution hangs when the into declaration is not provided #146
0.18.2 - 3 May 2016
- 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
0.18.1 - 26 Apr 2016
- 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.
0.18.0 - 11 Apr 2016
- Added `legacy` option to docker configuration properties.
Added support for `--cpuset-cpus` Docker command line option. See #115
- Added `region` option to AWS S3 config properties #116
- Added support for AWS S3 multipart uploads #112
- Added `NXF_TRACE` to enable application trace logging
- Added experimental support for Shifter containers
- Added experimental support for HTCondor scheduler
- Fixed Input file names staged into a subdirectory are not expanded properly #111
- Fixed Main script class name collides with variable names in global scope #113
- Fixed config file having a name as a top level config options raise a MissingPropertyException #117
- Fixed Process script errors should not be ignored #119
- Fixed timeline margin for long labels - fix #120
- Fixed Process `start` time is not reported correctly when using the Ignite executor #122
- Fixed Allow for a per-job memory limit for LSF executor #123
- Fixed Memory reservation should not be divided by the number of cpus #124
- Fixed Mixed content errors if timeline.html served over HTTPS #127
- Fixed Nextflow won't start if a proxy URL env variable contains a trailing slash #109
- Set poolSize as the number of avail cpus