forked from nextflow-io/nextflow
-
Notifications
You must be signed in to change notification settings - Fork 0
/
changelog.txt
3854 lines (3555 loc) · 187 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
===================
24.09.2-edge - 14 Oct 2024
- Add Google LS deprecation notice (#5400) [0ee1d9bc]
- Add hybrid workflow documentation for Azure (#5361) [f81f27de]
- Add more out formats to config command (#5399) [8acdb6e8]
- Change to scan.levels to scan.allowedLevels (#5401) [88a1b1b5]
- Fix inspect concretize option [0ee29a87]
- Manage moduleBinaries feature flag in the pipeline script (#5348) [dd5fd20f]
- Bump [email protected] [94273967]
- Bump [email protected] [fab01d58]
24.09.1-edge - 13 Oct 2024
- Add retry policy in Channel.fromSRA factory (#5389) [fb1c8b2e]
- Add retry policy to Google batch describe task (#5356) [64bb5a92]
- Add support for Wave container status API (#5384) [873703ad] [9ed18a88]
- Fix Identify default git branch when downloading pipelines (#3593) (#5375) [4f74fc37]
- Fix issue when retrying with stub (#5359) [324b611f]
- Fix include aborted in the ProgressRecord total count (#5365) [8eb0c393]
- Redirect logs to stderr during app bootstrap (#5206) [94918105]
- Remove unused reportsOpts (#5379) [e794e868]
- Sunsetting Spack support in Wave [3a54cb3b] [7bbba67b]
- Bump [email protected] [4204435e]
- Bump [email protected] [cdecb3f5]
24.09.0-edge - 2 Oct 2024
- Add Fusion version pinning info to Fusion config scope (#5294) [be1cac37]
- Add container tip in the task error report (#5299) [62e26043]
- Add support for Java 23 (#5329) [6e10c372]
- Add Platform workflow prefix in AWS Batch job names (#5318) [42dd4ba8]
- Fix AWS spot attempts with zero value (#5331) [bac2da12]
- Fix Azure Fusion env misses credentials when no key or SAS provided (#5328) [e11382c8]
- Fix CI build taking only the commit msg header [9e702c4d]
- Fix Inconsistency with camelCase and kebab-case config params #4702 (solve #4033) [349f4f6f]
- Fix XPath default de-serializer issue (#5339) [290f2d07]
- Fix failOnIgnore causes task monitor to stop submitting tasks (#5293) [d6870335]
- Fix large mermaid diagrams (#5302) [a46edfa0]
- Improve Wave build timeout handling (#5304) [05bef7e4]
- Include additional fields to manifest (#5314) [33fab52d]
- Remove `mini` from Flux submit command (#5229) [a0f69025]
- Update container handling with charliecloud (#5300) [8e6068db]
- Update Documentation structure (#4766) [25e5eba0]
- Update nextflow install docs (#5198) [7c453815]
- Bump groovy 4.0.23 (#5303) [fe3e3ac7]
- Bump [email protected] [179093dc]
- Bump [email protected] [41d37fa8]
- Bump [email protected] [e38980fb]
24.08.0-edge - 4 Sep 2024
- Add Google Batch warning when for conflicting disk image config (#5279) [96cb57cb]
- Add support for Google Batch used specified boot images (#5268) [0aaa6482]
- Disable AWS spot retry (#5215) [f28fcb25]
- Disable Google Batch automatic spot retries (#5223) [aad21533]
- Disable automatic detection of virtual threads (#5270) [b3ba2c2d]
- Fix missing .command.env when eval is used and task runs on a cloud env [4a6b54aa]
- Fix job array syntax for PBS/Torque executor (#5281) [d59f5fae]
- Fix k8s client status cond is possible null in podState (#5264) [46672415]
- Fix non-determinist behaviour of join operator with bag array as key (#5189) [e7dc0d69]
- Fix stage retry on corrupted HTTP downloads (#5275) [bf0cd326]
- Support Azure Managed Identities in Fusion configuration logic (#5278) [a0bf8b40]
- Use public.cr.seqera.io in place of AWS ECR [5a01f277]
- Wave client logs improvement [5a37e617]
- Bump amazoncorretto:21-al2023 [59aed581]
- Bump [email protected] [97c4e08f]
- Bump [email protected] [24133f2a]
- Bump [email protected] [29f49ba7]
- Bump [email protected] [bbc3adca]
24.07.0-edge - 8 Aug 2024
- Add runtime error for missing channel factory (#5170) [1f9210ab]
- Apply k8s.cpuLimits to kuberun driver pod (#5160) [4300adf1]
- Await build completion for all Wave containers [2b8117e9]
- Deprecate module addParams() and params() (#5200) [82c97f8c]
- Remove capsule launcher dependencies (#3395) [f15e4246]
- Fix AWS Cloudwatch access when using custom log group name [30195838]
- Fix Invalid AWS Fargate CPUs usage error reporting [d9c50e59]
- Fix Prevent AwS Batch retry the job execution when the container does not exist [4e218f22]
- Fix Prevent negative cpus values [af2e4ef7]
- Fix ProcessUnrecoverableException detection [17ec6c96]
- Fix aws logs group name (#5146) [643b16b0]
- Fix readAllBytes with http files (#5202) [7e90ce62]
- Improve Google Batch 5000x error class handling (#5141) [61b2205f]
- Improve docs [7703f0d0]
- Improve error message for topic channel feature flag (#5161) [c4d407fb]
- Improve fusion docs (#5166) [abdd78f1]
- Improve queue docs (#5154) [bc2fb409]
- Improve version checking [e7a879de]
- Link to other docs on the failOnIgnore option (#5122) [572f2116]
- Make Google Batch auto retry codes configurable (#5148) [e562ce06]
- More robust parsing of shm-size containerOptions (#5177) [b56802a3]
- Prevent default output/error logs for job arrays (#5152) [71f6ed0b]
- Bump amazon sdk to version 1.12.766 [cc6ec314]
- Bump gradle 8.9 [a437e97f]
- Bump jgit 6.10.0 [177dc474]
- Bump [email protected] [46c69d77]
- Bump [email protected] [26dcb604]
- Bump [email protected] [c171b601]
- Bump [email protected] [d7dd4611]
- Bump [email protected] [c1175157]
- Bump [email protected] [1eda221a]
- Bump [email protected] [257bebfd]
- Bump [email protected] [e8d643c2]
- Bump pf4j to version 3.12.0 [96117b9a]
- Bump wave-api to 0.11.1 [96ec4ded]
24.04.4 - 1 Aug 2024
- Fix parsing of shm-size containerOptions (#5177) [98cf0068]
- Fix aws logs group name (#5146) [b2ab651c]
- Update Azure batch deps [72576648]
- Bump [email protected] [19a7272f]
- Bump [email protected] [f2bcce99]
- Bump [email protected] [0ea1f102]
- Bump [email protected] [b13b5548]
- Bump wave-api to 0.11.1 [87828afd]
- Bump amazon sdk to version 1.12.766 [5ce42b79]
- Bump pf4j to version 3.12.0 [1a8f086a]
- Bump jgit 6.10.0 [cc2ccd81]
23.10.4 - 31 Jul 2024
- Add docker launcher [474427a5]
- Update Azure batch deps [e0c6d77d]
- Bump [email protected] [54683615]
- Bump [email protected] [084092f1]
- Bump [email protected] [de43b17e]
- Bump amazon sdk to version 1.12.766 [189f58ed]
- Bump pf4j to version 3.12.0 [8dfa4076]
- Bump jgit 6.10.0 [4cf6b9f7]
24.04.3 - 9 Jul 2024
- Add ability to override failOnError setting default via env variable (#5117) [6852429c]
- Fix normalization of consecutive slashes in uri path (#5114) [3f366b7e]
- Fix executions hangs on finalisation exception (#5070) [4c207c23]
- Bump [email protected] [55ec5ec5]
24.06.0-edge - 8 Jul 2024
- Add ability to override failOnError setting default via env variable (#5117) [72d78425]
- Add retry options to Azure Blob client (#5098) [7d5e5d2b]
- Add support for HyperQueue 0.17.0 or later [BREAKING] [b45f7c48]
- Adds example of error strategies to documentation (#5121) [e82b0dee]
- Fix docs for `failOnDuplicate` and `failOnMismatch` (#5113) [7d5c4824]
- Fix normalization of consecutive slashes in uri path (#5114) [18ec484f]
- Update Azure VMs and regions for 2024-07-01 (#5100) [12b027ee]
- Bump Fusion 2.4 (#5080) [0a8a484e]
- Bump Groovy 4.0.22 [284a6606]
- Bump [email protected] [28122b70]
- Bump [email protected] [a1c2a814]
- Bump [email protected] [a3dfba54]
- Bump amazoncorretto:17-al2023 to Dockerfile [5e03a7b7]
24.05.0-edge - 17 Jun 2024
- Add Managed Identity to Azure authentication documentation (#5062) [ab5b3eb2]
- Add support for Azure managed identity (#4897) [21ca16e6]
- Add support for EC-encrypted private keys for K8s executor [4dbb5193]
- Add workflow.failOnIgnore config option (#4686) [172edc38]
- Allow requester pays for S3 buckets (#5027) [0070c1b0]
- Dump threads on abort condition [e3740977]
- Enable build with Java 21 (#5030) [4c54db6a]
- Fix Azure system-assigned managed identity [a639a17d]
- Fix Java 22 version in launcher [29d6f1df]
- Fix executions hangs on finalisation exception (#5070) [38434b82]
- Fix support for Azure managed identity clientId [306814e7]
- Fix support for s5cmd 2.2.2 (#5069) [7e78bd4d]
- Fix the cleanup of local secret file (#5061) [e28537ca]
- Fix typo in error message [f5c2355b]
- Fix unique operator hangs when applied to value (#5053) [88b8ab0c]
- Improve retry strategy for Google cloud errors when writing task helper files (#5037) [f8b324ab]
- Remove GA4GH plugin (#5056) [0471b2e1]
- Remove ending slashes for publish targets [891ed117]
- Bump Gradle 8.8 final [ee54606c]
- Bump aws-sdk 1.12.740 [acad2a1f]
- Bump azure-compute-batch:1.0.0-beta.2 [c08dc49b]
- Bump azure-storage-blob 12.26.1 [c76ff5e7]
- Bump [email protected] [01922f13]
- Bump [email protected] [c064d209]
- Bump [email protected] [eeca7d67]
- Bump [email protected] [d3f53c19]
23.10.3 - 11 Jun 2024
- Bump [email protected] [6960daab]
- Bump [email protected] [fbd3c1b4]
- Bump [email protected] [f5b95820]
- Fix security vulnerabilities (#5057) [6d8765b8]
24.04.2 - 29 May 2024
- Fix handling of tags with slash on Bitbucket (#5031) [76cd305f]
- Fix the default for async finalizer (#5013) [f5fba709]
- Fix the invocation of function with gstring (#5020) [04317f0d]
- Fix escapes dollar char in local secret provider (#5021) [d8f8bf56]
- Improve Charliecloud registry handling (#5018) [42496dbc]
- Enable the use of Java 22 (#4970) [cbf24f9b]
23.10.2 - 28 May 2024
- Update Platform API endpoint (#4855) [04cedce0]
- Fix semaphore in parallel polling monitor (#4927) [d173ceab]
- Fix security vulnerabilities (#5014) [a28b404c]
- Bump [email protected] [3852dd1e]
- Bump [email protected] [d692711b]
- Bump [email protected] [b48a1423]
- Bump [email protected] [911c1624]
- Bump [email protected] [9d6b64c3]
- Bump [email protected] [f43964f8]
- Bump [email protected] [fb9059c7]
- Bump [email protected] [8c398620]
- Bump [email protected] [1d3726db]
24.04.1 - 20 May 2024
- Fix nf-google plugin dependency [725e2860]
- Fix nf-amazon plugin dependency [c234b09f]
- Bump [email protected] [633989a6]
- Bump [email protected] [e31f70e0]
24.04.0 - 20 May 2024
- Add 'preview' to workflow runtime metadata (#4985) [935bb1e5]
- Add enabled property to output dsl (#5008) [284415b1]
- Fix Taskbar API is not supported error [0ea09ccc]
- Fix inspect should not write history entry [c713ad51]
- Fix unexpected container resolution [a5ecf8a4]
- Improve icon loading error handling [c72e16f8]
- Remove Fusion symlink resolution (#5004) [071ea74c]
- Remove `seqera` and `defaults` from Conda default channels (#5003) [ec5ebd0b]
- Use protected visibility for updateStatus method [6871ba06]
- Workflow output definition (#4784) [cf0546b1]
- Bump Fusion 2.3 (#5005) [7176c113]
- Bump groovy-console 4.0.21-patch.2 [eb97831f]
- Bump [email protected] [96ee633d]
- Bump [email protected] [e8359042]
- Bump [email protected] [5dcb4c7a]
- Bump [email protected] [73c668a6]
24.04.0-edge - 13 May 2024
- Add Wave and Fusion info to workflow metadata (#4945) [bb7e1c8e]
- Add `k8s.cpuLimits` config option (#3027) [3c6e96d0]
- Add account config option for grid executors (#4975) [a09e37dd]
- Add git to docs deps [aa9e1273]
- Add resourceLimits directive (#2911) [7c9d965e]
- Add support for Job arrays (#3892) [ca9bc9d4]
- Add support for clusterOptions as a list of values (#4993) [dd173e33]
- Add threads dump for troubleshooting purposes [8992ebde]
- Fix Gstring casting exception when clusterOptions is a closure [74004fbd]
- Fix Missing error code when no entry is specified [f507e9a4]
- Fix NPE in LogsCheckpoint class [deb3076d]
- Fix Prevent maxForks less than zero [7676dd9c]
- Fix Use fully qualified S3 uris in error message (#4923) [f1cffd1b]
- Fix Wave container resolution with singularity and ociMode [54ad6241]
- Fix collectFile saving to GCS with sort: false (#4965) [1418553a]
- Fix console "Plugin manager not initialised" warn (#4989) [5ff44538]
- Fix console icon (#4991) [b8a23706]
- Fix docs formatting [c02e58c7]
- Fix docs snippet [6499649d]
- Fix flaky docs test (#4957) [ea8246f6]
- Fix groovy console issue (#4988) [b9bf6410]
- Fix job array docs (#4984) [6a3347ee]
- Fix missing include error message (#4981) [aad100e1]
- Fix script error text alignment (#4681) [1dc4e4e4]
- Fix security vulnerability in logback (#4947) [0ffcc4ca]
- Fix semaphore in parallel polling monitor (#4927) [5c37fcc2]
- Fix remove commented out test lines in Azure Batch Pool opts tests. (#4914) [cb607f07]
- Guarantees K8s pod name is unique on resume (#4959) [361cef84]
- Improve config resolution docs (#4950) [019eb86c]
- Improve documentation about azcopy installation requirements for custom Azure Batch worker pools (#4911) [5c410db8]
- Improve error message for image pull time-out for Singularity/Apptainer/Charliecloud (#4974) [73015fbd]
- Remove unused const [6e91285d]
- Run task finalisation asynchronously (#4890) [e0e94227]
- Strip auth secret from logs [acf63e0e]
- Update TES executor to TES API v1.1 (#4195) [7b32c2d6]
- Update aws.md to include Cluster access (#4951) [459d725b]
- Update developer diagrams (#4922) [dcff41a5]
- Update operator return types (#4976) [a614fbe7]
- Update stale documentation in overview.md (#4968) [6a58c6d7]
- Use for instead eachLine in error formatting [4a821f46]
- azure batch autopool feature more comprehensive documentation (#4941) [adbd8903]
- Bump Gradle 8.7 [8b5cf3cc]
- Bump [email protected] [830b032c]
- Bump [email protected] [163683c2]
- Bump [email protected] [6d99a22a]
- Bump [email protected] [89695ed3]
- Bump [email protected] [357b143a]
- Bump [email protected] [6c62a60a]
24.03.0-edge - 15 Apr 2024
- Add custom jobName for Google Batch [df40d55f]
- Add escher to name generator class [2e6496e2]
- Add retry policy to Google Batch client [c4981dcc]
- Add retry strategy for publishing (#4839) [c9c7032c]
- Add support for Azure custom startTask (#4913) [27d01e3a]
- Add task tip extension point [eadad5b8]
- Allow secrets to be used in pipeline script (#4171) [df866a24]
- Do not print a new line when stdout is empty (#4892) [658a5ec8]
- Fix Azure pool creation [2ee4d11e]
- Fix Use of secrets in the includeConfig path [00c9f226]
- Fix coloured ANSI log bug (#4898) [a04d6983]
- Fix eval output type via bash -c wrapping (#4887) [2165a14d]
- Fix exception handling in local executor [74d7d7a8]
- Fix support for GCS requester pays bucket option [d9d61cff]
- Fix test when missing Google secret [33dc3ce0]
- Improve Charliecloud support (#4879) [287471c0]
- Improve control on azcopy install (#4883) [01447d5c]
- Improve error message when Google creds file is corrupted [a550e52f]
- Improve getting started docs (#4764) [b59111b3]
- Improve retry logic for AWS Batch executor [62926c28]
- Nextflow launch script: improving search for JAVA_CMD (#4830) [ebbbe9e7]
- Publish built-in reports as Tower reports (#4760) [b710d923]
- Remove not needed dsl=2 + error in example (#4812) [7c5779d7]
- Remove unused code from AssetManager [77365165]
- Revert "Fix failing CI tests (#4861)" [7ba2e253]
- Update NameGenerator (#4907) [248201af]
- Update Platform API endpoint (#4855) [4842423a]
- Update Wave to API v1alpha2 (#4906) [9c350872]
- Update docs (#4852) [6e2d1a94]
- Updated docs on Google Cloud setup and credentials (#4896) [7e8b5e26]
- Updated dodcs note on singularity default command (#4825) [567f5334]
- Bump groovy 4.0.20 [66c1a164]
- Bump groovy 4.0.21 [9e08390b]
- Bump [email protected] [fc70dc8c]
- Bump [email protected] [b0c4e2c5]
- Bump [email protected] [6ae25fad]
- Bump [email protected] [967c2ac8]
- Bump [email protected] [ddda969e]
24.02.0-edge - 10 Mar 2024
- Add K8s job ttlSecondsAfterFinished option (#4434) [93627be6]
- Add NXF_CACHE_DIR environment var (#4655) [4b00170a]
- Add colours to ansi logs (#4573) [5e2ce9ed]
- Add eval output type (#4493) [df978113]
- Fix Always emit publish event for symlinks on resume (#4790) [bb5c4f9d]
- Fix Do not create local plugin path in embedded mode [9d6dd6a0]
- Fix Error while publishing S3 file with blanks [b74c0227]
- Fix Missing dependency for console command [baf29110]
- Fix typo in Azure Batch docs ('Azore') (#4735) [192bf8df]
- Fix typo in error message [a7f23305]
- Remove experimental admonition for podman [17d0dced]
- Remove square brackets from job name in LSF executor (#4799) [6e0ac72d]
- Remove unneeded const [09c957fb]
- Rename Tower -> Seqera Platform in docs and log messages (#4727) [7caffef9]
- Update Azure dependencies [1bcbaf0d]
- Update copyright info [e3089f0e]
- Use alias for HistoryFile.Record [17217a1c]
- minor cli docstring fix (#4759) [ee4b4a25]
- Bump Grengine 3.0.2 [42ca2b6f]
- Bump groovy 4.0.19 [854dc1f0]
- Bump snakeyaml 2.2 [07480779]
- Bump [email protected] [0eb84071]
- Bump [email protected] [d63be8c0]
- Bump [email protected] [57b7004e]
- Bump [email protected] [b7f703f5]
- Bump [email protected] [b8ffb180]
- Bump [email protected] [0c542eda]
- Bump amazoncorretto 17.0.10-al2023 [3e695ad9]
24.01.0-edge - 5 Feb 2024
- Add support for custom fuse device plugin (#4612) [a1e33193]
- Fix Ignore stored process message when ansi log is enabled (#4645) [f9ba47ef]
- Fix Wave container replicable checksum [da382ddf]
- Fix azure retry policy (#4638) [85bab699]
- Fix handling of wave.s5cmdConfigUrl setting (#4707) [3a19386d]
- Fix typo in Hyperqueue section (#4635) [d5a6a963]
- Fix typo in OCI mode warning message (#4633) [e216a876]
- Fix typo in the docs (#4636) [ci-skip] [4727f174]
- Improve detection of sys home variable [8812138f]
- Improve handling of publish error (#4703) [fc9f7685]
- LocalSecretsProvider: invalid permissions tests made more robust (#4663) [682a6806]
- Remove Glacier auto-retrieval (#4705) [5f0ec50d]
- Remove preview from cmd secret [dc040226]
- Set scratch default to false when using Fusion (#4675) [9d17e407]
- Slight change in wording for error message about userEmulation (#4680) [a9c8a841]
- Truncate max size exceeded error message (#4644) [36090b70]
- Use AZURE_STORAGE_SAS_TOKEN environment variable (#4627) [2e02afbf]
- Use canonical init method for plugins initialization [e7a20aff]
- Bump [email protected] [8b9905c7]
- Bump [email protected] [bfc94e46]
- Bump [email protected] [01ff0353]
- Bump [email protected] [3df34188]
- Bump [email protected] [e90d73a7]
- Bump [email protected] [4379c941]
- Bump [email protected] [2bc698c7]
- Bump [email protected] [07415ce1]
- Bump [email protected] [b991e14b]
- Bump Groovy 4 (#4443) [9d32503b]
- Bump actions/checkout@v4 [d1b3195e]
- Bump [email protected] + [email protected] [331ff425]
- Bump nextflow 23.12.0-edge as min version [63e83702]
- Bump tj-actions/changed-files from 35 to 41 in /.github/workflows (#4622) [d67aef5f]
23.10.1 - 12 Jan 2023
- Fix bug with Fusion symlink resolution (#4593) [f28c9e48]
- Fix Fusion symlinks when publishing files (#4348) [1fa5878a]
- Fix Inspect command fails with Singularity [25883df3]
- Fix Allow the use of error built-in function in onComplete handler (#4458) [4be10cd3]
- Fix Harden regular expression to used to strip secrets in logs (#4563) [0102d4d6]
- Fix custom notification template [40980bcb]
- Fix container environment with special chars (#4594) [f4e00601]
- Fix AZURE_STORAGE_SAS_TOKEN environment variable (#4627) [2e1cb413]
- Fix azure retry policy (#4638) [2bc3cf0e]
- Fix BitBucket get source API with custom branch [5ef75e32]
- Improve error details for AbortOperationException [9e795a62]
- Bump [email protected] [206f2614]
- Bump [email protected] [50bcad59]
23.04.5 - 12 Jan 2023
- Fix container environment with special chars (#4594) [663b2936]
23.12.0-edge - 20 Dec 2023
- Add AWS_SESSION_TOKEN to Fusion environment (#4581) [552f29b0]
- Add ability to disable Cloudinfo service (#4606) [f7251895]
- Add experimental support for Fargate compute type for AWS Batch (#3474) [47cf335b]
- Add support for Instance template to Google Batch [df7ed294]
- Add support for Singularity/Apptainer auto pull mode for OCI containers [b7f1a192]
- Fix BitBucket get source API with custom branch [58937831]
- Fix Fusion tags documentation (#4551) [687e2e96]
- Fix Harden regular expression to used to strip secrets in logs (#4563) [832bff24]
- Fix bug with Fusion symlink resolution (#4593) [09e85582]
- Fix container environment with special chars (#4594) [e0fe952f]
- Fix custom notification template [ccf4f59e]
- Fix fusion symlink test (#4604) [681ace86]
- Fix smoke tests [d3c2f330]
- Improve GLS tests [58590b1c]
- Load nf-amazon when AWS SES is enabled [887f06f4]
- Move build num & timestamp to BuildInfo class [ec8083d4]
- Move app version to BuildInfo class [c7d749e8]
- Remove deprecated Wave observer [0e009ef7]
- Remove undocumented userEmulation mode (#4596) [f6c79788]
- Remove unused DSL2 check [e9ee3b2c]
- Replace each iterator with class for [f7662e68]
- Bump [email protected] [0b40b7b9]
- Bump [email protected] [bcb20fcf]
- Bump [email protected] [aa981814]
- Bump [email protected] and [email protected] [9cb50035]
- Build optimizations (#4579) [5ad41e44]
23.11.0-edge - 24 Nov 2023
- Add `fusion.cacheSize` config option (#4518) [2faadc22]
- Add Topic channel type (experimental) (#4459) [921313d1]
- Add Google Batch native retry on spot termination (#4500) [ea1c1b70]
- Add Retry policy to Google Storage (#4524) [c271bb18]
- Add ability detect Google Batch spot interruption (#4462) [d49f02ae]
- Add doc tests, move some snippets to separate files (#3959) [0ff3b305]
- Add docs section on container requirements (#4501) [3fb29f78]
- Add labels field in Job request for Google Batch (#4538) [627c595e]
- Add note about limitations of glacier auto retrieval (#4514) [82e56799]
- Add note about local executor and enforcing resource limits (#4468) [6a0626f7]
- Add section about sharing modules (#4482) [3e66fba4]
- Add section on process directives to plugin docs (#4477) [d9ee9870]
- Add support for Azure low-priority pool (#4527) [8320ea10]
- Add support for FUSION_AWS_REGION (#4481) [8f8b09fa]
- Add support for Fusion when using Singularity OCI mode (#4508) [4f3aa631]
- Add support for K8s schedulerName pod spec (#4485) [dfc7b7c8]
- Add support for Singularity OCI mode (#4440) [f5362a7b]
- Allow the use of error built-in function in onComplete handler (#4458) [35a4424b]
- Fix Bug in JsonSplitter ordering [8ec14dd2]
- Fix Bypass Google Batch Price query if task cpus and memory are defined (#4521) [7f8f20d3]
- Fix Checkout remote tag if checkout remote branch fails (#4247) [b8907ccb]
- Fix Fusion symlinks when publishing files (#4348) [89f09fe0]
- Fix Inspect command fails with Singularity [f5bb829f]
- Fix ParamsMap copyWith param aliases (#4188) [b480ee0e]
- Fix Singularity docs [e952299f]
- Fix container hashing for Singularity + Wave containers [4c6f2e85]
- Fix detection of Conda local path made by Wave client (#4532) [4d5bc216]
- Fix doc tests to fail on test failure (#4505) [4d326551]
- Fix errors when NXF_HOME contains spaces (#4456) [fe5bea99]
- Fix Google Batch network/subnetwork docs (#4475) [27d132f3]
- Fix rounding error with long durations (#4496) [0356178b]
- Fix security vulnerabilities (#4513) [a310c777]
- Fix Use consistently NXF_TASK_WORKDIR (#4484) [48ee3c64]
- Improve error details for AbortOperationException [35609cb0]
- Improve operator docs (#4502) [38210e11]
- Makefile clean to also remove buildSrc/build (#4517) [2ccb05d0]
- Minor test improvements [171831ea]
- Minor types improvement for mix operator [91c1ab15]
- Normalise channel docs [b641d677]
- Remove deprecated TowerArchiver feature [ff8e06a3]
- Remove dsl1 deprecated code (part 2) [159effb1]
- Remove dsl1 deprecated code [2b433a52]
- Remove incorrect note about workflow inputs (#4509) [54bc0b7d]
- Return error if plugin version is not specified in offline mode (#4487) [f5d7246e]
- Update README.md with new branding color for Nextflow (#4412) [7a13b18b]
- Update background color of docs status badges (#4411) [3cb1c53c]
- Update logging filter for Google Batch provider. (#4488) [66a3ed19]
- Bump Gradle 8.4 and test vs Java 21 (#4450) [8cb2702c]
- Bump [email protected] [8e2d7879]
- Bump [email protected] [7c47d090]
- Bump [email protected] [65240b75]
- Bump [email protected] [725f0510]
- Bump [email protected] [a307686c]
- Bump [email protected] [e54ea007]
- Bump [email protected] [033ec92c]
- Bump [email protected] [836a44a5]
- Bump [email protected] [620523ef]
23.10.0 - 15 Oct 2023
- Add support for K8s hostPath [10c32325]
- Add AWS SES docs [b83e7148]
- Add -with-cloudcache instead of -cloudcache [ef530263]
- Add inspect command validation tests [882f369e]
- Improve warning complaining about tuple but mentioning set (#4400) [0ef48735]
- Improve `-dump-hashes` output adding json format (#4369) [5bdaac94]
- Improve error message on invalid file url prefix [82a3f405]
- Fix conda channels order [6672c6d7]
- Docs: Incorporate DSL2 features (#3793) [efd041cb]
- Docs: aws.batch.retrymode = 'built-in' (#4229) [d5a8098f]
- Docs: Update logos, fonts, and colors (#4407) [7814822c]
- Changelog minor changes [dfb5bf09]
- Bump [email protected] [795849d7]
23.09.3-edge - 10 Oct 2023
- Add -cloudcache CLI option (#4385) [73fda582]
- Add bioconda and seqera Conda default channels (#4359) [ff012dcd]
- Add codespell: config, workflow and have typos fixed (#4324) [e044b7a5]
- Add docs page on caching and resuming (#4371) [21190a3c]
- Add example of using the transpose operator with multiple items in element (#4364) [0bce2be0]
- Add setting to enable the use of sync command [f0d5cc5c]
- Improve S3 endpoint validation [2b9ae6aa]
- Improve Wave config validation [7d5a21b0]
- Improve Wave error handling [d47e8b07]
- Fix Google Batch do not stop running jobs (#4381) [3d6b7358]
- Incorporate README content into Nextflow docs (#4263) [74a0f998]
- Never say (nearly) Oops again (#4356) [4a39542b]
- Remove unsupported K8s device capability [be0cf0c2]
- Remove unused -dsl2 option [3cb91a15]
- Rename Microsoft AAD to Microsoft Entra (#4362) [5e3f2c0a]
- Return -1 when exitcode file is empty (#4354) [d26c42be]
- Support for Fusion unprivileged execution (#4387) [035e6e7b]
- Use HistoryFile.Record instead of Record type conflict [11c3aac5]
- Bump [email protected] [a84208a8]
- Bump [email protected] [b37b4014]
- Bump [email protected] [b4eb8b96]
- Bump [email protected] [5681ab13]
- Bump [email protected] [de1de6c7]
23.09.2-edge - 28 Sep 2023
- Add conda.enabled to conda config scope docs (#4320) [0b74c4e2]
- Add developer docs (#4065) [06843d87]
- Add fs stat command [a79056b7]
- Add more tests to container name [da7a1942]
- Add procps by default to Conda-based Wave builds [66b2d2d2]
- Add support for Java 21 (#4338) [ac1fc9ee]
- Add Mermaid diagram in HTML DAG (#4337) [0f3e263f]
- Default Conda basePackages to "conda-forge::procps-ng" [367af52f]
- Disable Tower container field for multiple images [b53936b0]
- Document `NXF_DISABLE_CHECK_LATEST` environment var (#4327) [4e3e9aca]
- Document `fs` CLI command (#4328) [1a680495]
- Document source of `vol_ctxt` and `inv_ctxt` trace metrics (#4333) [6525b0a1]
- Document when process directives are evaluated (#4217) [731a29a2]
- Fix List of S3 bucket for custom endpoint [4327fa58]
- Fix Prevent false positive resumable task [144e0a8a]
- Fix Prevent multi attempts to retrieve AWS creds [b30efe36]
- Fix allow_other vulnerability preventing google-batch submissions (#4332) [9b3741e3]
- Fix fs list command [29ab2f24]
- Fix minor typos in changelogs/source code (#4319) [4ce9f1df]
- Fix support for S3 custom endpoint with anonymous access [03752815]
- Fix use of GITHUB_TOKEN variable to access GitHub repo [afe3dc4f]
- Fix Wave does not support 'null' container engine [f3eba3d7]
- Fix Retry TimeoutException in azure file system (#4295) [79248355]
- Improve K8s unit tests (#4196) [5a43a32b]
- Improve Mermaid DAG rendering (#4070) [19587f40]
- Improve error report when exception is thrown in operator ctx [16f54a9c]
- Improve wave container name validation [73eb5a02]
- Minor improvements [fff3d7bd]
- Prevent cache invalidation for task directives (#4339) [aabb6c19]
- Remove line endings from container box id (#4334) [df41e54a]
- Bump Apache 2.0 license to tower client [e4a878b6]
- Bump [email protected] [3311172f]
- Bump [email protected] [a9b735ce]
- Bump [email protected] [7219d7f2]
- Bump [email protected] [91a935f9]
- Bump [email protected] [0cf2476c]
- Bump [email protected] [d0c47d49]
23.04.4 - 25 Sep 2023
- Fix use of GITHUB_TOKEN variable to access GitHub repo [108c6b55]
- Fix allow_other vulnerability preventing google-batch submissions (#4332) [4895d547]
- Fix Prevent false positive resumable task [aae87715]
- Fix Always emit publish event for cached task outputs (#4227) [c4cd53c2]
- Fix Too long Http connection pool timeout [ce5e9930]
- Bump [email protected] [d881728c]
23.09.1-edge - 11 Sep 2023
- Revert "Allow setting shell directive when using the trace file (#4210)" [9f9edcdc]
23.09.0-edge - 10 Sep 2023
- Add check for latest version (#4194) [3e8cd488]
- Add inspect command (#4069) [090c31ce]
- Add maxSubmitAwait (#3736) [5686bf1d]
- Add scripts logging for troubleshooting [c056a74e]
- Add support for Spack to Singularity builds [23c4ec1d]
- Add support for Wave native build for Singularity [8a434893]
- Add support for inputs and outputs arity [42504d3c]
- Add support for remote debug (#4266) [87e0648a]
- Add warning about using clusterOptions with process directives (#4248) [a68c1a3e]
- Add which to dockerfile build [817aa05b]
- Align Singularity experience with Docker (#4230) [a1e1d3ca] [c1cc60dd]
- Allow setting shell directive when using the trace file (#4210) [7d6ad624]
- Always emit publish event for cached task outputs (#4227) [62686ce8]
- Deprecated Wave report feature [80c5cb27]
- Disable staging script for remote work dir (#4282) [80f7cd46]
- Disable version check on CI tests [db79e13f]
- Docs improvement to clarify the usage of the bin dir (#4121) [2daa4172]
- Document API differences of process path inputs (#4189) [c37e00bc]
- Document use of local variables in closures (#4251) [05ff784a]
- Fix IOException should be thrown when failing to creare Azure directory [b0bdfd79]
- Fix Parallel execution of Conda corrupts data and packages (#4253) [976c282c]
- Fix Parse negative CLI params as numbers (#4238) [1ae70d5d]
- Fix Too long Http connection pool timeout [fa961e7f]
- Fix Wave build for Singularity files [a60ef72b]
- Fix Wave build when Conda package name is quoted [d19cb0b7]
- Fix failing test [2785ffe9]
- Fix fs cp command with remote file [366eedec]
- Fix printf command with negative exit code (#4213) [465468b0]
- Fix security deps in nf-azure plugin [c30d5211]
- Fix setting `executor.queueSize = 0` is ignored (#4228) [6664b578]
- Improve Wave handing of Conda envs [736ab9bb]
- Improve pod options documentation (#4274) [c3aa26e1]
- Make TraceRecord@store field public accessible [07582f0b]
- Remove -dsl1 and -dsl1 rub cli options [b6721b71]
- Remove experimental -dockerize option /2 [7def5542]
- Remove experimental -dockerize option [937c8fb7]
- Report an error on duplicate workflow name definitions (#4088) [fce9702e]
- Undocument internal NXF_DEBUG variable [7955db8d]
- Update AZ File share doc (#4235) [69d317b6]
- Update docs about splitCsv() operator (#4163) [1dfb621c]
- Update documentation of NXF_DEBUG (#4187) [a88a4245]
- Use sipHash24 in place of deprecated murmur32 for script aliasing [bb96763f]
- Bump groovy 3.0.19 [cb411208]
- Bump [email protected] [7e5d414e]
- Bump [email protected] [83410f39]
- Bump [email protected] [a9f6dd65]
23.08.1-edge - 17 Aug 2023
- Add 429 http status code to Wave retriable errors [8eb5f305]
- Add resource labels support for Azure Batch (#4178) [7b5e50a1]
- Apply K8s Pod metadata to Job (#4057) [4d918627]
- Document error about trailing backslash with space (#4180) [245afa5d]
- Enable cloud cache based on environment variable (#4160) [a66b0e63]
- Escape semicolons in paths (#4193) [552501ce]
- FIx nested InvocationTargetException (#4192) [67980f19]
- Fix Execution should fail if report or timeline file already exists [b238d7e2]
- Fix Process hangs when using flatten and finish errorStrategy [d99b3432]
- Fix `workflow.container` map resolution (#4190) [96ab8a69]
- Fix checkpoint thread termination (#4166) [2b449daa]
- Fix env output when changing task workdir [8e4d7fed]
- Fix if-guard on log.trace in trask processor inner class [50f6f6d5]
- Fix typos in source code comments (#4173) [e78bc37e]
- Improve Conda build error report [7b19fb03]
- Improve handling of name-only container env variables [3051cd13]
- Minor changes [7e58c945]
- Remove dockerize launcher classpath file (#4191) [2bae5198]
- Remove lock file from cloudcache (#4167) [6e6ea579]
- Update AWS instructions for creating a custom AMI (#4174) [563bff13]
- Update changelog [98f88a50]
- Update tip about modifying maps (#4153) [30036dbf]
- Use root user in Wave container based on micromamba (#4038) [a3a75ea2]
- Bump [email protected] [6670bb06]
- Bump [email protected] [fb8f6681]
- Bump [email protected] [d06b8365]
- Bump [email protected] [7555b17d]
23.04.3 - 11 Aug 2023
- Increase Wave client max attempts [8c67610a]
- Fix log typo [03e19ea2]
- Add 429 http status code to Wave retriable errors [a8b8c6c5]
- Improve handling Wave server errors [621c9665]
- Bump [email protected] [d7fa3f26]
- Bump corretto 17.0.8 [7a73a78f]
23.08.0-edge - 5 Aug 2023
- Add `-value` option to `config` command (#4142) [57e3100b]
- Add `deleteTasksOnCompletion` to Azure Batch configuration (#4114) [b14674dc]
- Add Tower logs checkpoint (#4132) [71dfecc2]
- Allow use virtual threads in Wave client [dd32f80a]
- Allow workflow entry from module import (#4128) [51f5c842]
- Disable cache backup/restore if cloudcache is used (#4125) [46e828e1]
- Document behavior of withName selector with included aliases (#4129) [8b7e3d48]
- Fix Option fixOwnership traverse parent directories [f2a2ea35]
- Fix Redirection http redirection across different hosts [fcdeec02]
- Fix Wave disable flag [8579e7a4]
- Fix bug with K8s resource labels (#4147) eu-west-1[3f4b8557]
- Fix glob resolution for remove files [19a72c40]
- Fix incorrect error message on missing comma (#4085) eu-west-1[a59af39f]
- Fix missing changelog for version 23.07.0-edge eu-west-1[9a33e936]
- Fix strict mode docs (#4150) [6b46b507]
- Improve plugin docs (#3957) [22638d46]
- Improve Wave config logging [547fad62]
- Improve TaskPollingMonitor logging [077ed5dd]
- Improve Wave and Fusion docs (#4149) [d2229bde]
- Increase Wave client max attempts [fe5dd497]
- Remove module all components import [a6d08c04]
- Restore Tower CacheManager for backward compatibility [6d269070]
- Bump amazoncorretto:17.0.8 [00eb145c]
- Bump [email protected] [78e4b278]
- Bump [email protected] [41c8c164]
- Bump [email protected] [5f33ac17]
- Bump [email protected] [981315ad]
23.07.0-edge - 23 Jul 2023
- Add CPU model name to trace files and traceRecord (#3946) [e0d91bf7]
- Add ability to disable CLI params type detection [9a1c584d]
- Add cloudcache plugin (#4097) [ac90cc26]
- Add missing header to Wave container await [d39866e6]
- Add remote bin support for TES in a workdir (#3990) [8a22168a]
- Add retry logic to wave image await [9fc1d3bd]
- Add rule to build Nextflow docker image for ARM (#4020) [705d55f5]
- Add support for AWS SSO credentials provider (#4045) [53e33cde]
- Add support for Wave container freeze [9a5903e6]
- Add support legacy Wave retry [73a1e7d4]
- Allow SLURM executor option `--mem-per-cpu` (#4023) [96c04e3b]
- Allow disabling the Wave requirement when Fusion is enabled [9180d633]
- Disable Singularity and Apptainer home mount by default (#4056) [a0ee4657]
- Document `NXF_WRAPPER_STAGE_FILE_THRESHOLD` environment variable (#4113) [bda47567]
- Fix AzFileSystem retry policy [ba9b6d18] [c2f3cc96]
- Fix Improve error message for invalid Azure URI [0f4d8867]
- Fix Treat HTTP headers as case insensitive (#4116) [97fd3358]
- Fix invalid detection of hierarchical namespace stub blobs as files (#4046) [ce06c877]
- Fix stage script in Fusion script launcher (#4109) [0933f47e]
- Ignore accelerator type for AWS Batch (#4043) [263ecca8]
- Implement Weblog feature as an external plugin [f9f2c338]
- Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf0]
- Improve Azure retry logging [de58697a]
- Improve description of channels and channel types (#4120) [8975734d]
- Improve handling Wave server errors [84f7a61a]
- Increase Azure min retry delay to 250ms [2e77e5e4]
- Remove default arch from wave request [f0e5c0c1]
- Remove logging of report JSON data (#4098) [099e5039]
- Wait for all child processes in nxf_parallel (#4050) [60a5f1a7]
- Bump Groovy 3.0.18 [207eb535]
- Bump micromamba 1.4.9 [6307f9b5]
- Bump [email protected] [57464746]
- Bump [email protected] [e1512f6a]
- Bump [email protected] [27e7f663]
- Bump [email protected] [1895efc4]
- Bump [email protected] [cb6242c4]
- Bump [email protected] [f98feb77]
- Bump [email protected] [6aede7c0]
- Bump [email protected] [3278d798]
- Bump [email protected] [2998db5d]
23.06.0-edge - 14 Jun 2023
- Add AWS Kms integration test [19449bf4]
- Add Wave containers reports (preview) [9d9e2758]
- Add disk resource with type option for google batch (#3861) [166b3638]
- Add httpConnectTimeout and httpReadTimeout to Google options (#3974) [49fa15f7]
- Add plugin cmd help description [d3788f9f]
- Add retry policy on Az blob operations [295bc1ff]
- Add retry policy to Wave http client [1daebeef]
- Add support for AWS SES as mail sending provider [df85d443]
- Add support for arch auto-detection to Wave [7b5fdaf0]
- Add wave.httpClient.connectTimeout config option [dd999a3c]
- Clarify tip about groupTuple size and groupKey (#3949) [e60d327f]
- Consolidate Wave retryPolicy options [7d7464fe]
- Enhanced support for Spack + Wave (#3998) [63ac03b3]
- Fix Google Batch default instance family types (#3960) [b5257cd7]
- Fix S3 path normalization [b75ec444]
- Fix access to public S3 bucket when no creds are provided (#3992) [cf8ba466] [680f0a90]
- Fix containerOptions when using Fusion [dcde7b7f]
- Fix dump pretty print to not modify input (#3955) [46c17ee3]
- Fix invalid machine type setting when no valid machine type is found (#3961) [5eb93971]
- Fix matching symlink files [d63af784]
- Fix missing options for JsonSplitter creation (#3958) [f991fe9e]
- Fix non-deterministic null container engine error [f227f2e5]
- Fix packing all including Wave [735b8d9c]
- Fix static compiler errors [f48a473c]
- Improve documentation on Nextflow scripts (#3953) [80050c03]
- Improve description of channels and channel types (#4120) [8975734d]
- Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf0]
- Minor change in Wave config [4da0442a]
- Prevent null exit code when Google batch is unable to access exit status [f68a39ec]
- Refactor Conda and Spack support for Wave to Java [36b9e226]
- Remove `--no-home` default option from charliecloud builder (#3956) [915074a4]
- Update workflow.revision max length to match the one in Tower (#4010) [1433a903]
- Bump amazocorretto:17.0.7 [c8aa1214]
- Bump azure-storage-blob:12.22.1 [2a36fa77]
- Bump [email protected] [2998db5d]
- Bump [email protected] [3278d798]
- Bump [email protected] [6aede7c0]
- Bump [email protected] [f98feb77]
- Bump [email protected] [1895efc4]
- Bump [email protected] [57464746]
- Bump [email protected] [cb6242c4]
23.04.2 - 8 Jun 2023
- Fix non-deterministic null container engine error [f93221ab]
- Add retry policy to Wave client [2f1532f6]
- Fix wave build docs [34a73022]
- Bump [email protected] [350201b5]
23.05.0-edge - 15 May 2023
- Add support for custom custom root directory to resolve relative paths (#3942) [f06bb1f7]
- Add `arch` directive support for Spack (#3786) [62dfc482]
- Add clone deep option to run and pull commands [b44b6453]
- Add fusion.exportStorageCredentials option [acb6aedf]
- Add groovy-yaml to core runtime [003e1f70]
- Add missing test env variables to CI build [a0e501bf]
- Add splitJson Operator (#3830) [4f58f695]
- Add support for Java 20 [3788a689]
- Add support for `time` directive in Azure Batch (#3869) [5c11a0d4]
- Add support for the Spack recipes to Wave build (#3636) [b03cbe70]
- Add Preview support for virtual threads (#3871) [5c429046]
- Convert docs to Markdown (#3196) [3cad402f]
- Deprecate DSL1 syntax for tap operator (#3004) [2be0edfe]
- Enable static compilation to missing classes (#3906) [c3c4b2f0]
- Fix -with-conda option in the docs (#3867) [9b350ba8]
- Fix AWS SSE env propagation to Fusion [e24608c3]
- Fix Apptainer rendering by removing superfluous space [36607ed1]
- Fix Azure jobs correctly deleted after completion (#3927) [b173a983]
- Fix Azure pool creation when using scaling formula (#3868) [79984a87]
- Fix DSL2 support in nextflow console (#3864) [0253f8d7]
- Fix K8s handling PodUnschedulableException (#3938) [5b756c63]
- Fix `interval` channel factory (#3848) [d001e4c7]
- Fix invalid warning on func import (#3807) [bb836960]
- Fix minor typo in nextflow subcommand (#3853) [dd3be3d1]
- Fix misleading error message on NoSuchFileException [f3dceba6]
- Fix missing SAS token fusion env for Azure [43015029]
- Fix problem args were not correctly represented in debug yaml (#3904) [eeb4b5c8]
- Fix string comparison in S3 client (#3875) [9344d294]
- Fix use of remote dir with local exec statement [850bc3d9]
- Fix Quote Singularity/Apptainer env values [586417ac]
- Improve handling default out param [91471970]
- Improve plugin test detection [29794bf4]
- Improve plugin updater err handling [f3d72f22]
- Improve task out redirect remove the use of mkfifo (#3863) [efedec74]
- Improve Use Docker stop instead of docker kill [32e6fd85]
- Improve Use separate script for long stage/unstage commands (#3851) [4343e333]
- Increase Azure default maxRetries to 10 [a017139f]
- Keep plugins-info content sorted [d5552ee6]
- Minor change on Docker-spack templates [e0e24bda]
- Refactor the AWS configuration (#3498) [a74e42d9]
- Remove `Channel.from` in favor of `Channel.of` from tests and docs (#3670) [aa8b72fa]
- Rename AmazonS3Client to S3Client [cc59596a]
- Rename com.upplication.s3fs package to nextflow.cloud.aws.nio [a2f3bb24]
- Run build CI tests on push to branches starting with `test*` or `dev*` (#3852) [7032e17c]
- Security fixes [973b7bea]
- Support enums in cache helper (#3901) [e4b977a4]
- Bump slf4j 2.0.7 and logback 1.4.6 [d7eae86e]
- Bump JGit 6.5 and use depth 1 when cloning repos [eda0845c]
- Bump aws-java-sdk-s3:1.12.429 [465171f5]
- Bump fusion 2.2 [f1ebe29a]
- Bump groovy 3.0.17 [cfe4ba56]
- Bump gson:2.10.1 [be555683]
- Bump micromamba:1.4.2 [334df1e0]
- Bump [email protected] [7d6d0108]
- Bump [email protected] [b06ffd0c]
- Bump [email protected] [2e0a15cd]
- Bump [email protected] [0c8fd7df]
- Bump [email protected] [a733b818]
- Bump [email protected] [12edf0e6]
- Bump [email protected] [69b6edde]
- Bump [email protected] [d05d51b4]
23.04.1 - 15 Apr 2023
- Add support for Java 20 [f6933db7]
- Fix use of remote dir with local exec statement [6ea1f68c]
- Fix Azure pool creation when using scaling formula (#3868) [84a808a5]
- Fix interval channel factory (#3848) [82ccf6ad]
- Fix invalid warning on func import (#3807) [4678ffe3]
- Improve plugin test detection [57cfb0d9]
- Improve plugin updater err handling [5627c69a]
- Security fixes [83e8fd6a]
- Bump [email protected] [d8cb763c]
- Bump [email protected] [b2354380]
- Bump [email protected] [22a68cfe]
- Bump gson:2.10.1 [83ca1e32]
- Bump [email protected] [b40b5165]
- Bump [email protected] [98a89154]
- Bump aws-java-sdk-s3:1.12.429 [b71ee0a3]
- Bump [email protected] [a5da54d3]
- Bump [email protected] [c90553c9]
22.10.8 - 15 Apr 2023
- Security fixes [fc2627bb]
- Add support for testing custom plugin uri [718d4562]
- Improve plugin updater err handling [84042082]
- Improve plugin test detection [e6c60a6c]
- Bump [email protected] [26b01b83]
- Bump [email protected] [2a886fe0]
- Bump [email protected] [b8769f1a]
- Bump [email protected] [89d902ec]
- Bump [email protected] [9b0f4bfb]
- Bump [email protected] [f7aaddc6]
- Bump [email protected] [7898cc04]
23.04.0 - 1 Apr 2023
- Add several names to the name generator feat:(#3790) [dfa2f6ca]
- Add support for Fusion to Azure Batch executor (#3209) [3d3cbfa2]
- Add support for testing custom plugin uri [227910ab]
- Add warnings for Azure named pools (#3819) [a2c71acf]
- Enable new pid namespace with Singularity & Apptainer [3601b014]
- Fix NoSuchMethodError String.stripIndent with Java 11 [308eafe6]
- Fix issue checking Google Batch script launcher type [39c3a517]
- Fix resolution of module resources [2c5a6878]
- Fix Relax caching across task retries [840e8432]
- Fix Java version for tests [7ce05c15]
- Remove extra context from workflow error message [38c8bd33]
- Revert "Enable Fusion on Google Batch tests" [2ba7ea54]
- Bump micromamba 1.4.1 [ec1439e6]
- Bump [email protected] [0f98b245]
- Bump [email protected] [e1732be9]
- Bump [email protected] [99477f79]
- Bump [email protected] [939195b5]
- Bump [email protected] [b7b5d4c9]
23.03.0-edge - 19 Mar 2023
- Add Azure batch pool virtualNetwork option (#3723) [e3917b8e]
- Add basePackages option to Wave config [7e827810]
- Add error message for missing container image with Google Batch (#3747) [6419e68f]
- Add notifyFilePublish optional source argument (#3737) [a65a9ff7]
- Add retry strategy on Bash wrapper write logic [1e38274a]
- Add support for AWS S3 Glacier Retrieval Tier (#3680) [fab6bd5e]
- Add sync invocation on job completion (#3678) [e29c4e4b]
- Add workflowId to Wave request [025ff9d0]
- Add Clone result list objects before output binding [38762080]
- Add plugins option to kuberun command (#3766) [6515294f]
- Fix Google Batch logging exception [d7e38e9e]
- Fix Java Matcher serialization [6aecc4ed]
- Fix Logger failure type detection [f1b89c1f]
- Fix Orphaned processes when using Singularity [7236f830]
- Fix groupTuple with mismatching tuple cardinality [1d32e2c2]
- Fix special chars escaping in container env [b93634e9]
- Fix commit revision type for Azure DevOps repos (#3721) [fb71767e]
- Improve DAG API (#3703) [21afb358]
- Improve Wave docs [7299dac9]
- Improve `fair` directive docs (#3677) [7ca7520f]
- Improve transpose and groupTuple examples in the docs (#3685) [7870dfc8]
- Increase pwd obfuscation min length [ba23d036]
- Make GroupKey cloneable (#3738) [0760b0fd]
- Prepare Nextflow for the CWS Plugin (#3727) [fd8bf709]
- Remove DNAnexus page from docs (#3695) [fa58c18c]
- Remove outdated FAQ page from docs (#3683) [e59c7fbb]
- Remove unused classes [9fa8d75b]
- Update Azure VM sizes (#3751) [1d06e9a6]
- Enable Fusion on Google Batch tests [2f1b1094]
- Bump groovy 3.0.16 [d3ff5dcb]
- Bump [email protected] [aa1b065d]
- Bump [email protected] [2aaaf2a7]
- Bump [email protected] [f358b008]
- Bump [email protected] [2395187d]
23.02.1-edge - 26 Feb 2023
- Add Fusion logs and tags config [09192078]
- Add support for NXF_DEBUG to K8s task handler [828583dc]
- Add support for Mamba HTTP based lock files [7fe88c84]
- Add container name validation [c3b6d9ab]
- Add Fusion for Google storage docs [34fcfe06]
- Improve K8s auth token discovery [44f8cc07]
- Bump [email protected] [1c697ab5]
- Bump amazoncorretto:17.0.6 [a33a6f47]
23.02.0-edge - 21 Feb 2023
- Add Fusion support for Google Batch (#3577) [d5fbab4f]
- Add Header provider to Google Batch client [20979929]
- Add Wave integration tests [c5faf971]
- Add errorStrategy validation [954cd921]
- Add Java install recommendations to docs (#3617) [7e9bee1e]
- Add nextflow tags to AWS Batch job def [b465ac52] [BREAKING]
- Add readOnlyInputs option for CharliecloudBuilder (#3590) [8ae001fc]
- Add refresh token to Wave request [41510e87]
- Add requirements for container images to run with Nextflow (#3586) [7af1cb66]
- Add support for Fusion to Slurm and LSF executors (#3516) [fbc95e6b]
- Add support for Fusion tags (#3609) [8385ec22] [BREAKING]
- Add support for the Spack package manager (#3580) [a5df62f6]
- Add the fcp tool option to file copy strategy (#3556) [2a224258]
- Add Fusion integration test
- Add Wave + Fusion test with Google Batch [b541c061]
- Add support for entryless Fusion configuration and Singularity support (#3584) [34a27733]
- Improve Fusion config [a1d08463]
- Ignore resource directives if -l option is specified in PBS executor (#3015) [28a67969]
- Improve K8s securityContext support [3f76240b]
- Improve AWS Batch error logging [8f4884c1]
- Improve secrets docs [9a3b4214]
- Improve Wave debug-task plugin command [cf3fd747]
- Improve Wave logging [fced3761]
- Increase Wave token duration to 30 mins [e1a712c2]
- Fix -with-apptainer cli option (#3621) [8c9588fe]
- Fix GH action tests step [bb890d9a]
- Fix Spack failing test [868374d3]
- Fix Tower doc links, fix typos (#3647) [1278e1a5]
- Fix Wave cli messages [10cf414b]
- Fix collectFile cache over remote storage [762ba19c]
- Fix output env var tokenize [40d56735]
- Fix plugin install version [59e9a91b]
- Fix race condition on Wave requests [f57fae2c]
- Fix serialization of S3 paths with spaces (#3565) [ce487624]
- Fix string literal method names with parens (#3604) [8278078a]
- Fix submit command in error message for grid executors that pipe wrapper script (#3548) [40ebd308]
- Fix typos in the documentation (#3640) [eccc1130]
- Fix unique fingerprint for Wave bundle resources [b59fa728]
- Log exception when an unexpected occurs (#3603) [9aeca99f]
- Minor change on container resolution [23d47ded]
- Refactor httpfs configuration [445218a8]
- Remove deprecated buckets field [0a355ac3]
- Remove leading/trailing special chars from tag [7d3cc707]
- Remove unused `-with-k8s` CLI option (#3624) [85b6e7d3]
- Update config.rst (#3655) [1555e188]
- Update Fusion docs [12782eeb]
- Bump Fusion 2.1 [f48ef5b3]
- Bump Groovy 3.0.15 [7a3ebc7d]
- Bump Micromamba 1.3.1 [aa2bf37e]
- Bump Spock 2.3 [9f0dac31]
- Bump [email protected] [b797fac2]
- Bump [email protected] [dd2f69dd]
- Bump [email protected] [8cb9fa35]
- Bump [email protected] [7ccca430]