forked from nextflow-io/nextflow
-
Notifications
You must be signed in to change notification settings - Fork 0
/
changelog.txt
2616 lines (2376 loc) · 127 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
===================
22.09.5-edge - 21 Sep 2022
- Use default wave strategy [abbfa7f4]
- Handle errors reported by tower report writer [0e814647]
- Fix AWS S3 copy object [b3b90d23]
22.09.4-edge - 19 Sep 2022
- Add Fusion display name [f789d457]
- Add container cleanup [cd2ae7dc]
- Add Wave interactive debug session [ce7fa651]
- Add support for wave build and cache repositories[692043ff]
- Add shutdown to Google Batch client [8f413cf7]
- Add native_id to Google Batch handler [352b4239]
- Add java sts library to enable use of IRSA in k8s (#3207) [62df42c3] <Vishwas>
- Add support for module custon bin dirs [77f55262]
- Add support for tower token to wave client [928d5b04]
- Update CLI docs (#3200) [8acebee6] <Marcel Ribeiro Dantas>
- Fix issue with empty report file [9cc4f079]
- Do not return resource bundle for root module [775c7ed9]
- Improve tower config [ee03c243]
- Bump groovy 3.0.13 [4a17e198]
22.09.3-edge - 10 Sep 2022
- Add fusion support to K8s executor (#3142) [6bb27b32]
- Fix shutdown/cleanup hooks invocation [f4185070]
- Fix Use smaller buffer size for S3 stream uploader [8c643074] [9926d15d]
- Fix Azure NPE on missing pool opts [d5c0aabd]
- Fix handling of targetDir when using Fusion fs [2091b272]
- Document aws.batch.retryMode config (#3195) [56f75e0c] <Abhinav Sharma>
22.09.2-edge - 7 Sep 2022
- Fix thread pool race condition on shutdown [8d2b0587]
- Fix Intermediate multipart upload requires a minimum size (#3193) [0b66aed6] <Jorge Aguilera>
- Fix fusion enable detection [3ef91512]
- Add before-afterScript warning to docs (#3167) [09464590] <Kibubu>
- Add httpReadTimeout and httpConnectTimeout config to K8s client [064f9bc4]
- Add support for Wave build & cache repos [98a275ba]
- Finalise secrets feature (#3161) [49021b82]
- Update executor retry config docs (#3001) [aed6c234]
- Change Azure test pool name [0c724504]
- Improve Wave error reporting [b11d0f11]
- Remove unneeded launcher file remapping [a255118d] <Paolo Di Tommaso>
- Update Azure vm types [80f5fbe4]
- Update docs logos (#3174) [529bad81] <Phil Ewels>
22.09.1-edge - 1 Sep 2022
- Add support for Charliecloud v0.28 (#3116) [84f43a33] <Patrick Hüther>
- Add Support for EC-encrypted keys for K8s client [fd759d09]
- Add support for Bridge batch scheduler (#3106) [343c17e6] <Eric Bonnet>
- Add fusion support to local executor [17160bb0] [6cfb51e7]
- Add getTags and getBranches to BitBucketServer [53bd89cd]
- Add retry strategy to httpfs client [55f9c87b]
- Add support for project resources [c2ad6566]
- Add mamba build options [987a13cb] <Paolo Di Tommaso>
- Fix Do not override tower endpoint in the config [41fb1ad0]
- Fix Hyperqueue job names must be less than 40 chars #3151 [8e43670b]
- Fix typo in ConfigBuilder.groovy (#3143) [659e6108] <Mike Lee>
- Fix Resume for dynamic resolved containers [13483ff2]
- Improve fusion env handling [10f35b60]
- Improve foreign file(s) cache detection logic [3a9352c8]
- Rename ModuleBundle to ResourcesBundle [0e51dc0f]
- Use quiet output mode for hyperqueue executor (#3103) [70a91fdf] <Ben Sherman>
- Wave improve conda settings [6f087fec]
- Improve secrets cmd (#3158) [115b2f3d] <Jorge Aguilera>
- Improve Wave resolution strategy [2eb700c6]
- Improve Az Batch err handling and testing [85d31e8d] <Paolo Di Tommaso>
- Bump google-cloud-batch 0.2.2
- Bump spock 2.2
22.09.0-edge - [SKIPPED]
22.08.2-edge - 16 Aug 2022
- Fix queueSize setting is not honoured by AWS Batch executor (again) #3117 [1733bb2e]
- Add `files()` method to docs (#3123) [00bb8896] <Ben Sherman>
- Refactor wave packing [bc876986]
- Improve logging [aa380d5f]
- Update dockerfile [e6329282]
22.08.1-edge - 11 Aug 2022
- Add support for disabling config include [e0859a12]
- Add experimental fusion support [1854f1f2]
- Add support for plugin provided function extension (#3079) [16230c2b] <Jorge Aguilera>
- Add support for AWS Batch logs group (#3092) [4ef043ac] <Ben Sherman>
- Add share identifier to Aws Batch (#3089) [c0253aba] <Ben Sherman>
- Improve Tower cache manager [0091afc5]
- Improve S3 copy via xfer manager [02d2beae]
- Reports a warning when using NXF vars in the config [009ec256]
- Make wake token cache duration config [5f955fc9]
- Patch unable to start non-core plugin [a55f58ff]
- Increase S3 upload chunk size to 100 MB [9c94a080]
- Change Google Batch disk directive to override boot disk size (#3097) [7e1c0686] <Ben Sherman>
- Fix queueSize setting is not honoured by AWS Batch executor (#3093) [d07bb52b] <Ben Sherman>
- Fix Allow disabling scratch with Google Batch [e8e5c721]
- Fix Emit relative path when relative parameter is set (#3072) [39797759] <Jorge Aguilera>
- Bump nf-wave@0.3.0 [e46d341d]
- Bump nf-tower@1.5.1 [cdc2be53]
- Bump nf-google@1.4.1 [c39935a5]
- Bump nf-amazon@1.10.0 [ccdf62d0]
22.08.0-edge - 1 Aug 2022
- Add warning to env config docs (#3083) [ca933c16] <Ben Sherman>
- Add -with-conda CLI option (#3073) [98b2ac80]
- Add simple wave plugin cli commands [8888b866]
- Add default wave plugin [7793a0ec]
- Add boot disk, cpu platform to google batch (#3058) [17a8483d] <Ben Sherman>
- Add support for GPU accelerator to Google Batch (#3056) [f34ad7f6] <Ben Sherman>
- Add support for archive dir to tower plugin [c234681a]
- Add support tower cache backup/restore [bc2f9d13]
- Add disk directive to google batch (#3057) [ec6e290c] <Ben Sherman>
- Add retry when Azure submit fails with OperationTimedOut [6a3f9742]
- Add warning when Google Batch quota is exceeded (#3066) [6b9c52ad] <Ben Sherman>
- Allow fully disabling history file [0a45f858]
- Allow the support function overloading and default parameters (#3011) [042d3857] <Jorge Aguilera>
- Improve S3 file upload/download via Transfer manager [7e8d2a5a] <Jorge Aguilera>
- Prevent overriding container entrypoint [b3a4bf85]
- Update FileTransfer pool settings [503aafce]
- Remove deprecated commands [93228b4b]
- Prevent nextflow config to break tower launch [e059a724]
- Refactor Google Batch executor to use Java API (#3044) [31a6e85c] <Ben Sherman>
- Fix Unable to disable scratch attribute with AWS Batch [1770f73a]
- Fix unit test setting explicit permissions for test files [1c821139] <Jorge Aguilera>
- Fix Default plugins are overriden by config plugins [46cf3bfa] <Paolo Di Tommaso>
- Fix S3 transfer download directory [b7bf9fe5]
- Fix NPE while setting S3 ObjectMetada #3031 [d6163431] <Jorge Aguilera>
- Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b]
- Fix AWS Batch job definition conflict (#3048) [e5084418]
- Fix JAVA_TOOL_OPTIONS breaking launch #1716 [0e7b416d]
- Fix add ps shared objects to Dockerfile (#3033) [1c23b40a] <Ben Sherman>
- Parallelize build integration tests [807800a3]
- Bump google-cloud-nio:0.124.8 [dfaa9d19]
- Bump groovy 3.0.12 [5c900b91]
- Bump Moment.js 2.29.4 [a9ced868]
- Bump gson@2.9.0 [12f17176]
- Bump nf-azure@0.13.4
- Bump nf-google@1.4.0
- Bump nf-tower@1.5.0
- Bump nf-wave@0.2.1
- Bump nf-amazon@1.9.0
22.04.5 - 15 Jul 2022
- Allow fully disabling history file [1a36c9bc]
22.07.1-edge - 13 Jul 2022
- Add support for Google Batch API v1 [4c116d58] [e85d87ee]
- Add time directive support for K8s executor (#2948) [2b6f70a8] <romanaduraciova>
- Add docs aws.client.s3PathStyleAccess config (#3000) [20005500] <Abhinav Sharma>
- Allow to override lsf.conf settings with nextflow config #2862 [dae191a1] <Paolo Di Tommaso>
- Allow hybrid containers execution [0af1bcb3]
- Improve error msg when script file cannot be read [52c2780e]
- Improve error reporting for custom function [877c7931] <Jorge Aguilera>
- Improve error message for missing plugin extension [4a43db84]
- Improve test #3019 [7c37e0be] <Paolo Di Tommaso>
- Rename kuberun -pod-image to -head-image [2576ba62] <Ben Sherman>
- Externalise sqldb plugin source code [17e80b4f] <Paolo Di Tommaso>
- Fix escape unstage outputs with double quotes #2912 #2904 #2790 [49ff02a6] <Ben Sherman>
- Fix Exception when settings AWS Batch containerOptions #3019 [89312ad8] <Paolo Di Tommaso>
- Fix Missing query param in http file (#2918) [43cc8511] <Paolo Di Tommaso>
- Fix Publish copy mode for S3 based path [085f6b2b]
- Fix Fail fast uploads to S3 (#2969) [7fd1a6e1] <Jorge Aguilera>
- Fix null script name in launch info [7118849f]
- Bump commons-code@1.15 [a06b4442]
- Bump jgit@6.2.0 [3331826f]
- Bump snakeyaml@1.30 [de62fd3f]
- Bump gson@2.8.9 [3234ddd5]
22.07.0-edge - [SKIPPED]
22.04.4 - 19 Jun 2022
- Fix Publish copy mode for s3 based path [bb510ce6]
- Add strict mode config setting [b0567e62]
- Update docker base image [b00c1418]
22.06.1-edge - 17 Jun 2022
- Fix CodeCommit creds handling + nf-codecommit@0.1.2 [70fc0745]
- Fix typo in log message [a8f8529d]
- Add more scientists to the list of random names [8d5b36a2] <Marcel Ribeiro Dantas>
22.06.0-edge - 9 Jun 2022
- Add AWS CodeCommit initial support [80fba6e9]
- Add support for 307 and 308 HTTP redirection [92382012]
- Add DirWatcher v2 [209c82cd]
- Add Moriondo in the list of random names [e0abca58]
- Add preview CLI option (#2914) [aa8f1aa4]
- Fix Git config resultion error [64436697]
- Fix StackOverflowError when dump all profiles (#2922) [28cd11a2] <Jorge Aguilera>
- Fix gradle warning message in nf-sqldb (#2921) [b09ceabe] <Jorge Aguilera>
- Fix log for LsfExecutror perTaskReserve attribute [7c3ec874] <Prete>
- Fix external pod deletion for jobs (#2915) [4dd1af7a] <xhejtman>
- Prevent function overloading in module definition [c0b522ab]
- Improve error message of non sensical include (#2623) [285fe49c] <Jorge Aguilera>
- Mount PWD path only when scratch is used [9b3c6e31]
- Stripe sensitive data into strings (#2908) [7fa4c86c] <Jorge Aguilera>
- Dump scm content when trace is enabled [c3117ada]
22.05.0-edge 25 May 2022
- Add Hyperqueue executor (#2896) [ffa5712e] <Henrik Nortamo>
- Add support for K8s Job resource [c70eb12d] <xhejtman>
- Add support for time process directive in GLS executor (#2880) [1402e183] <Florian De Temmerman>
- Add support for priviledge option for K8s containers [7ffe3a02]
- Add DSL1 option to docs (#2836) [d30841a5] <Jose Espinosa-Carrasco>
- Add support for container options to Azure Batch [3f4f00f9]
- Add support for move operation to AWS S3 [8c0ddfd5]
- Add K8s execution hostname in the trace file (#2828) [ebaef92a] <Fabian Lehmann>
- Add support for AWS S3 encyption using a custom KMS key [c1e45aa9] <Paolo Di Tommaso>
- Add support for Micromamba [383e023f]
- Add jaxb-api dependecy to nf-amazon [c1a09f87]
- Add strict mode config setting [ci fast] [696e70b5]
- Add -head-prescript option to kuberun (#2830) [9e387055]
- Fix missing err message on submit failure [233e67f0] (#2899)
- Fix resolve azure devops repositories when projectId is present [2500ff01] <Jorge Aguilera>
- Fix AthenaJdbc into distribution zip [853a1f2a] [4b3579d5] [70ef7ee3] <Jorge Aguilera>
- Fix Inconsistent bool parsing #2881 [40bf2b2a]
- Fix Unable to pull pipeline if config file is not in default branch (#2876) [4ee5b04f] <Jorge Aguilera>
- Fix Prevent crash when scratch dir does not exist (#2888) [9ef44ae5] <Fabian Lehmann>
- Fix DSL1 detection to invalid workflow keyword matching [fe0700b0] (#2879) <Jose Espinosa-Carrasco>
- Fix Aws Batch retry policy on spot reclaim [6e029b79]
- Fix 'false' string in config interpreted as true (#2865) [079a18ce] <Fabian Lehmann>
- Improve Git Provider config logging [d7dbca8ec]
- Improve K8s task handler [1822b2ca]
- Improve missing workflow err message [da101e8f] (#2871)
- Include revision in the Azure Repos provider when specified (#2861) [3342c767] <Jorge Aguilera>
- Remove unnecessary change dir echo [372d1f47]
- Abort execution when accessing undefined params with strict mode [93836081]
- Update docker base image [50cd7956]
- Update default SKU for Azure Batch (#2868) [9ea09dba] <Abhinav Sharma>]
- Update dependencies [405d9545]
- Refactoring to prevent name conflict [aba2671b]
- Few DSL syntax to explicit declaration of plugin extensions (#2820) [bfc4a067] <Jorge Aguilera>
- Sanitize k8s label and annotation keys, don't sanitize annotation value (#2843) [5287a984] <Ben Sherman>
- Docs improvement (#2835) [09e5bca3] <Ben Sherman>
- Bump Jgit 6.1 [7186348c]
- Bump Spock 2.1 [51100d16]
- Bump capsule 1.1.1 [20ec1697]
22.04.3 - 18 May 2022
- Fix dsl1 detection (#2879) [1a7ea0d1] <Jose Espinosa-Carrasco
22.04.2 - 16 May 2022
- Fix stackoverflow error when probe dsl [a05fcbea]
22.04.1 - 15 May 2022
- Improve dsl detection [739b959f]
- Improve missing workflow err message [f3fc081b] (#2871)
- Fix Aws Batch retry policy on spot reclaim [d855f0d9]
- Update default SKU for Azure Batch (#2868) [be60fc14]
- Bump nf-amazon 1.7.2
- Bump nf-azure 0.13.2
22.04.0 - 23 Apr 2022
- Improve error reporting (#2658) [e6ef017d] <Jorge Aguilera>
- Document params-file and improve self-update (#2673) [1e008f47] <Abhinav Sharma>
- Add support for AWS S3 anonymous credentials (#2810) [ae7ba35a]
- Add tolerations K8s pod option (#2763) [7f7cdadc] <Ben Sherman>
- Add support for batched queries to nf-sqldb plugin [3a9dad8b]
- Add `emitColumns` option fromQuery operator [6a6a6eac]
- Add mermaid DAG renderer [653f1e57]
- Fix missing SSE flag on AWS Batch job submit (#2809) [4b3e946d]
- Fix Task execution is not evicted on unexpected execution error (#2787) [05ea0c86] <Fabian Lehmann>
- Document params-file and improve self-update (#2673) [1e008f47] <Abhinav Sharma>
- Improve deprecation message (#2788) [720a84d7] <Fabian Lehmann>
- General docs improvements (#2800) [88acd26b] <Ben Sherman>
- Decrease Aws upload chunk size to 20 MB [086138fb]
- Improve error reporting (#2658) [e6ef017d] <Jorge Aguilera>
- Improve err reporting for Azure Batch [798bae1f]
- Rename echo directive to debug (#2776) [8f906aa5] <Ben Sherman>
- Remove embedded Read The Docs theme [728d545f] <Paolo Di Tommaso>
- Use a remote config in kuberun (#2781) [5485b699] <Fabian Lehmann>
- Start Github Actions also for edited PRs (#2796) [78f5c10f] <Fabian Lehmann>
- Deprecate isDsl2Final method [0f63f1a7]
- Document task object [1c83e21e] <Ben Sherman>
- Bump nf-sqldb@0.4.0 [a137e93a]
- Bump nf-amazon@1.7.1 [912b9bb2]
- Bump moment.js version2.29.2 [a229c1ed]
22.03.1-edge - 6 Apr 2022
- Fix default dsl env detection [b9a09bf6]
- Handle K8s timeout error - 500 status code (#2756) [89a1a46b] <xhejtman>
- Honour background option for kuberun command [b1b0ddd9] <kfrancisdev>
- Add Aws Batch native retry on spot reclaim [cd95e297]
- Improve Aws Batch error reporting [00443510]
- Add missing workflow err report [fa687789]
- Use local nextflow when packing docker image (#2757) [40271b08] <xhejtman>
- Add retry policy Azure create job [792820a2]
- Fix log message in nf-azure [80a0e937] <Manuele Simi>
- Prevent build on tag [5b660c73]
- Fix missing linux/amd64 platform on docker build [05f117d7]
22.03.0-edge - 27 Mar 2022
- Add experimental proxy reg [b3836691]
- Add api to access config raw value [977f6305]
- Add warning for invalid emit names [0045834c]
- Add retry policy on grid submit failure #2696 [673f560c]
- Add config tests #2422 [885993b1]
- Add ability to disable config names check [814a2605]
- Add azcopy fine grain config settings [3998a56b]
- Add binary compatibility with Java 8 [763ec999]
- Add retry policy to Az Batch operations [991c6175]
- Make DSL2 default syntax [4e9189ac] [0c80784a]
- Fix Reduce task command runner script size [6930408b]
- Fix K8s task retry strategy on node termination [bd093081]
- Fix use first config in stack when is into profile #2701 [44bdde8d] <Jorge Aguilera>
- Fix Allow comments after nextflow.enable.dsl (#2746) [6988638b] <Jorge Aguilera>
- Fix allow blank spaces in java path (#2690) [a966020e] <Jorge Aguilera>
- Improve AWS Batch job retry on spot termination [bd8f2e26] [72fbda848]
- Improve error reporting [55466be7]
- Undeprecate merge operation [1649944b]
- Bump support for Java 18 [f3a11e4c]
- Prevent invalid use of large maxForks values [5de0c200]
- Prevent race condition on thread pool creation [3e707a1d]
- Refactor AWS batch job unique token generation [d64f5a21]
- Decrese log verbosity [9237d587] [d1a5e5a8]
- Throw an error if a required secret is missing [8e5129d6]
- Wait for pod to stop running before shutdown (#2667) [505c5ad6]) <kfrancisdev>
- Restore AZ tests [858a4568]
22.02.1-edge - 3 Mar 2022
- Prevent multiple parsing of params file [38bb1f71]
22.02.0-edge - 25 Feb 2022
- Fix Prevent S3 tagging with empty list [ae7db466]
- Fix Azure repos tests [856aacf0]
- Fix isse on includeConfig resolution #2675 [6591a9e1]
- Fix NPE when accessing not existing Git file [6c79f8fd]
- Fix Batch Job name exceed max allowed size [e8b70ca3]
- Fix detect and skip bom mark in files (#2645) [02b06ba3] <Jorge Aguilera>
- Feature: Abort session if publish fails (#2643) [79b3836b] <Jorge Aguilera>
- Fix report overwrite cannot be disabled [202b5c9c] #2647
- Fix match bash interpreter irrespective the path [c2d2b9b2]
- Fix build warning + plugins assemble (#2634) [00dd143a] <Jorge Aguilera>
- Fix CITATION.cff and add automatic validation of your citation metadata [15698a45] <Faruk D>
- Bump nf-amazon@1.5.1 [a4496bb2]
- Bump nf-amazon@1.5.2 [e51139bb]
22.01.0-edge - 7 Feb 2022
- Add support for Tower reports (#2523) [de3d76349] <Jordi Deu-Pons>
- Add RateLimitExceededException when GitHub api limit is reached [ff123c605]
- Add fetch tags and branches to local git provider [e1de8e0ac]
- Add K8s priorityClassName pod option, updated tests (#2585) [51650f8c4] <Ben Sherman>
- Add securityContext pod option to docs (#2584) [19f16f0da] <Ben Sherman>
- Add automountServiceAccountToken option for k8s executor (#2562) [1b5908e4c] <xhejtman>
- Add warn about AWS CLI grandparent path in container (#2565) [67073b0c5] <Simon Li>
- Add affinity option to pod directive (#2522) [640cbed48](3 weeks ago) <Ben Sherman>
- Add ability to specify memory/cpu resources for the control pod (#2559) [13f3e036d] <xhejtman>
- Add `-entry` parameter to pass in k8s executor (#2525) [a96233af6] <xhejtman>
- Add AWS Athena JDBC driver for nf-sqldb plugin (#2500) [462575f05] <Abhinav Sharma>
- Fix process output 'env' as array (#2624) [0a246dc2c] <Jorge Aguilera>
- Fix make date format to change independent from system locale [d1e5f6e76] <Jorge Aguilera>
- Fix double access of params file [459ebab7b] <Paolo Di Tommaso>
- Fix Use account SAS token instead of service SAS token (#2576) [d5125975d] <Florian De Temmerman>
- Fix upload of nested directory outputs on azure (#2578) [85ad55225] [744447155] <Florian De Temmerman>
- Fix Docs Typo (#2556) [942be46f6] <Kibubu>
- Fix NXF_PARAMS_FILE is not recognised #2549 [62f5fe1d9]
- Fix failing tests (4 weeks ago) <Paolo Di Tommaso>
- Fix Unable to use output path with nested properties [ceceb0784]
- Fix Nextflow couldn't parse generated nextflow.config under some circumstances (#2496) [2dfbbc63c] <Fabian Lehmann>
- Fix invalid use of `var` keyword [8418cc8d6]
- Improve k8s executor throwing NodeTerminationException on node shutdown (#2590) [084c8d6ca] <Patrick Hüther>
- Improve docs on `include` statements (#2520) [9c140cee3] <Alexander Toenges>
- Improve core plugins info & logging [dfa544ac9]
- Improve Secrets handling [1c0ad4679] [329502d19] [[26b4be906]]
- Improve DSL2 documentation [048b026f2] [e2e8b5557] <Manuele Simi>
- Improve documentation (#2600) [787a1fd84] <Ben Sherman>
- Allow disabling history file unique check [c3677c311]
- Make S3 parallel download as default [b490f146d] [03dae9d6e]
- Run Azure integration tests only with Java 11 [0890ceeb3]
- Prepare for Java >= 11 build [8c0566fc3] [5ba16dd18] [405b67365]
- Use Standard_A3 instance type for Azure tests [67e7d3ab3] [b97b0010c]
- Refactor cache store using plugins [54bf7a61d]
- Update google cloud docs (#2594) [dfa867953] <Ben Sherman>
- Update the azure docs for registry [96baf288e] <Abhinav Sharma>
- Update copyright info [807a816a5]
- Remove gradle logs about tasks dependencies (#2618) [cae44e00b] <Jorge Aguilera>
- Remove Tika deps for nf-amazon module [95620d42b]
- Remove deprecated validExitStatuas directive [b3117e789] [2188d51a0]
- Remove support for Apache Ignite [d4dc1cfe1] [64d2773fd]
- Bump nf-amazon@1.5.0 as default plugin
- Bump Gradle 7.3.3 [f00bfb0d3]
- Bump nf-amazon@1.5.0 [40f90aa92] [[2bc16732e]]
21.12.1-edge - 22 Dec 2021
- Add tags attribute to publishDir directive [e78a997b5]
- Add ability to disable running jobs cancellation [a13af9a3c]
- Add ability to define containerProperties with using AWS Batch #2471 [ac7f1e71e] <Manuele Simi>
- Add NXF_JVM_ARGS env variable [7afb2deed]
- Improve paths validation [0849d583f]
- Include S3FS provider into nf-amazon plugin [3a7bf8c7a]
- Fix error reporting on missing script file #1951 [e1a0b240a]
- Fix singularity docs #2493 [c66cb3ba7] <Jose Espinosa-Carrasco>
- Fix cross compilation error cause by ByteBuffer [74916100f]
- Fix File staging race condition + beta AWS parallel downloader [b7c262de3]
- Fix enableAIAcaIssuers launcher flag [cd780aabd]
- Fix task index sequence generation [3447e735b]
- Fix Changes process directives invalidates tasks cache [967c1adff]
- Fix Interrupted download of staged files cause execution to fail #1552 [847789fad]
- Fix plugins start/stop for fs command [88d8be1f4]
- Fix for nested params with the same name #2485 [02de4147c] <Jay Carey>
- Fix race condition on plugin autoload status [ab00a50f5]
- Fix failing test with Java 17 [1c6183c92] [4daf8d0a1]
- Note on Azure Batch inactive pools #2483 [7fc116067] <Manuele Simi>
- Remove drip launcher [909f95279]
- Update azure test image [de9d5ee8c]
- Update logging library [a957db646]
- Bump nf-google@1.1.4 [93193a3f3]
- Bump version 21.12.0-edge [9cb7ee81f]
- Bump AWS sdk 1.12.129 [bd7ba1706]
- Bump logback 1.2.9 [29f260717]
- Bump Jsoup 1.14.3 [5776c0391]
- Bump corretto:17.0.1 [f7e047ea4]
21.12.0-edge - 22 Dec 2021 [SKIPPED]
21.10.6 - 21 Dec 2021
- Bump Slf4j 1.7.32
- Bump Logback 1.2.9
21.10.5 - 8 Dec 2021
- Fix race condition on plugin autoload status [73a0893ce]
21.11.0-edge - 5 Dec 2021
- Add process and workflow recursion (PREVIEW) [9f51155e9]
- Fix include no longer works for custom methods [6adfce099]
- Fix Azure executor fail to cleanup jobs on completion [533448be4]
- Fix Missing AWS SSE encryption for begin and exit task files #2452 [2c6665ef9]
- Fix false positive detection of publishDir conflict [6ea54eaea]
- Fix execution hang when reading empty error file [414240a1a]
- Test with java-17 LTS [c2141e826] <Abhinav Sharma>
- Improve plugins dev root detection [b095bee15]
- Change Azure test pool vmType [ad5ad97ab]
- Downgrade Google NIO library to version 0.121.2 [896ec3abd]
- Bump nf-amazon@1.3.4 - bump nxf-s3fs@1.1.3 (6 days ago)
- Bump nf-amazon@1.3.3 nf-google@1.1.3 nf-azure@0.11.2 [92f94bfeb]
- Bump gradle 7.3.1 [2c34a3a27]
21.10.4 - 30 Nov 2021
- Fix include no longer works for custom functions #2469 [e17f6155d]
- Bump nf-amazon@1.3.4 - bump nxf-s3fs@1.1.3 [be893dcb1]
21.10.3 - 23 Nov 2021
- Fix execution hang when reading empty error file [414240a1a]
21.10.2 - 22 Nov 2021
- Fix Azure executor fail to cleanup jobs on completion [4d5b71370]
- Fix Missing AWS SSE encryption for begin and exit task files #2452 [841e6101b]
- Fix Azure integration test [a8051bc01]
- Fix false positive detection of publishDir conflict [292b439ad]
- Make Azure executor logging less verbose [7452e386d]
- Change Azure test pool vmType [85682be7d]
- Downgrade Google NIO library to version 0.121.2 [66ae98820]
- Add java 16 and 17 to the launch.sh for debugging #2457 [3ff0a248e] <mmatthews06>
21.10.1 - 18 Nov 2021
- Fix Azure batch NPE when missing pool spec [84b2983f4]
- Fix Docker bin in image PATH #2445 [d30da377a] <Josh Chorlton>
- Fix failing test with Java 16 [f2d01888d]
- Fix AWS_RETRY_MODE var definition in Batch job [f1a58600d]
- Add docs for AWS endpoints for China region [e96c56d1e]
- Correct description of cross #2446 [e4c7f3d98]
- Dump resolved config when log trace is enabled [2580fb108]
- Bump nf-azure@0.11.1 [eb1e6fbd2]
- Bump nf-amazon@1.3.2 - bump nxf-s3fs@1.1.2 [ae9e885a8]
21.10.0 - 11 Nov 2021
- Add support for Java 17 [cb207cd64]
- Allow override Bash wrapper template files [e6e25ed7c]
- Fix issue with plugins local root sync [1d974a4eb]
- Fix Nextflow does not recognised Failed pod (#2430) [9c80cdea0] (3 days ago) <Mike Smoot>
- Fix Error reporting on Bash launcher creation failure [63e01c324]
- Fix Channel.fromSRA error one some project ids #2156 [dbcbac139]
- Fix Task completion percentage #2440
- Display no workflow warn if no main is defined [0f1295694]
- Invalidate task cache on directive change (EXPERIMENTAL) [62ded3421]
- Upgrade XmlParser used by SraExplorer [543b582b5]
- Use AWS Batch resources requirement for CPUs and memory [1cf2c379c]
- Bump Gradle 7.3 stable + GHA cache [4eaa4f25f]
21.09.1-edge - 28 Oct 2021
- Fix issue with config selectors and DSL2 [4d7d3e972]
- Fix issue evaluating dynamic errorStrategy with AWS Batch [8c6a5a6e2] [ce4d491b1]
- Fix verbose logging [92b113134]
- Fix docker image url [ed24a475d]
- Fix Temporary directories not deleted in on_exit #2406 [181bdf528] <Lukas Jelonek>
- Fix implict authentication for resources served by Tower [e30310b4f]
- Fix No more of 255 channels can be defined into a workflow context #2417 [7f91ecb39]
- Add tip about escaping variables in env scope #2366 <Ben Shealy>
- Add K8s env fieldPath option to pod directive #2363 <Ben Shealy>
- Improve AWS Batch error report fetching CloudWatch logs [b9f9578f1] [e229700ef]
- Improve docs about IAM policies for AWS Batch #2391 <Manuele Simi>
- Accommodate token in password field for Gitlab #2389 [ee32b7726] <Abhinav Sharma>
- Report a warning when main workflow is not defined [83aec6e8b]
- Bump nf-amazon 1.3.0
- Bump nf-tower@1.3.0
- Bump nf-google@1.1.2
21.09.0-edge - 12 Oct 2021
- Add secrets manager (preview) [da2a5ff1a] [2d66f83ca]
- Add Built-in support for Azure File Shares #2285 [a4c3e0ad5]
- Add Azure pool node SKU selection #2360 [9afcac756]
- Add support for protocol option to fromSRA #2087 [371f858ab]
- Add retry on AWS Job definition not-found error [452cae5d8]
- Add ability to define templates library at module level #2332 [7e7d52573]
- Add missing information for pulling images from private registry in Azure Batch #2355 [040e190bd]
- Add $NXF_CLI_OPTS env variable [7d57acca5]
- Add NXF_CACHE_MODE env variable [1c345c497]
- Fix asset directory consistent hashing via sha256 checksum [4c5c0ef41]
- Fix issue invoking extension method with GString params [570e5299c]
- Fix Prevent pipeline stopping when K8s pod is evicted [f9db9cc77]
- Fix clean command for Google storage [dc9625eb9]
- Fix plugins detection in local repo [6441a3882]
- Fix S3 canned ACL documentation #2334 [69216e292]
- Fix docker image build with recent docker [2aad36897] [1e485b32b]
- Fix amazon plugin is not used when using bucketDir option [6a8c50ad4]
- Fix Plugin dependency requirement overrides core plugin #2303 [4d1762fb3]
- Fix Make K8s ImagePullBackOff and ErrImagePull recoverable #2302 [766ffde40]
- Improve cache resume strategy [0b0eae225]
- Improve GH action build compressing integration tests [ab9d747d4]
- Prevent NPE if session is not set [83bb46d94]
- Remove deprecated attribute [50d63b6fb]
- Find newest matching plugin #2303 [e6cf79ff3]
- Documents noproxy variable #2325 [bc769b1b4]
- Bump Groovy 3.0.9 [dee2d6c99]
- Bump nf-sqldb@0.2.0
- Bump nf-amazon@1.2.1
- Bump nf-azure@0.11.0
- Bump nf-google@1.1.1
21.08.0-edge - 30 Aug 2021
- Fix plugin updater version logging [d162eb8b4]
- Fix Nextflow launcher breaks when java path contains blanks #2265 [8097a2a90]
- Fix docker build [efb2f449b]
- Fix NPE in AnsiLogObserver #2283 [cffc683df]
- Fix run script when fixing ownership in aws batch #2262
- Improve plugins auto start [283144474]
- Improve log error reporting [401863085]
- Improve handling of K8s node shutdown [67250c041]
- Update GitHub docs [4532b8e1e]
- Merge nf-sqldb 0.1.0
21.07.0-edge - 6 Aug 2021
- Add support for AWS_MAX_ATTEMPTS variable [3cc543589]
- Add app plugin to gradle build [007bc1cb4]
- Add self pid to tower client [d2e54ea22]
- Add support for head job operationId + log/out files [a7a76cf91]
- Add enable CA Issuers option to NF launcher [8f51dc787]
- Fix Clean cmd fails removing foreign files [8bf8ab720]
- Fix Prevent script var names conflicting with private names #2246 [82bbc180e]
- Fix ENA download URL #2239 [befbabbc8]
- Fix Tower client is not activated launching all packaging #2145 [c507518c2]
- Fix orphaned AWS Batch jobs after pipeline interruption #2169 [65e2a4d05]
- Fix Process error report on target exception #1896 [1bac3f17b]
- Fix Unexpected bool conversion on publishDir enable/overwrite attributes #2220 [651835d2d]
- Fix BatchCleanup toString method [ec9bb5648]
- Improve error reporting [49ac01dbb]
- Improve Unknown host error message [ad41d1e98]
- Improve AWS Batch task handler [eb1aff275]
- Use AWS cli standard retry mode by default [f2f1fdea4]
- Report warn on cache hashing failures [7bf93de06] [3b579c954]
21.04.3 [stable] - 21 Jl 2021
- Fix Tower client is not activated launching all packaging
21.04.2 [stable] - 12 Jul 2021
- Fix Plugin install lock file is not deleted #2103 [29c3e516c]
- Fix Default plugin version lookup [d340a221f]
- Fix BatchCleanup toString method [3c67fa3ae]
- Implicit variable projectDir breaks caching #2186 [7a4d1f1a2]
21.06.0-edge - 3 Jul 2021
- Add Keep alive option to Google LS executor [994222074]
- Add support for FTP proxy and proxy servers authentication [8ec33b04d]
- Add support for plugins groupping [aa5bc7d34]
- Add More details about the reason why a AWS Batch job has failed #2146 [27a4e88b2]
- Add support for extensions priority [ae083f1aa]
- Add stubRun attribute to workflow metadata #2164 [86cfc66fd]
- Add Run tasks under user accounts in Azure Batch #2157 [1c9fc4a40]
- Refactor GLS executor [2c86b79a4] [97fc49c09]
- Refactor AWS batch job def creation [89ce364c9] [986894287]
- Fix Default plugin version lookup [e0c8151d9]
- Fix Negative labels do not work as expected #2155 [491191811]
- Fix PublishDir overwriting task output files [190aa4eaf]
- Fix directory deletion strategy [b96fcedc8]
- Fix Implicit variable projectDir breaks caching #2186 [76417d273]
- Fix Prevent empty download array [9492cde5d]
- Fix output unstage with glob pattern [2d4c3dfcf]
- Fix Connection-reset crashes the workflow [3ee4fd0eb] [1400ded6d] [61bbc240a] [175c66584]
- Fix Slurm does not send soft kill message #2163 [f0ccfc7e8]
- Fix storeDir directive does not work with S3 #2141 [2e95a6a76]
- Fix maven local publish [05cfb7cf7]
- Fix GLS transfer attempts opts [f7c705db5]
- Fix build exportClasspath task [88d27f0c8]
- Fix PbsPro clusterOptions directive priority #2036 [75e3f225e]
- Disallow include nested within a workflow block [7dbf64bea]
- Upgrade AWS SDK minor version #2167 [296afaa8f]
- Improve gsutil transfer throughput [2da120b91]
- Improve config error reporting [6aa102430]
21.05.0-edge - 28 May 2021
- Add support for using mamba with conda (#2030) [10c8385b]
- Add AWS cli native error fail-over [fd7670ef]
- Add support for Container Registry to Az Batch executor (#2078) [12bf2da6]
- Add support for Tower workspace (#2097) [8a4dd3ab]
- Add support custom service account email in Google Cloud LifeSciences executor (#2044) [a642c9ea]
- Add support for Java 16 + Gradle 7 [caace1c5] [e2dd4510] [74e466e0] [1245ab1c] [bfc69fb6]
- Improve tower client error reporting [4efb6bf6]
- Fix Plugin install lock file is not deleted #2103 [b7fdffac]
- Fix Use caller runs policy of default thread pool #2021 [48b4e8ee]
- Fix Error reporting for malformed config [68e5ca18]
- Decrease max par transfers to 4 [c7ea816a]
- Prevent fetching aws instance type when missing container id [f5f96049]
- Use default opts for trace file creation [d8ae94bf]
- Improve Azure Batch executor error code and messages for failed Tasks (#2099) [1d5fa5d5]
- Bump groovy 3.0.8 [aa695e12]
- Bump snakeyaml@1.28 [8d361954]
21.04.1 [stable] - 14 May 2021
- Fix nested params file parse #2091
- Fix Malformed config error reporting #2105
- Fix Use default opts for trace file creation [09e6c6ac]
21.04.0 [stable] - 2 May 2021
- Fix NPE when AWS Batch job container is not returned [412b6fde]
- Fix execution hang when native task fail to submit #2060 [1253485d]
- Update preview message [e1eebdcd]
- Fix nf-ignite all packaging [72b6a428]
- Fix GS failing tests [be4f91e9]
- Fix AWS batch executor fails when using self-contained distribution #2058 [2e344c18]
- Fix groupTuple sort criteria with closure #2020 [28a579a9]
- Patch invalid double number cli parsing #2039 [4de4670c] [dcadaaeb]
- Update sphinx_rtd_theme 0.5.2 [4a165f43]
- Disable cpus option when running docker with legacy opt [1a7854a5]
21.04.0-edge - 8 Apr 2021
- Add readOnly flag to k8s volume mounts (#2013) [33bd24ac]
- Add Start default plugins on-demand #1964 [cf2a9d73]
- Add support for tower workspaceId [e2977688]
- Improve suppor for BitBucket server repos [eb946e27]
- Fix toInt/Long/Float/Double operator hangs with value channel [7c35d985]
- Fix regression caused by nested params handling #1923 [b25af49b]
- Fix Cache invalidation when repo is cloned between runs #1989 [ac526f38]
- Fix Invalid setting of TMP var with singularity #1997 [23f80121] [472cfbdd]
- Fix issue overriding nested params from cli #1923 [cfe6b1d1]
- Fix az path handling curly brackets globs #1969 [c78a1bbf]
- Fix Missing git credentials when checking last commit id [f101308e]
- Fix plugins version check against local installation [535c2bb5]
- Fix local dependant formatting #1962 [2a5cbac1]
- Fix Encode path parameter at GitLab getContentUrl [6f80f651]
- Fix Only use sudo rm with docker #1956 [f9490423]
- Prevent AZ NPE when missing vmtype + better logging #1992 [711362ca]
- Refactor params file var binding #1860 #1972 [330f044a]
- Prevent jobs names longer than 100 chars OAR exec [6daa21b9]
- Bump nf-azure@0.9.6 + nf-amazon@1.0.3 [aff1d355]
- Bump nf-amazon@1.0.3 - s3fs@1.0.9 - solve #1830 [b3b221c1]
- Bump nf-tower@1.1.0 [29fdd9f7]
- Bump nf-amazon@1.0.4 + nxf-s3fs@1.1.0 [c638af80]
- Bump nf-azure@0.9.7 [07c59946]
21.03.0-edge - 5 Mar 2021
- Add support for serializable ValueObject [8dfaadf3]
- Add abilitity to fetch revisioned git assets
- Add support for FixOwnership to AWS batch [24f83741]
- Add support for custom network to GLS #1810 [171f4aa8]
- Add ability to handle list of az vm types [00ced0b3]
- Add tower config scope to docs #1890 f2bd96fa
- Add charliecloud container environment from file (#1909) 4553648b
- Add azcopy tool install mode opts [9e9337d3]
- Update Az default vm type to Standard_D4_v3 [4c6e76b6]
- Update NF console dependency [a2d06e15]
- Remove CDN from timeline reports and make them offline readable #1927 [c0e5a941]
- Fix plugins install failing in some file systems #1882 [8cc43391]
- Fix catch failing commands in nxf_parallel #1884 [dd56f6c1]
- Fix missing error on empty process script [3607f84e]
- Fix GSL path de-serialization issue [c6cf784f]
- Fix Memory unit cannot be a negative number #1902 [abd1c9d9]
- Fix pod spec labels to start with numbers in addition to alphas [79740edf]
- Fix OAR executor log files #1761 [6f2ff4e4]
- Fix issue cause by sleep with subsecond argument [c4be8d00] [63974ac6]
- Fix az blob storage SAS permissions [18a33213]
- Fix sort human-readable tasks in report [6d68f28d]
21.02.0-edge - 1 Feb 2021
- Fix Issue when merging nested cli params #1856 [275e54c4] [fe37da6d]
- Fix job status detection on PBS pro #1840 [c1598908]
- Fix Issue when merging nested cli params #1856 (19 hours ago) <Paolo Di Tommaso>
- Revert the CPU/memory options being passed to singularity VM instead of singularity container [0d04e0f9]
- Add ability to specify plugins with cli [de91218f]
- Decrease upload/download process polling to 0.2secs [6ca2d6ca]
- Remove nf-amazon as default [e6810e90]
- Make plugin services singleton [cacd9328] [5787be6d]
- Make repository provider accessible to subclasses [988bccc6]
- Fix error on plugin downloading #1859 [77cabb3c]
21.01.1-edge - 15 Jan 2021
- Plugins stability improvements [8d849ec9] [bf093826]
- Charliecloud improvements [2242411a]
- Fix issue of FS discovery with dyn plugin loading [bf5e86df]
- Fix crash on startup when mem reported < 0 [095236b8]
- Fix and stability [e4b8afb5]
- Fix launcher on Java11 [c6b78034]
- Add plugins custom version manager (4 days ago) <Paolo Di Tommaso>
- Improve NF version checking [d33ea642]
- Bump plugins minor upgrade [f91bc21e]
21.01.0-edge - 04 Jan 2021
- Merge plugins feature [d959bfdb]
- Prevent twice access remote scm file [b2798556]
- Fix DAG edges not connected correctly #1486 [cece1161]
- Fix k8s executor must provide cpu resource requests #1570 [6896e923]
- Fix http/ftp read buffer size [a2886baf]
- Add support for OAuth Bearer auth [5823c280]
- Add support for basic auth for http/s file provider [6027fcba]
- Add User-Agent info to httpfs requests [222637de]
- Update CPU and RAM for containers (#1833) [ccf5c8ba]
- Move test containes to quay.io [7db053eb] [773be707] [c10a7f53]
20.12.0-edge - 12 Dec 2020
- Add support for charliecloud container engine #1809
- Fix glitch on K8s task progress update [668434f6]
- Upgrade to groovy 3.0.7 [27056035]
20.11.0-edge - 16 Nov 2020
- Fix Allow nextflow to handle http protocol for Singularity images #1791
- Fix params-file overrides config parameters [b03efcac]
- Fix println failing test #1621 [8c6f0f97] [9d2e5850]
- Let output env variables be optional (#1740) [3fca3655]
- Add stub-run feature #1774 [3de45c22] [e2d6d55b]
- Add overwrite option to trace/time/report/dag features #813 [a0615474]
- Allow nested CLI params #1182 [19ab8a8f] [df6204e3]
- Allow setting google projectId in nextflow config [223b5d6c]
- Make binDir accessible from the executor scope [1405a28f]
20.10.0 - 1 Nov 2020
- Add warning for AWS Batch mem request lower than 4 GB [e9240fc9]
- Fix issue with docker images tagged by SHA #1777
- Add support for Bitbucket tags and branches retrivial [5083066e]
- Add support for Tower client bearer authentication [532282ae]
- Fix Skip FS lock when Conda dir exist #1771
- Add support for Java 15 [b1f48884]
- Fix build with Gradle 6.7 [8d7227f0]
20.09.1-edge - 15 Oct Sep 2020
- Prevent USR1 signal to stop jobs #1753
- Add -main-script cli option [702ff64c]
- Improve Singularity image file caching #1706 [dd92772b]
- Fix unexpected default GLS action flags #1749
- Patch unpexpected error on tower serialization [f922324a]
20.09.0-edge - 23 Sep 2020
- Fix invalid error message on missing process #1719 [fc607f11]
- Deduplicate GS file + parallel up/downloads [29d37083]
- Deduplicate S3 file uploads [0b65d61f]
- Fix issue on GS path composition [276f0ed3]
- Add NXF_PARAMS_FILE env var [2e3c9232]
- Allow configurable container mounts [8dc0adf4]
- Refactor common Bash helper functions [22a0ff34] [502309b7]
- Fix race condition creating FTP file system #1725
- Fix invalid checkWarn method invocation [ba052a02]
- Move makeDigest into build.gradle file [a2b5de8f]
- Add variable NXF_CONFIG_FILE [83365aa3]
- Patch use of GString for fromSra apiKey option [a8b81ada]
- Use repository URL instead of Git clone URL [75a04d90]
- Fix Invalid exception capture for missing config [ce427924]
- Fix podman issue on duplicate mounts [661a40e9]
- Fix FromSra illegal character error [5a86d180]
- Fix Allow custom SCM file location #1657 [a90e66e3]
20.08.1-edge - 2 Sep 2020
- Add variable NXF_CONFIG_FILE [d15edcb8]
20.08.0-edge - 24 Aug 2020
- Merge Groovy3 runtime and support for Java 12/13/14
- Use repository URL instead of Git clone URL [102f8b01]
- Fix Invalid exception capture for missing config [8c7accca]
- Fix podman issue on duplicate mounts #1710 [d0cc38de]
- Fix FromSra illegal character error #1700 [a45decfb]
- Fix Allow custom SCM file location #1657 [7c27f895]
- Fix dynamic executors loading [7b9ce82f]
- Fix missing newline on cmd log stdout/err #1705 [1416a388]
- Fix k8s timeline start #1687 [24dff871]
- Remove unneeded parentheses from stdout declaration [dc029c04]
- Merge execution logs command docs [577ec744]
- Passing exact memory to TES executor in GiB #1696 [c8a15545]
- Improve docs replacing suscribe{println it} with view() [f84ccb6f] [cb2d607d]
- Use current environment Bash #1598 #1614 [e70ef87a]
- Include GA4GH support into the standalone binary (make pack) #1666 [e2175d45]
- Update Bitbucket docs [b9b57f83]
- Clone/Pull submodules recursively #1615 [5f20ab6a]
- Bump nf-ignite to version 1.1.0
20.07.1 - 24 Jul 2020
- see 20.07.0 and 20.07.0-RC1
20.07.0 - (skipped)
- Allow unqualified stdin/stdout defintions with DSL2 [bcdcaab6]
20.07.0-RC1 - 21 Jul 2020
- Add Dsl2 enable flag [08238109]
- Add check on invalid scope syntax definition [23c92021]
- Add channel as alias for Channel [05c358c9]
- Add DSL2 deprecation + clean up syntax [1b4b1307]
- Add DOI field to NF manifest #1676 [ec6ee223]
- Improve join duplicate detection [33eb9ef5]
- Improve mix operator error message [8074d714]
- Remove invalid log message [48b1b9f1]
- Fix hidden error message on fail fast run [3b4b377c]
- Disallow upwrapped includes + hard deprecation [19130f87]
- Suppress trap for SIGUSR1 signal #1656 [ca5bcf46]
- Improve error reporting on invalid task id [3921de1a]
20.06.0-edge - 5 Jul 2020
- Add more debug logging for AWS helper [2a62fdf7]
- Add join options failOnDuplicate and failOnMismatch [387366aa]
- Add strict mode flag [4ba5ac18]
- Add support for selecting minimum CPU platform on GCP (#1633) [afc4375d]
- Add missing trace fields to docs [bf2e1637]
- Fix Invalid GLS path composition in staging directories #1654 [e33fff98]
- Fix for feature 1647 that allows non gpu k8s accelerator resources. (#1649) [c1efa29d]
- Fix Issue accessing S3 bucket #1596 [ffc6f843]
- Fix Update getDomain method in ProviderConfig to support local repositories - #1492 (#1624) [651501ac]
20.05.0-edge - 31 May 2020
- Add support for NXF_LOG_NAME env var [cf496615]
- Add exception specialiation for ambiguous repo [a34b1d2a]
- Add support for tower_workflow_id env var [53188126]
- Add config profile names accessor [2784cdb8]
- Add support for Google Cloud buckets with Requester Pays set #1466 [bc9db8d8]
- Add Git tag and branch retrieval [7c97f23f]
- Fix PublishDir error caused by duplicates output files [5f3b69c1]
- Fix weird issue on config resolution [0d0fef4b]
- Fix resolution of malformed configs [fe213e41]
- Fix K8s labels and annotation normalization [6434b9d] #1577 #1584
- Fix minor git path provider ending slash [9888be29]
- Fix bugs in GA4GH TES support (#1589) [26708335]
20.04.1-edge - 19 Apr 2020
- Fix AWS auth with temporary security token [6a7b11b8]
20.04.0-edge - 13 Apr 2020
- Add SGE hr status handling (#1558) [f4db0049]
- Add moduleDir, projectDir and launchDir vars [7832a697] [576a5694]
- Add executor display name rendering [74c90ca9]
- Add ability to pipe custom fun [DSL2] [80bb6485]
- Add Aws Batch container image validation [e73951fa]
- Recognizes more UGE states (#1536) [4dacebbf]
- Prevent invalid process tag values [f2da1357]
- Report Tower backend error cause on failure [da8ac8f5]
- Fix Config cmd should resolve remote projects #889 [c2e0ac0b]
- Fix issue applying branch/multiMap to value channel [e69f39fa]
- Fix Kill signal is not propagated for Singularity container #1561
- Fix docs typos [d7261d2e]
- Fix Minor docs update #1545
- Revert "Bump jline 2.14.9" [ef7040cb]
- Deprecate validExitStatus directive #1564
- Improve error message [DSL2] [f8a0ee1c]
- Add sluper parse method for Path [a54fd03d]
- Report error message when accessing invalid out #1553 [83bd009c]
- Remove deprecated $ config syntax [0a31f9df]
- Remove deprecated workflow publish [DSL2] [1bd7b4a4]
- Remove support for workflow 'get' [d9b91149]
- Remove deprecated process output getter [013a323b]
- Remove deprecated out cardinal getters [414fae94]
- Remove deprecated gpu directive [f48b2c24]
- Minor executor logging [7f94299b]
- Minor improvement createDirIfNotExists API [34211675]
- Bump groovy 2.5.11
20.03.0-edge - 28 Mar 2020
- Add support for GLS private addr #1545 [a481b42b]
- Add AWS batch job def normalise function [79239f05]
- Fix Escape Singularity env variables #1535 [b651a371]
- Add Local executor file system check [ffc92926]
- Add Launch Id to Tower client [d768d2d1]
- Add workflow progress on completion [aea41f37]
- Remove deprecated onFlowStart method [14f12b5f]
- Minor method visibility change [43bc9697]
- Minor log change [130a963b]
- Fix docs broken link [0a1ec9a9]
- Fix typo CVS -> CSV #1500 [d89281c3]
20.02.0-edge - 29 Feb 2020
- Fix Unable to create AWS helper class warn #1504
- Fix Ansi log flickers when variable-length tags are used #1288
- Fix Directive maxForks may cause execution to hang #1432
- Fix Missing tag in ansi log #1503
- Fix PBSPRO res req should always include cpus #1510
- Deprecate workflow publish 7f315a63
20.01.0 - 12 Feb 2020
- Fix ansi logging and line count [4f5c7187]
- Fix Division by 0 in launcher script with Biocontainers #1488
- Fix Run name validation to 80 chars max #1491
- Add GitHub badge to README
- Add Bash version to issue template [78928546]
- Bump jline 2.14.9 [5df2b27e]
20.01.0-rc1 - 6 Feb 2020
- Add ability to extend module params #1484 [17c6acca]
- Add dsl2 command line opt [1cf544d5]
- Add GLS executor docs [574f2098] [7ce2597a]
- Add HTCondor detail on data sharing #1473 [f0af66de]
- Allow aliased process to inherit config settings [DSL2] [1c447e85]
- Allow module inclusion to inherit context params #1484
- Allow multiple inclusion from the same module [DSL2] [a9ae36f9]
- Fix Script template fails to render list of files #1478 [2e97bbbc]
- Fix process name validation when using legacy script [1543365c]
- Fix Early detection Dsl2 declaration #1468 [93a642aa]
- Fix Missing script validation checks #1468 [5d0cf145]
- Revert "Disable ansi log on non-tty env #1417" [98e6758b]
- Minor changes gradle build [619385f1]
- Minor AWS Batch api refactor [c20abc11]
- Improve foreign file detection [50508684]
- Improve GLS location validation [5b89ab50]
- Removed unused module flag [cf19cc9c]
- Update dsl2 docs [5c57c3a8]
20.01.0-edge - 20 Jan 2020
- Add Prevent negative progress stats [87cdddc6]
- Add More cloud tests [7a5dd828]
- Add support for UGE throttled jobs (Tr) #1461 [20408e4b]
- Add progress stats to tower client [781116a4] [138cf0b0]
- Add experimental Podman containers support (#1451) 026866cd
- Add support for Gexf format for DAG rendering [28bfe0ee]
- Improve ansi logging for multilines output [1ce978c3] [004e23eb]
- Improve progress stats and ansi log [0212ba16]
- Improve api to enable wr executor #1148 [21088ad3]
- Update tower trace client requests [138cf0b0]
- Enhance progress execution stats & tracking [a30e2b9a]
- Unexpected output when using Google Storage as work dir #1452
- Fix typos and minor changes [fb2f954f]
- Fix Operator splitFastq fails with PE option and DSL2 enabled #1390
- Fix Container entrypoint when using GLS executor #1291
- Fix GLS file unstaging #1406 [e67ef3be]
- Fix GLS unstage for file patterns #1406
- Fix Scratch directive does not work #1280 [644e9ac7] [6c7291fa]
- Fix Resume fails due to LevelDB exception #1358 [28fa3a6c]
- Fix Conda env activation #1195 [e3919275]
- Fix java command in launch script #1436 [f28b015f]
- Rename variable java to JAVA_BIN [086377d8]
- Removed unused compile deps [686bcd98]
- Bump capsule-maven 1.0.3.2 and fix broken env [004684e3]
- Bump capsule-maven 1.0.3.1 and seqera repo [62964eed]
19.12.0-edge - 20 Dec 2019
- Add GLS assigned zone discovery #1406
- Add Google Life sciences (GLS) executor improvements #1406 [ead29c11] [8228e9b4]
- Add GLS bootDiskSize support #1331 [f118798c] [af8fe16d]
- Add GLS job debugging #1351
- Fix NPE when file pattern is missing [1cbb6e49]
- Fix AWS cloud parsing for NVEe storage and tests
- Fix Disable ansi log on non-tty env #1417
- Fix Allow Singularity image path with blank #1368
- Fix Shell template invalid caching #1422
- Fix Task vars ordering may invalidate cache #1408
- Fix Join operator not matching gstrings #1394
- Fix sigpipe error caused by runner script #1332
- Fix Google Storage bucket with underscore is not recognized #1069 [85cd0cde]
- Fix fromFilePairs can't take list of paths #1405 [c00f5669]
- Refactor onFlowInit to onFlowCreate event [c477eeaf]
- Improve err msg when input files are remove from output [5d5744a8]
- Upgrade to Gradle 6.0.1 [e0c1a3ac]
19.11.0-edge - 2 Dec 2019
- Increase tasks.module to 255 [7332c606]
- Fix Allow the output of process env variables #69 [1c1befc7]
- Fix docs rounding issue #1350 [af824fc7]
- Fix Join operation incorrectly represented in DAG #1346 [9d83ed51]
- Fix Tiny typo in docs #1361
- Fix lost trace/report/timeline file name
- Fix invalid class exception [4308d6a4]
- Fix Invalid dynamic resolution of stageIn/OutMode directive #1374
- Fix No such property stackTraceDepth error #1387 [49450f67] [f5342e71]
- Fix Singularity env variables are not accessible #1386 [036af4a6]
- Fix PublishDir should not create dir when disabled #1381
- Fix Process hangs for non zero exit status #1344
- Fix Output stdout does not support emit attribute #1373
- Fix False positive warning when importing module #1349
- Fix HTCondor queue status command #1353 [a1addc8f]
- Fix Escape file names with blanks #1392
- Fix broken docs tutorial #1366
- Patch Duration unit cannot be a negative number #1384
- Handle ProviderMismatchException in CacheHelper (#1382) [cc584368] [3523f174]
- Introduce workflow take in place of get [DSL2] [e8cbbf08]
- Disable ansi log when using dockerized run [86bc2ada]
- Minor logging change [238b0e6c] [f5342e71] [b707882f] [ce97f073]
- Add multiMap in place of fork operator [afd671c8]
- Add Show Tower init response message as warning
- Add output path includeInputs docs [2ce7e861]
- Add metrics fields check #1360 [5b7f42e9] [caf9f137]
- Add console command to cli help #1347
- Add OAR executor #1343
- Add graphiviz to Docker image #1370
- Removed unused property [9c65426a]
19.10.0 - 21 Oct 2019
- Merge Use a delete function that doesn't follow symlinks #1337
- Merge Allow multiple mounts for the same K8s claim name [1d288a3d] #1284
- Make Google Pipelines logging less verbose [6edd9954]
- Merge Shifterimg workaround for ensuring image pulls #1327
- Merge Add ENDPOINT support for China regions #1323 [636cbfb5]
- Add limit on max field lengths sent by Tower [4d5cabc2]
- Add retry ability to Tower client for 500 class errors [c7f70fc5]