-
-
Notifications
You must be signed in to change notification settings - Fork 4
/
conformance_tests.yaml
3527 lines (3238 loc) · 103 KB
/
conformance_tests.yaml
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
# every "id" must be unique and have no spaces
# every "doc" must be unique
# "id" and "doc" should be meaningful
- job: tests/bwa-mem-job.json
tool: tests/bwa-mem-tool.cwl
output:
args: [bwa, mem, -t, '2', -I, '1,2,3,4', -m, '3',
chr20.fa,
example_human_Illumina.pe_1.fastq,
example_human_Illumina.pe_2.fastq]
id: cl_basic_generation
doc: General test of command line generation
tags: [ required, command_line_tool ]
- output:
args: [bwa, mem, chr20.fa,
"-XXX",
"-YYY", example_human_Illumina.pe_1.fastq,
"-YYY", example_human_Illumina.pe_2.fastq]
job: tests/bwa-mem-job.json
tool: tests/binding-test.cwl
id: nested_prefixes_arrays
doc: Test nested prefixes with arrays
tags: [ required, command_line_tool ]
- output:
args: [tmap, mapall, stage1, map1, --min-seq-length, '20', map2, --min-seq-length,
'20', stage2, map1, --max-seq-length, '20', --min-seq-length, '10', --seed-length,
'16', map2, --max-seed-hits, '-1', --max-seq-length, '20', --min-seq-length, '10']
job: tests/tmap-job.json
tool: tests/tmap-tool.cwl
id: nested_cl_bindings
doc: Test nested command line bindings
tags: [ schema_def, command_line_tool ]
- output:
args: [cat, hello.txt]
job: tests/cat-job.json
tool: tests/cat1-testcli.cwl
id: cl_optional_inputs_missing
doc: Test command line with optional input (missing)
tags: [ required, command_line_tool ]
- output:
args: [cat, -n, hello.txt]
job: tests/cat-n-job.json
tool: tests/cat1-testcli.cwl
id: cl_optional_bindings_provided
doc: Test command line with optional input (provided)
tags: [ required, command_line_tool ]
- output:
"foo": {
"checksum": "sha1$63da67422622fbf9251a046d7a34b7ea0fd4fead",
"class": "File",
"location": "foo.txt",
"size": 22
}
job: tests/cat-job.json
tool: tests/template-tool.cwl
id: initworkdir_expreng_requirements
doc: Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature
tags: [ initial_work_dir, inline_javascript, command_line_tool ]
- job: tests/cat-job.json
output:
output_file:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: output.txt
size: 13
tool: tests/cat3-tool.cwl
id: stdout_redirect_docker
doc: Test command execution in Docker with stdout redirection
tags: [ docker, command_line_tool ]
- job: tests/cat-job.json
tool: tests/cat3-tool-shortcut.cwl
output:
output_file:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: Any
size: 13
id: stdout_redirect_shortcut_docker
doc: Test command execution in Docker with shortcut stdout redirection
tags: [ docker, command_line_tool ]
- job: tests/cat-job.json
output:
output_file:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: cat-out
size: 13
tool: tests/cat3-tool-mediumcut.cwl
id: stdout_redirect_mediumcut_docker
doc: Test command execution in Docker with mediumcut stdout redirection
tags: [ docker, command_line_tool ]
- job: tests/empty.json
tool: tests/stderr.cwl
id: stderr_redirect
doc: Test command line with stderr redirection
output:
output_file:
class: File
checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
size: 4
location: error.txt
tags: [ shell_command, command_line_tool ]
- job: tests/empty.json
tool: tests/stderr-shortcut.cwl
id: stderr_redirect_shortcut
doc: Test command line with stderr redirection, brief syntax
output:
output_file:
class: File
checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
size: 4
location: Any
tags: [ shell_command, command_line_tool ]
- output:
output_file:
class: File
size: 4
checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
location: std.err
job: tests/empty.json
tool: tests/stderr-mediumcut.cwl
id: stderr_redirect_mediumcut
doc: Test command line with stderr redirection, named brief syntax
tags: [ shell_command, command_line_tool ]
- job: tests/cat-job.json
output:
output_txt:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: output.txt
size: 13
tool: tests/cat4-tool.cwl
id: stdinout_redirect_docker
doc: Test command execution in Docker with stdin and stdout redirection
tags: [ required, command_line_tool ]
- job: tests/empty.json
tool: tests/null-expression1-tool.cwl
output:
output: 1
id: expression_any
doc: Test default usage of Any in expressions.
tags: [ inline_javascript, expression_tool ]
- job: tests/null-expression1-job.json
tool: tests/null-expression1-tool.cwl
output:
output: 1
id: expression_any_null
doc: Test explicitly passing null to Any type inputs with default values.
tags: [ inline_javascript, expression_tool ]
- job: tests/null-expression2-job.json
tool: tests/null-expression1-tool.cwl
output:
output: 2
id: expression_any_string
doc: Testing the string 'null' does not trip up an Any with a default value.
tags: [ inline_javascript, expression_tool ]
- job: tests/empty.json
tool: tests/null-expression2-tool.cwl
should_fail: true
id: expression_any_nodefaultany
doc: Test Any without defaults cannot be unspecified.
tags: [ inline_javascript, expression_tool ]
- job: tests/null-expression1-job.json
tool: tests/null-expression2-tool.cwl
should_fail: true
id: expression_any_null_nodefaultany
doc: Test explicitly passing null to Any type without a default value.
tags: [ inline_javascript, expression_tool ]
- job: tests/null-expression2-job.json
tool: tests/null-expression2-tool.cwl
output:
output: 2
id: expression_any_nullstring_nodefaultany
doc: Testing the string 'null' does not trip up an Any without a default value.
tags: [ inline_javascript, expression_tool ]
- job: tests/any-type-job.json
tool: tests/any-type-compat.cwl
output:
output1: ["hello", "world"]
output2: ["foo", "bar"]
output3: hello
id: any_outputSource_compatibility
doc: Testing Any type compatibility in outputSource
tags: [ required, workflow ]
- job: tests/cat-job.json
output:
output:
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
class: File
location: output
size: 13
tool: tests/cat-tool.cwl
id: stdinout_redirect
doc: Test command execution in with stdin and stdout redirection
tags: [ required, command_line_tool ]
- job: tests/parseInt-job.json
output: {output: 42}
tool: tests/parseInt-tool.cwl
id: expression_parseint
doc: Test ExpressionTool with Javascript engine
tags: [ inline_javascript, expression_tool ]
- job: tests/wc-job.json
output: {output: 16}
tool: tests/wc2-tool.cwl
id: expression_outputEval
doc: Test outputEval to transform output
tags: [ inline_javascript, command_line_tool ]
- job: tests/wc-job.json
output: {count_output: 16}
tool: tests/count-lines1-wf.cwl
id: wf_wc_parseInt
doc: Test two step workflow with imported tools
tags: [ inline_javascript, workflow ]
- job: tests/wc-job.json
output: {count_output: 16}
tool: tests/count-lines2-wf.cwl
id: wf_wc_expressiontool
doc: Test two step workflow with inline tools
tags: [ inline_javascript, workflow ]
- job: tests/count-lines3-job.json
output:
count_output: [16, 1]
tool: tests/count-lines3-wf.cwl
id: wf_wc_scatter
doc: Test single step workflow with Scatter step
tags: [ scatter, inline_javascript, workflow ]
- job: tests/count-lines4-job.json
output:
count_output: [16, 1]
tool: tests/count-lines4-wf.cwl
id: wf_wc_scatter_multiple_merge
doc: >-
Test single step workflow with Scatter step and two data links connected to
same input, default merge behavior
tags: [ scatter, multiple_input, inline_javascript, workflow ]
- job: tests/count-lines6-job.json
output:
count_output: [32, 2]
tool: tests/count-lines6-wf.cwl
id: wf_wc_scatter_multiple_nested
doc: >-
Test single step workflow with Scatter step and two data links connected to
same input, nested merge behavior
tags: [ scatter, multiple_input, inline_javascript, workflow ]
- job: tests/count-lines6-job.json
output:
count_output: 34
tool: tests/count-lines7-wf.cwl
id: wf_wc_scatter_multiple_flattened
doc: >-
Test single step workflow with Scatter step and two data links connected to
same input, flattened merge behavior
tags: [ multiple_input, inline_javascript, workflow ]
- job: tests/count-lines4-job.json
output:
count_output: 16
tool: tests/count-lines13-wf.cwl
id: wf_wc_nomultiple
doc: >-
Test when step source is a single-item list and there is no
linkMerge, then it not wrapped in a list, and that
MultipleInputFeatureRequirement is not required.
tags: [ inline_javascript, workflow ]
- job: tests/count-lines4-job.json
output:
count_output: 16
tool: tests/count-lines19-wf.cwl
id: wf_wc_nomultiple_merge_nested
doc: >-
Test when step source is a single-item list and linkMerge is
listed, then it is wrapped in a list.
tags: [ inline_javascript, workflow ]
- job: tests/empty.json
output: {count_output: 1}
tool: tests/count-lines5-wf.cwl
id: wf_input_default_missing
doc: Test workflow with default value for input parameter (missing)
tags: [ inline_javascript, workflow ]
- job: tests/wc-job.json
output: {count_output: 16}
tool: tests/count-lines5-wf.cwl
id: wf_input_default_provided
doc: Test workflow with default value for input parameter (provided)
tags: [ inline_javascript, workflow ]
- job: tests/empty.json
output: {default_output: workflow_default}
tool: tests/echo-wf-default.cwl
id: wf_default_tool_default
doc: Test that workflow defaults override tool defaults
tags: [ required, workflow ]
- job: tests/env-job.json
output:
out:
class: File
checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519
location: out
size: 15
tool: tests/env-tool1.cwl
id: envvar_req
doc: Test EnvVarRequirement
tags: [ env_var, command_line_tool ]
- job: tests/scatter-job1.json
output:
out: ["foo one", "foo two", "foo three", "foo four"]
tool: tests/scatter-wf1.cwl
id: wf_scatter_single_param
doc: Test workflow scatter with single scatter parameter
tags: [ scatter, workflow ]
- job: tests/scatter-job2.json
output:
out: [["foo one three", "foo one four"], ["foo two three", "foo two four"]]
tool: tests/scatter-wf2.cwl
id: wf_scatter_two_nested_crossproduct
doc: Test workflow scatter with two scatter parameters and nested_crossproduct join method
tags: [ scatter, workflow ]
- job: tests/scatter-job2.json
output:
out: ["foo one three", "foo one four", "foo two three", "foo two four"]
tool: "tests/scatter-wf3.cwl#main"
id: wf_scatter_two_flat_crossproduct
doc: Test workflow scatter with two scatter parameters and flat_crossproduct join method
tags: [ scatter, workflow ]
- job: tests/scatter-job2.json
output:
out: ["foo one three", "foo two four"]
tool: "tests/scatter-wf4.cwl#main"
id: wf_scatter_two_dotproduct
doc: Test workflow scatter with two scatter parameters and dotproduct join method
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job1.json
output:
out: []
tool: tests/scatter-wf1.cwl
id: wf_scatter_emptylist
doc: Test workflow scatter with single empty list parameter
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job2.json
output:
out: [[], []]
tool: tests/scatter-wf2.cwl
id: wf_scatter_nested_crossproduct_secondempty
doc: Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job3.json
output:
out: []
tool: "tests/scatter-wf3.cwl#main"
id: wf_scatter_nested_crossproduct_firstempty
doc: Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job2.json
output:
out: []
tool: "tests/scatter-wf3.cwl#main"
id: wf_scatter_flat_crossproduct_oneempty
doc: Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job4.json
output:
out: []
tool: "tests/scatter-wf4.cwl#main"
id: wf_scatter_dotproduct_twoempty
doc: Test workflow scatter with two empty scatter parameters and dotproduct join method
tags: [ scatter, workflow ]
- tool: tests/echo-tool.cwl
job: tests/env-job.json
output:
{"out": "hello test env\n"}
id: any_input_param
doc: Test Any type input parameter
tags: [ required, command_line_tool ]
- job: tests/wc-job.json
output: {count_output: 16}
tool: tests/count-lines8-wf.cwl
id: nested_workflow
doc: Test nested workflow
tags: [ subworkflow, workflow, inline_javascript ]
- job: tests/env-job.json
output:
out:
class: File
checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519
location: out
size: 15
tool: tests/env-wf1.cwl
id: requirement_priority
doc: Test requirement priority
tags: [ env_var, workflow ]
- job: tests/env-job.json
output:
out:
class: File
checksum: sha1$cdc1e84968261d6a7575b5305945471f8be199b6
location: out
size: 9
tool: tests/env-wf2.cwl
id: requirement_override_hints
doc: Test requirements override hints
tags: [ env_var, workflow ]
- job: tests/env-job.json
output:
out:
class: File
checksum: sha1$cdc1e84968261d6a7575b5305945471f8be199b6
location: out
size: 9
tool: tests/env-wf3.cwl
id: requirement_workflow_steps
doc: Test requirements on workflow steps
tags: [ env_var, workflow ]
- job: tests/empty.json
output: {count_output: 16}
tool: tests/count-lines9-wf.cwl
id: step_input_default_value
doc: Test default value on step input parameter
tags: [ inline_javascript, workflow ]
- job: tests/empty.json
output: {count_output: 16}
tool: tests/count-lines11-wf.cwl
id: step_input_default_value_nosource
doc: Test use default value on step input parameter with empty source
tags: [ inline_javascript, workflow ]
- job: tests/file1-null.json
output: {count_output: 16}
tool: tests/count-lines11-wf.cwl
id: step_input_default_value_nullsource
doc: Test use default value on step input parameter with null source
tags: [ inline_javascript, workflow ]
- job: tests/cat-job.json
output: {count_output: 1}
tool: tests/count-lines11-wf.cwl
id: step_input_default_value_overriden
doc: Test default value on step input parameter overridden by provided source
tags: [ inline_javascript, workflow ]
- job: tests/revsort-job.json
output:
output:
class: File
checksum: sha1$b9214658cc453331b62c2282b772a5c063dbd284
location: output.txt
size: 1111
tool: tests/revsort.cwl
id: wf_simple
doc: Test simple workflow
tags: [ required, workflow ]
- job: tests/cat-job.json
output:
output_file:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: output.txt
size: 13
tool: tests/cat5-tool.cwl
id: hints_unknown_ignored
doc: Test unknown hints are ignored.
tags: [ required, command_line_tool ]
- job: tests/search-job.json
output:
outfile:
class: File
checksum: sha1$e2dc9daaef945ac15f01c238ed2f1660f60909a0
location: result.txt
size: 142
indexedfile: {
"location": "input.txt",
"class": "File",
"checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",
"secondaryFiles": [
{
"location": "input.txt.idx1",
"class": "File",
"checksum": "sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44",
"size": 1500
},
{
"location": "input.idx2",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"location": "input.txt.idx3",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"location": "input.txt.idx4",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"location": "input.txt.idx5",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"location": "input.idx6.txt",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"class": "File",
"location": "input.txt.idx7",
"size": 0
},
{
"checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
"class": "File",
"location": "hello.txt",
"size": 13
},
{
"class": "Directory",
"listing": [{
"basename": "index",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"class": "File",
"location": "index",
"size": 0
}],
"location": "input.txt_idx8",
}
],
"size": 1111
}
tool: "tests/search.cwl#main"
id: initial_workdir_secondary_files_expr
doc: >-
Test InitialWorkDirRequirement linking input files and capturing secondaryFiles
on input and output. Also tests the use of a variety of parameter references
and expressions in the secondaryFiles field.
tags: [ initial_work_dir, inline_javascript, workflow ]
- job: tests/rename-job.json
output:
outfile:
class: File
checksum: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
location: fish.txt
size: 1111
tool: tests/rename.cwl
id: rename
doc: >-
Test InitialWorkDirRequirement with expression in filename.
tags: [ initial_work_dir, command_line_tool ]
- job: tests/string-job.json
output:
out:
class: File
checksum: sha1$6a47aa22b2a9d13a66a24b3ee5eaed95ce4753cf
location: example.conf
size: 16
tool: tests/iwdr-entry.cwl
id: initial_workdir_trailingnl
doc: Test if trailing newline is present in file entry in InitialWorkDir
tags: [ initial_work_dir, command_line_tool ]
- job: tests/wc-job.json
output:
output: 16
tool: tests/wc4-tool.cwl
id: inline_expressions
doc: >-
Test inline expressions
tags: [ inline_javascript, command_line_tool ]
- job: tests/schemadef-job.json
output:
output:
location: output.txt
size: 12
class: File
checksum: "sha1$f12e6cfe70f3253f70b0dbde17c692e7fb0f1e5e"
tool: tests/schemadef-tool.cwl
id: schemadef_req_tool_param
doc: >-
Test SchemaDefRequirement definition used in tool parameter
tags: [ schema_def, command_line_tool ]
- job: tests/schemadef-job.json
output:
output:
location: output.txt
size: 12
class: File
checksum: "sha1$f12e6cfe70f3253f70b0dbde17c692e7fb0f1e5e"
tool: tests/schemadef-wf.cwl
id: schemadef_req_wf_param
doc: >-
Test SchemaDefRequirement definition used in workflow parameter
tags: [ schema_def, workflow ]
- job: tests/empty.json
output: {
"t1": {
"bar": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
}
},
"t10": true,
"t11": true,
"t12": null,
"t13": "-zab1",
"t14": "-zab1",
"t15": "-zab1",
"t16": "-zab1",
"t17": "zab1 zab1",
"t18": "zab1 zab1",
"t19": "zab1 zab1",
"t2": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t20": "zab1 zab1",
"t21": "2 2",
"t22": "true true",
"t23": "true true",
"t24": "null null",
"t25": "b",
"t26": "b b",
"t3": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t4": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t5": "zab1",
"t6": "zab1",
"t7": "zab1",
"t8": "zab1",
"t9": 2,
"t27": null,
"t28": 3
}
tool: tests/params.cwl
id: param_evaluation_noexpr
doc: Test parameter evaluation, no support for JS expressions
tags: [ required, command_line_tool ]
- job: tests/empty.json
output: {
"t1": {
"bar": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
}
},
"t10": true,
"t11": true,
"t12": null,
"t13": "-zab1",
"t14": "-zab1",
"t15": "-zab1",
"t16": "-zab1",
"t17": "zab1 zab1",
"t18": "zab1 zab1",
"t19": "zab1 zab1",
"t2": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t20": "zab1 zab1",
"t21": "2 2",
"t22": "true true",
"t23": "true true",
"t24": "null null",
"t25": "b",
"t26": "b b",
"t3": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t4": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t5": "zab1",
"t6": "zab1",
"t7": "zab1",
"t8": "zab1",
"t9": 2,
"t27": null,
"t28": 3
}
tool: tests/params2.cwl
id: param_evaluation_expr
doc: >-
Test parameter evaluation, with support for JS expressions
tags: [ inline_javascript, command_line_tool ]
- output: {}
job: tests/cat-job.json
tool: tests/metadata.cwl
id: metadata
doc: Test metadata
tags: [ required, command_line_tool ]
- job: tests/formattest-job.json
output:
output:
"location": "output.txt"
"format": "http://edamontology.org/format_2330"
"size": 1111
"class": "File"
"checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f"
tool: tests/formattest.cwl
id: format_checking
doc: >-
Test simple format checking.
tags: [ required, command_line_tool ]
- job: tests/formattest2-job.json
output:
output:
"location": "output.txt"
"format": "http://edamontology.org/format_1929"
"size": 12010
"class": "File"
"checksum": "sha1$971d88faeda85a796752ecf752b7e2e34f1337ce"
tool: tests/formattest2.cwl
id: format_checking_subclass
doc: >-
Test format checking against ontology using subclassOf.
tags: [ required, command_line_tool ]
- job: tests/formattest2-job.json
output:
output:
"location": "output.txt"
"format": "http://edamontology.org/format_1929"
"size": 12010
"class": "File"
"checksum": "sha1$971d88faeda85a796752ecf752b7e2e34f1337ce"
tool: tests/formattest3.cwl
id: format_checking_equivalentclass
doc: >-
Test format checking against ontology using equivalentClass.
tags: [ required, command_line_tool ]
- tool: tests/optional-output.cwl
job: tests/cat-job.json
output:
optional_file: null
output_file:
location: output.txt
size: 13
class: "File"
checksum: "sha1$47a013e660d408619d894b20806b1d5086aab03b"
id: output_secondaryfile_optional
doc: >-
Test optional output file and optional secondaryFile on output.
tags: [ docker, command_line_tool ]
- job: tests/empty.json
output:
out: "\n"
tool: tests/vf-concat.cwl
id: valuefrom_ignored_null
doc: Test that valueFrom is ignored when the parameter is null
tags: [ inline_javascript, command_line_tool ]
- job: tests/cat-job.json
output:
out: "a string\n"
tool: tests/vf-concat.cwl
id: valuefrom_secondexpr_ignored
doc: Test that second expression in concatenated valueFrom is not ignored
tags: [ inline_javascript, command_line_tool ]
- job: tests/step-valuefrom-wf.json
output: {count_output: 16}
tool: tests/step-valuefrom-wf.cwl
id: valuefrom_wf_step
doc: Test valueFrom on workflow step.
tags: [ step_input, inline_javascript, workflow ]
- job: tests/step-valuefrom-job.json
output: {val: "3\n"}
tool: tests/step-valuefrom2-wf.cwl
id: valuefrom_wf_step_multiple
doc: Test valueFrom on workflow step with multiple sources
tags: [ step_input, inline_javascript, multiple_input, workflow ]
- job: tests/step-valuefrom-job.json
output: {val: "3\n"}
tool: tests/step-valuefrom3-wf.cwl
id: valuefrom_wf_step_other
doc: Test valueFrom on workflow step referencing other inputs
tags: [ step_input, inline_javascript, workflow ]
- job: tests/record-output-job.json
output:
"orec": {
"ofoo": {
"location": "foo",
"size": 1111,
"class": "File",
"checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"
},
"obar": {
"location": "bar",
"size": 12010,
"class": "File",
"checksum": "sha1$aeb3d11bdf536511649129f4077d5cda6a324118"
}
}
tool: tests/record-output.cwl
id: record_output_binding
doc: Test record type output binding.
tags: [ shell_command, command_line_tool ]
- job: tests/empty.json
output: {
"foo": {
"location": "foo",
"class": "File",
"checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
"size": 4
}
}
tool: tests/test-cwl-out.cwl
id: docker_json_output_path
doc: >-
Test support for reading cwl.output.json when running in a Docker container
and just 'path' is provided.
tags: [ shell_command, command_line_tool ]
- job: tests/empty.json
output: {
"foo": {
"location": "foo",
"class": "File",
"checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
"size": 4
}
}
tool: tests/test-cwl-out2.cwl
id: docker_json_output_location
doc: >-
Test support for reading cwl.output.json when running in a Docker container
and just 'location' is provided.
tags: [ shell_command, command_line_tool ]
- job: tests/empty.json
output: {
"foo": {
"location": "foo",
"class": "File",
"checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
"size": 4
}
}
tool: tests/test-cwl-out3.cwl
id: json_output_path_relative
doc: >-
Test support for reading cwl.output.json where 'path' is relative path in output dir.
tags: [ required, command_line_tool ]
- job: tests/empty.json
output: {
"foo": {
"location": "foo",
"class": "File",
"checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
"size": 4
}
}
tool: tests/test-cwl-out4.cwl
id: json_output_location_relative
doc: >-
Test support for reading cwl.output.json where 'location' is relative reference to output dir.
tags: [ required, command_line_tool ]
- job: tests/abc.json
output:
files: [{
"location": "a",
"size": 0,
"class": "File",