-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathCNVSomaticPairWorkflow.cwl
1311 lines (1282 loc) · 41.2 KB
/
CNVSomaticPairWorkflow.cwl
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
#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
id: CNVSomaticPairWorkflow
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
- id: common_sites
type: File
- id: intervals
type: File
- id: blacklist_intervals
type: File?
- id: tumor_bam
type: File
secondaryFiles:
- ^.bai
- id: normal_bam
type: File[]?
default: []
secondaryFiles:
- ^.bai
- id: read_count_pon
type: File
- id: ref_fasta
type: File
secondaryFiles:
- .fai
- ^.dict
- id: gatk_docker
type: string
- id: gatk4_jar_override
type:
- File
- string?
- id: preemptible_attempts
type: int?
- id: emergency_extra_disk
type: int?
- id: padding
type: int?
- id: bin_length
type: int?
- id: mem_gb_for_preprocess_intervals
type: int?
- id: collect_counts_format
type: string?
- id: mem_gb_for_collect_counts
type: int?
- id: minimum_base_quality
type: string?
- id: mem_gb_for_collect_allelic_counts
type: int?
- id: number_of_eigensamples
type: int?
- id: mem_gb_for_denoise_read_counts
type: int?
- id: max_num_segments_per_chromosome
type: int?
- id: min_total_allele_count
type: int?
- id: min_total_allele_count_normal
type: int?
- id: genotyping_homozygous_log_ratio_threshold
type: float?
- id: genotyping_base_error_rate
type: float?
- id: kernel_variance_copy_ratio
type: float?
- id: kernel_variance_allele_fraction
type: float?
- id: kernel_scaling_allele_fraction
type: float?
- id: kernel_approximation_dimension
type: int?
- id: window_sizes
type: int[]?
default: [8, 16, 32, 64, 128, 256]
- id: num_changepoints_penalty_factor
type: float?
- id: minor_allele_fraction_prior_alpha
type: float?
- id: num_samples_copy_ratio
type: int?
- id: num_burn_in_copy_ratio
type: int?
- id: num_samples_allele_fraction
type: int?
- id: num_burn_in_allele_fraction
type: int?
- id: smoothing_threshold_copy_ratio
type: float?
- id: smoothing_threshold_allele_fraction
type: float?
- id: max_num_smoothing_iterations
type: int?
- id: num_smoothing_iterations_per_fit
type: int?
- id: mem_gb_for_model_segments
type: int?
- id: neutral_segment_copy_ratio_lower_bound
type: float?
- id: neutral_segment_copy_ratio_upper_bound
type: float?
- id: outlier_neutral_segment_copy_ratio_z_score_threshold
type: float?
- id: calling_copy_ratio_z_score_threshold
type: float?
- id: mem_gb_for_call_copy_ratio_segments
type: int?
- id: minimum_contig_length
type: int?
- id: mem_gb_for_plotting
type: int?
outputs:
- id: preprocessed_intervals
type: File
outputSource: PreprocessIntervals/preprocessed_intervals
- id: read_counts_entity_ids
type: string
outputSource: CollectCountsTumor/entity_id
- id: read_counts_tumor
type: File
outputSource: CollectCountsTumor/counts
- id: allelic_counts_entity_id_tumor
type: string
outputSource: CollectAllelicCountsTumor/entity_id
- id: allelic_counts_tumor
type: File
outputSource: CollectAllelicCountsTumor/allelic_counts
- id: denoised_copy_ratios_tumor
type: File
outputSource: DenoiseReadCountsTumor/denoised_copy_ratios
- id: standardized_copy_ratios_tumor
type: File
outputSource: DenoiseReadCountsTumor/standardized_copy_ratios
- id: het_allelic_counts_tumor
type: File
outputSource: ModelSegmentsTumor/het_allelic_counts
- id: normal_het_allelic_counts_tumor
type: File
outputSource: ModelSegmentsTumor/normal_het_allelic_counts
- id: copy_ratio_only_segments_tumor
type: File
outputSource: ModelSegmentsTumor/copy_ratio_only_segments
- id: copy_ratio_legacy_segments_tumor
type: File
outputSource: ModelSegmentsTumor/copy_ratio_legacy_segments
- id: allele_fraction_legacy_segments_tumor
type: File
outputSource: ModelSegmentsTumor/allele_fraction_legacy_segments
- id: modeled_segments_begin_tumor
type: File
outputSource: ModelSegmentsTumor/modeled_segments_begin
- id: copy_ratio_parameters_begin_tumor
type: File
outputSource: ModelSegmentsTumor/copy_ratio_parameters_begin
- id: allele_fraction_parameters_begin_tumor
type: File
outputSource: ModelSegmentsTumor/allele_fraction_parameters_begin
- id: modeled_segments_tumor
type: File
outputSource: ModelSegmentsTumor/modeled_segments
- id: copy_ratio_parameters_tumor
type: File
outputSource: ModelSegmentsTumor/copy_ratio_parameters
- id: allele_fraction_parameters_tumor
type: File
outputSource: ModelSegmentsTumor/allele_fraction_parameters
- id: called_copy_ratio_segments_tumor
type: File
outputSource: CallCopyRatioSegmentsTumor/called_copy_ratio_segments
- id: called_copy_ratio_legacy_segments_tumor
type: File
outputSource: CallCopyRatioSegmentsTumor/called_copy_ratio_legacy_segments
- id: denoised_copy_ratios_plot_tumor
type: File
outputSource: PlotDenoisedCopyRatiosTumor/denoised_copy_ratios_plot
- id: standardized_MAD_tumor
type: File
outputSource: PlotDenoisedCopyRatiosTumor/standardized_MAD
- id: standardized_MAD_value_tumor
type: float
outputSource: PlotDenoisedCopyRatiosTumor/standardized_MAD_value
- id: denoised_MAD_tumor
type: File
outputSource: PlotDenoisedCopyRatiosTumor/denoised_MAD
- id: denoised_MAD_value_tumor
type: float
outputSource: PlotDenoisedCopyRatiosTumor/denoised_MAD_value
- id: delta_MAD_tumor
type: File
outputSource: PlotDenoisedCopyRatiosTumor/delta_MAD
- id: delta_MAD_value_tumor
type: float
outputSource: PlotDenoisedCopyRatiosTumor/delta_MAD_value
- id: scaled_delta_MAD_tumor
type: File
outputSource: PlotDenoisedCopyRatiosTumor/scaled_delta_MAD
- id: scaled_delta_MAD_value_tumor
type: float
outputSource: PlotDenoisedCopyRatiosTumor/scaled_delta_MAD_value
- id: modeled_segments_plot_tumor
type: File
outputSource: PlotModeledSegmentsTumor/modeled_segments_plot
- id: read_counts_entity_id_normal
type: string?
outputSource: UnScatter_read_counts_entity_id_normal/string_
- id: read_counts_normal
type: File?
outputSource: UnScatter_read_counts_normal/File_
- id: allelic_counts_entity_id_normal
type: string?
outputSource: UnScatter_allelic_counts_entity_id_normal/string_
- id: allelic_counts_normal
type: File?
outputSource: UnScatter_allelic_counts_normal/File_
- id: denoised_copy_ratios_normal
type: File?
outputSource: UnScatter_denoised_copy_ratios_normal/File_
- id: standardized_copy_ratios_normal
type: File?
outputSource: UnScatter_standardized_copy_ratios_normal/File_
- id: het_allelic_counts_normal
type: File?
outputSource: UnScatter_het_allelic_counts_normal/File_
- id: normal_het_allelic_counts_normal
type: File?
outputSource: UnScatter_normal_het_allelic_counts_normal/File_
- id: copy_ratio_only_segments_normal
type: File?
outputSource: UnScatter_copy_ratio_only_segments_normal/File_
- id: copy_ratio_legacy_segments_normal
type: File?
outputSource: UnScatter_copy_ratio_legacy_segments_normal/File_
- id: allele_fraction_legacy_segments_normal
type: File?
outputSource: UnScatter_allele_fraction_legacy_segments_normal/File_
- id: modeled_segments_begin_normal
type: File?
outputSource: UnScatter_modeled_segments_begin_normal/File_
- id: copy_ratio_parameters_begin_normal
type: File?
outputSource: UnScatter_copy_ratio_parameters_begin_normal/File_
- id: allele_fraction_parameters_begin_normal
type: File?
outputSource: UnScatter_allele_fraction_parameters_begin_normal/File_
- id: modeled_segments_normal
type: File?
outputSource: UnScatter_modeled_segments_normal/File_
- id: copy_ratio_parameters_normal
type: File?
outputSource: UnScatter_copy_ratio_parameters_normal/File_
- id: allele_fraction_parameters_normal
type: File?
outputSource: UnScatter_allele_fraction_parameters_normal/File_
- id: called_copy_ratio_segments_normal
type: File?
outputSource: UnScattercalled_copy_ratio_segments_normal/File_
- id: called_copy_ratio_legacy_segments_normal
type: File?
outputSource: UnScattercalled_copy_ratio_legacy_segments_normal/File_
- id: denoised_copy_ratios_plot_normal
type: File?
outputSource: UnScatterdenoised_copy_ratios_plot/File_
- id: standardized_MAD_normal
type: File?
outputSource: UnScatterstandardized_MAD/File_
- id: standardized_MAD_value_normal
type: float?
outputSource: UnScatterstandardized_MAD_value/float_
- id: denoised_MAD_normal
type: File?
outputSource: UnScatterdenoised_MAD/File_
- id: denoised_MAD_value_normal
type: float?
outputSource: UnScatterdenoised_MAD_value/float_
- id: delta_MAD_normal
type: File?
outputSource: UnScatterdelta_MAD/File_
- id: delta_MAD_value_normal
type: float?
outputSource: UnScatterdelta_MAD_value/float_
- id: scaled_delta_MAD_normal
type: File?
outputSource: UnScatterscaled_delta_MAD/File_
- id: scaled_delta_MAD_value_normal
type: float?
outputSource: UnScatterscaled_delta_MAD_value/float_
- id: modeled_segments_plot_normal
type: File?
outputSource: UnScattermodeled_segments_plot/File_
steps:
- id: PreprocessIntervals
in:
- id: intervals
source: intervals
- id: common_sites
source: common_sites
- id: blacklist_intervals
source: blacklist_intervals
- id: ref_fasta
source: ref_fasta
- id: padding
source: padding
- id: bin_length
source: bin_length
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_preprocess_intervals
- id: disk_space_gb
valueFrom:
${
var ref_size = Math.ceil(inputs.ref_fasta.size + inputs.ref_fasta.secondaryFiles[0].size + inputs.ref_fasta.secondaryFiles[1].size);
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
return(ref_size+disk_pad);
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/PreprocessIntervals.cwl
out:
- id: preprocessed_intervals
- id: CollectCountsTumor
in:
- id: intervals
source: PreprocessIntervals/preprocessed_intervals
- id: bam
source: tumor_bam
- id: ref_fasta
source: ref_fasta
- id: enable_indexing
default: false
- id: format
source: collect_counts_format
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_collect_counts
- id: emergency_extra_disk
source: emergency_extra_disk
- id: common_sites
source: common_sites
- id: disk_space_gb
valueFrom:
${
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
var tumor_bam_size = Math.ceil(inputs.bam.size + inputs.bam.secondaryFiles[0].size);
return(tumor_bam_size + Math.ceil(inputs.intervals.size) + disk_pad);
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/CollectCounts.cwl
out:
- id: entity_id
- id: counts
- id: CollectAllelicCountsTumor
in:
- id: intervals
source: intervals
- id: common_sites
source: common_sites
- id: bam
source: tumor_bam
- id: ref_fasta
source: ref_fasta
- id: minimum_base_quality
source: minimum_base_quality
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_collect_allelic_counts
- id: emergency_extra_disk
source: emergency_extra_disk
- id: disk_space_gb
valueFrom:
${
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
var ref_size = Math.ceil(inputs.ref_fasta.size + inputs.ref_fasta.secondaryFiles[0].size + inputs.ref_fasta.secondaryFiles[1].size);
var tumor_bam_size = Math.ceil(inputs.bam.size + inputs.bam.secondaryFiles[0].size);
return(tumor_bam_size + ref_size + disk_pad);
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/CollectAllelicCounts.cwl
out:
- id: entity_id
- id: allelic_counts
- id: DenoiseReadCountsTumor
in:
- id: entity_id
source: CollectCountsTumor/entity_id
- id: read_counts
source: CollectCountsTumor/counts
- id: read_count_pon
source: read_count_pon
- id: number_of_eigensamples
source: number_of_eigensamples
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_denoise_read_counts
- id: emergency_extra_disk
source: emergency_extra_disk
- id: intervals
source: intervals
- id: common_sites
source: common_sites
- id: disk_space_gb
valueFrom:
${
var read_count_pon_size = Math.ceil(inputs.read_count_pon.size);
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
return(read_count_pon_size + Math.ceil(inputs.read_counts.size) + disk_pad)
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/DenoiseReadCounts.cwl
out:
- id: standardized_copy_ratios
- id: denoised_copy_ratios
- id: CollectAllelicCountsNormal
scatter: bam
in:
- id: common_sites
source: common_sites
- id: bam
source: normal_bam
- id: ref_fasta
source: ref_fasta
- id: minimum_base_quality
source: minimum_base_quality
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_collect_allelic_counts
- id: emergency_extra_disk
source: emergency_extra_disk
- id: intervals
source: intervals
- id: disk_space_gb
valueFrom:
${
var ref_size = Math.ceil(inputs.ref_fasta.size + inputs.ref_fasta.secondaryFiles[0].size + inputs.ref_fasta.secondaryFiles[1].size);
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
var normal_bam_size = 0;
if (inputs.bam){
normal_bam_size = Math.ceil(inputs.bam.size + inputs.bam.secondaryFiles[0].size);
}
return(normal_bam_size + ref_size + disk_pad);
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/CollectAllelicCounts.cwl
out:
- id: entity_id
- id: allelic_counts
- id: UnScatter_allelic_counts_entity_id_normal
in:
- id: input_array
source: CollectAllelicCountsNormal/entity_id
run: tools/UnScatterString.cwl
out:
- id: string_
- id: UnScatter_allelic_counts_normal
in:
- id: input_array
source: CollectAllelicCountsNormal/allelic_counts
run: tools/UnScatterFile.cwl
out:
- id: File_
- id: ModelSegmentsTumor
in:
- id: entity_id
source: CollectCountsTumor/entity_id
- id: denoised_copy_ratios
source: DenoiseReadCountsTumor/denoised_copy_ratios
- id: allelic_counts
source: CollectAllelicCountsTumor/allelic_counts
- id: normal_allelic_counts
source: UnScatter_allelic_counts_normal/File_
- id: max_num_segments_per_chromosome
source: max_num_segments_per_chromosome
- id: min_total_allele_count
source: min_total_allele_count
- id: min_total_allele_count_normal
source: min_total_allele_count_normal
- id: genotyping_homozygous_log_ratio_threshold
source: genotyping_homozygous_log_ratio_threshold
- id: genotyping_base_error_rate
source: genotyping_base_error_rate
- id: kernel_variance_copy_ratio
source: kernel_variance_copy_ratio
- id: kernel_variance_allele_fraction
source: kernel_variance_allele_fraction
- id: kernel_scaling_allele_fraction
source: kernel_scaling_allele_fraction
- id: kernel_approximation_dimension
source: kernel_approximation_dimension
- id: window_sizes
source: window_sizes
- id: num_changepoints_penalty_factor
source: num_changepoints_penalty_factor
- id: minor_allele_fraction_prior_alpha
source: minor_allele_fraction_prior_alpha
- id: num_samples_copy_ratio
source: num_samples_copy_ratio
- id: num_burn_in_copy_ratio
source: num_burn_in_copy_ratio
- id: num_samples_allele_fraction
source: num_samples_allele_fraction
- id: num_burn_in_allele_fraction
source: num_burn_in_allele_fraction
- id: smoothing_threshold_copy_ratio
source: smoothing_threshold_copy_ratio
- id: smoothing_threshold_allele_fraction
source: smoothing_threshold_allele_fraction
- id: max_num_smoothing_iterations
source: max_num_smoothing_iterations
- id: num_smoothing_iterations_per_fit
source: num_smoothing_iterations_per_fit
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_model_segments
- id: emergency_extra_disk
source: emergency_extra_disk
- id: intervals
source: intervals
- id: common_sites
source: common_sites
- id: normal_bam
source: normal_bam
- id: disk_space_gb
source: [UnScatter_allelic_counts_normal/File_, DenoiseReadCountsTumor/denoised_copy_ratios, CollectAllelicCountsTumor/allelic_counts]
valueFrom:
${
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
var model_segments_normal_portion = 0;
if (inputs.normal_bam.length > 0){
model_segments_normal_portion = Math.ceil(self[0].size);
}
return(Math.ceil(self[1].size) + Math.ceil(self[2].size) + model_segments_normal_portion + disk_pad);
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/ModelSegments.cwl
out:
- id: het_allelic_counts
- id: normal_het_allelic_counts
- id: copy_ratio_only_segments
- id: copy_ratio_legacy_segments
- id: allele_fraction_legacy_segments
- id: modeled_segments_begin
- id: copy_ratio_parameters_begin
- id: allele_fraction_parameters_begin
- id: modeled_segments
- id: copy_ratio_parameters
- id: allele_fraction_parameters
- id: CallCopyRatioSegmentsTumor
in:
- id: entity_id
source: CollectCountsTumor/entity_id
- id: copy_ratio_segments
source: ModelSegmentsTumor/copy_ratio_only_segments
- id: neutral_segment_copy_ratio_lower_bound
source: neutral_segment_copy_ratio_lower_bound
- id: neutral_segment_copy_ratio_upper_bound
source: neutral_segment_copy_ratio_upper_bound
- id: outlier_neutral_segment_copy_ratio_z_score_threshold
source: outlier_neutral_segment_copy_ratio_z_score_threshold
- id: calling_copy_ratio_z_score_threshold
source: calling_copy_ratio_z_score_threshold
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_call_copy_ratio_segments
- id: ref_fasta
source: ref_fasta
- id: emergency_extra_disk
source: emergency_extra_disk
- id: intervals
source: intervals
- id: common_sites
source: common_sites
- id: disk_space_gb
source: [DenoiseReadCountsTumor/denoised_copy_ratios, ModelSegmentsTumor/copy_ratio_only_segments]
valueFrom:
${
var ref_size = Math.ceil(inputs.ref_fasta.size + inputs.ref_fasta.secondaryFiles[0].size + inputs.ref_fasta.secondaryFiles[1].size);
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
return(Math.ceil(self[0].size) + Math.ceil(self[1].size) + disk_pad);
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/CallCopyRatioSegments.cwl
out:
- id: called_copy_ratio_segments
- id: called_copy_ratio_legacy_segments
- id: PlotDenoisedCopyRatiosTumor
in:
- id: entity_id
source: CollectCountsTumor/entity_id
- id: standardized_copy_ratios
source: DenoiseReadCountsTumor/standardized_copy_ratios
- id: denoised_copy_ratios
source: DenoiseReadCountsTumor/denoised_copy_ratios
- id: ref_fasta_dict
valueFrom: $(inputs.ref_fasta.secondaryFiles[1])
- id: minimum_contig_length
source: minimum_contig_length
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: ref_fasta
source: ref_fasta
- id: emergency_extra_disk
source: emergency_extra_disk
- id: intervals
source: intervals
- id: common_sites
source: common_sites
- id: disk_space_gb
source: [DenoiseReadCountsTumor/standardized_copy_ratios, DenoiseReadCountsTumor/denoised_copy_ratios, ModelSegmentsTumor/het_allelic_counts, ModelSegmentsTumor/modeled_segments]
valueFrom:
${
var ref_size = Math.ceil(inputs.ref_fasta.size + inputs.ref_fasta.secondaryFiles[0].size + inputs.ref_fasta.secondaryFiles[1].size);
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
return(ref_size + Math.ceil(self[0].size) + Math.ceil(self[1].size) + Math.ceil(self[2].size) + Math.ceil(self[3].size) + disk_pad)
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/PlotDenoisedCopyRatios.cwl
out:
- id: denoised_copy_ratios_plot
- id: standardized_MAD
- id: standardized_MAD_value
- id: denoised_MAD
- id: denoised_MAD_value
- id: delta_MAD
- id: delta_MAD_value
- id: scaled_delta_MAD
- id: scaled_delta_MAD_value
- id: PlotModeledSegmentsTumor
in:
- id: entity_id
source: CollectCountsTumor/entity_id
- id: denoised_copy_ratios
source: DenoiseReadCountsTumor/denoised_copy_ratios
- id: het_allelic_counts
source: ModelSegmentsTumor/het_allelic_counts
- id: modeled_segments
source: ModelSegmentsTumor/modeled_segments
- id: ref_fasta
source: ref_fasta
- id: ref_fasta_dict
valueFrom: $(inputs.ref_fasta.secondaryFiles[1])
- id: minimum_contig_length
source: minimum_contig_length
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: preemptible_attempts
source: preemptible_attempts
run: tools/PlotModeledSegments.cwl
out:
- id: modeled_segments_plot
- id: CollectCountsNormal
scatter: bam
in:
- id: intervals
source: PreprocessIntervals/preprocessed_intervals
- id: bam
source: normal_bam
- id: ref_fasta
source: ref_fasta
- id: enable_indexing
default: false
- id: format
source: collect_counts_format
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_collect_counts
- id: emergency_extra_disk
source: emergency_extra_disk
- id: common_sites
source: common_sites
- id: disk_space_gb
valueFrom:
${
var normal_bam_size = 0;
if (inputs.bam){
normal_bam_size = Math.ceil(inputs.bam.size + inputs.bam.secondaryFiles[0].size);
}
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
return(normal_bam_size + Math.ceil(inputs.intervals.size) + disk_pad);
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/CollectCounts.cwl
out:
- id: entity_id
- id: counts
- id: UnScatter_read_counts_entity_id_normal
in:
- id: input_array
source: CollectCountsNormal/entity_id
run: tools/UnScatterString.cwl
out:
- id: string_
- id: UnScatter_read_counts_normal
in:
- id: input_array
source: CollectCountsNormal/counts
run: tools/UnScatterFile.cwl
out:
- id: File_
- id: DenoiseReadCountsNormal
scatter: normal_bam
in:
- id: normal_bam
source: normal_bam
- id: entity_id
source: UnScatter_read_counts_entity_id_normal/string_
- id: read_counts
source: UnScatter_read_counts_normal/File_
- id: read_count_pon
source: read_count_pon
- id: number_of_eigensamples
source: number_of_eigensamples
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_denoise_read_counts
- id: emergency_extra_disk
source: emergency_extra_disk
- id: intervals
source: intervals
- id: common_sites
source: common_sites
- id: disk_space_gb
valueFrom:
${
var read_count_pon_size = Math.ceil(inputs.read_count_pon.size)
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
return(read_count_pon_size + Math.ceil(inputs.read_counts.size) + disk_pad)
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/DenoiseReadCounts.cwl
out:
- id: standardized_copy_ratios
- id: denoised_copy_ratios
- id: UnScatter_standardized_copy_ratios_normal
in:
- id: input_array
source: DenoiseReadCountsNormal/standardized_copy_ratios
run: tools/UnScatterFile.cwl
out:
- id: File_
- id: UnScatter_denoised_copy_ratios_normal
in:
- id: input_array
source: DenoiseReadCountsNormal/denoised_copy_ratios
run: tools/UnScatterFile.cwl
out:
- id: File_
- id: ModelSegmentsNormal
scatter: normal_bam
in:
- id: normal_bam
source: normal_bam
- id: entity_id
source: UnScatter_read_counts_entity_id_normal/string_
- id: denoised_copy_ratios
source: UnScatter_denoised_copy_ratios_normal/File_
- id: allelic_counts
source: UnScatter_allelic_counts_normal/File_
- id: max_num_segments_per_chromosome
source: max_num_segments_per_chromosome
- id: min_total_allele_count
source: min_total_allele_count
- id: min_total_allele_count_normal
source: min_total_allele_count_normal
- id: genotyping_homozygous_log_ratio_threshold
source: genotyping_homozygous_log_ratio_threshold
- id: genotyping_base_error_rate
source: genotyping_base_error_rate
- id: kernel_variance_copy_ratio
source: kernel_variance_copy_ratio
- id: kernel_variance_allele_fraction
source: kernel_variance_allele_fraction
- id: kernel_scaling_allele_fraction
source: kernel_scaling_allele_fraction
- id: kernel_approximation_dimension
source: kernel_approximation_dimension
- id: window_sizes
source: window_sizes
- id: num_changepoints_penalty_factor
source: num_changepoints_penalty_factor
- id: minor_allele_fraction_prior_alpha
source: minor_allele_fraction_prior_alpha
- id: num_samples_copy_ratio
source: num_samples_copy_ratio
- id: num_burn_in_copy_ratio
source: num_burn_in_copy_ratio
- id: num_samples_allele_fraction
source: num_samples_allele_fraction
- id: num_burn_in_allele_fraction
source: num_burn_in_allele_fraction
- id: smoothing_threshold_copy_ratio
source: smoothing_threshold_copy_ratio
- id: smoothing_threshold_allele_fraction
source: smoothing_threshold_allele_fraction
- id: max_num_smoothing_iterations
source: max_num_smoothing_iterations
- id: num_smoothing_iterations_per_fit
source: num_smoothing_iterations_per_fit
- id: gatk4_jar_override
source: gatk4_jar_override
- id: gatk_docker
source: gatk_docker
- id: mem_gb
source: mem_gb_for_model_segments
- id: emergency_extra_disk
source: emergency_extra_disk
- id: intervals
source: intervals
- id: common_sites
source: common_sites
- id: disk_space_gb
source: [DenoiseReadCountsNormal/denoised_copy_ratios, UnScatter_allelic_counts_normal/File_]
valueFrom:
${
var gatk4_override_size = 0;
if(inputs.gatk4_jar_override){
var gatk4_override_size = Math.ceil(inputs.gatk4_jar_override.size);
}
var emergency_extra_disk_size = 0;
if(inputs.emergency_extra_disk){
var emergency_extra_disk_size = inputs.emergency_extra_disk;
}
var disk_pad = 20 + Math.ceil(inputs.intervals.size) + Math.ceil(inputs.common_sites.size) + gatk4_override_size + emergency_extra_disk_size;
return(Math.ceil(self[0].size) + Math.ceil(self[1].size) + disk_pad)
}
- id: preemptible_attempts
source: preemptible_attempts
run: tools/ModelSegments.cwl
out:
- id: het_allelic_counts
- id: normal_het_allelic_counts
- id: copy_ratio_only_segments
- id: copy_ratio_legacy_segments
- id: allele_fraction_legacy_segments
- id: modeled_segments_begin
- id: copy_ratio_parameters_begin
- id: allele_fraction_parameters_begin
- id: modeled_segments
- id: copy_ratio_parameters
- id: allele_fraction_parameters
- id: UnScatter_het_allelic_counts_normal
in:
- id: input_array
source: ModelSegmentsNormal/het_allelic_counts
run: tools/UnScatterFile.cwl
out:
- id: File_
- id: UnScatter_normal_het_allelic_counts_normal
in:
- id: input_array