Skip to content

Commit 1bc2b34

Browse files
SHuang-BroadSHuang-Broad
committed
CC create two other helper scripts that need more review
1 parent 6f61cad commit 1bc2b34

4 files changed

Lines changed: 641 additions & 0 deletions

File tree

‎ALL_CALLABLES_IN_TASK_FOLDER.tsv‎

Lines changed: 280 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,280 @@
1+
name class file_path line_number
2+
Minimap2 task wdl/tasks/Alignment/AlignReads.wdl 5
3+
SAMtoPAF task wdl/tasks/Alignment/AlignReads.wdl 147
4+
HaploTagBam task wdl/tasks/Alignment/WhatsHap.wdl 5
5+
Phase task wdl/tasks/Alignment/WhatsHap.wdl 80
6+
Stats task wdl/tasks/Alignment/WhatsHap.wdl 157
7+
Canu workflow wdl/tasks/Assembly/Canu.wdl 5
8+
Correct task wdl/tasks/Assembly/Canu.wdl 60
9+
Trim task wdl/tasks/Assembly/Canu.wdl 118
10+
Assemble task wdl/tasks/Assembly/Canu.wdl 175
11+
Flye workflow wdl/tasks/Assembly/Flye.wdl 5
12+
Assemble task wdl/tasks/Assembly/Flye.wdl 35
13+
Hifiasm workflow wdl/tasks/Assembly/Hifiasm.wdl 6
14+
AssembleForHaplotigs task wdl/tasks/Assembly/Hifiasm.wdl 72
15+
AssembleForAltContigs task wdl/tasks/Assembly/Hifiasm.wdl 169
16+
RaconPolish task wdl/tasks/Assembly/Racon.wdl 3
17+
CollectParentsKmerStats workflow wdl/tasks/Preprocessing/CollectParentsKmerStats.wdl 5
18+
ParentalReadsRepartitionAndMerylConfigure task wdl/tasks/Preprocessing/CollectParentsKmerStats.wdl 92
19+
PrintMerylMemory task wdl/tasks/Preprocessing/CollectParentsKmerStats.wdl 233
20+
MerylCount task wdl/tasks/Preprocessing/CollectParentsKmerStats.wdl 254
21+
MerylMergeAndSubtract task wdl/tasks/Preprocessing/CollectParentsKmerStats.wdl 369
22+
Guppy workflow wdl/tasks/Preprocessing/Guppy.wdl 16
23+
ListFast5s task wdl/tasks/Preprocessing/Guppy.wdl 99
24+
Basecall task wdl/tasks/Preprocessing/Guppy.wdl 138
25+
MakeSequencingSummary task wdl/tasks/Preprocessing/Guppy.wdl 238
26+
MakeFinalSummary task wdl/tasks/Preprocessing/Guppy.wdl 283
27+
FinalizeBasecalls task wdl/tasks/Preprocessing/Guppy.wdl 337
28+
Process workflow wdl/tasks/Preprocessing/Longbow.wdl 16
29+
Peek task wdl/tasks/Preprocessing/Longbow.wdl 147
30+
Annotate task wdl/tasks/Preprocessing/Longbow.wdl 189
31+
Filter task wdl/tasks/Preprocessing/Longbow.wdl 234
32+
Segment task wdl/tasks/Preprocessing/Longbow.wdl 291
33+
Extract task wdl/tasks/Preprocessing/Longbow.wdl 338
34+
Correct task wdl/tasks/Preprocessing/Longbow.wdl 573
35+
Stats task wdl/tasks/Preprocessing/Longbow.wdl 689
36+
Demultiplex task wdl/tasks/Preprocessing/Longbow.wdl 734
37+
MedakaPolish task wdl/tasks/Preprocessing/Medaka.wdl 5
38+
AlignedMetrics workflow wdl/tasks/QC/AlignedMetrics.wdl 6
39+
MakeChrIntervalList task wdl/tasks/QC/AlignedMetrics.wdl 108
40+
MosDepth task wdl/tasks/QC/AlignedMetrics.wdl 150
41+
MosDepthOverBed task wdl/tasks/QC/AlignedMetrics.wdl 212
42+
MosDepthWGS task wdl/tasks/QC/AlignedMetrics.wdl 261
43+
SummarizeDepth task wdl/tasks/QC/AlignedMetrics.wdl 346
44+
CoverageTrack task wdl/tasks/QC/AlignedMetrics.wdl 390
45+
FlagStats task wdl/tasks/QC/AlignedMetrics.wdl 438
46+
ReadNamesAndLengths task wdl/tasks/QC/AlignedMetrics.wdl 480
47+
FilterMQ0Reads task wdl/tasks/QC/AlignedMetrics.wdl 522
48+
ComputeBedCoverage task wdl/tasks/QC/AlignedMetrics.wdl 566
49+
ReadMetrics task wdl/tasks/QC/AlignedMetrics.wdl 613
50+
BamToBed task wdl/tasks/QC/AlignedMetrics.wdl 665
51+
VerifyBamID task wdl/tasks/QC/Contamination.wdl 3
52+
ListGenotypedVCFs task wdl/tasks/QC/Fingerprinting.wdl 5
53+
PickGenotypeVCF task wdl/tasks/QC/Fingerprinting.wdl 40
54+
FilterGenotypesVCF task wdl/tasks/QC/Fingerprinting.wdl 81
55+
ExtractGenotypingSites task wdl/tasks/QC/Fingerprinting.wdl 128
56+
MergeGenotypingSites task wdl/tasks/QC/Fingerprinting.wdl 171
57+
ExtractRelevantGenotypingReads task wdl/tasks/QC/Fingerprinting.wdl 206
58+
ResetCLRBaseQual task wdl/tasks/QC/Fingerprinting.wdl 265
59+
CheckFingerprint task wdl/tasks/QC/Fingerprinting.wdl 327
60+
CheckCLRFingerprint task wdl/tasks/QC/Fingerprinting.wdl 423
61+
ReheaderFullGRCh38VCFtoNoAlt task wdl/tasks/QC/Fingerprinting.wdl 516
62+
FPCheckAoU workflow wdl/tasks/QC/FPCheckAoU.wdl 6
63+
ResolveFPVCFPath task wdl/tasks/QC/FPCheckAoU.wdl 108
64+
ReheaderFullGRCh38VCFtoNoAlt task wdl/tasks/QC/FPCheckAoU.wdl 162
65+
Quast task wdl/tasks/QC/Quast.wdl 5
66+
SummarizeQuastReport task wdl/tasks/QC/Quast.wdl 80
67+
SummarizeCoverages task wdl/tasks/QC/SexConcordance.wdl 3
68+
MakeACall task wdl/tasks/QC/SexConcordance.wdl 37
69+
RemoveMasSeqTruncatedReads task wdl/tasks/Transcriptomics/MASSeq.wdl 5
70+
AdjustUmiSequenceWithAdapterAlignment task wdl/tasks/Transcriptomics/MASSeq.wdl 59
71+
FilterMasSeqReads task wdl/tasks/Transcriptomics/MASSeq.wdl 153
72+
RenameSingleCellBamTagsForMasIsoSeqV0 task wdl/tasks/Transcriptomics/MASSeq.wdl 231
73+
RestoreSingleCellBamTagsForMasIsoSeqV0 task wdl/tasks/Transcriptomics/MASSeq.wdl 290
74+
CreateCountMatrixFromAnnotatedBam task wdl/tasks/Transcriptomics/Postprocessing_Tasks.wdl 5
75+
AggregateUmiAdjustmentStats task wdl/tasks/Transcriptomics/Postprocessing_Tasks.wdl 72
76+
MergeBarcodeCounts task wdl/tasks/Transcriptomics/Postprocessing_Tasks.wdl 182
77+
CreateCountMatrixAnndataFromTsv task wdl/tasks/Transcriptomics/Postprocessing_Tasks.wdl 240
78+
CreateCountMatrixAnndataFromEquivalenceClasses task wdl/tasks/Transcriptomics/Postprocessing_Tasks.wdl 326
79+
SubsetCountsMatrixByGenes task wdl/tasks/Transcriptomics/Postprocessing_Tasks.wdl 425
80+
QuantifyGffComparison task wdl/tasks/Transcriptomics/Postprocessing_Tasks.wdl 469
81+
CombineEqClassFiles task wdl/tasks/Transcriptomics/Postprocessing_Tasks.wdl 564
82+
CopyEqClassInfoToTag task wdl/tasks/Transcriptomics/Postprocessing_Tasks.wdl 638
83+
SplitBamBySampleAndCellBarcodeTask task wdl/tasks/Transcriptomics/Preprocessing_Tasks.wdl 5
84+
DownsampleToIsoSeqEquivalent task wdl/tasks/Transcriptomics/Preprocessing_Tasks.wdl 52
85+
DemuxMasSeqDataByIndex task wdl/tasks/Transcriptomics/Preprocessing_Tasks.wdl 95
86+
MergeDemuxMasSeqByIndexLogs task wdl/tasks/Transcriptomics/Preprocessing_Tasks.wdl 138
87+
SplitBamByContig task wdl/tasks/Transcriptomics/Preprocessing_Tasks.wdl 227
88+
ConvertSplicedBamToGff task wdl/tasks/Transcriptomics/Preprocessing_Tasks.wdl 285
89+
GffCompare task wdl/tasks/Transcriptomics/Preprocessing_Tasks.wdl 336
90+
RestoreOriginalReadNames task wdl/tasks/Transcriptomics/Preprocessing_Tasks.wdl 420
91+
CorrectUmisWithSetCover task wdl/tasks/Transcriptomics/Preprocessing_Tasks.wdl 478
92+
Run_Group task wdl/tasks/Transcriptomics/UMI_Tools.wdl 5
93+
AssignChildLongReadsGivenParentalKmerStats workflow wdl/tasks/Utility/AssignChildLongReads.wdl 8
94+
AssignChildLongReads task wdl/tasks/Utility/AssignChildLongReads.wdl 83
95+
GetReadGroupInfo task wdl/tasks/Utility/BAMutils.wdl 9
96+
GetReadGroupLines task wdl/tasks/Utility/BAMutils.wdl 63
97+
GatherBamMetadata task wdl/tasks/Utility/BAMutils.wdl 105
98+
CountReadGroups task wdl/tasks/Utility/BAMutils.wdl 166
99+
InferSampleName task wdl/tasks/Utility/BAMutils.wdl 199
100+
ValidateSamFile task wdl/tasks/Utility/BAMutils.wdl 244
101+
SamtoolsFlagStats task wdl/tasks/Utility/BAMutils.wdl 329
102+
ParseFlagStatsJson task wdl/tasks/Utility/BAMutils.wdl 397
103+
CountMethylCallReads task wdl/tasks/Utility/BAMutils.wdl 439
104+
CountAlignmentRecords task wdl/tasks/Utility/BAMutils.wdl 498
105+
StreamingBamErrored task wdl/tasks/Utility/BAMutils.wdl 574
106+
CountAlignmentRecordsByFlag task wdl/tasks/Utility/BAMutils.wdl 607
107+
GetDuplicateReadnamesInQnameSortedBam task wdl/tasks/Utility/BAMutils.wdl 713
108+
ResetSamplename task wdl/tasks/Utility/BAMutils.wdl 776
109+
FilterBamByLen task wdl/tasks/Utility/BAMutils.wdl 850
110+
GatherReadsWithoutMethylCalls task wdl/tasks/Utility/BAMutils.wdl 959
111+
SubsetBamToLocusLocal task wdl/tasks/Utility/BAMutils.wdl 1034
112+
DeduplicateQuerynameSortedBam task wdl/tasks/Utility/BAMutils.wdl 1108
113+
BamToFastq task wdl/tasks/Utility/BAMutils.wdl 1182
114+
GetPileup task wdl/tasks/Utility/BAMutils.wdl 1277
115+
BamToRelevantPileup task wdl/tasks/Utility/BAMutils.wdl 1332
116+
SamtoolsReset task wdl/tasks/Utility/BAMutils.wdl 1431
117+
QuerynameSortBamWithSamtools task wdl/tasks/Utility/BAMutils.wdl 1509
118+
QuerynameSortBamWithPicard task wdl/tasks/Utility/BAMutils.wdl 1580
119+
SplitNameSortedUbam task wdl/tasks/Utility/BAMutils.wdl 1648
120+
SplitByRG task wdl/tasks/Utility/BAMutils.wdl 1722
121+
ShardAlignedBam task wdl/tasks/Utility/BAMutils.wdl 1802
122+
MergeBamsWithSamtools task wdl/tasks/Utility/BAMutils.wdl 1928
123+
MergeBamsQuerynameSortedWithPicard task wdl/tasks/Utility/BAMutils.wdl 1997
124+
PreprocessIntervals task wdl/tasks/Utility/cnv_common_tasks.wdl 6
125+
AnnotateIntervals task wdl/tasks/Utility/cnv_common_tasks.wdl 60
126+
FilterIntervals task wdl/tasks/Utility/cnv_common_tasks.wdl 115
127+
CollectCounts task wdl/tasks/Utility/cnv_common_tasks.wdl 186
128+
CollectAllelicCounts task wdl/tasks/Utility/cnv_common_tasks.wdl 289
129+
ScatterIntervals task wdl/tasks/Utility/cnv_common_tasks.wdl 348
130+
PostprocessGermlineCNVCalls task wdl/tasks/Utility/cnv_common_tasks.wdl 419
131+
CollectSampleQualityMetrics task wdl/tasks/Utility/cnv_common_tasks.wdl 521
132+
CollectModelQualityMetrics task wdl/tasks/Utility/cnv_common_tasks.wdl 562
133+
Stats task wdl/tasks/Utility/FastqUtils.wdl 6
134+
FilterByLength task wdl/tasks/Utility/FastqUtils.wdl 65
135+
FilterByLenSeqTk task wdl/tasks/Utility/FastqUtils.wdl 100
136+
FinalizeToFile task wdl/tasks/Utility/Finalize.wdl 5
137+
FinalizeToDir task wdl/tasks/Utility/Finalize.wdl 64
138+
FinalizeTarGzContents task wdl/tasks/Utility/Finalize.wdl 147
139+
WriteCompletionFile task wdl/tasks/Utility/Finalize.wdl 207
140+
WriteNamedFile task wdl/tasks/Utility/Finalize.wdl 247
141+
CompressAndFinalize task wdl/tasks/Utility/Finalize.wdl 288
142+
FinalizeAndCompress task wdl/tasks/Utility/Finalize.wdl 359
143+
TarGZFilesAndSave task wdl/tasks/Utility/Finalize.wdl 428
144+
TarGZFiles task wdl/tasks/Utility/GeneralUtils.wdl 6
145+
GetTodayDate task wdl/tasks/Utility/GeneralUtils.wdl 39
146+
CollapseArrayOfStrings task wdl/tasks/Utility/GeneralUtils.wdl 57
147+
CoerceMapToArrayOfPairs task wdl/tasks/Utility/GeneralUtils.wdl 85
148+
CoerceArrayOfPairsToMap task wdl/tasks/Utility/GeneralUtils.wdl 120
149+
MergeMaps task wdl/tasks/Utility/GeneralUtils.wdl 145
150+
MapToTsv task wdl/tasks/Utility/GeneralUtils.wdl 196
151+
ConcatenateFiles task wdl/tasks/Utility/GeneralUtils.wdl 225
152+
Unzip task wdl/tasks/Utility/GeneralUtils.wdl 251
153+
SendEmailNotification task wdl/tasks/Utility/GeneralUtils.wdl 284
154+
ConvertToHailMT task wdl/tasks/Utility/Hail.wdl 5
155+
MASIsoSeqReport task wdl/tasks/Utility/JupyterNotebooks.wdl 5
156+
FindSequencingSummaryFiles task wdl/tasks/Utility/ONTUtils.wdl 5
157+
GetRunInfo task wdl/tasks/Utility/ONTUtils.wdl 77
158+
ListFiles task wdl/tasks/Utility/ONTUtils.wdl 126
159+
PartitionManifest task wdl/tasks/Utility/ONTUtils.wdl 181
160+
DeduplicateBam task wdl/tasks/Utility/ONTUtils.wdl 232
161+
FindBams task wdl/tasks/Utility/PBUtils.wdl 5
162+
GetRunInfo task wdl/tasks/Utility/PBUtils.wdl 56
163+
ShardLongReads task wdl/tasks/Utility/PBUtils.wdl 117
164+
CCS task wdl/tasks/Utility/PBUtils.wdl 199
165+
ExtractHifiReads task wdl/tasks/Utility/PBUtils.wdl 281
166+
MergeCCSReports task wdl/tasks/Utility/PBUtils.wdl 365
167+
ExtractUncorrectedReads task wdl/tasks/Utility/PBUtils.wdl 418
168+
Demultiplex task wdl/tasks/Utility/PBUtils.wdl 474
169+
MakeDetailedDemultiplexingReport task wdl/tasks/Utility/PBUtils.wdl 565
170+
MakeSummarizedDemultiplexingReport task wdl/tasks/Utility/PBUtils.wdl 618
171+
MakePerBarcodeDemultiplexingReports task wdl/tasks/Utility/PBUtils.wdl 669
172+
RefineTranscriptReads task wdl/tasks/Utility/PBUtils.wdl 728
173+
ClusterTranscripts task wdl/tasks/Utility/PBUtils.wdl 785
174+
PolishTranscripts task wdl/tasks/Utility/PBUtils.wdl 850
175+
Align task wdl/tasks/Utility/PBUtils.wdl 908
176+
PBIndex task wdl/tasks/Utility/PBUtils.wdl 1007
177+
CollapseTranscripts task wdl/tasks/Utility/PBUtils.wdl 1067
178+
SummarizeCCSReport task wdl/tasks/Utility/PBUtils.wdl 1122
179+
SummarizeXMLMetadata task wdl/tasks/Utility/PBUtils.wdl 1185
180+
SummarizePBI task wdl/tasks/Utility/PBUtils.wdl 1238
181+
GetLengthsFromBam task wdl/tasks/Utility/ReadLengths.wdl 5
182+
GetLengthsFromFastq task wdl/tasks/Utility/ReadLengths.wdl 48
183+
GetNumReadsAndShorts task wdl/tasks/Utility/ReadLengths.wdl 91
184+
Dyst task wdl/tasks/Utility/ReadLengths.wdl 125
185+
Peaker task wdl/tasks/Utility/ReadLengths.wdl 157
186+
ReverseYield task wdl/tasks/Utility/ReadLengths.wdl 188
187+
Skewness task wdl/tasks/Utility/ReadLengths.wdl 214
188+
SplitSoftClippedReads task wdl/tasks/Utility/SoftClipper.wdl 3
189+
SplitSoftClippedReadsAssisted task wdl/tasks/Utility/SoftClipper.wdl 61
190+
Quantify task wdl/tasks/Utility/StringTie2.wdl 5
191+
ExtractTranscriptSequences task wdl/tasks/Utility/StringTie2.wdl 73
192+
CompareTranscriptomes task wdl/tasks/Utility/StringTie2.wdl 134
193+
GetDefaultDir task wdl/tasks/Utility/Utils.wdl 5
194+
PrepareManifest task wdl/tasks/Utility/Utils.wdl 54
195+
EchoManifest task wdl/tasks/Utility/Utils.wdl 101
196+
ChunkManifest task wdl/tasks/Utility/Utils.wdl 150
197+
SortBam task wdl/tasks/Utility/Utils.wdl 201
198+
SortSam task wdl/tasks/Utility/Utils.wdl 260
199+
MakeChrIntervalList task wdl/tasks/Utility/Utils.wdl 326
200+
FastaToSam task wdl/tasks/Utility/Utils.wdl 383
201+
CountFastqRecords task wdl/tasks/Utility/Utils.wdl 433
202+
CountFastaRecords task wdl/tasks/Utility/Utils.wdl 489
203+
CountBamRecords task wdl/tasks/Utility/Utils.wdl 540
204+
FilterListOfStrings task wdl/tasks/Utility/Utils.wdl 600
205+
FilterReadsBySamFlags task wdl/tasks/Utility/Utils.wdl 652
206+
DownsampleSam task wdl/tasks/Utility/Utils.wdl 715
207+
GrepCountBamRecords task wdl/tasks/Utility/Utils.wdl 783
208+
GrepCountUniqueBamRecords task wdl/tasks/Utility/Utils.wdl 843
209+
Sum task wdl/tasks/Utility/Utils.wdl 904
210+
Uniq task wdl/tasks/Utility/Utils.wdl 953
211+
Timestamp task wdl/tasks/Utility/Utils.wdl 1003
212+
BamToTable task wdl/tasks/Utility/Utils.wdl 1050
213+
ConvertReads task wdl/tasks/Utility/Utils.wdl 1101
214+
BamToBed task wdl/tasks/Utility/Utils.wdl 1155
215+
BamToFastq task wdl/tasks/Utility/Utils.wdl 1207
216+
MergeFastqs task wdl/tasks/Utility/Utils.wdl 1260
217+
MergeBams task wdl/tasks/Utility/Utils.wdl 1322
218+
Index task wdl/tasks/Utility/Utils.wdl 1382
219+
FilterReadsWithTagValues task wdl/tasks/Utility/Utils.wdl 1436
220+
SubsetBam task wdl/tasks/Utility/Utils.wdl 1500
221+
ExcludeRegionsFromBam task wdl/tasks/Utility/Utils.wdl 1576
222+
SelectFirstNReads task wdl/tasks/Utility/Utils.wdl 1637
223+
ResilientSubsetBam task wdl/tasks/Utility/Utils.wdl 1697
224+
SplitBam task wdl/tasks/Utility/Utils.wdl 1791
225+
Bamtools task wdl/tasks/Utility/Utils.wdl 1851
226+
FilterBamOnTag task wdl/tasks/Utility/Utils.wdl 1906
227+
Cat task wdl/tasks/Utility/Utils.wdl 1965
228+
ListBamContigs task wdl/tasks/Utility/Utils.wdl 2025
229+
ComputeGenomeLength task wdl/tasks/Utility/Utils.wdl 2076
230+
ListFilesOfType task wdl/tasks/Utility/Utils.wdl 2130
231+
StopWorkflow task wdl/tasks/Utility/Utils.wdl 2187
232+
InferSampleName task wdl/tasks/Utility/Utils.wdl 2206
233+
CheckOnSamplenames task wdl/tasks/Utility/Utils.wdl 2252
234+
FixSampleName task wdl/tasks/Utility/Utils.wdl 2283
235+
ComputeAllowedLocalSSD task wdl/tasks/Utility/Utils.wdl 2359
236+
RandomZoneSpewer task wdl/tasks/Utility/Utils.wdl 2405
237+
ShardReads task wdl/tasks/Utility/Utils.wdl 2444
238+
GetCurrentTimestampString task wdl/tasks/Utility/Utils.wdl 2523
239+
GetRawReadGroup task wdl/tasks/Utility/Utils.wdl 2565
240+
FailWithWarning task wdl/tasks/Utility/Utils.wdl 2622
241+
SplitDelimitedString task wdl/tasks/Utility/Utils.wdl 2663
242+
ConstructMap task wdl/tasks/Utility/Utils.wdl 2695
243+
MapToTsv task wdl/tasks/Utility/Utils.wdl 2727
244+
MergePerChrCalls task wdl/tasks/Utility/VariantUtils.wdl 5
245+
MergeAndSortVCFs task wdl/tasks/Utility/VariantUtils.wdl 73
246+
CollectDefinitions task wdl/tasks/Utility/VariantUtils.wdl 207
247+
GetVCFSampleName task wdl/tasks/Utility/VariantUtils.wdl 279
248+
SubsetVCF task wdl/tasks/Utility/VariantUtils.wdl 326
249+
ZipAndIndexVCF task wdl/tasks/Utility/VariantUtils.wdl 385
250+
IndexVCF task wdl/tasks/Utility/VariantUtils.wdl 439
251+
FixSnifflesVCF task wdl/tasks/Utility/VariantUtils.wdl 491
252+
CallAssemblyVariants workflow wdl/tasks/VariantCalling/CallAssemblyVariants.wdl 6
253+
AlignAsPAF task wdl/tasks/VariantCalling/CallAssemblyVariants.wdl 47
254+
Paftools task wdl/tasks/VariantCalling/CallAssemblyVariants.wdl 93
255+
Work workflow wdl/tasks/VariantCalling/CallSmallVariants.wdl 11
256+
Work workflow wdl/tasks/VariantCalling/CallStructuralVariants.wdl 8
257+
Run workflow wdl/tasks/VariantCalling/Clair.wdl 10
258+
Clair task wdl/tasks/VariantCalling/Clair.wdl 64
259+
Run workflow wdl/tasks/VariantCalling/DeepVariant.wdl 7
260+
DV task wdl/tasks/VariantCalling/DeepVariant.wdl 117
261+
DV_gpu task wdl/tasks/VariantCalling/DeepVariant.wdl 209
262+
JointCall workflow wdl/tasks/VariantCalling/GLNexus.wdl 6
263+
GetRanges task wdl/tasks/VariantCalling/GLNexus.wdl 87
264+
ShardVCFByRanges task wdl/tasks/VariantCalling/GLNexus.wdl 141
265+
Call task wdl/tasks/VariantCalling/GLNexus.wdl 200
266+
CompressAndIndex task wdl/tasks/VariantCalling/GLNexus.wdl 266
267+
ConcatBCFs task wdl/tasks/VariantCalling/GLNexus.wdl 316
268+
MarginPhase task wdl/tasks/VariantCalling/MarginPhase.wdl 5
269+
RunPBSV workflow wdl/tasks/VariantCalling/PBSV.wdl 5
270+
Discover task wdl/tasks/VariantCalling/PBSV.wdl 67
271+
Call task wdl/tasks/VariantCalling/PBSV.wdl 175
272+
Run workflow wdl/tasks/VariantCalling/PhaseSmallVariantsAndTagBam.wdl 7
273+
Sniffles2 workflow wdl/tasks/VariantCalling/Sniffles2.wdl 7
274+
SampleSV task wdl/tasks/VariantCalling/Sniffles2.wdl 57
275+
MergeCall task wdl/tasks/VariantCalling/Sniffles2.wdl 138
276+
NanoPlotFromSummary task wdl/tasks/Visualization/NanoPlot.wdl 5
277+
NanoPlotFromRichFastqs task wdl/tasks/Visualization/NanoPlot.wdl 101
278+
NanoPlotFromBam task wdl/tasks/Visualization/NanoPlot.wdl 182
279+
NanoPlotFromUBam task wdl/tasks/Visualization/NanoPlot.wdl 262
280+
SimpleRscript task wdl/tasks/Visualization/VisualizeResourceUsage.wdl 3

0 commit comments

Comments
 (0)