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broadinstitute · Dec 11, 2024 · 7883336 · 7883336
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commit 7883336
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diff --git a/dot/AlignAndCheckFingerprintCCS.dot b/dot/AlignAndCheckFingerprintCCS.dot
@@ -33,8 +33,8 @@ digraph {
 		"call-saveFPRes" [label=saveFPRes shape=cds]
 		"if-L112C5" [label="" height=0 margin=0 style=invis width=0]
 	}
-	"call-Guess" -> "call-ShardLongReads"
 	"call-arbitrary" -> "call-ShardLongReads"
+	"call-Guess" -> "call-ShardLongReads"
 	"call-ShardLongReads" -> "scatter-L62C9-unaligned_bam" [lhead="cluster-scatter-L62C9-unaligned_bam"]
 	"call-AlignReads" -> "call-MergeAlignedReads"
 	"call-MergeAlignedReads" -> "decl-aBAM"
@@ -43,8 +43,8 @@ digraph {
 	"call-AlignReadsTogether" -> "decl-aBAI"
 	"decl-aBAM" -> "call-IndexAlignedReads"
 	"decl-aBAM" -> "call-CollectPacBioAlignedMetrics"
-	"call-IndexAlignedReads" -> "call-CollectPacBioAlignedMetrics"
 	"decl-aBAI" -> "call-CollectPacBioAlignedMetrics"
+	"call-IndexAlignedReads" -> "call-CollectPacBioAlignedMetrics"
 	"call-CollectPacBioAlignedMetrics" -> "call-saveAlnMetrics"
 	"decl-aBAM" -> "call-FPCheckAoU"
 	"decl-aBAI" -> "call-FPCheckAoU"

diff --git a/dot/BenchmarkVCFs.dot b/dot/BenchmarkVCFs.dot
@@ -116,8 +116,8 @@ digraph {
 	"call-CreateIntervalList" -> "call-StratConvertIntervals"
 	"call-StratConvertIntervals" -> "decl-stratBeds"
 	"call-StratConvertIntervals" -> "decl-stratILs"
-	"decl-stratBeds" -> "scatter-L198C5-strat" [lhead="cluster-scatter-L198C5-strat"]
 	"decl-stratILs" -> "scatter-L198C5-strat" [lhead="cluster-scatter-L198C5-strat"]
+	"decl-stratBeds" -> "scatter-L198C5-strat" [lhead="cluster-scatter-L198C5-strat"]
 	"call-CreateIntervalList" -> "call-ConfidenceConvertIntervals"
 	"call-ConfidenceConvertIntervals" -> "call-CheckForVariantsEval"
 	"call-ConfidenceConvertIntervals" -> "call-CheckForVariantsTruth"
@@ -131,24 +131,24 @@ digraph {
 	"call-StandardVcfEval" -> "call-CountUNKVcfEval"
 	"call-CheckForVariantsTruth" -> "decl-areVariants"
 	"call-CheckForVariantsEval" -> "decl-areVariants"
+	"call-StandardVcfEval" -> "call-SummariseVcfEval"
+	"call-CountUNKVcfEval" -> "call-SummariseVcfEval"
 	"call-VcfEvalWriteXMLfile" -> "call-SummariseVcfEval"
 	"decl-areVariants" -> "call-SummariseVcfEval"
-	"call-CountUNKVcfEval" -> "call-SummariseVcfEval"
-	"call-StandardVcfEval" -> "call-SummariseVcfEval"
-	"call-StandardVcfEval" -> "decl-annotatedVcfsList"
 	"decl-outputPrefix" -> "decl-annotatedVcfsList"
+	"call-StandardVcfEval" -> "decl-annotatedVcfsList"
 	"call-ConfidenceConvertIntervals" -> "decl-annotatedVcfsList"
 	"decl-annotatedVcfsList" -> "scatter-L315C5-indelCombo" [lhead="cluster-scatter-L315C5-indelCombo"]
 	"call-EvalIndelLengthVcfEval" -> "call-VcfEvalIndelWriteXMLfile"
-	"call-EvalIndelLengthVcfEval" -> "call-VcfEvalSummariseForIndelSelection"
 	"call-VcfEvalIndelWriteXMLfile" -> "call-VcfEvalSummariseForIndelSelection"
+	"call-EvalIndelLengthVcfEval" -> "call-VcfEvalSummariseForIndelSelection"
 	"decl-actualVariantSelectors" -> "scatter-L383C5-selectorCombo" [lhead="cluster-scatter-L383C5-selectorCombo"]
 	"decl-annotatedVcfsList" -> "scatter-L383C5-selectorCombo" [lhead="cluster-scatter-L383C5-selectorCombo"]
 	"call-EvalSelectorVcfEval" -> "call-VcfEvalSelectorWriteXMLfile"
-	"call-VcfEvalSelectorWriteXMLfile" -> "call-VcfEvalSummariseForVariantSelection"
 	"call-EvalSelectorVcfEval" -> "call-VcfEvalSummariseForVariantSelection"
-	"call-VcfEvalSummariseForIndelSelection" -> "decl-summaries"
+	"call-VcfEvalSelectorWriteXMLfile" -> "call-VcfEvalSummariseForVariantSelection"
 	"call-VcfEvalSummariseForVariantSelection" -> "decl-summaries"
 	"call-SummariseVcfEval" -> "decl-summaries"
+	"call-VcfEvalSummariseForIndelSelection" -> "decl-summaries"
 	"decl-summaries" -> "call-CombineSummaries"
 }
diff --git a/dot/BroadOnPremMalariaPipeline_1_Alignment_and_Variant_Calling.dot b/dot/BroadOnPremMalariaPipeline_1_Alignment_and_Variant_Calling.dot
@@ -47,10 +47,10 @@ digraph {
 	"call-t_012_IndexRealignIndels" -> "call-t_012_BQSR"
 	"call-t_011_RealignIndels" -> "call-t_012_BQSR"
 	"call-t_012_BQSR" -> "call-t_013_IndexBQSR"
-	"call-t_013_IndexBQSR" -> "call-t_013_HaplotypeCaller"
 	"call-t_012_BQSR" -> "call-t_013_HaplotypeCaller"
-	"call-t_013_IndexBQSR" -> "call-t_014_HaplotypeCallerGvcfMode"
+	"call-t_013_IndexBQSR" -> "call-t_013_HaplotypeCaller"
 	"call-t_012_BQSR" -> "call-t_014_HaplotypeCallerGvcfMode"
+	"call-t_013_IndexBQSR" -> "call-t_014_HaplotypeCallerGvcfMode"
 	"call-t_013_HaplotypeCaller" -> "call-t_015_VariantRecalibrator"
 	"call-t_013_HaplotypeCaller" -> "call-t_016_SortCompressIndexRawVCF"
 	"call-t_015_VariantRecalibrator" -> "call-t_017_SortCompressIndexVCF"

diff --git a/dot/CallVariantsONT.dot b/dot/CallVariantsONT.dot
@@ -57,12 +57,12 @@ digraph {
 		"if-L189C5" [label="" height=0 margin=0 style=invis width=0]
 	}
 	"call-SmallVariantsScatterPrepp" -> "scatter-L86C9-c" [lhead="cluster-scatter-L86C9-c"]
-	"call-SmallVariantsScatter" -> "call-Clair"
 	"call-arbitrary" -> "call-Clair"
+	"call-SmallVariantsScatter" -> "call-Clair"
 	"call-Clair" -> "call-MergeAndSortClairVCFs"
 	"call-Clair" -> "call-MergeAndSortClair_gVCFs"
-	"call-size_balanced_scatter" -> "call-Pepper"
 	"call-arbitrary" -> "call-Pepper"
+	"call-size_balanced_scatter" -> "call-Pepper"
 	"call-Pepper" -> "call-MergeDeepVariantGVCFs"
 	"call-Pepper" -> "call-MergeDeepVariantPhasedVCFs"
 	"call-Pepper" -> "call-MergeDeepVariantVCFs"

diff --git a/dot/CallVariantsPBCCS.dot b/dot/CallVariantsPBCCS.dot
@@ -56,12 +56,12 @@ digraph {
 		"if-L197C5" [label="" height=0 margin=0 style=invis width=0]
 	}
 	"call-SmallVariantsScatterPrepp" -> "scatter-L83C9-c" [lhead="cluster-scatter-L83C9-c"]
-	"call-SmallVariantsScatter" -> "call-Clair"
 	"call-arbitrary" -> "call-Clair"
+	"call-SmallVariantsScatter" -> "call-Clair"
 	"call-Clair" -> "call-MergeAndSortClairVCFs"
 	"call-Clair" -> "call-MergeAndSortClair_gVCFs"
-	"call-size_balanced_scatter" -> "call-CCSPepper"
 	"call-arbitrary" -> "call-CCSPepper"
+	"call-size_balanced_scatter" -> "call-CCSPepper"
 	"call-CCSPepper" -> "call-MergeDeepVariantGVCFs"
 	"call-CCSPepper" -> "call-MergeDeepVariantVCFs"
 	"call-CCSPepper" -> "call-MergeBams"

diff --git a/dot/CollectPacBioAlignedMetrics.dot b/dot/CollectPacBioAlignedMetrics.dot
@@ -11,10 +11,10 @@ digraph {
 	"call-SummarizeAlignedQ15PBI" [label=SummarizeAlignedQ15PBI shape=cds]
 	"call-NanoPlotFromBam" [label=NanoPlotFromBam shape=cds]
 	"call-CustomMetricsSummaryToFile" [label=CustomMetricsSummaryToFile shape=cds]
-	"call-SummarizeAlignedQ15PBI" -> "call-CustomMetricsSummaryToFile"
 	"call-SummarizeAlignedQ5PBI" -> "call-CustomMetricsSummaryToFile"
+	"call-SummarizeAlignedQ15PBI" -> "call-CustomMetricsSummaryToFile"
 	"call-SummarizeAlignedQ12PBI" -> "call-CustomMetricsSummaryToFile"
-	"call-SummarizeAlignedQ10PBI" -> "call-CustomMetricsSummaryToFile"
 	"call-NanoPlotFromBam" -> "call-CustomMetricsSummaryToFile"
+	"call-SummarizeAlignedQ10PBI" -> "call-CustomMetricsSummaryToFile"
 	"call-SummarizeAlignedQ7PBI" -> "call-CustomMetricsSummaryToFile"
 }
diff --git a/dot/DownloadFromFTP.dot b/dot/DownloadFromFTP.dot
@@ -16,6 +16,6 @@ digraph {
 	}
 	"call-GetFileManifest" -> "call-ComputeDiskSize"
 	"call-ComputeDiskSize" -> "if-L48C9" [lhead="cluster-if-L48C9"]
-	"call-ComputeDiskSize" -> "call-DownloadFTPFile"
 	"call-GetFileManifest" -> "call-DownloadFTPFile"
+	"call-ComputeDiskSize" -> "call-DownloadFTPFile"
 }
diff --git a/dot/FPCheckAoU.dot b/dot/FPCheckAoU.dot
@@ -17,9 +17,9 @@ digraph {
 	"call-ReheaderFullGRCh38VCFtoNoAlt" -> "call-FilterGenotypesVCF"
 	"call-FilterGenotypesVCF" -> "call-ExtractGenotypingSites"
 	"call-ExtractGenotypingSites" -> "call-ExtractRelevantGenotypingReads"
-	"call-ExtractRelevantGenotypingReads" -> "call-CheckFingerprint"
 	"call-GetVCFSampleName" -> "call-CheckFingerprint"
 	"call-FilterGenotypesVCF" -> "call-CheckFingerprint"
+	"call-ExtractRelevantGenotypingReads" -> "call-CheckFingerprint"
 	"call-CheckFingerprint" -> "decl-lod_expected_sample_t"
 	"decl-lod_expected_sample_t" -> "decl-status"
 }
diff --git a/dot/FindBamIdentity.dot b/dot/FindBamIdentity.dot
@@ -52,14 +52,14 @@ digraph {
 	"call-MergeGenotypingSites" -> "call-ExtractRelevantGenotypingReads"
 	"call-ExtractRelevantGenotypingReads" -> "call-ResetCLRBaseQual"
 	"call-FilterGenotypesVCF" -> "scatter-L75C5-vcf" [lhead="cluster-scatter-L75C5-vcf"]
-	"call-ExtractRelevantGenotypingReads" -> "call-CheckFingerprint"
 	"call-GetVCFSampleName" -> "call-CheckFingerprint"
+	"call-ExtractRelevantGenotypingReads" -> "call-CheckFingerprint"
 	"call-CheckFingerprint" -> "decl-non_clr_lod"
-	"call-ResetCLRBaseQual" -> "call-CheckCLRFingerprint"
 	"call-GetVCFSampleName" -> "call-CheckCLRFingerprint"
+	"call-ResetCLRBaseQual" -> "call-CheckCLRFingerprint"
 	"call-CheckCLRFingerprint" -> "decl-clr_lod"
-	"decl-clr_lod" -> "call-FindMaxLOD"
 	"decl-non_clr_lod" -> "call-FindMaxLOD"
+	"decl-clr_lod" -> "call-FindMaxLOD"
 	"call-FindMaxLOD" -> "if-L113C5" [lhead="cluster-if-L113C5"]
 	"call-FindMaxLOD" -> "decl-matching_vcf"
 	"call-PickGenotypeVCF" -> "decl-matching_vcf"

diff --git a/dot/Guppy.dot b/dot/Guppy.dot
@@ -27,11 +27,11 @@ digraph {
 	"call-Basecall" -> "call-SumPassingFastqs"
 	"call-Basecall" -> "call-SumFailingFastqs"
 	"call-Basecall" -> "call-MakeSequencingSummary"
-	"call-Basecall" -> "call-MakeFinalSummary"
 	"call-TimestampStopped" -> "call-MakeFinalSummary"
+	"call-Basecall" -> "call-MakeFinalSummary"
 	"call-Basecall" -> "call-UniqueBarcodes"
-	"call-MakeSequencingSummary" -> "call-FinalizeBasecalls"
 	"call-UniqueBarcodes" -> "call-FinalizeBasecalls"
-	"call-MakeFinalSummary" -> "call-FinalizeBasecalls"
+	"call-MakeSequencingSummary" -> "call-FinalizeBasecalls"
 	"call-Basecall" -> "call-FinalizeBasecalls"
+	"call-MakeFinalSummary" -> "call-FinalizeBasecalls"
 }
diff --git a/dot/HaplotypeCaller.dot b/dot/HaplotypeCaller.dot
@@ -33,6 +33,6 @@ digraph {
 	"call-CallVariantsWithHC" -> "call-MergeVariantCalledBamOuts"
 	"call-MergeVariantCalledBamOuts" -> "call-IndexBamout"
 	"call-MergeGVCFs" -> "call-ReblockHcGVCF"
-	"call-ReblockHcGVCF" -> "call-CollapseGVCFtoVCF"
 	"decl-actual_interval_list" -> "call-CollapseGVCFtoVCF"
+	"call-ReblockHcGVCF" -> "call-CollapseGVCFtoVCF"
 }
diff --git a/dot/LRCNVs.dot b/dot/LRCNVs.dot
@@ -32,23 +32,23 @@ digraph {
 	"call-CollectModelQualityMetrics" [label=CollectModelQualityMetrics shape=cds]
 	"call-PreprocessIntervals" -> "call-AnnotateIntervals"
 	"call-PreprocessIntervals" -> "call-CollectCounts"
-	"call-PreprocessIntervals" -> "call-FilterIntervals"
 	"call-AnnotateIntervals" -> "call-FilterIntervals"
 	"call-CollectCounts" -> "call-FilterIntervals"
+	"call-PreprocessIntervals" -> "call-FilterIntervals"
 	"call-FilterIntervals" -> "call-DetermineGermlineContigPloidyCohortMode"
 	"call-CollectCounts" -> "call-DetermineGermlineContigPloidyCohortMode"
 	"call-FilterIntervals" -> "call-ScatterIntervals"
 	"call-ScatterIntervals" -> "scatter-L261C5-scatter_index" [lhead="cluster-scatter-L261C5-scatter_index"]
-	"call-ScatterIntervals" -> "call-GermlineCNVCallerCohortMode"
-	"call-DetermineGermlineContigPloidyCohortMode" -> "call-GermlineCNVCallerCohortMode"
 	"call-AnnotateIntervals" -> "call-GermlineCNVCallerCohortMode"
 	"call-CollectCounts" -> "call-GermlineCNVCallerCohortMode"
+	"call-DetermineGermlineContigPloidyCohortMode" -> "call-GermlineCNVCallerCohortMode"
+	"call-ScatterIntervals" -> "call-GermlineCNVCallerCohortMode"
 	"call-GermlineCNVCallerCohortMode" -> "decl-call_tars_sample_by_shard"
 	"call-CollectCounts" -> "scatter-L317C5-sample_index" [lhead="cluster-scatter-L317C5-sample_index"]
+	"decl-call_tars_sample_by_shard" -> "call-PostprocessGermlineCNVCalls"
 	"call-GermlineCNVCallerCohortMode" -> "call-PostprocessGermlineCNVCalls"
 	"call-DetermineGermlineContigPloidyCohortMode" -> "call-PostprocessGermlineCNVCalls"
 	"call-CollectCounts" -> "call-PostprocessGermlineCNVCalls"
-	"decl-call_tars_sample_by_shard" -> "call-PostprocessGermlineCNVCalls"
 	"call-PostprocessGermlineCNVCalls" -> "call-CollectSampleQualityMetrics"
 	"call-CollectCounts" -> "call-CollectSampleQualityMetrics"
 	"call-GermlineCNVCallerCohortMode" -> "call-CollectModelQualityMetrics"

diff --git a/dot/Longbow.dot b/dot/Longbow.dot
@@ -36,8 +36,8 @@ digraph {
 	"decl-lbmodel" -> "call-t_07_PadUMI"
 	"call-t_05_RemoveMasSeqTruncatedReads" -> "call-t_07_PadUMI"
 	"decl-lbmodel" -> "if-L83C5" [lhead="cluster-if-L83C5"]
-	"decl-lbmodel" -> "call-t_08_PadCBC"
 	"call-t_07_PadUMI" -> "call-t_08_PadCBC"
+	"decl-lbmodel" -> "call-t_08_PadCBC"
 	"call-t_08_PadCBC" -> "call-t_09_Correct"
 	"decl-lbmodel" -> "call-t_09_Correct"
 	"call-t_07_PadUMI" -> "decl-bam_for_umi_adjustment"

diff --git a/dot/ONTAssembleWithCanu.dot b/dot/ONTAssembleWithCanu.dot
@@ -17,8 +17,8 @@ digraph {
 	"call-summaryQ" [label=summaryQ shape=cds]
 	"decl-q_metrics" [label=q_metrics shape=plaintext]
 	"call-ListFilesOfType" -> "call-MergeFastqs"
-	"call-ComputeGenomeLength" -> "call-Canu"
 	"call-MergeFastqs" -> "call-Canu"
+	"call-ComputeGenomeLength" -> "call-Canu"
 	"call-MergeFastqs" -> "call-MedakaPolish"
 	"call-Canu" -> "call-MedakaPolish"
 	"call-MedakaPolish" -> "call-Quast"

diff --git a/dot/ONTAssembleWithFlye.dot b/dot/ONTAssembleWithFlye.dot
@@ -19,10 +19,10 @@ digraph {
 	"call-summaryQ" [label=summaryQ shape=cds]
 	"decl-q_metrics" [label=q_metrics shape=plaintext]
 	"call-ListFilesOfType" -> "call-MergeFastqs"
-	"call-ComputeGenomeLength" -> "call-Flye"
 	"call-MergeFastqs" -> "call-Flye"
-	"call-Flye" -> "call-MedakaPolish"
+	"call-ComputeGenomeLength" -> "call-Flye"
 	"call-MergeFastqs" -> "call-MedakaPolish"
+	"call-Flye" -> "call-MedakaPolish"
 	"call-MedakaPolish" -> "call-Quast"
 	"call-MedakaPolish" -> "call-CallAssemblyVariants"
 	"call-Flye" -> "call-FinalizeAsmUnpolished"

diff --git a/dot/ONTFlowcell.dot b/dot/ONTFlowcell.dot
@@ -44,10 +44,10 @@ digraph {
 	"call-ListFilesOfType" -> "call-NanoPlotFromRichFastqs"
 	"call-NanoPlotFromRichFastqs" -> "decl-nanoplot_map"
 	"call-NanoPlotFromSummary" -> "decl-nanoplot_map"
-	"call-ListFilesOfType" -> "decl-manifest"
 	"call-ListFastqs" -> "decl-manifest"
-	"decl-PU" -> "decl-RG"
+	"call-ListFilesOfType" -> "decl-manifest"
 	"decl-DT" -> "decl-RG"
+	"decl-PU" -> "decl-RG"
 	"decl-manifest" -> "call-PartitionFastqManifest"
 	"call-PartitionFastqManifest" -> "scatter-L95C5-manifest_chunk" [lhead="cluster-scatter-L95C5-manifest_chunk"]
 	"decl-RG" -> "call-AlignReads"

diff --git a/dot/ONTFlowcellFromMultipleBasecalls.dot b/dot/ONTFlowcellFromMultipleBasecalls.dot
@@ -30,12 +30,12 @@ digraph {
 	"call-MergeAllReads" -> "decl-bai"
 	"decl-bam" -> "call-RemoveDuplicates"
 	"decl-bai" -> "call-RemoveDuplicates"
-	"call-RemoveDuplicates" -> "decl-usable_bam"
 	"decl-bam" -> "decl-usable_bam"
+	"call-RemoveDuplicates" -> "decl-usable_bam"
 	"call-RemoveDuplicates" -> "decl-usable_bai"
 	"decl-bai" -> "decl-usable_bai"
-	"decl-usable_bam" -> "call-coverage"
 	"decl-usable_bai" -> "call-coverage"
+	"decl-usable_bam" -> "call-coverage"
 	"decl-usable_bam" -> "call-FinalizeAlignedBam"
 	"decl-usable_bai" -> "call-FinalizeAlignedBai"
 	"call-coverage" -> "call-FinalizeRegionalCoverage"

diff --git a/dot/ONTMethylation.dot b/dot/ONTMethylation.dot
@@ -64,16 +64,16 @@ digraph {
 	"call-MakeChrIntervalList" -> "scatter-L91C5-c" [lhead="cluster-scatter-L91C5-c"]
 	"call-MergeVarMappings" -> "call-SubsetBam"
 	"call-IndexVariants" -> "call-SubsetVCF"
-	"call-SubsetVCF" -> "call-PhaseVariants"
 	"call-SubsetBam" -> "call-PhaseVariants"
-	"call-PhaseVariants" -> "call-Haplotag"
+	"call-SubsetVCF" -> "call-PhaseVariants"
 	"call-MergeVarMappings" -> "call-Haplotag"
+	"call-PhaseVariants" -> "call-Haplotag"
 	"call-PhaseVariants" -> "call-MergePerChrCalls"
 	"call-Haplotag" -> "call-MergeHaplotagBams"
-	"call-MergeModifiedBaseCallDBs" -> "call-ExtractHaplotypeReads"
-	"call-MergeVariantDBs" -> "call-ExtractHaplotypeReads"
 	"call-MergePerChrCalls" -> "call-ExtractHaplotypeReads"
 	"call-MergeHaplotagBams" -> "call-ExtractHaplotypeReads"
+	"call-MergeVariantDBs" -> "call-ExtractHaplotypeReads"
+	"call-MergeModifiedBaseCallDBs" -> "call-ExtractHaplotypeReads"
 	"call-MergeVariantDBs" -> "call-CallHaplotype1Variants"
 	"call-MergeModifiedBaseCallDBs" -> "call-CallHaplotype1Variants"
 	"call-ExtractHaplotypeReads" -> "call-CallHaplotype1Variants"

diff --git a/dot/ONTProcessBasecall.dot b/dot/ONTProcessBasecall.dot
@@ -48,10 +48,10 @@ digraph {
 	"call-ListFilesOfType" -> "call-NanoPlotFromRichFastqs"
 	"call-NanoPlotFromRichFastqs" -> "decl-nanoplot_map"
 	"call-NanoPlotFromSummary" -> "decl-nanoplot_map"
-	"call-ListFilesOfType" -> "decl-manifest"
 	"call-ListFastqs" -> "decl-manifest"
-	"decl-PU" -> "decl-RG"
+	"call-ListFilesOfType" -> "decl-manifest"
 	"decl-DT" -> "decl-RG"
+	"decl-PU" -> "decl-RG"
 	"decl-manifest" -> "call-PartitionFastqManifest"
 	"call-PartitionFastqManifest" -> "scatter-L98C5-manifest_chunk" [lhead="cluster-scatter-L98C5-manifest_chunk"]
 	"decl-RG" -> "call-AlignReads"

diff --git a/dot/ONTWholeGenome.dot b/dot/ONTWholeGenome.dot
@@ -105,17 +105,17 @@ digraph {
 	"call-MergeAllReads" -> "decl-bai"
 	"decl-bam" -> "call-RemoveDuplicates"
 	"decl-bai" -> "call-RemoveDuplicates"
-	"call-RemoveDuplicates" -> "decl-usable_bam"
 	"decl-bam" -> "decl-usable_bam"
+	"call-RemoveDuplicates" -> "decl-usable_bam"
 	"call-RemoveDuplicates" -> "decl-usable_bai"
 	"decl-bai" -> "decl-usable_bai"
-	"decl-usable_bam" -> "call-coverage"
 	"decl-usable_bai" -> "call-coverage"
+	"decl-usable_bam" -> "call-coverage"
 	"decl-usable_bam" -> "call-FinalizeBam"
 	"decl-usable_bai" -> "call-FinalizeBai"
 	"call-coverage" -> "call-FinalizeRegionalCoverage"
-	"decl-usable_bai" -> "call-CallVariants"
 	"decl-usable_bam" -> "call-CallVariants"
+	"decl-usable_bai" -> "call-CallVariants"
 	"call-CallVariants" -> "call-FinalizePBSV"
 	"call-CallVariants" -> "call-FinalizePBSVtbi"
 	"call-CallVariants" -> "call-FinalizeSniffles"

diff --git a/dot/PBAssembleWithHifiasm.dot b/dot/PBAssembleWithHifiasm.dot
@@ -51,8 +51,8 @@ digraph {
 	"decl-dummy_b" -> "if-L73C5" [lhead="cluster-if-L73C5"]
 	"decl-dummy" -> "if-L73C5" [lhead="cluster-if-L73C5"]
 	"decl-ccs_fq" -> "call-CompressAndFinalizeMergedFQ"
-	"call-CompressAndFinalizeMergedFQ" -> "decl-finalized_merged_fq_path"
 	"call-FinalizeMergedFQ" -> "decl-finalized_merged_fq_path"
+	"call-CompressAndFinalizeMergedFQ" -> "decl-finalized_merged_fq_path"
 	"call-Hifiasm" -> "call-FinalizeHifiasmPrimaryGFA"
 	"call-Hifiasm" -> "call-FinalizeHifiasmPrimaryFA"
 	"call-Hifiasm" -> "call-FinalizeHifiasmAlternateGFA"

diff --git a/dot/PBCCSWholeGenome.dot b/dot/PBCCSWholeGenome.dot
@@ -107,8 +107,8 @@ digraph {
 	"decl-bai" -> "call-FinalizeBai"
 	"decl-pbi" -> "call-FinalizePbi"
 	"call-coverage" -> "call-FinalizeRegionalCoverage"
-	"decl-bam" -> "call-CallVariants"
 	"decl-bai" -> "call-CallVariants"
+	"decl-bam" -> "call-CallVariants"
 	"call-CallVariants" -> "call-FinalizePBSV"
 	"call-CallVariants" -> "call-FinalizePBSVtbi"
 	"call-CallVariants" -> "call-FinalizeSniffles"