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broadinstitute · Dec 6, 2024 · 73e5ef0 · 73e5ef0
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diff --git a/dot/AlignAndCheckFingerprintCCS.dot b/dot/AlignAndCheckFingerprintCCS.dot
@@ -37,16 +37,16 @@ digraph {
 	"call-arbitrary" -> "call-ShardLongReads"
 	"call-ShardLongReads" -> "scatter-L62C9-unaligned_bam" [lhead="cluster-scatter-L62C9-unaligned_bam"]
 	"call-AlignReads" -> "call-MergeAlignedReads"
-	"call-AlignReadsTogether" -> "decl-aBAM"
 	"call-MergeAlignedReads" -> "decl-aBAM"
-	"call-AlignReadsTogether" -> "decl-aBAI"
+	"call-AlignReadsTogether" -> "decl-aBAM"
 	"call-MergeAlignedReads" -> "decl-aBAI"
+	"call-AlignReadsTogether" -> "decl-aBAI"
 	"decl-aBAM" -> "call-IndexAlignedReads"
+	"decl-aBAM" -> "call-CollectPacBioAlignedMetrics"
 	"call-IndexAlignedReads" -> "call-CollectPacBioAlignedMetrics"
 	"decl-aBAI" -> "call-CollectPacBioAlignedMetrics"
-	"decl-aBAM" -> "call-CollectPacBioAlignedMetrics"
 	"call-CollectPacBioAlignedMetrics" -> "call-saveAlnMetrics"
-	"decl-aBAI" -> "call-FPCheckAoU"
 	"decl-aBAM" -> "call-FPCheckAoU"
+	"decl-aBAI" -> "call-FPCheckAoU"
 	"call-FPCheckAoU" -> "call-saveFPRes"
 }
diff --git a/dot/AlignedMetrics.dot b/dot/AlignedMetrics.dot
@@ -28,8 +28,8 @@ digraph {
 	}
 	"call-MakeChrIntervalList" -> "scatter-L33C5-chr_info" [lhead="cluster-scatter-L33C5-chr_info"]
 	"call-MosDepth" -> "call-SummarizeDepth"
-	"call-AlignedReadMetrics" -> "call-FFYieldAligned"
 	"call-AlignedFlagStats" -> "call-FFYieldAligned"
+	"call-AlignedReadMetrics" -> "call-FFYieldAligned"
 	"call-MosDepth" -> "call-FFCoverageFullDist"
 	"call-MosDepth" -> "call-FFCoverageGlobalDist"
 	"call-MosDepth" -> "call-FFCoverageRegionDist"

diff --git a/dot/BenchmarkVCFs.dot b/dot/BenchmarkVCFs.dot
@@ -125,19 +125,19 @@ digraph {
 	"call-CheckForVariantsEval" -> "if-L248C9" [lhead="cluster-if-L248C9"]
 	"decl-outputPrefix" -> "call-StandardVcfEval"
 	"call-ConfidenceConvertIntervals" -> "call-StandardVcfEval"
+	"call-StandardVcfEval" -> "call-VcfEvalWriteXMLfile"
 	"decl-outputPrefix" -> "call-VcfEvalWriteXMLfile"
 	"call-ConfidenceConvertIntervals" -> "call-VcfEvalWriteXMLfile"
-	"call-StandardVcfEval" -> "call-VcfEvalWriteXMLfile"
 	"call-StandardVcfEval" -> "call-CountUNKVcfEval"
 	"call-CheckForVariantsTruth" -> "decl-areVariants"
 	"call-CheckForVariantsEval" -> "decl-areVariants"
-	"call-StandardVcfEval" -> "call-SummariseVcfEval"
+	"call-VcfEvalWriteXMLfile" -> "call-SummariseVcfEval"
 	"decl-areVariants" -> "call-SummariseVcfEval"
 	"call-CountUNKVcfEval" -> "call-SummariseVcfEval"
-	"call-VcfEvalWriteXMLfile" -> "call-SummariseVcfEval"
+	"call-StandardVcfEval" -> "call-SummariseVcfEval"
+	"call-StandardVcfEval" -> "decl-annotatedVcfsList"
 	"decl-outputPrefix" -> "decl-annotatedVcfsList"
 	"call-ConfidenceConvertIntervals" -> "decl-annotatedVcfsList"
-	"call-StandardVcfEval" -> "decl-annotatedVcfsList"
 	"decl-annotatedVcfsList" -> "scatter-L315C5-indelCombo" [lhead="cluster-scatter-L315C5-indelCombo"]
 	"call-EvalIndelLengthVcfEval" -> "call-VcfEvalIndelWriteXMLfile"
 	"call-EvalIndelLengthVcfEval" -> "call-VcfEvalSummariseForIndelSelection"

diff --git a/dot/BroadOnPremMalariaPipeline_1_Alignment_and_Variant_Calling.dot b/dot/BroadOnPremMalariaPipeline_1_Alignment_and_Variant_Calling.dot
@@ -36,21 +36,21 @@ digraph {
 	"call-t_002_RevertSam" -> "call-t_003_Bam2Fastq"
 	"call-t_003_Bam2Fastq" -> "decl-fq_e1"
 	"call-t_003_Bam2Fastq" -> "decl-fq_e2"
-	"decl-fq_e1" -> "call-t_005_FilterOutHumanReads"
 	"decl-fq_e2" -> "call-t_005_FilterOutHumanReads"
+	"decl-fq_e1" -> "call-t_005_FilterOutHumanReads"
 	"call-t_005_FilterOutHumanReads" -> "call-t_006_AlignReads"
 	"call-t_006_AlignReads" -> "call-t_008_SortAlignedBam"
 	"call-t_008_SortAlignedBam" -> "call-t_009_MarkDuplicates"
 	"call-t_009_MarkDuplicates" -> "call-t_010_ReorderSam"
 	"call-t_010_ReorderSam" -> "call-t_011_RealignIndels"
 	"call-t_011_RealignIndels" -> "call-t_012_IndexRealignIndels"
-	"call-t_011_RealignIndels" -> "call-t_012_BQSR"
 	"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_012_BQSR" -> "call-t_013_HaplotypeCaller"
 	"call-t_013_IndexBQSR" -> "call-t_013_HaplotypeCaller"
-	"call-t_012_BQSR" -> "call-t_014_HaplotypeCallerGvcfMode"
+	"call-t_012_BQSR" -> "call-t_013_HaplotypeCaller"
 	"call-t_013_IndexBQSR" -> "call-t_014_HaplotypeCallerGvcfMode"
+	"call-t_012_BQSR" -> "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
@@ -61,15 +61,15 @@ digraph {
 	"call-arbitrary" -> "call-Clair"
 	"call-Clair" -> "call-MergeAndSortClairVCFs"
 	"call-Clair" -> "call-MergeAndSortClair_gVCFs"
-	"call-arbitrary" -> "call-Pepper"
 	"call-size_balanced_scatter" -> "call-Pepper"
+	"call-arbitrary" -> "call-Pepper"
 	"call-Pepper" -> "call-MergeDeepVariantGVCFs"
 	"call-Pepper" -> "call-MergeDeepVariantPhasedVCFs"
 	"call-Pepper" -> "call-MergeDeepVariantVCFs"
 	"call-Pepper" -> "call-MergeBams"
 	"call-MakeChrIntervalList" -> "scatter-L198C13-c" [lhead="cluster-scatter-L198C13-c"]
-	"call-SubsetBam" -> "call-RunPBSV"
 	"call-arbitrary" -> "call-RunPBSV"
+	"call-SubsetBam" -> "call-RunPBSV"
 	"call-SubsetBam" -> "call-InferSampleName"
 	"call-RunPBSV" -> "call-MergePBSVVCFs"
 	"call-arbitrary" -> "call-PBSVslow"

diff --git a/dot/CallVariantsPBCCS.dot b/dot/CallVariantsPBCCS.dot
@@ -60,16 +60,16 @@ digraph {
 	"call-arbitrary" -> "call-Clair"
 	"call-Clair" -> "call-MergeAndSortClairVCFs"
 	"call-Clair" -> "call-MergeAndSortClair_gVCFs"
-	"call-arbitrary" -> "call-CCSPepper"
 	"call-size_balanced_scatter" -> "call-CCSPepper"
+	"call-arbitrary" -> "call-CCSPepper"
 	"call-CCSPepper" -> "call-MergeDeepVariantGVCFs"
 	"call-CCSPepper" -> "call-MergeDeepVariantVCFs"
 	"call-CCSPepper" -> "call-MergeBams"
 	"call-arbitrary" -> "call-MarginPhase"
 	"call-MergeDeepVariantVCFs" -> "call-MarginPhase"
 	"call-MakeChrIntervalList" -> "scatter-L206C13-c" [lhead="cluster-scatter-L206C13-c"]
-	"call-SubsetBam" -> "call-RunPBSV"
 	"call-arbitrary" -> "call-RunPBSV"
+	"call-SubsetBam" -> "call-RunPBSV"
 	"call-RunPBSV" -> "call-MergePBSVVCFs"
 	"call-arbitrary" -> "call-PBSVslow"
 	"call-PBSVslow" -> "call-ZipAndIndexPBSV"

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-NanoPlotFromBam" -> "call-CustomMetricsSummaryToFile"
-	"call-SummarizeAlignedQ12PBI" -> "call-CustomMetricsSummaryToFile"
+	"call-SummarizeAlignedQ15PBI" -> "call-CustomMetricsSummaryToFile"
 	"call-SummarizeAlignedQ5PBI" -> "call-CustomMetricsSummaryToFile"
+	"call-SummarizeAlignedQ12PBI" -> "call-CustomMetricsSummaryToFile"
 	"call-SummarizeAlignedQ10PBI" -> "call-CustomMetricsSummaryToFile"
+	"call-NanoPlotFromBam" -> "call-CustomMetricsSummaryToFile"
 	"call-SummarizeAlignedQ7PBI" -> "call-CustomMetricsSummaryToFile"
-	"call-SummarizeAlignedQ15PBI" -> "call-CustomMetricsSummaryToFile"
 }
diff --git a/dot/CollectParentsKmerStats.dot b/dot/CollectParentsKmerStats.dot
@@ -16,6 +16,6 @@ digraph {
 	"call-PrintMerylMemory" -> "call-MerylCount"
 	"call-ParentalReadsRepartitionAndMerylConfigure" -> "call-MerylCount"
 	"call-PrintMerylMemory" -> "call-MerylMergeAndSubtract"
-	"call-ParentalReadsRepartitionAndMerylConfigure" -> "call-MerylMergeAndSubtract"
 	"call-MerylCount" -> "call-MerylMergeAndSubtract"
+	"call-ParentalReadsRepartitionAndMerylConfigure" -> "call-MerylMergeAndSubtract"
 }
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-GetFileManifest" -> "call-DownloadFTPFile"
 	"call-ComputeDiskSize" -> "call-DownloadFTPFile"
+	"call-GetFileManifest" -> "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
@@ -52,11 +52,11 @@ digraph {
 	"call-MergeGenotypingSites" -> "call-ExtractRelevantGenotypingReads"
 	"call-ExtractRelevantGenotypingReads" -> "call-ResetCLRBaseQual"
 	"call-FilterGenotypesVCF" -> "scatter-L75C5-vcf" [lhead="cluster-scatter-L75C5-vcf"]
-	"call-GetVCFSampleName" -> "call-CheckFingerprint"
 	"call-ExtractRelevantGenotypingReads" -> "call-CheckFingerprint"
+	"call-GetVCFSampleName" -> "call-CheckFingerprint"
 	"call-CheckFingerprint" -> "decl-non_clr_lod"
-	"call-GetVCFSampleName" -> "call-CheckCLRFingerprint"
 	"call-ResetCLRBaseQual" -> "call-CheckCLRFingerprint"
+	"call-GetVCFSampleName" -> "call-CheckCLRFingerprint"
 	"call-CheckCLRFingerprint" -> "decl-clr_lod"
 	"decl-clr_lod" -> "call-FindMaxLOD"
 	"decl-non_clr_lod" -> "call-FindMaxLOD"

diff --git a/dot/Guppy.dot b/dot/Guppy.dot
@@ -19,19 +19,19 @@ digraph {
 	"call-UniqueBarcodes" [label=UniqueBarcodes shape=cds]
 	"call-FinalizeBasecalls" [label=FinalizeBasecalls shape=cds]
 	"call-ListFast5s" -> "decl-ns"
-	"call-ListFast5s" -> "call-PartitionFast5Manifest"
 	"decl-ns" -> "call-PartitionFast5Manifest"
+	"call-ListFast5s" -> "call-PartitionFast5Manifest"
 	"call-PartitionFast5Manifest" -> "scatter-L44C5-chunk_index" [lhead="cluster-scatter-L44C5-chunk_index"]
 	"call-PartitionFast5Manifest" -> "call-Basecall"
 	"call-Basecall" -> "call-TimestampStopped"
 	"call-Basecall" -> "call-SumPassingFastqs"
 	"call-Basecall" -> "call-SumFailingFastqs"
 	"call-Basecall" -> "call-MakeSequencingSummary"
-	"call-TimestampStopped" -> "call-MakeFinalSummary"
 	"call-Basecall" -> "call-MakeFinalSummary"
+	"call-TimestampStopped" -> "call-MakeFinalSummary"
 	"call-Basecall" -> "call-UniqueBarcodes"
-	"call-MakeFinalSummary" -> "call-FinalizeBasecalls"
-	"call-UniqueBarcodes" -> "call-FinalizeBasecalls"
 	"call-MakeSequencingSummary" -> "call-FinalizeBasecalls"
+	"call-UniqueBarcodes" -> "call-FinalizeBasecalls"
+	"call-MakeFinalSummary" -> "call-FinalizeBasecalls"
 	"call-Basecall" -> "call-FinalizeBasecalls"
 }
diff --git a/dot/LRCNVs.dot b/dot/LRCNVs.dot
@@ -32,24 +32,24 @@ digraph {
 	"call-CollectModelQualityMetrics" [label=CollectModelQualityMetrics shape=cds]
 	"call-PreprocessIntervals" -> "call-AnnotateIntervals"
 	"call-PreprocessIntervals" -> "call-CollectCounts"
-	"call-CollectCounts" -> "call-FilterIntervals"
 	"call-PreprocessIntervals" -> "call-FilterIntervals"
 	"call-AnnotateIntervals" -> "call-FilterIntervals"
-	"call-CollectCounts" -> "call-DetermineGermlineContigPloidyCohortMode"
+	"call-CollectCounts" -> "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-CollectCounts" -> "call-GermlineCNVCallerCohortMode"
 	"call-ScatterIntervals" -> "call-GermlineCNVCallerCohortMode"
-	"call-AnnotateIntervals" -> "call-GermlineCNVCallerCohortMode"
 	"call-DetermineGermlineContigPloidyCohortMode" -> "call-GermlineCNVCallerCohortMode"
+	"call-AnnotateIntervals" -> "call-GermlineCNVCallerCohortMode"
+	"call-CollectCounts" -> "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-CollectCounts" -> "call-PostprocessGermlineCNVCalls"
 	"call-DetermineGermlineContigPloidyCohortMode" -> "call-PostprocessGermlineCNVCalls"
-	"call-CollectCounts" -> "call-CollectSampleQualityMetrics"
+	"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
@@ -33,17 +33,17 @@ digraph {
 	"call-t_02_Annotate" -> "call-t_03_Filter"
 	"call-t_03_Filter" -> "call-t_04_Segment"
 	"call-t_04_Segment" -> "call-t_05_RemoveMasSeqTruncatedReads"
-	"call-t_05_RemoveMasSeqTruncatedReads" -> "call-t_07_PadUMI"
 	"decl-lbmodel" -> "call-t_07_PadUMI"
+	"call-t_05_RemoveMasSeqTruncatedReads" -> "call-t_07_PadUMI"
 	"decl-lbmodel" -> "if-L83C5" [lhead="cluster-if-L83C5"]
-	"call-t_07_PadUMI" -> "call-t_08_PadCBC"
 	"decl-lbmodel" -> "call-t_08_PadCBC"
-	"decl-lbmodel" -> "call-t_09_Correct"
+	"call-t_07_PadUMI" -> "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"
 	"call-t_09_Correct" -> "decl-bam_for_umi_adjustment"
-	"decl-lbmodel" -> "call-t_10_AdjustUmiSequenceWithAdapterAlignment"
 	"decl-bam_for_umi_adjustment" -> "call-t_10_AdjustUmiSequenceWithAdapterAlignment"
+	"decl-lbmodel" -> "call-t_10_AdjustUmiSequenceWithAdapterAlignment"
 	"decl-lbmodel" -> "if-L115C5" [lhead="cluster-if-L115C5"]
 	"call-t_09_Correct" -> "call-AggregateCorrectLogStats"
 	"call-t_10_AdjustUmiSequenceWithAdapterAlignment" -> "call-Extract"

diff --git a/dot/ONTAssembleWithCanu.dot b/dot/ONTAssembleWithCanu.dot
@@ -19,8 +19,8 @@ digraph {
 	"call-ListFilesOfType" -> "call-MergeFastqs"
 	"call-ComputeGenomeLength" -> "call-Canu"
 	"call-MergeFastqs" -> "call-Canu"
-	"call-Canu" -> "call-MedakaPolish"
 	"call-MergeFastqs" -> "call-MedakaPolish"
+	"call-Canu" -> "call-MedakaPolish"
 	"call-MedakaPolish" -> "call-Quast"
 	"call-MedakaPolish" -> "call-CallAssemblyVariants"
 	"call-Canu" -> "call-FinalizeAsmUnpolished"

diff --git a/dot/ONTMethylation.dot b/dot/ONTMethylation.dot
@@ -64,22 +64,22 @@ digraph {
 	"call-MakeChrIntervalList" -> "scatter-L91C5-c" [lhead="cluster-scatter-L91C5-c"]
 	"call-MergeVarMappings" -> "call-SubsetBam"
 	"call-IndexVariants" -> "call-SubsetVCF"
-	"call-SubsetBam" -> "call-PhaseVariants"
 	"call-SubsetVCF" -> "call-PhaseVariants"
-	"call-MergeVarMappings" -> "call-Haplotag"
+	"call-SubsetBam" -> "call-PhaseVariants"
 	"call-PhaseVariants" -> "call-Haplotag"
+	"call-MergeVarMappings" -> "call-Haplotag"
 	"call-PhaseVariants" -> "call-MergePerChrCalls"
 	"call-Haplotag" -> "call-MergeHaplotagBams"
 	"call-MergeModifiedBaseCallDBs" -> "call-ExtractHaplotypeReads"
-	"call-MergeHaplotagBams" -> "call-ExtractHaplotypeReads"
 	"call-MergeVariantDBs" -> "call-ExtractHaplotypeReads"
 	"call-MergePerChrCalls" -> "call-ExtractHaplotypeReads"
-	"call-ExtractHaplotypeReads" -> "call-CallHaplotype1Variants"
-	"call-MergeModifiedBaseCallDBs" -> "call-CallHaplotype1Variants"
+	"call-MergeHaplotagBams" -> "call-ExtractHaplotypeReads"
 	"call-MergeVariantDBs" -> "call-CallHaplotype1Variants"
-	"call-ExtractHaplotypeReads" -> "call-CallHaplotype2Variants"
-	"call-MergeModifiedBaseCallDBs" -> "call-CallHaplotype2Variants"
+	"call-MergeModifiedBaseCallDBs" -> "call-CallHaplotype1Variants"
+	"call-ExtractHaplotypeReads" -> "call-CallHaplotype1Variants"
 	"call-MergeVariantDBs" -> "call-CallHaplotype2Variants"
+	"call-MergeModifiedBaseCallDBs" -> "call-CallHaplotype2Variants"
+	"call-ExtractHaplotypeReads" -> "call-CallHaplotype2Variants"
 	"call-MergePerChrCalls" -> "decl-vcf"
 	"call-MergePerChrCalls" -> "decl-tbi"
 	"call-MergeHaplotagBams" -> "decl-bam"

diff --git a/dot/PBAssembleWithHifiasm.dot b/dot/PBAssembleWithHifiasm.dot
@@ -45,14 +45,14 @@ digraph {
 	"call-primary_h0_h1_quast" -> "call-primary_h0_h1_quast_summary"
 	"decl-ccs_fq" -> "decl-dummy"
 	"decl-dummy" -> "decl-dummy_b"
-	"decl-dummy" -> "if-L70C5" [lhead="cluster-if-L70C5"]
 	"decl-dummy_b" -> "if-L70C5" [lhead="cluster-if-L70C5"]
+	"decl-dummy" -> "if-L70C5" [lhead="cluster-if-L70C5"]
 	"decl-ccs_fq" -> "call-FinalizeMergedFQ"
-	"decl-dummy" -> "if-L73C5" [lhead="cluster-if-L73C5"]
 	"decl-dummy_b" -> "if-L73C5" [lhead="cluster-if-L73C5"]
+	"decl-dummy" -> "if-L73C5" [lhead="cluster-if-L73C5"]
 	"decl-ccs_fq" -> "call-CompressAndFinalizeMergedFQ"
-	"call-FinalizeMergedFQ" -> "decl-finalized_merged_fq_path"
 	"call-CompressAndFinalizeMergedFQ" -> "decl-finalized_merged_fq_path"
+	"call-FinalizeMergedFQ" -> "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-bai" -> "call-CallVariants"
 	"decl-bam" -> "call-CallVariants"
+	"decl-bai" -> "call-CallVariants"
 	"call-CallVariants" -> "call-FinalizePBSV"
 	"call-CallVariants" -> "call-FinalizePBSVtbi"
 	"call-CallVariants" -> "call-FinalizeSniffles"