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amplicon.wdl
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amplicon.wdl
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version 1.0
import "modules/preparePanelCaptureTmpDirs.wdl" as runPreparePanelCaptureTmpDirs
import "modules/fastp.wdl" as runFastp
import "modules/bwaSamtools.wdl" as runBwaSamtools
import "modules/sambambaIndex.wdl" as runSambambaIndex
import "modules/bedToGatkIntervalList.wdl" as runBedToGatkIntervalList
import "modules/gatkSplitIntervals.wdl" as runGatkSplitIntervals
import "modules/gatkBaseRecalibrator.wdl" as runGatkBaseRecalibrator
import "modules/gatkGatherBQSRReports.wdl" as runGatkGatherBQSRReports
import "modules/gatkApplyBQSR.wdl" as runGatkApplyBQSR
import "modules/gatkLeftAlignIndels.wdl" as runGatkLeftAlignIndels
import "modules/gatkGatherBamFiles.wdl" as runGatkGatherBamFiles
import "modules/samtoolsSort.wdl" as runSamtoolsSort
import "modules/samtoolsCramConvert.wdl" as runSamtoolsCramConvert
import "modules/samtoolsCramIndex.wdl" as runSamtoolsCramIndex
import "modules/crumble.wdl" as runCrumble
import "modules/sambambaFlagStat.wdl" as runSambambaFlagStat
import "modules/gatkCollectMultipleMetrics.wdl" as runGatkCollectMultipleMetrics
import "modules/gatkCollectInsertSizeMetrics.wdl" as runGatkCollectInsertSizeMetrics
import "modules/gatkBedToPicardIntervalList.wdl" as runGatkBedToPicardIntervalList
import "modules/computePoorCoverage.wdl" as runComputePoorCoverage
import "modules/samtoolsBedCov.wdl" as runSamtoolsBedCov
import "modules/computeCoverage.wdl" as runComputeCoverage
import "modules/computeCoverageClamms.wdl" as runComputeCoverageClamms
import "modules/gatkCollectHsMetrics.wdl" as runGatkCollectHsMetrics
import "modules/deepVariant.wdl" as runDeepVariant
import "modules/bcftoolsNorm.wdl" as runBcftoolsNorm
import "modules/compressIndexVcf.wdl" as runCompressIndexVcf
import "modules/jvarkitVcfPolyX.wdl" as runJvarkitVcfPolyX
import "modules/gatkSortVcf.wdl" as runGatkSortVcf
import "modules/bcftoolsStats.wdl" as runBcftoolsStats
# import "modules/gatkVariantEval.wdl" as runGatkVariantEval
import "modules/refcallFiltration.wdl" as runRefCallFiltration
import "modules/gatkVariantFiltrationDv.wdl" as runGatkVariantFiltrationDv
import "modules/gatkHaplotypeCaller.wdl" as runGatkHaplotypeCaller
import "modules/gatkGatherVcfs.wdl" as runGatkGatherVcfs
# import "modules/qualimapBamQc.wdl" as runQualimapBamQc
import "modules/gatkSplitVcfs.wdl" as runGatkSplitVcfs
import "modules/gatkVariantFiltrationSnp.wdl" as runGatkVariantFiltrationSnp
import "modules/gatkVariantFiltrationIndel.wdl" as runGatkVariantFiltrationIndel
import "modules/gatkMergeVcfs.wdl" as runGatkMergeVcfs
import "modules/anacoreUtilsMergeVCFCallers.wdl" as runAnacoreUtilsMergeVCFCallers
import "modules/gatkUpdateVCFSequenceDictionary.wdl" as runGatkUpdateVCFSequenceDictionary
import "modules/cleanUpPanelCaptureTmpDirs.wdl" as runCleanUpPanelCaptureTmpDirs
import "modules/multiqc.wdl" as runMultiqc
workflow amplicon {
meta {
author: "David BAUX"
email: "david.baux(at)chu-montpellier.fr"
version: "1.2.2"
date: "2024-10-07"
}
input {
# variables declarations
## conda
String condaBin
## envs
String fastpEnv = "fastpEnv"
String bwaEnv = "bwaEnv"
String samtoolsEnv = "samtoolsEnv"
String vcftoolsEnv = "vcftoolsEnv"
String sambambaEnv = "sambambaEnv"
String bedtoolsEnv = "bedtoolsEnv"
String crumbleEnv = "crumbleEnv"
String bcftoolsEnv = "bcftoolsEnv"
String multiqcEnv = "multiqcEnv"
String singularityEnv = "singularityEnv"
String anacoreEnv = "anacoreEnv"
## queues
String defQueue = "prod"
String avxQueue = "avx"
## resources
Int cpuHigh
Int cpuLow
# Int avxCpu
Int memoryLow
Int memoryHigh
# memoryLow = scattered tasks =~ mem_per_cpu in HPC or not
# memoryHigh = one cpu tasks => high mem ex 10Gb
## Global
String sampleID
String suffix1
String suffix2
File fastqR1
File fastqR2
String genomeVersion
File refFasta
File refFai
File refDict
File intervalBedFile
String intervalBaitBed = ""
File intervalBaitBedFile = if intervalBaitBed == "" then intervalBedFile else intervalBaitBed
String workflowType
String outDir
Boolean debug = false
## Bioinfo execs
String fastpExe = "fastp"
String bwaExe = "bwa"
String samtoolsExe = "samtools"
String sambambaExe = "sambamba"
String bedToolsExe = "bedtools"
String bcftoolsExe = "bcftools"
String bgZipExe = "bgzip"
String tabixExe = "tabix"
String multiqcExe = "multiqc"
String vcftoolsExe = "vcftools"
String crumbleExe = "crumble"
String gatkExe = "gatk"
String ldLibraryPath
String vcfPolyXJar
## Anacore-Utils custom mergeVCF script
File mergeVCFMobiDL
## Standard execs
String awkExe = "awk"
String sedExe = "sed"
String sortExe = "sort"
String javaExe = "java"
String cromwellJar
## fastp
String noFiltering = ""
## bwaSamtools
String platform
File refAmb
File refAnn
File refBwt
File refPac
File refSa
## sambambaIndex
## gatk splitintervals
String subdivisionMode
## gatk Base recal
File knownSites1
File knownSites1Index
File knownSites2
File knownSites2Index
File knownSites3
File knownSites3Index
## cram conversion
File refFastaGz
File refFaiGz
File refFaiGzi
## crumble
Boolean doCrumble = true
## gatk-picard
String variantEvalEV = "MetricsCollection"
## computePoorCoverage
Int bedtoolsLowCoverage
Int bedToolsSmallInterval
## computeCoverage
Int minCovBamQual
## haplotypeCaller
String swMode
String emitRefConfidence = "NONE"
## DeepVariant
# String referenceFasta
String modelType
# String bedFile
String data
String refData
# String dvOut
String outputMnt
String dvExe
String singularityExe = "singularity"
String dvSimg
## VcSuffix
String dvSuffix = ".dv"
String hcSuffix = ".hc"
}
# Tasks calls
call runPreparePanelCaptureTmpDirs.preparePanelCaptureTmpDirs {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GenomeVersion = genomeVersion
}
call runFastp.fastp {
input:
Queue = defQueue,
CondaBin = condaBin,
FastpEnv = fastpEnv,
Cpu = cpuHigh,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
FastpExe = fastpExe,
Version = true,
NoFiltering = noFiltering,
FastqR1 = fastqR1,
FastqR2 = fastqR2,
Suffix1 = suffix1,
Suffix2 = suffix2,
DirsPrepared = preparePanelCaptureTmpDirs.dirsPrepared
}
###################################################################################
#
# Alignment and post-alignment processing + QC
#
###################################################################################
call runBwaSamtools.bwaSamtools {
input:
Queue = defQueue,
CondaBin = condaBin,
BwaEnv = bwaEnv,
Cpu = cpuHigh,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
FastqR1 = fastp.fastpR1,
FastqR2 = fastp.fastpR2,
SamtoolsExe = samtoolsExe,
BwaExe = bwaExe,
Version = true,
Platform = platform,
RefFasta = refFasta,
RefAmb = refAmb,
RefAnn = refAnn,
RefBwt = refBwt,
RefPac = refPac,
RefSa = refSa
}
call runSambambaIndex.sambambaIndex as firstIndexing {
input:
Queue = defQueue,
CondaBin = condaBin,
SambambaEnv = sambambaEnv,
Cpu = cpuHigh,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
SambambaExe = sambambaExe,
Version = true,
BamFile = bwaSamtools.sortedBam
}
call runBedToGatkIntervalList.bedToGatkIntervalList {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
IntervalBedFile = intervalBedFile,
AwkExe = awkExe,
DirsPrepared = preparePanelCaptureTmpDirs.dirsPrepared,
}
call runGatkSplitIntervals.gatkSplitIntervals {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
Version = true,
GatkInterval = bedToGatkIntervalList.gatkIntervals,
SubdivisionMode = subdivisionMode,
ScatterCount = cpuHigh
}
scatter (interval in gatkSplitIntervals.splittedIntervals) {
call runGatkBaseRecalibrator.gatkBaseRecalibrator {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
GatkInterval = interval,
BamFile = bwaSamtools.sortedBam,
BamIndex = firstIndexing.bamIndex,
KnownSites1 = knownSites1,
KnownSites1Index = knownSites1Index,
KnownSites2 = knownSites2,
KnownSites2Index = knownSites2Index,
KnownSites3 = knownSites3,
KnownSites3Index = knownSites3Index
}
}
call runGatkGatherBQSRReports.gatkGatherBQSRReports {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RecalTables = gatkBaseRecalibrator.recalTable
}
# scatter (interval in gatkSplitIntervals.splittedIntervals) {
# https://gatk.broadinstitute.org/hc/en-us/community/posts/360077410652-What-interval-should-be-used-when-doing-the-BaseRecalibrator-for-exome-data?page=1#community_comment_360014580731
call runGatkApplyBQSR.gatkApplyBQSR {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
# GatkInterval = interval,
BamFile = bwaSamtools.sortedBam,
BamIndex = firstIndexing.bamIndex,
GatheredRecaltable = gatkGatherBQSRReports.gatheredRecalTable
}
call runGatkLeftAlignIndels.gatkLeftAlignIndels {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
# GatkInterval = interval,
BamFile = gatkApplyBQSR.recalBam
}
# }
# call runGatkGatherBamFiles.gatkGatherBamFiles {
# input:
# Queue = defQueue,
# Cpu = cpuLow,
# Memory = memoryHigh,
# SampleID = sampleID,
# OutDir = outDir,
# WorkflowType = workflowType,
# GatkExe = gatkExe,
# LAlignedBams = gatkLeftAlignIndels.lAlignedBam
# }
call runSamtoolsSort.samtoolsSort {
input:
Queue = defQueue,
CondaBin = condaBin,
SamtoolsEnv = samtoolsEnv,
Cpu = cpuHigh,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
SamtoolsExe = samtoolsExe,
BamFile = gatkLeftAlignIndels.lAlignedBam
}
call runSambambaIndex.sambambaIndex as finalIndexing {
input:
Queue = defQueue,
CondaBin = condaBin,
SambambaEnv = sambambaEnv,
Cpu = cpuHigh,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
SambambaExe = sambambaExe,
BamFile = samtoolsSort.sortedBam
}
call runSamtoolsCramConvert.samtoolsCramConvert {
input:
Queue = defQueue,
CondaBin = condaBin,
SamtoolsEnv = samtoolsEnv,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
SamtoolsExe = samtoolsExe,
BamFile = samtoolsSort.sortedBam,
RefFastaGz = refFastaGz,
RefFaiGz = refFaiGz,
RefFaiGzi = refFaiGzi
}
call runSamtoolsCramIndex.samtoolsCramIndex {
input:
Queue = defQueue,
CondaBin = condaBin,
SamtoolsEnv = samtoolsEnv,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
SamtoolsExe = samtoolsExe,
CramFile = samtoolsCramConvert.cram,
CramSuffix = ""
}
if (doCrumble) {
call runCrumble.crumble {
input:
Queue = defQueue,
CondaBin = condaBin,
CrumbleEnv = crumbleEnv,
Cpu = cpuHigh,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
CrumbleExe = crumbleExe,
Version = true,
LdLibraryPath = ldLibraryPath,
InputFile = samtoolsCramConvert.cram,
InputFileIndex = samtoolsCramIndex.cramIndex,
FileType = "cram"
}
call runSamtoolsCramIndex.samtoolsCramIndex as crumbleIndexing {
input:
Queue = defQueue,
CondaBin = condaBin,
SamtoolsEnv = samtoolsEnv,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
SamtoolsExe = samtoolsExe,
Version = true,
CramFile = crumble.crumbled,
CramSuffix = ".crumble"
}
}
call runSambambaFlagStat.sambambaFlagStat {
input:
Queue = defQueue,
CondaBin = condaBin,
SambambaEnv = sambambaEnv,
Cpu = cpuHigh,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
SambambaExe = sambambaExe,
BamFile = samtoolsSort.sortedBam
}
call runGatkCollectMultipleMetrics.gatkCollectMultipleMetrics {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
BamFile = samtoolsSort.sortedBam
}
call runGatkCollectInsertSizeMetrics.gatkCollectInsertSizeMetrics {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
BamFile = samtoolsSort.sortedBam
}
call runGatkBedToPicardIntervalList.gatkBedToPicardIntervalList as gatkBedToPicardIntervalListTarget {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
IntervalBedFile = intervalBedFile,
RefDict = refDict,
GatkExe = gatkExe,
DirsPrepared = preparePanelCaptureTmpDirs.dirsPrepared
}
call runGatkBedToPicardIntervalList.gatkBedToPicardIntervalList as gatkBedToPicardIntervalListBait {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
Bait = true,
IntervalBedFile = intervalBaitBedFile,
RefDict = refDict,
GatkExe = gatkExe,
DirsPrepared = preparePanelCaptureTmpDirs.dirsPrepared
}
call runComputePoorCoverage.computePoorCoverage {
input:
Queue = defQueue,
CondaBin = condaBin,
BedtoolsEnv = bedtoolsEnv,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GenomeVersion = genomeVersion,
BedToolsExe = bedToolsExe,
AwkExe = awkExe,
SortExe = sortExe,
IntervalBedFile = intervalBedFile,
BedtoolsLowCoverage = bedtoolsLowCoverage,
BedToolsSmallInterval = bedToolsSmallInterval,
BamFile = samtoolsSort.sortedBam
}
call runSamtoolsBedCov.samtoolsBedCov {
input:
Queue = defQueue,
CondaBin = condaBin,
SamtoolsEnv = samtoolsEnv,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
SamtoolsExe = samtoolsExe,
IntervalBedFile = intervalBedFile,
BamFile = samtoolsSort.sortedBam,
BamIndex = finalIndexing.bamIndex,
MinCovBamQual = minCovBamQual
}
call runComputeCoverage.computeCoverage {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
AwkExe = awkExe,
SortExe = sortExe,
BedCovFile = samtoolsBedCov.BedCovFile
}
call runComputeCoverageClamms.computeCoverageClamms {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
AwkExe = awkExe,
SortExe = sortExe,
BedCovFile = samtoolsBedCov.BedCovFile
}
call runGatkCollectHsMetrics.gatkCollectHsMetrics {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
BamFile = samtoolsSort.sortedBam,
BaitIntervals = gatkBedToPicardIntervalListBait.picardIntervals,
TargetIntervals = gatkBedToPicardIntervalListTarget.picardIntervals
}
###################################################################################
#
# Variant Calling 1: DeepVariant
#
###################################################################################
call runDeepVariant.deepVariant {
input:
Queue = avxQueue,
CondaBin = condaBin,
SingularityEnv = singularityEnv,
Cpu = cpuHigh,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
DvExe = dvExe,
GatkExe = gatkExe,
SingularityExe = singularityExe,
Version = true,
DvSimg = dvSimg,
BamFile = samtoolsSort.sortedBam,
BamIndex = finalIndexing.bamIndex,
RefFastaGz = refFastaGz,
IntervalBedFile = intervalBedFile,
ModelType = modelType,
Data = data,
RefData = refData,
OutDir = outDir,
Output = outputMnt,
VcSuffix = dvSuffix
}
call runRefCallFiltration.refCallFiltration {
input:
Queue = defQueue,
CondaBin = condaBin,
VcftoolsEnv = vcftoolsEnv,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
VcSuffix = dvSuffix,
VcftoolsExe = vcftoolsExe,
Version = true,
VcfToRefCalled = deepVariant.DeepVcf
}
call runGatkSortVcf.gatkSortVcf as gatkSortVcfDv {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
VcSuffix = dvSuffix,
UnsortedVcf = refCallFiltration.noRefCalledVcf
}
call runJvarkitVcfPolyX.jvarkitVcfPolyX as jvarkitVcfPolyxDv {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
JavaExe = javaExe,
VcfPolyXJar = vcfPolyXJar,
VcSuffix = dvSuffix,
Version = true,
Vcf = gatkSortVcfDv.sortedVcf,
VcfIndex = gatkSortVcfDv.sortedVcfIndex
}
call runGatkVariantFiltrationDv.gatkVariantFiltrationDv {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
Vcf = jvarkitVcfPolyxDv.polyxedVcf,
VcfIndex = jvarkitVcfPolyxDv.polyxedVcfIndex,
VcSuffix = dvSuffix,
LowCoverage = bedtoolsLowCoverage
}
call runBcftoolsNorm.bcftoolsNorm as bcftoolsNormDv {
input:
Queue = defQueue,
CondaBin = condaBin,
BcftoolsEnv = bcftoolsEnv,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
BcftoolsExe = bcftoolsExe,
VcSuffix = dvSuffix,
Version = true,
SortedVcf = gatkVariantFiltrationDv.filteredVcf
}
call runCompressIndexVcf.compressIndexVcf as compressIndexVcfDv {
input:
Queue = defQueue,
CondaBin = condaBin,
SamtoolsEnv = samtoolsEnv,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
BgZipExe = bgZipExe,
TabixExe = tabixExe,
VcSuffix = dvSuffix,
Version = true,
VcfFile = bcftoolsNormDv.normVcf
}
call runBcftoolsStats.bcftoolsStats as bcftoolsStatsDv {
input:
Queue = defQueue,
CondaBin = condaBin,
BcftoolsEnv = bcftoolsEnv,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
BcftoolsExe = bcftoolsExe,
VcSuffix = dvSuffix,
VcfFile = compressIndexVcfDv.bgZippedVcf,
VcfFileIndex = compressIndexVcfDv.bgZippedVcfIndex
}
#not ready for production (gath 4.1.4.0) and toooooooo loooooonnnnggggg
#call runGatkVariantEval.gatkVariantEval as gatkVariantEvalDv{
# input:
# Queue = defQueue,
# CondaBin = condaBin,
# Cpu = cpuHigh,
# Memory = memoryLow,
# SampleID = sampleID,
# OutDir = outDir,
# WorkflowType = workflowType,
# GatkExe = gatkExe,
# VariantEvalEV = variantEvalEV,
# VcSuffix = dvSuffix,
# VcfFile = bcftoolsNormDv.normVcf,
# RefFasta = refFasta,
# RefFai = refFai,
# RefDict = refDict,
# DbSNP = knownSites3,
# DbSNPIndex = knownSites3Index
#}
###################################################################################
#
# Variant Calling 2: Haplotype Caller
#
###################################################################################
scatter (interval in gatkSplitIntervals.splittedIntervals) {
call runGatkHaplotypeCaller.gatkHaplotypeCaller {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
DbSNP = knownSites3,
DbSNPIndex = knownSites3Index,
GatkInterval = interval,
BamFile = samtoolsSort.sortedBam,
BamIndex = finalIndexing.bamIndex,
SwMode = swMode,
EmitRefConfidence = emitRefConfidence
}
}
call runGatkGatherVcfs.gatkGatherVcfs {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
Version = true,
HcVcfs = gatkHaplotypeCaller.hcVcf,
VcSuffix = hcSuffix
}
call runJvarkitVcfPolyX.jvarkitVcfPolyX as jvarkitVcfPolyxHc {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
JavaExe = javaExe,
VcfPolyXJar = vcfPolyXJar,
VcSuffix = hcSuffix,
Vcf = gatkGatherVcfs.gatheredHcVcf,
VcfIndex = gatkGatherVcfs.gatheredHcVcfIndex
}
call runGatkSplitVcfs.gatkSplitVcfs {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
VcSuffix = hcSuffix,
GatkExe = gatkExe,
Vcf = jvarkitVcfPolyxHc.polyxedVcf,
VcfIndex = jvarkitVcfPolyxHc.polyxedVcfIndex
}
call runGatkVariantFiltrationSnp.gatkVariantFiltrationSnp {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
Vcf = gatkSplitVcfs.snpVcf,
VcfIndex = gatkSplitVcfs.snpVcfIndex,
LowCoverage = bedtoolsLowCoverage
}
call runGatkVariantFiltrationIndel.gatkVariantFiltrationIndel {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
Vcf = gatkSplitVcfs.indelVcf,
VcfIndex = gatkSplitVcfs.indelVcfIndex,
LowCoverage = bedtoolsLowCoverage
}
call runGatkMergeVcfs.gatkMergeVcfs {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
Vcfs = [gatkVariantFiltrationSnp.filteredSnpVcf, gatkVariantFiltrationIndel.filteredIndelVcf],
VcSuffix = hcSuffix
}
call runGatkSortVcf.gatkSortVcf as gatkSortVcfHc {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
VcSuffix = hcSuffix,
UnsortedVcf = gatkMergeVcfs.mergedVcf
}
call runBcftoolsNorm.bcftoolsNorm as bcftoolsNormHc {
input:
Queue = defQueue,
CondaBin = condaBin,
BcftoolsEnv = bcftoolsEnv,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
BcftoolsExe = bcftoolsExe,
VcSuffix = hcSuffix,
SortedVcf = gatkSortVcfHc.sortedVcf
}
# not ready for production (gath 4.1.4.0) and toooooooo loooooonnnnggggg
# call runGatkVariantEval.gatkVariantEval as gatkVariantEvalHc{
# input:
# Queue = defQueue,
# CondaBin = condaBin,
# Cpu = cpuLow,
# Memory = memoryHigh,
# SampleID = sampleID,
# OutDir = outDir,
# WorkflowType = workflowType,
# GatkExe = gatkExe,
# VariantEvalEV = variantEvalEV,
# VcSuffix = hcSuffix,
# VcfFile = bcftoolsNormHc.normVcf,
# RefFasta = refFasta,
# RefFai = refFai,
# RefDict = refDict,
# DbSNP = knownSites3,
# DbSNPIndex = knownSites3Index
# }
call runCompressIndexVcf.compressIndexVcf as compressIndexVcfHc {
input:
Queue = defQueue,
CondaBin = condaBin,
SamtoolsEnv = samtoolsEnv,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
BgZipExe = bgZipExe,
TabixExe = tabixExe,
VcSuffix = hcSuffix,
VcfFile = bcftoolsNormHc.normVcf
}
call runBcftoolsStats.bcftoolsStats as bcftoolsStatsHc {
input:
Queue = defQueue,
CondaBin = condaBin,
BcftoolsEnv = bcftoolsEnv,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
BcftoolsExe = bcftoolsExe,
VcSuffix = hcSuffix,
VcfFile = compressIndexVcfHc.bgZippedVcf,
VcfFileIndex = compressIndexVcfHc.bgZippedVcfIndex
}
call runAnacoreUtilsMergeVCFCallers.anacoreUtilsMergeVCFCallers {
input:
Queue = defQueue,
CondaBin = condaBin,
AnacoreEnv = anacoreEnv,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
MergeVCFMobiDL = mergeVCFMobiDL,
Vcfs = [bcftoolsNormHc.normVcf, bcftoolsNormDv.normVcf],
Callers = ["HaplotypeCaller", "DeepVariant"]
}
call runGatkUpdateVCFSequenceDictionary.gatkUpdateVCFSequenceDictionary {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
GatkExe = gatkExe,
RefFasta = refFasta,
RefFai = refFai,
RefDict = refDict,
Vcf = anacoreUtilsMergeVCFCallers.mergedVcf
}
call runCompressIndexVcf.compressIndexVcf as compressIndexMergedVcf {
input:
Queue = defQueue,
CondaBin = condaBin,
SamtoolsEnv = samtoolsEnv,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
BgZipExe = bgZipExe,
TabixExe = tabixExe,
VcSuffix = '',
VcfFile = gatkUpdateVCFSequenceDictionary.refUpdatedVcf
}
if (!debug) {
String dataPath = "~{outDir}~{sampleID}/~{workflowType}/"
if (doCrumble) {
call runCleanUpPanelCaptureTmpDirs.cleanUpPanelCaptureTmpDirs as cleanUpPanelCaptureTmpDirsDoCrumble {
input:
Queue = defQueue,
Cpu = cpuLow,
Memory = memoryLow,
SampleID = sampleID,
OutDir = outDir,
WorkflowType = workflowType,
FinalFile1 = compressIndexMergedVcf.bgZippedVcf,
FinalFile2 = crumbleIndexing.cramIndex,
JavaExe = javaExe,
CromwellJar = cromwellJar,
BamArray = ["~{dataPath}" + basename(gatkGatherBQSRReports.gatheredRecalTable), "~{dataPath}" + basename(gatkApplyBQSR.recalBam), "~{dataPath}" + basename(gatkApplyBQSR.recalBamIndex), "~{dataPath}" + basename(gatkLeftAlignIndels.lAlignedBam), "~{dataPath}" + basename(gatkLeftAlignIndels.lAlignedBamIndex), "~{dataPath}" + basename(samtoolsSort.sortedBam), "~{dataPath}" + basename(finalIndexing.bamIndex), "~{dataPath}" + basename(samtoolsCramConvert.cram),"~{dataPath}" + basename(samtoolsCramIndex.cramIndex)],
VcfArray = ["~{dataPath}" + basename(refCallFiltration.noRefCalledVcf),"~{dataPath}" + basename(gatkSortVcfDv.sortedVcf),"~{dataPath}" + basename(gatkSortVcfDv.sortedVcfIndex),"~{dataPath}" + basename(jvarkitVcfPolyxDv.polyxedVcf),"~{dataPath}" + basename(jvarkitVcfPolyxDv.polyxedVcfIndex),"~{dataPath}" + basename(gatkVariantFiltrationDv.filteredVcf),"~{dataPath}" + basename(gatkVariantFiltrationDv.filteredVcfIndex), "~{dataPath}" + basename(gatkGatherVcfs.gatheredHcVcf), "~{dataPath}" + basename(gatkGatherVcfs.gatheredHcVcfIndex), "~{dataPath}" + basename(jvarkitVcfPolyxHc.polyxedVcf), "~{dataPath}" + basename(jvarkitVcfPolyxHc.polyxedVcfIndex), "~{dataPath}" + basename(gatkSplitVcfs.snpVcf), "~{dataPath}" + basename(gatkSplitVcfs.snpVcfIndex), "~{dataPath}" + basename(gatkSplitVcfs.indelVcf), "~{dataPath}" + basename(gatkSplitVcfs.indelVcfIndex), "~{dataPath}" + basename(gatkVariantFiltrationSnp.filteredSnpVcf), "~{dataPath}" + basename(gatkVariantFiltrationSnp.filteredSnpVcfIndex), "~{dataPath}" + basename(gatkVariantFiltrationIndel.filteredIndelVcf), "~{dataPath}" + basename(gatkVariantFiltrationIndel.filteredIndelVcfIndex), "~{dataPath}" + basename(gatkMergeVcfs.mergedVcf), "~{dataPath}" + basename(gatkMergeVcfs.mergedVcfIndex), "~{dataPath}" + basename(gatkSortVcfHc.sortedVcf), "~{dataPath}" + basename(gatkSortVcfHc.sortedVcfIndex), "~{dataPath}" + basename(compressIndexVcfHc.bgZippedVcf), "~{dataPath}" + basename(compressIndexVcfHc.bgZippedVcfIndex), "~{dataPath}" + basename(compressIndexVcfDv.bgZippedVcf), "~{dataPath}" + basename(compressIndexVcfDv.bgZippedVcfIndex), "~{dataPath}" + basename(anacoreUtilsMergeVCFCallers.mergedVcf)]
}
call runMultiqc.multiqc as multiqcDoCrumble {
input:
Queue = defQueue,
CondaBin = condaBin,
MultiqcEnv = multiqcEnv,
Cpu = cpuLow,
Memory = memoryHigh,
SampleID = sampleID,