panelCaptureDuo.wdl

import "modules/preparePanelCaptureTmpDirs.wdl" as runPreparePanelCaptureTmpDirs
import "modules/fastqcDuo.wdl" as runFastqcDuo
import "modules/gatkBedToPicardIntervalList.wdl" as runGatkBedToPicardIntervalList
import "modules/gatkHaplotypeCallerDuo.wdl" as runGatkHaplotypeCallerDuo
import "modules/gatkGatherVcfs.wdl" as runGatkGatherVcfs
import "modules/qualimapBamQc.wdl" as runQualimapBamQc
import "modules/jvarkitVcfPolyX.wdl" as runJvarkitVcfPolyX
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/gatkSortVcf.wdl" as runGatkSortVcf
import "modules/bcftoolsNorm.wdl" as runBcftoolsNorm
import "modules/compressIndexVcf.wdl" as runCompressIndexVcf
#import "modules/deepVariant.wdl" as runDeepVariant
import "modules/refcallFiltration.wdl" as runRefCallFiltration
import "modules/gatkHardFilteringVcf.wdl" as runGatkHardFilteringVcf
import "modules/bcftoolsStats.wdl" as runBcftoolsStats
# import "modules/gatkVariantEval.wdl" as runGatkVariantEval
# import "modules/gatkCombineVariants.wdl" as runGatkCombineVariants
# import "modules/rtgMergeVcfs.wdl" as runRtgMerge
# import "modules/fixVcfHeaders.wdl" as runFixVcfHeaders
#import "modules/crumble.wdl" as runCrumble
#import "modules/anacoreUtilsMergeVCFCallers.wdl" as runAnacoreUtilsMergeVCFCallers
import "modules/gatkUpdateVCFSequenceDictionary.wdl" as runGatkUpdateVCFSequenceDictionary
import "modules/cleanUpPanelCaptureDuoTmpDirs.wdl" as runCleanUpPanelCaptureDuoTmpDirs
import "modules/multiqc.wdl" as runMultiqc
import "modules/toolVersions.wdl" as runToolVersions
import "modules/alignement.wdl" as alignDNA
workflow panelCaptureDuo {
	meta {
		author: "Olivier Ardouin"
		email: "o-ardouin(at)chu-montpellier.fr"
		version: "0.0.2"
		date: "2021-05-29"
	}
	# variables declarations
	## Resources
	Int cpuHigh
	Int cpuLow
	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 FatherSampleID
	String suffix1
	String suffix2
	File fastqR1
	File FatherFastqR1
	File fastqR2
	File FatherFastqR2
	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 fastqcExe
	String bwaExe
	String samtoolsExe
	String sambambaExe
	String bedToolsExe
	String qualimapExe
	String bcfToolsExe
	String bgZipExe
	String tabixExe
	String multiqcExe
	String gatkExe
	## Standard execs
	String awkExe
	String sedExe
	String sortExe
	String javaExe
	## 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
	## gatk-picard
	String variantEvalEV = "MetricsCollection"
	## computePoorCoverage
	Int bedtoolsLowCoverage
	Int bedToolsSmallInterval
	## computeCoverage
	Int minCovBamQual
	## haplotypeCaller
	String swMode
	String emitRefConfidence = "NONE"
	## jvarkit
	String vcfPolyXJar
	## ConvertCramtoCrumble
	String crumbleExe
	String ldLibraryPath
	## DeepVariant
	String referenceFasta
	String modelType
	String bedFile
	String data
	String refData
	String dvOut
	String outputMnt
	String deepExe
	String singularity
	String singularityImg
	## RefCallFiltration
	String vcftoolsExe
	## VcSuffix
	String dvSuffix = ".dv"
	String hcSuffix = ".hc"
	## Anacore-Utils mcustom mergeVCF script
	File mergeVCFMobiDL


	# Tasks calls
	call runPreparePanelCaptureTmpDirs.preparePanelCaptureTmpDirs {
		input:
		Cpu = cpuLow,
		Memory = memoryHigh,
		SampleID = sampleID,
		OutDir = outDir,
		WorkflowType = workflowType
	}
	# RunFastqc on all FASTQs
	call runFastqcDuo.fastqc {
		input:
		Cpu = cpuHigh,
		Memory = memoryLow,
		SampleID = sampleID,
		FatherSampleID = FatherSampleID,
		OutDir = outDir,
		WorkflowType = workflowType,
		FastqcExe = fastqcExe,
		FastqR1 = fastqR1,
		FatherFastqR1 = FatherFastqR1,
		FastqR2 = fastqR2,
		FatherFastqR2 = FatherFastqR2,
		Suffix1 = suffix1,
		Suffix2 = suffix2,
		DirsPrepared = preparePanelCaptureTmpDirs.dirsPrepared
	}
	call runGatkBedToPicardIntervalList.gatkBedToPicardIntervalList as gatkBedToPicardIntervalListTarget {
		input:
		Cpu = cpuLow,
		Memory = memoryHigh,
		SampleID = sampleID,
		OutDir = outDir,
		WorkflowType = workflowType,
		IntervalBedFile = intervalBedFile,
		RefDict = refDict,
		GatkExe = gatkExe,
		DirsPrepared = preparePanelCaptureTmpDirs.dirsPrepared
	}
	call runGatkBedToPicardIntervalList.gatkBedToPicardIntervalList as gatkBedToPicardIntervalListBait {
 		input:
 		Cpu = cpuLow,
 		Memory = memoryHigh,
 		SampleID = sampleID,
 		OutDir = outDir,
 		WorkflowType = workflowType,
 		Bait = true,
 		IntervalBedFile = intervalBaitBedFile,
 		RefDict = refDict,
 		GatkExe = gatkExe,
 		DirsPrepared = preparePanelCaptureTmpDirs.dirsPrepared
 	}

	#Call alignement SubWorkflow
	call alignDNA.alignDNA as alignCI {
		input:
		## Resources
  	CpuHigh = cpuHigh,
  	CpuLow = cpuLow,
  	memoryLow = memoryLow,
  	memoryHigh = memoryHigh,
    ## Global
    sampleID = sampleID,
    CIsDIR = sampleID,
  	fastqR1 = fastqR1,
  	fastqR2 = fastqR2,
		refFasta = refFasta,
  	refFai = refFai,
  	refDict = refDict,
  	intervalBedFile = intervalBedFile,
  	workflowType = workflowType,
  	outDir = outDir,
		genomeVersion = genomeVersion,
    ## Bioinfo execs,
  	bwaExe = bwaExe,
  	samtoolsExe = samtoolsExe,
  	sambambaExe = sambambaExe,
		bedToolsExe = bedToolsExe,
    ## Standard execs
		sortExe = sortExe,
  	awkExe = awkExe,
  	gatkExe = gatkExe,
  	## bwaSamtools
  	platform = platform,
  	refAmb = refAmb,
  	refAnn = refAnn,
  	refBwt = refBwt,
  	refPac = refPac,
  	refSa = refSa,
		# CRAM conversion
		refFastaGz = refFastaGz,
		refFaiGz = refFaiGz,
		refFaiGzi = refFaiGzi,
		#Comvert Cram to CrumbleExe
		crumbleExe = crumbleExe,
		ldLibraryPath = ldLibraryPath,
  	## sambambaIndex
  	## gatk splitintervals
  	subdivisionMode = subdivisionMode,
  	## gatk Base recal
  	knownSites1 = knownSites1,
  	knownSites1Index = knownSites1Index,
  	knownSites2 = knownSites2,
  	knownSites2Index = knownSites2Index,
  	knownSites3 = knownSites3,
  	knownSites3Index = knownSites3Index,
		DirsPrepared = preparePanelCaptureTmpDirs.dirsPrepared,
		## compute LowCoverage
		minCovBamQual = minCovBamQual,
		## computePoorCoverage
		bedtoolsLowCoverage = bedtoolsLowCoverage,
		bedToolsSmallInterval = bedToolsSmallInterval,
		## Picard HSmetrix
		BaitIntervals = gatkBedToPicardIntervalListBait.picardIntervals,
		TargetIntervals = gatkBedToPicardIntervalListTarget.picardIntervals
	}

	call alignDNA.alignDNA as alignFather {
		input:
		## Resources
  	CpuHigh = cpuHigh,
  	CpuLow = cpuLow,
  	memoryLow = memoryLow,
  	memoryHigh = memoryHigh,
    ## Global
    sampleID = FatherSampleID,
    CIsDIR = sampleID,
  	fastqR1 = FatherFastqR1,
  	fastqR2 = FatherFastqR2,
		refFasta = refFasta,
  	refFai = refFai,
  	refDict = refDict,
  	intervalBedFile = intervalBedFile,
  	workflowType = workflowType,
  	outDir = outDir,
		genomeVersion = genomeVersion,
    ## Bioinfo execs,
  	bwaExe = bwaExe,
  	samtoolsExe = samtoolsExe,
  	sambambaExe = sambambaExe,
		bedToolsExe = bedToolsExe,
    ## Standard execs
		sortExe = sortExe,
  	awkExe = awkExe,
  	gatkExe = gatkExe,
  	## bwaSamtools
  	platform = platform,
  	refAmb = refAmb,
  	refAnn = refAnn,
  	refBwt = refBwt,
  	refPac = refPac,
  	refSa = refSa,
  	## sambambaIndex
		# CRAM conversion
		refFastaGz = refFastaGz,
		refFaiGz = refFaiGz,
		refFaiGzi = refFaiGzi,
		#Comvert Cram to CrumbleExe
		crumbleExe = crumbleExe,
		ldLibraryPath = ldLibraryPath,
  	## gatk splitintervals
  	subdivisionMode = subdivisionMode,
  	## gatk Base recal
  	knownSites1 = knownSites1,
  	knownSites1Index = knownSites1Index,
  	knownSites2 = knownSites2,
  	knownSites2Index = knownSites2Index,
  	knownSites3 = knownSites3,
  	knownSites3Index = knownSites3Index,
		DirsPrepared = preparePanelCaptureTmpDirs.dirsPrepared,
		## compute LowCoverage
		minCovBamQual = minCovBamQual,
		## computePoorCoverage
		bedtoolsLowCoverage = bedtoolsLowCoverage,
		bedToolsSmallInterval = bedToolsSmallInterval,
		## Picard HSmetrix
		BaitIntervals = gatkBedToPicardIntervalListBait.picardIntervals,
		TargetIntervals = gatkBedToPicardIntervalListTarget.picardIntervals
	}

##############################################HaplotypeCaller######################@
	scatter (interval in alignCI.splittedIntervals) {
		call runGatkHaplotypeCallerDuo.gatkHaplotypeCallerDuo {
			input:
			Cpu = cpuLow,
			Memory = memoryHigh,
			SampleID = sampleID,
			OutDir = outDir,
			WorkflowType = workflowType,
			GatkExe = gatkExe,
			RefFasta = refFasta,
			RefFai = refFai,
			RefDict = refDict,
			DbSNP = knownSites3,
			DbSNPIndex = knownSites3Index,
			GatkInterval = interval,
			BamFile = alignCI.bam,
			BamIndex = alignCI.idx,
			BamFileFather = alignFather.bam,
			BamIndexFather = alignFather.idx,
			SwMode = swMode,
			EmitRefConfidence = emitRefConfidence
		}
	}
	output {
		Array[File] hcVcfs = gatkHaplotypeCallerDuo.hcVcf
	}
	call runGatkGatherVcfs.gatkGatherVcfs {
		input:
		Cpu = cpuLow,
		Memory = memoryHigh,
		SampleID = sampleID,
		OutDir = outDir,
		WorkflowType = workflowType,
		GatkExe = gatkExe,
		HcVcfs = hcVcfs,
		VcSuffix = hcSuffix
	}
	call runJvarkitVcfPolyX.jvarkitVcfPolyX as jvarkitVcfPolyxHc {
		input:
		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:
		Cpu = cpuLow,
		Memory = memoryHigh,
		SampleID = sampleID,
		OutDir = outDir,
		WorkflowType = workflowType,
		VcSuffix = hcSuffix,
		GatkExe = gatkExe,
		Vcf = jvarkitVcfPolyxHc.polyxedVcf,
		VcfIndex = jvarkitVcfPolyxHc.polyxedVcfIndex
	}
	call runGatkVariantFiltrationSnp.gatkVariantFiltrationSnp {
		input:
		Cpu = cpuLow,
		Memory = memoryHigh,
		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:
		Cpu = cpuLow,
		Memory = memoryHigh,
		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:
		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:
		Cpu = cpuLow,
		Memory = memoryHigh,
		SampleID = sampleID,
		OutDir = outDir,
		WorkflowType = workflowType,
		GatkExe = gatkExe,
		VcSuffix = hcSuffix,
		UnsortedVcf = gatkMergeVcfs.mergedVcf
	}
	call runBcftoolsNorm.bcftoolsNorm as bcftoolsNormHc {
		input:
		Cpu = cpuLow,
		Memory = memoryHigh,
		SampleID = sampleID,
		OutDir = outDir,
		WorkflowType = workflowType,
		BcfToolsExe = bcfToolsExe,
		VcSuffix = hcSuffix,
		SortedVcf = gatkSortVcfHc.sortedVcf
	}

	call runCompressIndexVcf.compressIndexVcf as compressIndexVcfHc {
		input:
		Cpu = cpuLow,
		Memory = memoryHigh,
		SampleID = sampleID,
		OutDir = outDir,
		WorkflowType = workflowType,
		BgZipExe = bgZipExe,
		TabixExe = tabixExe,
		VcSuffix = hcSuffix,
		# NormVcf = bcftoolsNormHc.normVcf
		VcfFile = gatkSortVcfHc.sortedVcf
	}

	call runBcftoolsStats.bcftoolsStats as bcftoolsStatsHc {
		input:
		Cpu = cpuLow,
		Memory = memoryHigh,
		SampleID = sampleID,
		OutDir = outDir,
		WorkflowType = workflowType,
		BcfToolsExe = bcfToolsExe,
		VcSuffix = hcSuffix,
		VcfFile = compressIndexVcfHc.bgZippedVcf,
		VcfFileIndex = compressIndexVcfHc.bgZippedVcfIndex
	}

	if (!debug) {
		String dataPath = "${outDir}${sampleID}/${workflowType}/"
		call runCleanUpPanelCaptureDuoTmpDirs.cleanUpPanelCaptureDuoTmpDirs {
			input:
			Cpu = cpuLow,
			Memory = memoryHigh,
			SampleID = sampleID,
			OutDir = outDir,
			WorkflowType = workflowType,
			FinalFile1 = compressIndexVcfHc.bgZippedVcf,
			FinalFile2 = alignCI.CrumbleIndex,
			FinalFile3 = alignFather.CrumbleIndex,
		}

		call runMultiqc.multiqc {
			input:
			Cpu = cpuLow,
			Memory = memoryHigh,
			SampleID = sampleID,
			OutDir = outDir,
			WorkflowType = workflowType,
			MultiqcExe = multiqcExe,
			Vcf = cleanUpPanelCaptureDuoTmpDirs.finalFile1
		}
	}
	call runToolVersions.toolVersions {
		input:
		Cpu = cpuLow,
		Memory = memoryHigh,
		SampleID = sampleID,
		OutDir = outDir,
		WorkflowType = workflowType,
		GenomeVersion = genomeVersion,
    FastqcExe = fastqcExe,
    BwaExe = bwaExe,
    SamtoolsExe = samtoolsExe,
    SambambaExe = sambambaExe,
    BedToolsExe = bedToolsExe,
    QualimapExe = qualimapExe,
    BcfToolsExe = bcfToolsExe,
    BgZipExe = bgZipExe,
    CrumbleExe = crumbleExe,
    TabixExe = tabixExe,
    MultiqcExe = multiqcExe,
    GatkExe = gatkExe,
    JavaExe= javaExe,
    VcfPolyXJar = vcfPolyXJar,
		Vcf = cleanUpPanelCaptureDuoTmpDirs.finalFile1
    }
	output {
		File? FinalVcf = cleanUpPanelCaptureDuoTmpDirs.finalFile1
		File FinalCram = alignCI.Crumble
		File FinalCramIndex = alignCI.CrumbleIndex
		File FinalCramFather = alignFather.Crumble
		File FinalCramIndexFather = alignFather.CrumbleIndex
		File VersionFile = toolVersions.versionFile
	}
}