modifs for callcaching behaviour, removed useles files, modified fina…

…l outputs

modules/bwaSamtools.wdl

@@ -12,7 +12,8 @@ task bwaSamtools {
 	String BwaExe
 	String Platform
 	File RefFasta
-	File RefFai
+	#File RefFai
+	#RefFai useles for bwa
 	#index files for bwa
 	File RefAmb
 	File RefAnn
@@ -32,4 +33,4 @@ task bwaSamtools {
 		File sortedBam = "${OutDir}${SampleID}/${WorkflowType}/${SampleID}.bam"
 		#File sortedBamIndex = "${OutDir}${SampleID}/${WorkflowType}/${SampleID}.bam.bai"
 	}
-}
+}

modules/cleanUpPanelCaptureTmpDirs.wdl

@@ -6,8 +6,10 @@ task cleanUpPanelCaptureTmpDirs {
 	String WorkflowType
 	File FinalVcf
 	Array[String] BamArray
-	String FinalBam
-	String FinalBamIndex
+	#String FinalBam
+	#String FinalBamIndex
+	#String FinalCram
+	#String FinalCramIndex
 	Array[String] VcfArray
 	command {
 		if [ -d "${OutDir}${SampleID}/${WorkflowType}/splitted_intervals" ];then \
@@ -24,12 +26,12 @@ task cleanUpPanelCaptureTmpDirs {
 		fi
 		rm ${sep=" " BamArray} 
 		rm ${sep=" " VcfArray}
-		#mv "${FinalBam}" "${OutDir}${SampleID}/${WorkflowType}/${SampleID}.bam"
-		#mv "${FinalBamIndex}" "${OutDir}${SampleID}/${WorkflowType}/${SampleID}.bam.bai"
 	}
 	output {
-		File finalBam = "${FinalBam}"
-		File finalBamIndex = "${FinalBamIndex}"
+		#File finalBam = "${FinalBam}"
+		#File finalBamIndex = "${FinalBamIndex}"
+		#File finalCram = "${FinalCram}"
+		#File finalCramIndex = "${FinalCramIndex}"
 		File finalVcf = "${FinalVcf}"
 	}
-}
+}

modules/computeCoverage.wdl

@@ -11,9 +11,9 @@ task computeCoverage {
 	command <<<
 		${SortExe} -k1,1 -k2,2n -k3,3n ${BedCovFile} \
 		| ${AwkExe}  'BEGIN {OFS="\t"}{a=($3-$2+1);b=($7/a);print $1,$2,$3,$4,b,"+","+"}' \
-		> "${OutDir}/${SampleID}/${WorkflowType}/coverage/${SampleID}_coverage.tsv"
+		> "${OutDir}${SampleID}/${WorkflowType}/coverage/${SampleID}_coverage.tsv"
 	>>>
 	output {
-		File TsvCoverageFile = "${OutDir}/${SampleID}/${WorkflowType}/coverage/${SampleID}_coverage.tsv"
+		File TsvCoverageFile = "${OutDir}${SampleID}/${WorkflowType}/coverage/${SampleID}_coverage.tsv"
 	}
 }

modules/computeCoverageClamms.wdl

@@ -11,9 +11,9 @@ task computeCoverageClamms {
 	command <<<
 		${SortExe} -k1,1 -k2,2n -k3,3n ${BedCovFile} \
 		| awk '{ printf "%s\t%d\t%d\t%.6g\n", $1, $2, $3, $NF/($3-$2); }' \
-		> "${OutDir}/${SampleID}/${WorkflowType}/coverage/${SampleID}_coverage.bed"
+		> "${OutDir}${SampleID}/${WorkflowType}/coverage/${SampleID}_coverage.bed"
 	>>>
 	output {
-		File ClammsCoverageFile = "${OutDir}/${SampleID}/${WorkflowType}/coverage/${SampleID}_coverage.bed"
+		File ClammsCoverageFile = "${OutDir}${SampleID}/${WorkflowType}/coverage/${SampleID}_coverage.bed"
 	}
 }

modules/computePoorCoverage.wdl

@@ -21,9 +21,9 @@ task computePoorCoverage {
 		| ${BedToolsExe} merge -c 4 -o distinct -i - \
 		| ${AwkExe} -v small_intervall="${BedToolsSmallInterval}" \
 		'BEGIN {OFS="\t";print "#chr","start","end","region","size bp","type","UCSC link"} {a=($3-$2+1);if(a<small_intervall) {b="SMALL_INTERVAL"} else {b="OTHER"};url="http://genome-euro.ucsc.edu/cgi-bin/hgTracks?db='${GenomeVersion}'&position="$1":"$2-10"-"$3+10"&highlight='${GenomeVersion}'."$1":"$2"-"$3;print $0, a, b, url}' \
-		> "${OutDir}/${SampleID}/${WorkflowType}/coverage/${SampleID}_poor_coverage.tsv"
+		> "${OutDir}${SampleID}/${WorkflowType}/coverage/${SampleID}_poor_coverage.tsv"
 	>>>
 	output {
-		File poorCoverageFile = "${OutDir}/${SampleID}/${WorkflowType}/coverage/${SampleID}_poor_coverage.tsv"
+		File poorCoverageFile = "${OutDir}${SampleID}/${WorkflowType}/coverage/${SampleID}_poor_coverage.tsv"
 	}
 }

modules/gatkHaplotypeCaller.wdl

@@ -15,6 +15,8 @@ task gatkHaplotypeCaller {
 	String intervalName = basename("${GatkInterval}", ".intervals")
 	File BamFile
 	File BamIndex
+	#when callcaching on, seem to keep Bam and index in the same directory for HC execution
+	Pair[File, File] Bam = (BamFile, BamIndex)
 	String SwMode
 	command {
 		${SrunLow} ${GatkExe} HaplotypeCaller \
@@ -28,4 +30,4 @@ task gatkHaplotypeCaller {
 	output {
 		File hcVcf = "${OutDir}${SampleID}/${WorkflowType}/vcfs/${SampleID}.${intervalName}.vcf"
 	}
-}
+}

modules/multiqc.wdl

@@ -6,9 +6,9 @@ task multiqc {
 	String MultiqcExe
 	File Vcf
 	command {
-		${SrunLow} ${MultiqcExe} -o "${OutDir}${SampleID}/${WorkflowType}/" -n "${SampleID}_multiqc" "${OutDir}${SampleID}/${WorkflowType}/"
+		${SrunLow} ${MultiqcExe} -o "${OutDir}${SampleID}/${WorkflowType}/" -n "${SampleID}_multiqc" "${OutDir}${SampleID}/${WorkflowType}/" -f
 	}
 	output {
 		File multiqcHtml = "${OutDir}${SampleID}/${WorkflowType}/${SampleID}_multiqc.html"
 	}
-}
+}

panelCapture.wdl

@@ -38,6 +38,11 @@ import "modules/cleanUpPanelCaptureTmpDirs.wdl" as runCleanUpPanelCaptureTmpDirs
 import "modules/multiqc.wdl" as runMultiqc
 
 workflow panelCapture {
+	meta {
+		author: "David Baux"
+		email: "david.baux(at)inserm.fr"
+	}
+	#variables declarations
 	#global
 	String srunHigh
 	String srunLow
@@ -145,7 +150,7 @@ workflow panelCapture {
 		BwaExe = bwaExe,
 		Platform = platform,
 		RefFasta = refFasta,
-		RefFai = refFai,
+		#RefFai = refFai,
 		RefAmb = refAmb,
 		RefAnn = refAnn,
 		RefBwt = refBwt,
@@ -558,8 +563,10 @@ workflow panelCapture {
 		WorkflowType = workflowType,
 		FinalVcf = compressIndexVcf.bgZippedVcf,
 		BamArray = ["${dataPath}" + basename(sambambaMarkDup.markedBam), "${dataPath}" + basename(sambambaMarkDup.markedBamIndex), "${dataPath}" + basename(gatkGatherBQSRReports.gatheredRecalTable), "${dataPath}" + basename(gatkGatherBamFiles.gatheredBam)],
-		FinalBam = "${dataPath}" + basename(samtoolsSort.sortedBam),
-		FinalBamIndex = "${dataPath}" + basename(finalIndexing.bamIndex),
+		#FinalBam = "${dataPath}" + basename(samtoolsSort.sortedBam),
+		#FinalBamIndex = "${dataPath}" + basename(finalIndexing.bamIndex),
+		#FinalCram = "${dataPath}" + basename(samtoolsCramConvert.cram),
+		#FinalCramIndex = "${dataPath}" + basename(samtoolsCramIndex.cramIndex),
 		VcfArray = ["${dataPath}" + basename(gatkGatherVcfs.gatheredHcVcf), "${dataPath}" + basename(gatkGatherVcfs.gatheredHcVcfIndex), "${dataPath}" + basename(jvarkitVcfPolyX.polyxedVcf), "${dataPath}" + basename(jvarkitVcfPolyX.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), "${dataPath}" + basename(gatkSortVcf.sortedVcf), "${dataPath}" + basename(gatkSortVcf.sortedVcfIndex)]
 	}
 	call runMultiqc.multiqc {
@@ -571,6 +578,11 @@ workflow panelCapture {
 		MultiqcExe = multiqcExe,
 		Vcf = cleanUpPanelCaptureTmpDirs.finalVcf
 	}
-
-
+	output {
+		File FinalVcf = cleanUpPanelCaptureTmpDirs.finalVcf
+		#FinalBam = "${dataPath}" + basename(samtoolisSort.sortedBam),
+		#FinalBamIndex = "${dataPath}" + basename(finalIndexing.bamIndex),
+		File FinalCram = samtoolsCramConvert.cram
+		File FinalCramIndex = samtoolsCramIndex.cramIndex
+	}
 }