Merge pull request #279 from RoanKanninga/master

fixing Manta WGS + wgs resource parameters for Gavin
molgenis · Aug 16, 2021 · 33e2e1c · 33e2e1c
2 parents 5decff4 + 809c4c4
commit 33e2e1c
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Showing 6 changed files with 25 additions and 19 deletions.
diff --git a/parameters_resources_wgs.csv b/parameters_resources_wgs.csv
@@ -17,7 +17,7 @@ mem_protocols_DecisionTree,5gb
 mem_protocols_DetermineTrio,1gb
 mem_protocols_FastQC,2gb
 mem_protocols_FlagstatMetrics,1gb
-mem_protocols_Gavin,4gb
+mem_protocols_Gavin,24gb
 mem_protocols_GenderCalculate,3gb
 mem_protocols_GenderCheck,3gb
 mem_protocols_InSilicoConcordance,25gb
@@ -116,7 +116,7 @@ walltime_protocols_PrepareFastQ,05:59:00
 walltime_protocols_SnpEff,05:59:00
 walltime_protocols_SnpFiltration,05:59:00
 walltime_protocols_SplitIndelsAndSNPs,05:59:00
-walltime_protocols_VariantCalling,05:59:00
+walltime_protocols_VariantCalling,15:59:00
 walltime_protocols_VariantGenotyping,05:59:00
 walltime_protocols_VcfToTable,05:59:00
 walltime_protocols_XHMM,05:59:00

diff --git a/protocols/CopyToResultsDir.sh b/protocols/CopyToResultsDir.sh
@@ -71,7 +71,7 @@ printf '%s\n' '.. finished.'
 printf 'Copying GAVIN results to results directory .'
 for sample in "${UNIQUESAMPLES[@]}"
 do
-	if [ -f "${intermediateDir}/${sample}.GAVIN.rlv.vcf" ]
+	if [ -f "${intermediateDir}/${sample}.GAVIN.rlv.vcf.gz" ]
 	then
 		rsync -a "${intermediateDir}/${sample}.GAVIN.rlv.vcf.gz" "${projectResultsDir}/variants/GAVIN/"
 		printf '.'

diff --git a/protocols/CoverageCalculations.sh b/protocols/CoverageCalculations.sh
@@ -135,7 +135,7 @@ then
 					echo "${sampleNameID}: percentage $percentage ($count/$totalcount) is more than 10 procent, skipped"
 					echo "${sampleNameID}: percentage $percentage ($count/$totalcount) is more than 10 procent, skipped" >> "${projectResultsDir}/coverage/${externalSampleID}.rejected"
 				else
-					rsync -a "${sampleNameID}.${perTarget}.coveragePerTarget.txt" "${projectResultsDir}/coverage/CoveragePerBase/${Gender,,}/"
+					rsync -a "${sampleNameID}.${perTarget}.coveragePerTarget.txt" "${projectResultsDir}/coverage/CoveragePerTarget/${Gender,,}/"
 				fi
 			fi
 		fi

diff --git a/protocols/CreateExternSamplesProjects.sh b/protocols/CreateExternSamplesProjects.sh
@@ -128,22 +128,28 @@ then
 	echo "Bedfile does not exist! Exiting"
         exit 1
 fi
-if [[ "${capturingKitProject,,}" == *"exoom"* || "${capturingKitProject,,}" == *"exome"* || "${capturingKitProject,,}" == *"all_exon_v1"* || "${capturingKitProject,,}" == *"wgs"* ]]
+if [[ "${capturingKitProject,,}" == *"exoom"* || "${capturingKitProject,,}" == *"exome"* || "${capturingKitProject,,}" == *"all_exon_v1"* ]]
 then
-	resourcesParameters="${EBROOTNGS_DNA}/parameters_resources_exome.csv"
 	batching="_chr"
-        if [ ! -e "${coveragePerTargetDir}/${captKit}/${captKit}" ]
-        then
+	resourcesParameters="${EBROOTNGS_DNA}/parameters_resources_exome.csv"
+	if [ ! -e "${coveragePerTargetDir}/${captKit}/${captKit}" ]
+	then
 		echo "Bedfile in ${coveragePerTargetDir} does not exist! Exiting"
-                exit 1
-        fi
+		echo "ls ${coveragePerTargetDir}/${captKit}/${captKit}"
+		exit 1
+	fi
+elif [[ "${capturingKitProject,,}" == *"wgs"* ]]
+then
+	batching="_chr"
+	resourcesParameters="${EBROOTNGS_DNA}/parameters_resources_wgs.csv"
 else
 	resourcesParameters="${EBROOTNGS_DNA}/parameters_resources_exome.csv"
 	if [ ! -e "${coveragePerBaseDir}/${captKit}/${captKit}" ]
-        then
+	then
 		echo "Bedfile in ${coveragePerBaseDir} does not exist! Exiting"
-                exit 1
-        fi
+		echo "ls ${coveragePerTargetDir}/${captKit}/${captKit}"
+		exit 1
+	fi
 fi
 
 if [ -f ".compute.properties" ];

diff --git a/protocols/CreateInhouseProjects.sh b/protocols/CreateInhouseProjects.sh
@@ -210,15 +210,15 @@ then
 elif [[ "${capturingKitProject,,}" == *"wgs"* ]]
 then
 	batching="_chr"
-        resourcesParameters="${EBROOTNGS_DNA}/parameters_resources_exome.csv"
+	resourcesParameters="${EBROOTNGS_DNA}/parameters_resources_wgs.csv"
 else
 	resourcesParameters="${EBROOTNGS_DNA}/parameters_resources_exome.csv"
 	if [ ! -e "${coveragePerBaseDir}/${captKit}/${captKit}" ]
-        then
-                echo "Bedfile in ${coveragePerBaseDir} does not exist! Exiting"
+	then
+		echo "Bedfile in ${coveragePerBaseDir} does not exist! Exiting"
 		echo "ls ${coveragePerTargetDir}/${captKit}/${captKit}"
-                exit 1
-        fi
+		exit 1
+	fi
 fi
 
 if [ "${captKit}" == *"ONCO"* ]

diff --git a/protocols/Manta.sh b/protocols/Manta.sh
@@ -136,5 +136,5 @@ then
 
 else
 	echo "WGS sample, just copy"
-	cp "${mantaDir}/results/variants/"{candidateSV,candidateSmallIndels,diploidSV}".vcf.gz."{,tbi} "${mantaDir}/results/variants/real/"
+	cp "${mantaDir}/results/variants/"{candidateSV,candidateSmallIndels,diploidSV}".vcf.gz"{,.tbi} "${mantaDir}/results/variants/real/"
 fi