Merge pull request #178 from RoanKanninga/master

added MantaAnnotation

protocols/MantaAnnotation.sh

@@ -27,7 +27,7 @@ ${checkStage}
 makeTmpDir "${intermediateDir}"
 tmpIntermediateDir="${MC_tmpFile}"
 
-for i in  "candidateSV" "diploidSV"
+for i in  "diploidSV"
 do
 	echo "running $i"
 	if [ -f "${mantaDir}/results/variants/real/${i}.vcf.gz" ]

workflow.csv

@@ -10,7 +10,7 @@ s09a_Manta,protocols/Manta.sh,s07_MarkDuplicates
 s09b_Convading,protocols/Convading.sh,s07_MarkDuplicates
 s09c_XHMM,protocols/XHMM.sh,s07_MarkDuplicates
 s09d_DecisionTree,protocols/DecisionTree.sh,s09b_Convading;s09c_XHMM
-#s09e_MantaAnnotation,protocols/MantaAnnotation.sh,s09a_Manta
+s09e_MantaAnnotation,protocols/MantaAnnotation.sh,s09a_Manta
 s10_GenderCalculate,protocols/GenderCalculate.sh,s07_MarkDuplicates
 s11_CramConversion,protocols/CramConversion.sh,s07_MarkDuplicates
 s12_MakeDedupBamMd5,protocols/MakeDedupBamMd5.sh,s07_MarkDuplicates
@@ -37,7 +37,6 @@ s24b_CompressingProjectVcf,protocols/CompressingFinalVcf.sh,s22_MergeIndelsAndSn
 s25_VcfToTable,protocols/VcfToTable.sh,s22_MergeIndelsAndSnps
 s26_InSilicoConcordance,protocols/InSilicoConcordance.sh,s25_VcfToTable
 s27a_QCStats,protocols/QCStats.sh,s14a_CollectMultipleMetrics;s14b_CollectHSMetrics;s14c_CollectGCBiasMetrics;s14d_CollectBamIndexMetrics;s26_InSilicoConcordance
-#s27b_QCReport,protocols/QCReport.sh,s27a_QCStats
-s27c_MultiQC,protocols/MultiQC.sh,s14a_CollectMultipleMetrics;s14b_CollectHSMetrics;s14c_CollectGCBiasMetrics;s14d_CollectBamIndexMetrics;s26_InSilicoConcordance
-s28_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s09d_DecisionTree.sh;s23b_GeneNetwork;s27b_QCReport;s13_CoverageCalculations;s27c_MultiQC
+s27b_MultiQC,protocols/MultiQC.sh,s14a_CollectMultipleMetrics;s14b_CollectHSMetrics;s14c_CollectGCBiasMetrics;s14d_CollectBamIndexMetrics;s26_InSilicoConcordance
+s28_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s09d_DecisionTree.sh;s23b_GeneNetwork;s13_CoverageCalculations;s27b_MultiQC
 s29_CopyToResultsDir,protocols/CopyToResultsDir.sh,s09e_MantaAnnotation;s24a_CompressingSampleVcf;s24b_CompressingProjectVcf;s28_CountAllFinishedFiles