Merge pull request #220 from RoanKanninga/master

changed order in workflow + updated vcfanno version

parameters.csv

@@ -34,7 +34,7 @@ samtoolsVersion,SAMtools/1.2-${toolChain}
 seqTkVersion,seqtk/1.2-${toolChain}
 snpEffVersion,snpEff/4.3t-Java-1.8.0_74
 htsLibVersion,HTSlib/1.3.2-${toolChain}
-vcfAnnoVersion,vcfanno/v0.2.9
+vcfAnnoVersion,vcfanno/v0.3.1
 bcfToolsVersion,BCFtools/1.6-${toolChain}
 tabixVersion,tabix/0.2.6-${toolChain}
 vepVersion,VEP/90.5

workflow.csv

@@ -1,25 +1,25 @@
 step,protocol,dependencies
 s01_PrepareFastQ,protocols/PrepareFastQ.sh,
-s02_FastQC,protocols/FastQC.sh,s01_PrepareFastQ;fastq1=peEnd1BarcodePhiXRecodedFqGz;fastq2=peEnd2BarcodePhiXRecodedFqGz
-s03_BwaAlignAndSortSam,protocols/BwaAlignAndSortSam.sh,s01_PrepareFastQ;fastq1=peEnd1BarcodePhiXRecodedFqGz;fastq2=peEnd2BarcodePhiXRecodedFqGz
-s04_MergeBam,protocols/MergeBam.sh,s03_BwaAlignAndSortSam;inputMergeBam=alignedSortedBam;inputMergeBamIdx=alignedSortedBamIdx
+s02_BwaAlignAndSortSam,protocols/BwaAlignAndSortSam.sh,s01_PrepareFastQ;fastq1=peEnd1BarcodePhiXRecodedFqGz;fastq2=peEnd2BarcodePhiXRecodedFqGz
+s03_FastQC,protocols/FastQC.sh,s01_PrepareFastQ;fastq1=peEnd1BarcodePhiXRecodedFqGz;fastq2=peEnd2BarcodePhiXRecodedFqGz
+s04_MergeBam,protocols/MergeBam.sh,s02_BwaAlignAndSortSam;inputMergeBam=alignedSortedBam;inputMergeBamIdx=alignedSortedBamIdx
 s05_BaseRecalibrator,protocols/BaseRecalibrator.sh,s04_MergeBam;dbSnp=dbSNP137Vcf
 s06_MarkDuplicates,protocols/MarkDuplicates.sh,s04_MergeBam
-s07_Flagstat,protocols/FlagstatMetrics.sh,s06_MarkDuplicates
-s08_Manta,protocols/Manta.sh,s06_MarkDuplicates
-s09a_Convading,protocols/Convading.sh,s06_MarkDuplicates
-s09b_XHMM,protocols/XHMM.sh,s06_MarkDuplicates
-s09c_DecisionTree,protocols/DecisionTree.sh,s09a_Convading;s09b_XHMM
-s10_GenderCalculate,protocols/GenderCalculate.sh,s06_MarkDuplicates
-s11_CramConversion,protocols/CramConversion.sh,s06_MarkDuplicates
-s12_MakeDedupBamMd5,protocols/MakeDedupBamMd5.sh,s06_MarkDuplicates
-s13_CoverageCalculations,protocols/CoverageCalculations.sh,s06_MarkDuplicates
-s14a_CollectMultipleMetrics,protocols/CollectMultipleMetrics.sh,s06_MarkDuplicates
-s14b_CollectHSMetrics,protocols/CollectHSMetrics.sh,s06_MarkDuplicates
-s14c_CollectBamIndexMetrics,protocols/CollectBamIndexMetrics.sh,s06_MarkDuplicates
-s14d_CollectGCBiasMetrics,protocols/CollectGCBiasMetrics.sh,s06_MarkDuplicates
-s15_GenderCheck,protocols/GenderCheck.sh,s10_GenderCalculate;s14b_CollectHSMetrics
-s16a_VariantCalling,protocols/VariantCalling.sh,s15_GenderCheck;s05_BaseRecalibrator;dbSnp=dbSNP137Vcf
+s07_GenderCalculate,protocols/GenderCalculate.sh,s06_MarkDuplicates
+s08a_CollectMultipleMetrics,protocols/CollectMultipleMetrics.sh,s06_MarkDuplicates
+s08b_CollectHSMetrics,protocols/CollectHSMetrics.sh,s06_MarkDuplicates
+s08c_CollectBamIndexMetrics,protocols/CollectBamIndexMetrics.sh,s06_MarkDuplicates
+s08d_CollectGCBiasMetrics,protocols/CollectGCBiasMetrics.sh,s06_MarkDuplicates
+s09_GenderCheck,protocols/GenderCheck.sh,s10_GenderCalculate;s08b_CollectHSMetrics
+s10_Flagstat,protocols/FlagstatMetrics.sh,s06_MarkDuplicates
+s11_Manta,protocols/Manta.sh,s06_MarkDuplicates
+s12a_Convading,protocols/Convading.sh,s06_MarkDuplicates
+s12b_XHMM,protocols/XHMM.sh,s06_MarkDuplicates
+s12c_DecisionTree,protocols/DecisionTree.sh,s12a_Convading;s12b_XHMM
+s13_CramConversion,protocols/CramConversion.sh,s06_MarkDuplicates
+s14_MakeDedupBamMd5,protocols/MakeDedupBamMd5.sh,s06_MarkDuplicates
+s15_CoverageCalculations,protocols/CoverageCalculations.sh,s06_MarkDuplicates
+s16a_VariantCalling,protocols/VariantCalling.sh,s09_GenderCheck;s05_BaseRecalibrator;dbSnp=dbSNP137Vcf
 s16b_GenotypeVariants,protocols/VariantGenotyping.sh,s16a_VariantCalling;dbSnp=dbSNP137Vcf
 s17_AnnotateVcf,protocols/AnnotateVcf.sh,s16b_GenotypeVariants
 s18_SnpEff,protocols/SnpEff.sh,s17_AnnotateVcf
@@ -36,6 +36,6 @@ s25a_CompressingSampleVcf,protocols/CompressingFinalVcf.sh,s22_MergeIndelsAndSnp
 s25b_CompressingProjectVcf,protocols/CompressingFinalVcf.sh,s22_MergeIndelsAndSnps;finalVcf=projectFinalVcf
 s26_VcfToTable,protocols/VcfToTable.sh,s22_MergeIndelsAndSnps
 s27_InSilicoConcordance,protocols/InSilicoConcordance.sh,s26_VcfToTable
-s28_MultiQC,protocols/MultiQC.sh,s14a_CollectMultipleMetrics;s14b_CollectHSMetrics;s14c_CollectGCBiasMetrics;s14d_CollectBamIndexMetrics;s27_InSilicoConcordance
-s29_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s08_Manta;s09c_DecisionTree.sh;s24c_CartegeniaFiltering;s13_CoverageCalculations;s28_MultiQC
+s28_MultiQC,protocols/MultiQC.sh,s08a_CollectMultipleMetrics;s08b_CollectHSMetrics;s08c_CollectGCBiasMetrics;s08d_CollectBamIndexMetrics;s27_InSilicoConcordance
+s29_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s11_Manta;s12c_DecisionTree.sh;s24c_CartegeniaFiltering;s15_CoverageCalculations;s28_MultiQC
 s30_CopyToResultsDir,protocols/CopyToResultsDir.sh,s08_Manta;s25a_CompressingSampleVcf;s25b_CompressingProjectVcf;s29_CountAllFinishedFiles