Additional files

parameters.molgenis.csv

queue,mem,walltime,nodes,ppn,defaultInterpreter,stage,checkStage,WORKDIR,root,group,tmp,resDir,toolDir,projectDir,fastqcMod,bwaMod,picardMod,RMod,gatkMod,snpEffMod,varScanMod,samtoolsMod,vcfToolsMod,genomeLatSpecies,genomeSpecies,genomeBuild,genomeGrchBuild,ensemblVersion,onekgGenomeFasta,onekgGenomeFastaIdxBase,onekgGenomeFastaDict,goldStandardVcf,goldStandardVcfIdx,oneKgPhase1SnpsVcf,oneKgPhase1SnpsVcfIdx,oneKgPhase1IndelsVcf,oneKgPhase1IndelsVcfIdx,${resDir}/${genomeBuild}/variants/1000G_Phase3/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz,dbsnpVcf,dbsnpVcfIdx,exacVcf,exacVcfIdx,indelRealignmentTargets,snpEffStats,motifBin,nextProtBin,pwmsBin,regulation_CD4Bin,regulation_GM06990Bin,regulation_GM12878Bin,regulation_H1ESCBin,regulation_HeLaS3Bin,regulation_HepG2Bin,regulation_HMECBin,regulation_HSMMBin,regulation_HUVECBin,regulation_IMR90Bin,regulation_K562bBin,regulation_K562Bin,regulation_NHABin,regulation_NHEKBin,snpEffectPredictorBin,dbnsfp,dbnsfpTbi,oneKgP1wgsVcf,oneKgP1wgsVcfIdx,cosmicDir,cosmicVersion,cosmicVcf,cosmicVcfIdx,normalAnnotPl,nugBcSplitterPl,GenerateTableDescriptionByVcfHeaderPl,RVersion,vcfToolsVersion,plotScriptPl,slopTargetsList,scatterIntervallistDir,scatterList,genesRefFlat,rRnaIntervalList,fastqcDir,fastqcZipExt,singleEndfastqcZip,pairedEndfastqcZip1,pairedEndfastqcZip2,nTreads,bwaAlignmentDir,bwaSam,nugeneDir,nugeneTool,nugeneOutputPrefix,nugeneNodupsBam,nugeneNodupsBai,nugeneAddOrReplaceGroupsDir,nugeneAddOrReplaceGroupsBam,nugeneAddOrReplaceGroupsBai,nugeneCalculateHsMetricsDir,nugeneCalculateHsMetricsLog,nugeneCalculateHsMetricsPerTargetCov,addOrReplaceGroupsDir,addOrReplaceGroupsBam,addOrReplaceGroupsBai,nugeneRgDir,nugeneBam,nugeneBai,MergeBamFilesDir,MergeBamFilesBam,MergeBamFilesBai,markDuplicatesDir,markDuplicatesBam,markDuplicatesBai,markDuplicatesMetrics,collectRnaSeqMetricsDir,collectRnaSeqMetrics,collectRnaSeqMetricsChart,collectMultipleMetricsDir,collectMultipleMetricsPrefix,calculateHsMetricsDir,calculateHsMetricsLog,calculateHsMetricsPerTargetCov,indelRealignmentDir,realignmentIntervals,indelRealignmentBam,indelRealignmentBai,bsqrDir,bsqrBam,bsqrBai,bsqrBeforeGrp,analyseCovarsDir,bsqrAfterGrp,analyseCovariatesPdf,haplotyperDir,haplotyperRealignmentBam,haplotyperRealignmentBai,haplotyperScatVcf,haplotyperScatVcfIdx,haplotyperVcf,haplotyperVcfIdx,annotatorDir,snpEffGatkAnnotVcf,snpEffGatkAnnotVcfIdx,gatkAnnotVcf,gatkAnnotVcfIdx,snpEffAnnotVcf,snpEffAnnotVcfIdx,annotVcf,annotVcfIdx,custAnnotVcf,custAnnotVcfIdx,variantFiltDir,snvRawVcf,snvRawVcfIdx,indelMnpRawVcf,indelMnpRawVcfIdx,snvVcf,snvVcfIdx,indelMnpVcf,indelMnpVcfIdx,tableDir,snvTable,indelMnpTable,snvRawTable,indelMnpRawTable,snvDescrTable,indelMnpDescrTable,xlsxDir,snvXlsx,indelMnpXlsx,snvRawXlsx,indelMnpRawXlsx,snvDescrXlsx,indelMnpDescrXlsx,gHaplotyperDir,haplotyperGvcf,haplotyperGvcfIdx,mergeGvcf,mergeGvcfIdx,genotypedVcf,genotypedVcfIdx,gannotatorDir,gsnpEffVcf,gsnpEffVcfIdx,gannotVcf,gannotVcfIdx,varscanDir,varscanCopynumberPrefix,varscanCopynumber,varscanCopycaller,varscanCopycallerHomdels,varscanInputBam,varscanInputBai,varscanInputBamBai,controlvarscanInputBam,controlvarscanInputBai,controlvarscanInputBamBai,segFile,segmentsPlotPdf,cnvPlotPdf,scriptDir,projectMarkdown,targetsList
gcc,4,23:59:00,1,1,#!/bin/bash,module load,module list,/gcc/,${WORKDIR},umcg-oncogenetics,tmp01,${root}/resources/,${root}/tools/,/gcc/groups/${group}/${tmp}/projects/${project}/,FastQC/0.11.3-Java-1.7.0_80,BWA/0.7.12-goolf-1.7.20,picard/1.130-Java-1.7.0_80,R/3.2.0-goolf-1.7.20-Java-1.7.0_80,GATK/3.3-0-Java-1.7.0_80,snpEff/4.1d-Java-1.7.0_80,VarScan/2.3.9-Java-1.7.0_80,SAMtools/1.2-goolf-1.7.20,VCFtools/0.1.12b-goolf-1.7.20-Perl-5.20.2-bare,Homo_sapiens,human,b37,GRCh37,75,${resDir}/${genomeBuild}/indices/human_g1k_v37.fasta,${onekgGenomeFasta},${resDir}/${genomeBuild}/indices/human_g1k_v37.dict,${resDir}/${genomeBuild}/sv/1000G/Mills_and_1000G_gold_standard.indels.b37.vcf,${goldStandardVcf}.idx,${resDir}/${genomeBuild}/snp/1000G/1000G_phase1.snps.high_confidence.b37.vcf,${oneKgPhase1SnpsVcf}.idx,${resDir}/${genomeBuild}/sv/1000G/1000G_phase1.indels.b37.vcf,${oneKgPhase1IndelsVcf}.idx,,${resDir}/${genomeBuild}/snp/dbSNP/dbsnp_138.b37.vcf,${dbsnpVcf}.idx,${resDir}/ExAC/release0.3/ExAC.r0.3.sites.vep.vcf.gz,${exacVcf}.tbi,${resDir}/${genomeBuild}/intervals/1000G_phase1.indels_Mills_and_1000G_gold_standard.indels.b37.human_g1k_v37.intervals,${annotatorDir}/${project}.snpEff.summary.html,/gcc/resources/snpEff/3.6c/GRCh37.75/motif.bin,/gcc/resources/snpEff/3.6c/GRCh37.75/nextProt.bin,/gcc/resources/snpEff/3.6c/GRCh37.75/pwms.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_CD4.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_GM06990.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_GM12878.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_H1ESC.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_HeLa-S3.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_HepG2.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_HMEC.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_HSMM.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_HUVEC.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_IMR90.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_K562b.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_K562.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_NH-A.bin,${resDir}/snpEff/3.6c/GRCh37.75/regulation_NHEK.bin,${resDir}/snpEff/3.6c/GRCh37.75/snpEffectPredictor.bin,${resDir}/dbNSFP/2.7/dbNSFP2.7.txt.gz,${resDir}/dbNSFP/2.7/dbNSFP2.7.txt.gz.tbi,${resDir}/,${resDir}/,${resDir}/Cosmic/,v70,${cosmicDir}/${cosmicVersion}/CosmicCodingMuts.ensembl.vcf,${cosmicVcf}.idx,/gcc/tools/scripts/Vcf_tools_misc/ForGerardTeMeermanVcfAnnotation0.0.2.pl,/gcc/groups/oncogenetics/tmp01/tools/NugeneBarcodesAsReadgroup/dist/NugeneDigitalSplitter.pl,/gcc/tools/scripts/Vcf_tools_misc/GenerateTableDescriptionByVcfHeader.pl,3.0.2,0.1.12a,${scriptDir}/PlotVarscan/PlotFloatsOnInterVals0.0.3.pl,${projectDir}/targets.slop100.list,${projectDir}/scatter/,${projectDir}/scatter/temp_${scatterIDs}_of_*/scattered.intervals ,${resDir}/picard-tools/Ensembl${ensemblVersion}/${genomeLatSpecies}.${genomeGrchBuild}.${ensemblVersion}.refflat,${resDir}//picard-tools/Ensembl${ensemblVersion}/${genomeLatSpecies}.${genomeGrchBuild}.${ensemblVersion}.rrna.interval_list,${projectDir}/fastqc/,_fastqc.zip,${fastqcDir}/${internalId}_${sampleName}.fq${fastqcZipExt},${fastqcDir}/${internalId}_${sampleName}_1.fq${fastqcZipExt},${fastqcDir}/${internalId}_${sampleName}_2.fq${fastqcZipExt},8,${projectDir}/bwa/,${bwaAlignmentDir}${internalId}_${sampleName}.sam,${projectDir}/nugeneRmdups/,${"/gcc/groups/oncogenetics/tmp01/projects/NugeneValidation/Test/NuGEN_DupAnalysisTool_v5.1.5/runN6pipeline.sh"},${nugeneDir}/${sampleName},${nugeneOutputPrefix}_n6dupsRemoved_sorted.bam,${nugeneOutputPrefix}_n6dupsRemoved_sorted.bam.bai,${projectDir}/addOrReplaceReadGroupsNugene/,${nugeneAddOrReplaceGroupsDir}${internalId}_${sampleName}.bam,${nugeneAddOrReplaceGroupsDir}${internalId}_${sampleName}.bai,${projectDir}/hsMetricsNugene/, ${nugeneCalculateHsMetricsDir}/${internalId}_${sampleName}.hsmetrics.log, ${nugeneCalculateHsMetricsDir}/${internalId}_${sampleName}.hsmetrics.pertargetcov.tsv,${projectDir}/addOrReplaceReadGroups/,${addOrReplaceGroupsDir}${internalId}_${sampleName}.bam,${addOrReplaceGroupsDir}${internalId}_${sampleName}.bai,${projectDir}/nugeneReadgroups/,${nugeneRgDir}${internalId}_${sampleName}.bam,${nugeneRgDir}${internalId}_${sampleName}.bai,${projectDir}/MergeBams/,${MergeBamFilesDir}${sampleName}.bam,${MergeBamFilesDir}${sampleName}.bai,${projectDir}/markDuplicates/,${markDuplicatesDir}${sampleName}.bam,${markDuplicatesDir}${sampleName}.bai,${markDuplicatesDir}${sampleName}.metrics.log,${projectDir}/collectRnaSeqMetrics/,${collectRnaSeqMetricsDir}${sampleName}.rna_metrics.log,${collectRnaSeqMetricsDir}${sampleName}.chart.pdf,${projectDir}/multipleMetrics/,${collectMultipleMetricsDir}/${sampleName},${projectDir}/HsMetrics/, ${calculateHsMetricsDir}/${sampleName}.hsmetrics.log, ${calculateHsMetricsDir}/${sampleName}.hsmetrics.pertargetcov.tsv,${projectDir}/indelRealignment/,${indelRealignmentDir}/realignmentIntervals.list,${indelRealignmentDir}${sampleName}.bam,${indelRealignmentDir}${sampleName}.bai,${projectDir}/baseQualityScoreRecalibration/,${bsqrDir}${sampleName}.bam,${bsqrDir}${sampleName}.bai,${bsqrDir}${sampleName}.before.grp,${projectDir}/CovariantAnalysis/,${bsqrDir}${sampleName}.after.grp,${analyseCovarsDir}/${sampleName}.analysecovariates.pdf,${projectDir}/haplotypeCaller/,${haplotyperDir}${sampleName}.bam,${haplotyperDir}${sampleName}.bam,${haplotyperDir}${project}.${scatterIDs}.vcf,${haplotyperScatVcf}.idx,${haplotyperDir}${project}.vcf,${haplotyperVcf}.idx,${projectDir}/VariantAnnotation/,${annotatorDir}/${project}.snpEffGatk.intermediate.vcf,${snpEffGatkAnnotVcf}.idx,${annotatorDir}/${project}.annot.intermediate.vcf,${gatkAnnotVcf}.idx,${annotatorDir}/${project}.snpEff.intermediate.vcf,${snpEffAnnotVcf}.idx,${annotatorDir}/${project}.annot.vcf,${annotVcf}.idx,${annotatorDir}/${project}.annot.cust.${controlSampleName}.vcf,${custAnnotVcf}.idx,${projectDir}/variantfiltering/,${variantFiltDir}/${project}.${controlSampleName}.snv.raw.vcf,${snvRawVcf}.idx,${variantFiltDir}/${project}.${controlSampleName}.indelmnp.raw.vcf,${indelMnpRawVcf}.idx,${variantFiltDir}/${project}.${controlSampleName}.snv.vcf,${snvVcf}.idx,${variantFiltDir}/${project}.${controlSampleName}.indelmnp.vcf,${indelMnpVcf}.idx,${projectDir}/tables/,${tableDir}/${project}.${controlSampleName}.snv.tsv,${tableDir}/${project}.${controlSampleName}.indelmnp.tsv,${tableDir}/${project}.${controlSampleName}.snv.raw.tsv,${tableDir}/${project}.${controlSampleName}.indelmnp.raw.tsv,${tableDir}/${project}.snv.description.tsv,${tableDir}/${project}.indelmnp.description.tsv,${projectDir}/xlsx/,${xlsxDir}/${project}.${controlSampleName}.snv.xlsx,${xlsxDir}/${project}.${controlSampleName}.indelmnp.xlsx,${xlsxDir}/${project}.${controlSampleName}.snv.raw.xlsx,${xlsxDir}/${project}.${controlSampleName}.indelmnp.raw.xlsx,${xlsxDir}/${project}.snv.description.xlsx,${xlsxDir}/${project}.indelmnp.description.xlsx,${projectDir}/haplotypeCallerGvf/,${gHaplotyperDir}${sampleName}.g.vcf,${haplotyperGvcf}.idx,${gHaplotyperDir}${project}.g.vcf,${mergeGvcf}.idx,${gHaplotyperDir}${project}.gg.vcf,${genotypedVcf}.idx,${projectDir}/GVariantAnnotation/,${gannotatorDir}/${project}.snpEff.vcf,${gsnpEffVcf}.idx,${gannotatorDir}/${project}.annot.vcf,${gannotVcf}.idx,${projectDir}/varscan.${controlSampleName}/,${varscanDir}/${sampleName}.cn,${varscanCopynumberPrefix}.copynumber,${varscanCopynumberPrefix}.called,${varscanCopynumberPrefix}.called.homdels,${indelRealignmentBam},${indelRealignmentBai},${indelRealignmentBai},${indelRealignmentDir}${controlSampleName}.bam,${indelRealignmentDir}${controlSampleName}.bai,${indelRealignmentDir}${controlSampleName}.bai,${varscanDir}/${sampleName}.cn.seg,${varscanDir}/${sampleName}.cn.called.pdf,${varscanDir}/${sampleName}.cn.called.pdf,/gcc/tools/scripts/,${projectDir}/${project}.summary.Rmd,/groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/samplesheet.csv

samplesheet.csv.tmp.csv

scatter_id.csv

weavecommand

!#/bin/bash
#need a little remoddeling
bash /groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/test/molgenis-compute-core-1.0.0-SNAPSHOT/molgenis_compute.sh \
 --generate\
 -p /groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/parameters.molgenis.csv\
 -p /groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/samplesheet.csv.tmp.csv\
 -p /groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/scatter_id.csv\
 -w /groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/workflow_test.csv\
 --backend pbs\
 --weave\
 -rundir /groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/groups/umcg-oncogenetics/tmp04/projects/something.20140402.104325-2/jobs\
 -header /groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/test/molgenis-compute-core-1.0.0-SNAPSHOT/templates/localhost//header.ftl\
 -submit /groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/test/molgenis-compute-core-1.0.0-SNAPSHOT/templates/localhost//submit.ftl\
 -footer /groups/umcg-oncogenetics/tmp04/git/molgenis-c5-TumorNormal/test/molgenis-compute-core-1.0.0-SNAPSHOT/templates/localhost//footer.ftl