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parameters.hisat.csv
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parameters.hisat.csv
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##### BACKEND #####
stage,module load
checkStage,module list
jobname,jobname
##### Tools and versions #####
jdkVersion,Java/1.7.0_80
NGSUtilsVersion,ngs-utils
fastqcVersion,FastQC/0.11.3-Java-1.7.0_80
samtoolsVersion,SAMtools/1.2-foss-2015b
RVersion,R/3.2.1-foss-2015b
wkhtmltopdfVersion,wkhtmltopdf/0.11.0_rc1-static-amd64
picardVersion,picard/1.130-Java-1.7.0_80
anacondaVersion,Anaconda/1.8.0-Linux-x86_64
htseqVersion,HTSeq/0.6.1p1-foss-2015b
hisatVersion,hisat/0.1.5-beta-foss-2015b
starVersion,STAR/2.5.1b-foss-2015b
pythonVersion,Python/2.7.10-foss-2015b
gatkVersion,GATK/3.6-Java-1.8.0_74
ghostscriptVersion,Ghostscript/9.16-foss-2015b
kallistoVersion,Kallisto/0.43.0-goolf-1.7.20
BBMapVersion,BBMap/35.69-Java-1.7.0_80
multiqcVersion,multiqc/1.0-foss-2015b-Python-2.7.11
picardJar,picard.jar
mergeSamFilesJar,MergeSamFiles
processReadCountsJar,ProcessReadCounts.jar
##### GENERAL DIRECTORIES #####
tmpDataDir,${workDir}/${tmpName}/
tmpTmpDataDir,${tmpDataDir}/tmp/
sourcesDir,${root}/sources/
softwareDir,${root}/software/
scriptDir,${softwareDir}/scripts/
##### RAW DATA FILES/DIRS #####
allRawNgsPrmDataDir,${permanentDir}/rawdata/ngs
allRawtmpDataDir,${tmpDataDir}/rawdata/
allRawNgstmpDataDir,${allRawtmpDataDir}/ngs/
rawtmpDataDir,${allRawNgstmpDataDir}/${runPrefix}
logsDir,${tmpDataDir}/logs
srInputFile,${rawtmpDataDir}/${filePrefix}.fq.gz
peEnd1FqGz,${rawtmpDataDir}/${filePrefix}_1.fq.gz
peEnd2FqGz,${rawtmpDataDir}/${filePrefix}_2.fq.gz
peEnd1BarcodeFqGz,${rawFile}_1.${rawFileExt}
peEnd2BarcodeFqGz,${rawFile}_2.${rawFileExt}
peEnd1BarcodeFq,${rawFile}_1.fq
srBarcodeFqGz,${rawFile}.${rawFileExt}
srBarcodeFq,${intermediateDir}/${filePrefix}_${barcode}.fq
leftbarcode,${projectRawtmpDataDir}/${filePrefix}_${barcode}_1
rightbarcode,${projectRawtmpDataDir}/${filePrefix}_${barcode}_2
leftbarcodefq,${leftbarcode}.fq
rightbarcodefq,${rightbarcode}.fq
leftbarcodefqgz,${leftbarcodefq}.gz
rightbarcodefqgz,${rightbarcodefq}.gz
workflowFile,$MC_HOME/NGS_RNA_seq_pipeline/workflow.csv
##### GENOME,INDEX,ANNOTATION FILES #####
ensembleDir,${dataDir}/ftp.ensembl.org/pub/release-${ensembleReleaseVersion}/gtf/${speciesFileName}/
geneAnnotationTxt,${ensembleDir}/${annotationFileName}.${ensembleReleaseVersion}.annotation.geneIds.txt.gz
annotationGtf,${ensembleDir}/${annotationFileName}.${ensembleReleaseVersion}.gtf
annotationRefFlat,${ensembleDir}/${annotationFileName}.${ensembleReleaseVersion}.gtf.annotation.refFlat
annotationIntervalList,${ensembleDir}/${annotationFileName}.${ensembleReleaseVersion}.rrna.interval_list
dbsnpVcf,${dbSNPDir}${dbSNPFileID}.vcf
##### PREFIXES,POSTFIXES #####
rawFileExt,fq.gz
runPrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}
rawFile,${projectRawtmpDataDir}/${filePrefix}_${barcode}
filePrefix,${runPrefix}_L${lane}
library,${filePrefix}
##### Projects #####
generalProjectDir,${tmpDataDir}/projects/
projectDir,${generalProjectDir}/${project}/${runid}
projectRawtmpDataDir,${projectDir}/rawdata/ngs/
projectRawArraytmpDataDir,${projectDir}/rawdata/array/
intermediateDir,${tempDir}/${project}/${runid}/
projectPrefix,${intermediateDir}/${project}
projectJobsDir,${projectDir}/jobs/
projectLogsDir,${projectDir}/logs/
projectResultsDir,${projectDir}/results/
projectQcDir,${projectDir}/qc/
##### Protocols 0,1a,1b, (FastQC,HisatAlignment,MergeBam) #####
peEnd1BarcodeFastQcZip,${intermediateDir}/${filePrefix}_${barcode}_1.fq_fastqc.zip
peEnd2BarcodeFastQcZip,${intermediateDir}/${filePrefix}_${barcode}_2.fq_fastqc.zip
srBarcodeFastQcZip,${intermediateDir}/${filePrefix}_${barcode}.fq_fastqc.zip
BarcodeFastQcFolder,${intermediateDir}/${filePrefix}_${barcode}.fq_fastqc
BarcodeFastQcFolderPE,${intermediateDir}/${filePrefix}_${barcode}_1.fq_fastqc
alignedSam,${intermediateDir}/${filePrefix}_${barcode}.sam
alignedBam,${intermediateDir}/${filePrefix}_${barcode}.bam
alignedFilteredBam,${intermediateDir}/${filePrefix}_${barcode}.bam
alignedFilteredBai,${intermediateDir}/${filePrefix}_${barcode}.bai
sortedBam,${intermediateDir}/${filePrefix}_${barcode}.sorted.bam
sortedBai,${intermediateDir}/${filePrefix}_${barcode}.sorted.bai
addOrReplaceGroupsBam,${intermediateDir}/${filePrefix}_${barcode}.rg.sorted.bam
addOrReplaceGroupsBai,${intermediateDir}/${filePrefix}_${barcode}.rg.sorted.bai
sampleMergedBam,${intermediateDir}/${externalSampleID}.sorted.merged.bam
sampleMergedBai,${intermediateDir}/${externalSampleID}.sorted.merged.bai
sampleMergedDedupBam,${intermediateDir}/${externalSampleID}.sorted.merged.dedup.bam
sampleMergedDedupBai,${intermediateDir}/${externalSampleID}.sorted.merged.dedup.bai
starLogFile,${intermediateDir}/${externalSampleID}.hisat.final.log,
fragmentLength,200
##### Protocols 4,5a,5b,5c (SplitAndTrim,GatkHaplotypeCallerGvcf,GatkMergeGvcf,GatkGenotypeGvcf) #####
splitAndTrimBam,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.bam
splitAndTrimBai,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.bai
IndelRealignedBam,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.realigned.bam
IndelRealignedBai,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.realigned.bai
bqsrBeforeGrp,${intermediateDir}${externalSampleID}.before.grp
bqsrBam,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.realigned.bqsr.bam
bqsrBai,${intermediateDir}${externalSampleID}.sorted.merged.dedup.splitAndTrim.realigned.bqsr.bai
GatkHaplotypeCallerGvcf,${intermediateDir}${externalSampleID}.GatkHaplotypeCallerGvcf.g.vcf
GatkHaplotypeCallerGvcfidx,${intermediateDir}${externalSampleID}.GatkHaplotypeCallerGvcf.g.vcf.idx
GatkMergeGvcf,${intermediateDir}${externalSampleID}.MergeGvcf.g.vcf
GatkMergeGvcfidx,${intermediateDir}.MergeGvcf.g.vcf.idx
projectBatchGenotypedVariantCalls,${projectPrefix}.variant.calls.genotyped.chr${chr}.vcf
projectBatchCombinedVariantCalls,${projectPrefix}.variant.calls.combined.chr${chr}.g.vcf
##### Protocols 2,7 (QCStats, QC_Report) #####
collectMultipleMetricsPrefix,${intermediateDir}${externalSampleID}
flagstatMetrics,${intermediateDir}${externalSampleID}.flagstat
idxstatsMetrics,${intermediateDir}${externalSampleID}.idxstats
dupStatMetrics,${intermediateDir}${externalSampleID}.mdupmetrics
rnaSeqMetrics,${intermediateDir}${externalSampleID}.collectrnaseqmetrics
alignmentMetrics,${intermediateDir}${externalSampleID}.alignment_summary_metrics
insertsizeMetrics,${intermediateDir}${externalSampleID}.insertsizemetrics
insertsizeMetricspdf,${intermediateDir}${externalSampleID}.insert_size_histogram.pdf
insertsizeMetricspng,${intermediateDir}${externalSampleID}.insert_size_histogram.png
qcMatricsList,${intermediateDir}/${project}_qcMatricsList.txt
gcPlotList,${intermediateDir}/${project}_gcPlotList.txt
recreateinsertsizepdfR,createInsertSizePlot.R
qcMatrics,${intermediateDir}/${externalSampleID}.total.qc.metrics.table
##### Protocols 3,6 (HTSeq count, MakeExpressionTable) #####
sampleHTseqExpressionText,${intermediateDir}/${externalSampleID}.htseq.txt
projectHTseqExpressionTable,${intermediateDir}/${project}.expression.genelevel.v${ensembleReleaseVersion}.htseq.txt.table