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parameters.csv
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parameters.csv
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defaultInterpreter,#!/bin/bash
stage,module load
checkStage,module list
### Tool versions ####
bcl2fastqVersion,bcl2fastq2/2.20.0-GCC-11.3.0
perlPlusVersion,PerlPlus/5.34.1-GCCcore-11.3.0-v22.11.1
interopVersion,interop/1.2.0-foss-2022a
#### Prefixes ####
filePrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}
runPrefix,${filePrefix}_L${lane}
##### GENERAL DIRECTORIES #####
dataDir,${root}/data/
rawDataDir,${workDir}/rawdata
ngsDir,${rawDataDir}/ngs/${filePrefix}/
arrayDir,${rawDataDir}/array
runID,run_${run}
generatedScriptsDir,${workDir}/generatedscripts/NGS_Demultiplexing/${filePrefix}/
logsDir,${workDir}/logs/
runDir,${workDir}/runs/NGS_Demultiplexing/${filePrefix}/
runJobsDir,${runDir}/jobs/
runResultsDir,${runDir}/results/
prepKitsDir,${dataDir}/Prepkits/
intermediateDir,${workDir}/tmp/NGS_Demultiplexing/${filePrefix}/
bcl2fastqDir,${nextSeqRunDataDir}/${project}
sampleSheet,${workDir}/generatedscripts/NGS_Demultiplexing/${filePrefix}/${filePrefix}.csv
MCsampleSheet,${intermediateDir}/status_samples.csv
sourcesDir,${root}/sources/
adapterStringency,0.9
createPerSampleFinalReportPl,CreateFinalReportPerSample.pl
finalReportResultDir,${nextSeqRunDataDir}/finalreports/
fastqExtension,.fq
gzipExtension,.gz
md5sumExtension,.md5
filenameSuffixPE1,1
filenameSuffixPE2,2
filenameSuffixDiscardedReads,DISCARDED
fastqFilenameSR,${runPrefix}${fastqExtension}
fastqFilenamePE1,${runPrefix}_${filenameSuffixPE1}${fastqExtension}
fastqFilenamePE2,${runPrefix}_${filenameSuffixPE2}${fastqExtension}
compressedFastqFilenameSR,${fastqFilenameSR}${gzipExtension}
compressedFastqFilenamePE1,${fastqFilenamePE1}${gzipExtension}
compressedFastqFilenamePE2,${fastqFilenamePE2}${gzipExtension}
demultiplexedSampleFastqFilenameSR,${runPrefix}_${barcode}${fastqExtension}
demultiplexedSampleFastqFilenamePE1,${runPrefix}_${barcode}_${filenameSuffixPE1}${fastqExtension}
demultiplexedSampleFastqFilenamePE2,${runPrefix}_${barcode}_${filenameSuffixPE2}${fastqExtension}
demultiplexedDiscardedFastqFilenameSR,${runPrefix}_${filenameSuffixDiscardedReads}${fastqExtension}
demultiplexedDiscardedFastqFilenamePE1,${runPrefix}_${filenameSuffixDiscardedReads}_${filenameSuffixPE1}${fastqExtension}
demultiplexedDiscardedFastqFilenamePE2,${runPrefix}_${filenameSuffixDiscardedReads}_${filenameSuffixPE2}${fastqExtension}
compressedDemultiplexedSampleFastqFilenameSR,${demultiplexedSampleFastqFilenameSR}${gzipExtension}
compressedDemultiplexedSampleFastqFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${gzipExtension}
compressedDemultiplexedSampleFastqFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${gzipExtension}
compressedDemultiplexedDiscardedFastqFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${gzipExtension}
compressedDemultiplexedDiscardedFastqFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${gzipExtension}
compressedDemultiplexedDiscardedFastqFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${gzipExtension}
demultiplexedSampleFastqChecksumFilenameSR,${demultiplexedSampleFastqFilenameSR}${md5sumExtension}
demultiplexedSampleFastqChecksumFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${md5sumExtension}
demultiplexedSampleFastqChecksumFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${md5sumExtension}
demultiplexedDiscardedFastqChecksumFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${md5sumExtension}
demultiplexedDiscardedFastqChecksumFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${md5sumExtension}
demultiplexedDiscardedFastqChecksumFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${md5sumExtension}