sof202
commented
9 months ago Here is a comprehensive list of all affected files:
integrative/chromHMM/jobSubmission/bootstrapBinarise.sh integrative/chromHMM/jobSubmission/bootstrapPeakCalling.sh general/jobSubmission/copyFiles.sh general/jobSubmission/findError.sh general/jobSubmission/batchDownload.sh general/jobSubmission/replaceName.sh integrative/segway/jobSubmission/segwayBin.sh integrative/segway/jobSubmission/2_learnSegway.sh integrative/segway/jobSubmission/bamtoBig.sh integrative/segway/jobSubmission/1_genomeDataGroup.sh integrative/segway/jobSubmission/1_genomeData.sh integrative/chromHMM/jobSubmission/calcStateQCMetrics.sh integrative/chromHMM/jobSubmission/runLDSCNeuralPeaks.sh integrative/chromHMM/jobSubmission/2_chmmMergeBinary.sh integrative/chromHMM/jobSubmission/runChromatinStateEnrichments.sh integrative/chromHMM/jobSubmission/1_chmmBinarise.sh integrative/chromHMM/jobSubmission/3_chmmLearnModel.sh integrative/chromHMM/jobSubmission/bootstrapBinarise.sh integrative/chromHMM/jobSubmission/4_chmmCompareModels.sh integrative/chromHMM/jobSubmission/calcBootstrapStateQCMetrics.sh array/DNAm/preprocessing/jobSubmission/1_runDNAmQC.sh array/DNAm/analysis/neuralCellComposition/jobSubmission/testCTModels.sh array/DNAm/analysis/EWAS/jobSubmission/runEWAS.sh array/DNAm/analysis/QTLs/jobSubmission/runQTLs.sh array/DNAm/analysis/QTLs/jobSubmission/prepQTLData.sh array/DNAm/analysis/methodsDevelopment/jobSubmission/simulateCellSpecificEWAS.sh sequencing/BSSeq/jobSubmission/segwayBin.sh sequencing/BSSeq/jobSubmission/3_collateS1QCMetrics.sh sequencing/BSSeq/jobSubmission/1_batchRunAlignment.sh sequencing/longReadseq/jobSubmission/squanti3BatchArray.sh sequencing/longReadseq/jobSubmission/06_talonLabelReadsBatchArray.sh sequencing/longReadseq/jobSubmission/04_minimap2AlignmentBatchArray.sh sequencing/longReadseq/jobSubmission/03_pychopperBatchArray.sh sequencing/ChIPSeq/jobSubmission/bamtoBigwig.sh sequencing/ChIPSeq/jobSubmission/1_batchRunAlignment.sh sequencing/ChIPSeq/jobSubmission/2_batchRunPeakCalling.sh sequencing/ChIPSeq/jobSubmission/4_collateStage1QCMetrics.sh sequencing/ChIPSeq/jobSubmission/peakCallingByGroup.sh sequencing/DNAhydroxy/jobSubmission/batchPeakCallingByGroup.sh sequencing/DNAhydroxy/jobSubmission/batchQCMetrics.sh sequencing/ATACSeq/preprocessing/jobSubmission/1_batchRunAlignment.sh sequencing/ATACSeq/preprocessing/jobSubmission/7_batchRunGenotypeConcordance.sh sequencing/ATACSeq/preprocessing/jobSubmission/5_batchFormatSexChrs.sh sequencing/ATACSeq/preprocessing/jobSubmission/4_collateStage1QCMetrics.sh sequencing/ATACSeq/preprocessing/jobSubmission/3_batchRunPeakCalling.sh sequencing/ATACSeq/preprocessing/jobSubmission/8_batchRunGenotypeSearch.sh sequencing/ATACSeq/jobSubmission/9_idrAnalysis.sh sequencing/ATACSeq/jobSubmission/groupPeakCallingHMMR.sh sequencing/ATACSeq/jobSubmission/subsetNmix.sh sequencing/ATACSeq/jobSubmission/samplePeakCallingHMMR.sh sequencing/ATACSeq/jobSubmission/macsTools.sh sequencing/ATACSeq/jobSubmission/1_batchRunAlignment.sh sequencing/ATACSeq/jobSubmission/7_batchRunGenotypeConcordance.sh sequencing/ATACSeq/jobSubmission/7_2_batchRunGenotypeSearch.sh sequencing/ATACSeq/jobSubmission/correctFripBAMPE.sh sequencing/ATACSeq/jobSubmission/8_batchPeakCallingByGroup.sh sequencing/ATACSeq/jobSubmission/5_batchFormatSexChrs.sh sequencing/ATACSeq/jobSubmission/scoping.sh sequencing/ATACSeq/jobSubmission/4_collateStage1QCMetrics.sh sequencing/ATACSeq/jobSubmission/testPeakCallingbyGroup.sh sequencing/ATACSeq/jobSubmission/3_batchRunPeakCalling.sh sequencing/ATACSeq/jobSubmission/batchFormatSexChrs.sh sequencing/ATACSeq/jobSubmission/10_diffAnalysis.sh
Contact Details
s.o.fletcher@exeter.ac.uk
Path to affected file
Type of refactor
Code optimisation, Code understandability improvement
Description of required code refactor
Currently, line 29 reads:
cd $SLURM_SUBMIT_DIRConsidering that this is the first
cdcommand in this script, this command is not doing anything and therefore can be removed to increase understandability.