Infinite loop on quoted strings containing comma's

[mmterpstra]

Compute does not handle qouted strings with comma's correctly. The parameterfile supplied below gets compute in an infinite loop due to the following three parameter values:

,"chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY","c(chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22)","c(chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr20,chr21,chr22)"

A (confirmed) workaround is to change the comma's to tabs and then replace them in the actual script.

parameter file supplied to compute

queue,group,user,data,projectDir,logsDir,fastqcMod,bwaMod,picardMod,picardOldMod,RMod,gatkMod,snpEffMod,varScanMod,samtoolsMod,bcftoolsMod,vcfToolsMod,pipelineUtilMod,parallelMod,tableToXlsxMod,digiRgMod,nudupMod,bbmapMod,bedtoolsMod,hisat2Mod,htseqMod,fusioncatcherMod,RmarkMod,mantaMod,lancetMod,freebayesMod,lofreqMod,multiqcMod,cnvlibMod,ichorcnaMod,convadingMod,resDir,fusioncatcherDataDir,probeFa,probeBed,probeRnaFa,probeRnaBed,ampliconsBed,genomeLatSpecies,genomeSpecies,genomeBuild,genomeGrchBuild,ensemblVersion,bundle,onekgGenomeFasta,onekgGenomeFastaIdxBase,onekgGenomeFastaDict,goldStandardVcf,goldStandardVcfIdx,oneKgPhase1SnpsVcf,oneKgPhase1SnpsVcfIdx,oneKgPhase1IndelsVcf,oneKgPhase1IndelsVcfIdx,popStratifiedVcf,popStratifiedVcfIdx,dbsnp138Vcf,dbsnp138VcfIdx,dbsnpVcf,dbsnpVcfIdx,indelRealignmentTargets,snpeffDataDir,snpeffGrcData,motifBin,nextProtBin,pwmsBin,regulation_CD4Bin,regulation_GM06990Bin,regulation_GM12878Bin,regulation_H1ESCBin,regulation_HeLaS3Bin,regulation_HepG2Bin,regulation_HMECBin,regulation_HSMMBin,regulation_HUVECBin,regulation_IMR90Bin,regulation_K562Bin,regulation_NHABin,regulation_NHEKBin,snpEffectPredictorBin,dbnsfp,dbnsfpTbi,gnomadDir,gnomadVcf,gnomadVcfIdx,clinvarDir,clinvarVcf,clinvarVcfIdx,clinvarPapuVcf,clinvarPapuVcfIdx,cosmicDir,cosmicVersion,cosmicVcf,cosmicVcfIdx,ichorcnaChromosomes,ichorcnaChrs,ichorcnaChrtrain,genesRefFlat,rRnaIntervalList,ensemblAnnotationGtf
regular,umcg-gcc,umcg-mterpstra,/data/${user}/apps/data/,/scratch/${user}/projects/${project}/,/data/umcg-mterpstra/umcg-oncogenetics/git/molgenis-c5-TumorNormal/log/,FastQC/0.11.5-Java-1.7.0_80,BWA/0.7.15-foss-2016a,picard/2.20.8-foss-2016a-Java-1.8.0_192,picard/1.140-foss-2016a-Java-1.8.0_74,R/3.2.2-foss-2016a-bioconductor,GATK/3.8-0-foss-2016a-Java-1.8.0_121,snpEff/4.1g-Java-1.7.0_80,VarScan/2.4.3-Java-1.7.0_80,SAMtools/1.3.1-foss-2016a,BCFtools/1.6-foss-2016a,VCFtools/0.1.12b-foss-2016a-Perl-5.20.2-bare,pipeline-util/0.8.12-foss-2016a-Perl-5.20.2-bare,parallel/20160622-foss-2016a,TableToXlsx/0.3.0-foss-2016a-Perl-5.20.2-bare,DigitalBarcodeReadgroups/0.1.10-foss-2016a-Perl-5.20.2-bare,nudup.py/740d9fe-foss-2016a-Python-2.7.11,BBMap/35.69-Java-1.7.0_80,BEDTools/2.25.0-foss-2016a,hisat2/2.0.4-foss-2016a-Python-2.7.11,HTSeq/0.6.1p1-foss-2016a-Python-2.7.11,FusionCatcher/0.99.6a-foss-2016a-Python-2.7.11,markdown/0.7.7-foss-2016a-R-3.2.2-bioconductor,manta/1.1.0-foss-2016a,Lancet/v1.0.5-foss-2016a,freebayes/1.1.0-foss-2016a-961e5f3,LoFreq/2.1.3.1-foss-2016a-Python-2.7.12,multiqc/1.0-foss-2016a-Python-2.7.11,cnvlib/0.9.1-foss-2016a-Python-2.7.11,R-bundle-ichorCNA/0.2.0-foss-2016a-R-3.3.3-bioconductor,CoNVaDING/1.3.13-foss-2016a-Perl-5.22.1-bare,${data}/resources/,/data/umcg-mterpstra/apps/data/resources/fusioncatcher/ensembl_v84-fusioncatcher0.99.6a/,${data}/resources/probeSeq_RDonly_ET1262F_2_182.rc.fasta,${data}/resources/probeSeq_RDonly_ET1262F_2_182.bed,${data}/resources/target_ET1508R_3a_782_3b_783_probeSeq.fasta,${data}/resources/target_ET1508R_3a_782_3b_783_probeSeq.bed,none,Homo_sapiens,human,hg38,GRCh38,86,${data}/ftp.broadinstitute.org/bundle/bundle17jan2020/${genomeBuild}/,${bundle}/Homo_sapiens_assembly38.fasta,${bundle}/BWA/0.7.15-foss-2016a/Homo_sapiens_assembly38.fasta,${onekgGenomeFasta}.dict,${bundle}/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz,${goldStandardVcf}.tbi,${bundle}/1000G_phase1.snps.high_confidence.hg38.vcf.gz,${oneKgPhase1SnpsVcf}.tbi,${bundle}/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz,${oneKgPhase1IndelsVcf}.tbi,${bundle}/hapmap_3.3_grch38_pop_stratified_af.vcf.gz,${popStratifiedVcf}.tbi,${bundle}/dbsnp_138.hg38.vcf.gz,${dbsnpVcf}.tbi,${bundle}/dbsnp_146.hg38.vcf.gz,${dbsnpVcf}.tbi,${bundle}/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz,${data}/snpEff/4.3/,${snpeffDataDir}/${genomeGrchBuild}.${ensemblVersion}/,${snpeffGrcData}/motif.bin,${snpeffGrcData}/nextProt.bin,${snpeffGrcData}/pwms.bin,${snpeffGrcData}/regulation_CD4.bin,${snpeffGrcData}/regulation_GM06990.bin,${snpeffGrcData}/regulation_GM12878.bin,${snpeffGrcData}/regulation_H1ESC.bin,${snpeffGrcData}/regulation_HeLa-S3.bin,${snpeffGrcData}/regulation_HepG2.bin,${snpeffGrcData}/regulation_HMEC.bin,${snpeffGrcData}/regulation_HSMM.bin,${snpeffGrcData}/regulation_HUVEC.bin,${snpeffGrcData}/regulation_IMR90.bin,${snpeffGrcData}/regulation_K562.bin,${snpeffGrcData}/regulation_NH-A.bin,${snpeffGrcData}/regulation_NHEK.bin,${snpeffGrcData}/snpEffectPredictor.bin,${data}/dbNSFP/4.0a/dbNSFP4.0a.txt.gz,${dbnsfp}.tbi,${data}/storage.googleapis.com/gnomad-public/release/3.0/vcf/,${gnomadDir}/genomes/genomes/gnomad.genomes.r3.0.sites.vcf.gz,${gnomadVcf}.tbi,${data}/ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/,${clinvarDir}/clinvar_20200210_Homo_sapiens_assembly38.vcf.gz,${clinvarVcf}.tbi,${clinvarDir}/clinvar_20200210_Homo_sapiens_assembly38.vcf.gz,${clinvarPapuVcf}.tbi,${data}/sftp-cancer.sanger.ac.uk/files/grch38/cosmic/,v90,${cosmicDir}/${cosmicVersion}/VCF/CosmicCodingMuts_Homo_sapiens_assembly38.vcf.gz,${cosmicVcf}.tbi,"chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY","c(chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22)","c(chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr20,chr21,chr22)",${data}/ftp.ensembl.org/pub/release-${ensemblVersion}/gtf/homo_sapiens/${genomeLatSpecies}.${genomeGrchBuild}.${ensemblVersion}.refflat,${data}/ftp.ensembl.org/pub/release-${ensemblVersion}/gtf/homo_sapiens/${genomeLatSpecies}.${genomeGrchBuild}.${ensemblVersion}.rrna.interval_list,${data}/ftp.ensembl.org/pub/release-${ensemblVersion}/gtf/homo_sapiens/${genomeLatSpecies}.${genomeGrchBuild}.${ensemblVersion}.gtf