# # #----------------------------------------------------#
# # # Create scripts and directories for runs or reruns
# # #----------------------------------------------------#
#
# resultsdir=data$resultsdir[i]
# participantid=data$participantid[i]
# tumourplatekey=data$tumourplatekey[i]
# normalplatekey=data$normalplatekey[i]
# tumourbam=data$tumourbam[i]
# normalbam=data$normalbam[i]
# gender=data$gender[i]
# project.code=data$project.code[i]
# bb1done=F
# ccubeexists=data$ccubeexists[i]
# vcfdir=NA
# ccubedir=NA
# ccubepurity=NA
# vcffilepath=data$vcffilepath[i]
#
#
# # # Using Beagle, original rerun order (DPC, CCube, VAFpeaks)
# CreateScriptsDirsBeagle <- function(resultsdir,
# participantid,
# tumourplatekey,
# normalplatekey,
# tumourbam,
# normalbam,
# gender,
# project.code,
# bb1done,
# ccubeexists,
# vcfdir,
# ccubedir,
# ccubepurity,
# vcffilepath) {
#
# # define gender true false
# if (gender=="Female") {gendertrue = "FALSE"}
# if (gender=="Male") {gendertrue = "TRUE"}
#
# # Make config file for peaks run (make this more manipulable later, just using standard for now)
# system(paste0("cp ",resultsdir,"peakconfigfile.R ",
# resultsdir,"tumo",tumourplatekey,"_norm",normalplatekey,"/",
# tumourplatekey,"_peakconfigfile.R"))
#
# # # if don't yet have a first BB run
# # if (bb1done==F) {
# # create overall sample dir
# sampledir = paste0(resultsdir,"tumo",tumourplatekey,"_norm",normalplatekey)
# dir.create(sampledir)
#
# # create subdirs & subsubdirs
# dir.create(paste0(sampledir,"/A-GetAlleleCounts"))
# dir.create(paste0(sampledir,"/B-RunBAFLogR"))
# dir.create(paste0(sampledir,"/C-RunGCcorrect"))
# dir.create(paste0(sampledir,"/D-GenerateImputeInputFromAlleleFrequencies"))
# dir.create(paste0(sampledir,"/E-RunBeagle5"))
# # dir.create(paste0(sampledir,"/E-RunImpute"))
# # dir.create(paste0(sampledir,"/F-CombineImputeOutputs"))
# dir.create(paste0(sampledir,"/G-GetHaplotypedBAFs"))
# # dir.create(paste0(sampledir,"/H-CleanUp"))
# dir.create(paste0(sampledir,"/I-PlotHaplotypedData"))
# dir.create(paste0(sampledir,"/J-CombineBAFfiles"))
# dir.create(paste0(sampledir,"/K-SegmentBAFphased"))
# dir.create(paste0(sampledir,"/L-FitCopyNumber"))
# dir.create(paste0(sampledir,"/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/N-wrapup"))
# # dir.create(paste0(sampledir,"/O-Postprocessing"))
# dir.create(paste0(sampledir,"/P-DPC1"))
# dir.create(paste0(sampledir,"/P-DPC1/DPPrep"))
# dir.create(paste0(sampledir,"/P-DPC1/DPClust"))
# dir.create(paste0(sampledir,"/Q-AssessBB1DPC1"))
# dir.create(paste0(sampledir,"/R-BB2"))
# dir.create(paste0(sampledir,"/R-BB2/L-FitCopyNumber"))
# dir.create(paste0(sampledir,"/R-BB2/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/R-BB2/O-Postprocessing"))
# dir.create(paste0(sampledir,"/S-DPC2"))
# dir.create(paste0(sampledir,"/S-DPC2/DPPrep"))
# dir.create(paste0(sampledir,"/S-DPC2/DPClust"))
# dir.create(paste0(sampledir,"/T-AssessBB2DPC2"))
# dir.create(paste0(sampledir,"/U-BB3"))
# dir.create(paste0(sampledir,"/U-BB3/L-FitCopyNumber"))
# dir.create(paste0(sampledir,"/U-BB3/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/U-BB3/O-Postprocessing"))
# dir.create(paste0(sampledir,"/V-DPC3"))
# dir.create(paste0(sampledir,"/V-DPC3/DPPrep"))
# dir.create(paste0(sampledir,"/V-DPC3/DPClust"))
# dir.create(paste0(sampledir,"/W-AssessBB3DPC3"))
# dir.create(paste0(sampledir,"/X-BB4"))
# dir.create(paste0(sampledir,"/X-BB4/L-FitCopyNumber"))
# dir.create(paste0(sampledir,"/X-BB4/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/X-BB4/O-Postprocessing"))
# dir.create(paste0(sampledir,"/Y-DPC4"))
# dir.create(paste0(sampledir,"/Y-DPC4/DPPrep"))
# dir.create(paste0(sampledir,"/Y-DPC4/DPClust"))
# dir.create(paste0(sampledir,"/Z-AssessBB4DPC4"))
# dir.create(paste0(sampledir,"/ZZ-BB_WGD"))
# dir.create(paste0(sampledir,"/ZZ-BB_WGD/L-FitCopyNumber"))
# dir.create(paste0(sampledir,"/ZZ-BB_WGD/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/ZZ-BB_WGD/O-Postprocessing"))
# dir.create(paste0(sampledir,"/ZZ-DPC_WGD"))
# dir.create(paste0(sampledir,"/ZZ-DPC_WGD/DPPrep"))
# dir.create(paste0(sampledir,"/ZZ-DPC_WGD/DPClust"))
# dir.create(paste0(sampledir,"/ZZ-AssessBBDPC_WGD"))
# dir.create(paste0(sampledir,"/logs"))
#
# # create basic config file (parameters will be added later if reruns are required)
# config=matrix(nrow=43,ncol=1)
# config[1,1]=paste0("RUN_DIR=",resultsdir)
# config[2,1]=paste0("LOG_DIR=",sampledir,"/logs/")
# config[3,1]=paste0("OUTPUT_DIR=",sampledir)
# config[4,1]=paste0("SAMPLE_PATH=",sampledir)
# config[5,1]="PIPELINE_DIR=/home/AFrangou/battenberg-lsf-pipeline"
# config[6,1]=paste0("TUMOURNAME=",tumourplatekey)
# config[7,1]=paste0("IS_MALE=",gendertrue)
# config[8,1]=paste0("NORMALNAME=",normalplatekey)
# config[9,1]=paste0("TUMOURBAM=",tumourbam)
# config[10,1]=paste0("NORMALBAM=",normalbam)
# config[11,1]="PLATFORM_GAMMA=1"
# config[12,1]="PHASING_GAMMA=1"
# config[13,1]="SEGMENTATION_GAMMA=10"
# config[14,1]="CLONALITY_DIST_METRIC=0"
# config[15,1]="ASCAT_DIST_METRIC=1"
# config[16,1]="MIN_PLOIDY=1.6"
# config[17,1]="MAX_PLOIDY=4.8"
# config[18,1]="MIN_RHO=0.13"
# config[19,1]="MAX_RHO=1.02"
# config[20,1]="MIN_GOODNESS_OF_FIT=0.63"
# config[21,1]="BALANCED_THRESHOLD=0.51"
# config[22,1]="IMPUTEINFOFILE=/home/AFrangou/ALL_100G_phase1integrated_v3_impute/impute_info.txt"
# config[23,1]="IMPUTE_EXE=/home/AFrangou/impute_v2.3.2_x86_64_static/impute2"
# config[24,1]=paste0("SEED=",as.integer(Sys.time()))
# config[25,1]="MAX_CN_STATE=250"
# config[26,1]="SV_BREAKPOINTS_FILE=NA"
# config[27,1]="PROBLEMLOCI=/home/AFrangou/probloci_270415.txt"
# config[28,1]="G1000_PREFIX_HG38=/home/AFrangou/battenberg_1000genomesloci2012_v3_hg38/hg38_alleleFiles_feb22_chr"
# config[29,1]="G1000_PREFIX_AC_HG38=/home/AFrangou/battenberg_1000genomesloci2012_v3_hg38/hg38_lociFiles_feb22_chr"
# config[30,1]="G1000_PREFIX=/home/AFrangou/battenberg_1000genomesloci2012_v3/1000genomesAlleles2012_chr"
# config[31,1]="G1000_PREFIX_AC=/home/AFrangou/runallelecounter/1000genomesloci2012/1000genomesloci2012_chr"
# config[32,1]="GCCORRECTPREFIX=/home/AFrangou/battenberg_wgs_gc_correction_1000g_v3/1000_genomes_GC_corr_filled_chr_"
# config[33,1]="MIN_NORMAL_DEPTH=10"
# config[34,1]="ALLELECOUNTER=/home/AFrangou/bin/alleleCounter-FixVAF"
# config[35,1]=paste0("PARTICIPANTID=",participantid)
# config[36,1]=paste0("VCFFILEPATH=",vcffilepath)
# config[37,1]=paste0("CCUBEDIR=",ccubedir)
# config[38,1]=paste0("CCUBEPURITY=",ccubepurity)
# config[39,1]="SHAPEIT_EXE=/home/AFrangou/bin/shapeit"
# config[40,1]="SHAPEITINFOFILE=/home/AFrangou/ALL_100G_phase1integrated_v3_impute/impute_info_shapeit.txt"
# config[41,1]="BEAGLE_JAR=/re_gecip/cancer_sarcoma/0.sharedResources/0.4.software/Beagle5.1/beagle.25Nov19.28d.jar"
# config[42,1]="BEAGLE_REF=/re_gecip/cancer_sarcoma/0.sharedResources/0.2.referenceFiles/Battenberg_hg38/beagle5/chr"
# config[43,1]="BEAGLE_PLINK=/re_gecip/cancer_sarcoma/0.sharedResources/0.2.referenceFiles/Battenberg_hg38/beagle5/plink.chr"
#
#
#
# write.table(config,paste0(sampledir,"/",tumourplatekey,"_configfile.txt"),
# quote=F,
# col.names=F,
# row.names=F)
#
# # create script for first Battenberg run
# header=matrix(nrow=51,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
#
# header[4,1]="# Get allele frequencies"
# header[5,1]="# Tumour"
# header[6,1]=paste0('bsub -J"GetAlleleFrequenciesTumour_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/GetAlleleFrequenciesTumour.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetAlleleCounts_tumour.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[7,1]="# Normal"
# header[8,1]=paste0('bsub -J"GetAlleleFrequenciesNormal_',
# normalplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/GetAlleleFrequenciesNormal.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetAlleleCounts_normal.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[10,1]="# Remove 'chr' from alleleCounter output, array"
# header[11,1]=paste0('bsub -w"done(GetAlleleFrequenciesTumour_',
# tumourplatekey,'[1-23]) && done(GetAlleleFrequenciesNormal_',
# normalplatekey,'[1-23])" -J"RunRemoveCHR_',tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,'/logs/RemoveCHR.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/RemoveCHR.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# # header[13,1]=paste0("# Convert alleleCounter output back to hg37")
# # header[14,1]=paste0('bsub -w"done(RunRemoveCHR_',tumourplatekey,')" -J"RunSwitchback_hg38_to_hg37_',
# # tumourplatekey,'[1-23]" -q short -P ',project.code,
# # ' -o ',sampledir,'/logs/Switchback_hg38_to_hg37.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/Switchback_hg38_to_hg37.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[16,1]="# Get BAF and logR"
# header[17,1]=paste0('bsub -w"done(RunRemoveCHR_',
# tumourplatekey,'[1-23])" -J"RunBAFLogR_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,'/logs/RunBAFLogR.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunBAFLogR.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[19,1]='# RunGCCorrect_wgs'
# header[20,1]=paste0('bsub -w "done(RunBAFLogR_',tumourplatekey,
# ')" -J"runGCcorrect_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,'/logs/runGCcorrect',tumourplatekey,
# '.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunGCcorrect_wgs.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[22,1]='# Perform phasing'
# header[23,1]='# GenerateImputeInputFromAlleleFrequencies'
# header[24,1]=paste0('bsub -w "done(RunRemoveCHR_',
# tumourplatekey,'[1-23])" -J"GenerateImputeInputs_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/GenerateImputeInputs.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GenerateImputeInputFromAlleleFrequencies.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[26,1]='# Convert Impute2 to Beagle5 input'
# header[27,1]=paste0('bsub -w "done(GenerateImputeInputs_',
# tumourplatekey,'[1-23])" -J"ConvertImputeInputToBeagleInput_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/ConvertImputeInputToBeagleInput.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertImputeInputToBeagleInput.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
#
# header[29,1]='# RunBeagle5'
# header[30,1]=paste0('bsub -w "done(ConvertImputeInputToBeagleInput_',
# tumourplatekey,'[*])" -J"RunBeagle5_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/RunBeagle5.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunBeagle5.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[32,1]='# Convert Beagle output to impute output'
# header[33,1]=paste0('bsub -w"done(RunBeagle5_',tumourplatekey,
# '[*])" -J"ConvertBeagleOutputToImputeOutput_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,' -o ',
# sampledir,'/logs/ConvertBeagleOutputToImputeOutput.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/WriteBeagleAsImpute.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[35,1]='# GetHaplotypeBAFs'
# header[36,1]=paste0('bsub -w"done(ConvertBeagleOutputToImputeOutput_',
# tumourplatekey,'[*])" -J"GetHaplotypedBAFs_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/GetHaplotypedBAFs.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetHaplotypedBAFs.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# # header[35,1]='# CleanUp'
# # header[36,1]=paste0('bsub -w"done(GetHaplotypedBAFs_',
# # tumourplatekey,'[*])" -J"CleanUp_',
# # tumourplatekey,'[1-23]" -q short -P ',project.code,
# # ' -o ',sampledir,
# # '/logs/CleanUp.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/CleanUp.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
# #
# header[38,1]='# PlotHaplotypedData'
# header[39,1]=paste0('bsub -w"done(GetHaplotypedBAFs_',
# tumourplatekey,'[*])" -J"PlotHaplotypedData_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/PlotHaplotypedData.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/PlotHaplotypedData.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[41,1]='# CombineBAFfiles'
# header[42,1]=paste0('bsub -w"done(PlotHaplotypedData_',
# tumourplatekey,'[1-23])" -J"CombineBAFfiles_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,'/logs/CombineBAFfiles.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CombineBAFfiles.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[44,1]='# Segmentation and copy number calling'
# header[45,1]=paste0('bsub -w"done(CombineBAFfiles_',
# tumourplatekey,')" -J"SegmentBAFphased_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,'/logs/SegmentBAFphased.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/SegmentBAFphased.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[47,1]=paste0('bsub -w"done(SegmentBAFphased_',
# tumourplatekey,') && done(runGCcorrect_',
# tumourplatekey,')" -J"FitCopyNumber_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/FitCopyNumber.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/FitCopyNumber.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[49,1]=paste0('bsub -w"done(FitCopyNumber_',
# tumourplatekey,')" -J"CallSubclones_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/CallSubclones.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# # header[51,1]=paste0('bsub -w"done(CallSubclones_',
# # tumourplatekey,')" -J"wrapup_',
# # tumourplatekey,'" -q short -P ',project.code,
# # ' -o ',sampledir,'/logs/wrapup.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/wrapup.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[which(is.na(header[,1])),]=""
# write.table(header,paste0(sampledir,'/',tumourplatekey,"_submission.sh"),quote=F,col.names=F,row.names=F)
#
# # } else if (bb1done==T) {
# #
# # sampledir = paste0(resultsdir,"tumo",tumourplatekey,"_norm",normalplatekey)
# #
# # # make additional directories for reruns
# # dir.create(paste0(sampledir,"/O-Postprocessing"))
# # dir.create(paste0(sampledir,"/P-DPC1"))
# # dir.create(paste0(sampledir,"/P-DPC1/DPPrep"))
# # dir.create(paste0(sampledir,"/P-DPC1/DPClust"))
# # dir.create(paste0(sampledir,"/Q-AssessBB1DPC1"))
# # dir.create(paste0(sampledir,"/R-BB2"))
# # dir.create(paste0(sampledir,"/R-BB2/L-FitCopyNumber"))
# # dir.create(paste0(sampledir,"/R-BB2/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/R-BB2/O-Postprocessing"))
# # dir.create(paste0(sampledir,"/S-DPC2"))
# # dir.create(paste0(sampledir,"/S-DPC2/DPPrep"))
# # dir.create(paste0(sampledir,"/S-DPC2/DPClust"))
# # dir.create(paste0(sampledir,"/T-AssessBB2DPC2"))
# # dir.create(paste0(sampledir,"/U-BB3"))
# # dir.create(paste0(sampledir,"/U-BB3/L-FitCopyNumber"))
# # dir.create(paste0(sampledir,"/U-BB3/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/U-BB3/O-Postprocessing"))
# # dir.create(paste0(sampledir,"/V-DPC3"))
# # dir.create(paste0(sampledir,"/V-DPC3/DPPrep"))
# # dir.create(paste0(sampledir,"/V-DPC3/DPClust"))
# # dir.create(paste0(sampledir,"/W-AssessBB3DPC3"))
# # dir.create(paste0(sampledir,"/X-BB4"))
# # dir.create(paste0(sampledir,"/X-BB4/L-FitCopyNumber"))
# # dir.create(paste0(sampledir,"/X-BB4/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/X-BB4/O-Postprocessing"))
# # dir.create(paste0(sampledir,"/Y-DPC4"))
# # dir.create(paste0(sampledir,"/Y-DPC4/DPPrep"))
# # dir.create(paste0(sampledir,"/Y-DPC4/DPClust"))
# # dir.create(paste0(sampledir,"/Z-AssessBB4DPC4"))
# #
# # # add participant ID to the config file
# # system(paste0("echo PARTICIPANTID=",participantid,
# # " >> ",
# # sampledir,"/",
# # tumourplatekey,"_configfile.txt"))
# # # add vcffilepath to the config file
# # system(paste0("echo VCFFILEPATH=",vcffilepath,
# # " >> ",
# # sampledir,"/",
# # tumourplatekey,"_configfile.txt"))
# # # add ccubefilepath to the config file
# # system(paste0("echo CCUBEDIR=",ccubedir,
# # " >> ",
# # sampledir,"/",
# # tumourplatekey,"_configfile.txt"))
# # # add ccube purity to config file
# # system(paste0("echo CCUBEPURITY=",if(!is.na(ccubepurity)){ccubepurity/100}else{ccubepurity},
# # " >> ",
# # sampledir,"/",
# # tumourplatekey,"_configfile.txt"))
# #
# # }
#
# # create script for first DPClust run (does subclones conversion, DPPrep, DPClust)
# # this happens for all samples, whether first BB has run or not
# header=matrix(nrow=17,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# # header[4,1]="# Convert subclones file from BB1 to hg38"
# # if (bb1done==T) {
# # header[5,1]=paste0('bsub -J"ConvertSubclones1_',
# # tumourplatekey,'"',
# # # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# # ' -q short -P ',project.code,
# # ' -o ',sampledir,"/logs/ConvertSubclones1.%J.out",
# # ' -e ',sampledir,"/logs/ConvertSubclones1.%J.err",
# # ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
# # } else if (bb1done==F) {
# # header[5,1]=paste0('bsub -w"done(wrapup_',tumourplatekey,')"' ,
# # ' -J"ConvertSubclones1_',
# # tumourplatekey,'"',
# # # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# # ' -q short -P ',project.code,
# # ' -o ',sampledir,"/logs/ConvertSubclones1.%J.out",
# # ' -e ',sampledir,"/logs/ConvertSubclones1.%J.err",
# # ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
# # }
# header[4,1]=paste0('bsub -w"done(FitCopyNumber_',
# tumourplatekey,')" -J"CallSubclones_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/CallSubclones.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[6,1]=""
# header[7,1]="# RunDPPrep1"
# header[8,1]=paste0('bsub -w"done(CallSubclones_',tumourplatekey,')"',
# ' -J"DPPrep_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPPrep.%J.out",
# ' -e ',sampledir,"/logs/DPPrep.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPPrep.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[9,1]=""
# header[10,1]="# RunDPClust1"
# header[11,1]=paste0('bsub -w"done(DPPrep_',tumourplatekey,')"',
# ' -J"DPClust_',tumourplatekey,'"',
# # ' -R"select[mem>16000] rusage[mem=16000]" -M16000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPClust.%J.out",
# ' -e ',sampledir,"/logs/DPClust.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPClust.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[12,1]=""
# header[13,1]="# Assess PASS/FAIL status based on outcome of DPClust"
# header[14,1]=paste0('bsub -w"done(DPClust_',tumourplatekey,')"',
# ' -J"AssessBBDPC_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/AssessBBDPC1.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[15,1]=""
# header[16,1]="# Assess PASS/FAIL status based on outcome of peak calling"
# header[17,1]=paste0('bsub -w"done(AssessBBDPC_',tumourplatekey,')"',
# ' -J"AssessBBDPC_Peaks_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_Peaks.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_Peaks.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ComputePeaksVAF_B.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# write.table(header,paste0(sampledir,'/Run1.sh'),quote=F,col.names=F,row.names=F)
#
#
# # create script for second run if a rerun is needed (so Setup, FCN, CS, Convert, DPPrep, DPClust, Assess)
# header=matrix(nrow=26,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# header[4,1]="# Set up run 2 (rerun 1) parameters"
# header[5,1]=paste0('bsub -w"done(AssessBBDPC_Peaks_',tumourplatekey,')" -J"SetUpRun2_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/SetUpRun2.%J.out",
# ' -e ',sampledir,"/logs/SetUpRun2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/SetUpRun2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[6,1]=""
# header[7,1]="# Run BB FitCopyNumber 2"
# header[8,1]=paste0('bsub -w"done(SetUpRun2_',tumourplatekey,')"',
# ' -J"FitCopyNumber2_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/FitCopyNumber_run2.%J.out",
# ' -e ',sampledir,"/logs/FitCopyNumber_run2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/FitCopyNumber_run2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[9,1]=""
# header[10,1]="# Run BB CallSubclones 2"
# header[11,1]=paste0('bsub -w"done(FitCopyNumber2_',tumourplatekey,')"',
# ' -J"CallSubclones_run2_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/CallSubclones_run2.%J.out",
# ' -e ',sampledir,"/logs/CallSubclones_run2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones_run2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[12,1]=""
# header[13,1]="# Convert subclones from CallSubclones 2"
# header[14,1]=paste0('bsub -w"done(CallSubclones_run2_',tumourplatekey,')"',
# ' -J"ConvertSubclones2_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/ConvertSubclones2.%J.out",
# ' -e ',sampledir,"/logs/ConvertSubclones2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[15,1]=""
# header[16,1]="# Run DPPrep 2"
# header[17,1]=paste0('bsub -w"done(ConvertSubclones2_',tumourplatekey,')"',
# ' -J"DPPrep2_',tumourplatekey,'"',
# # ' -R"select[mem>8000] rusage[mem=8000]" -M8000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPPrep2.%J.out",
# ' -e ',sampledir,"/logs/DPPrep2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPPrep2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[18,1]=""
# header[19,1]="# Run DPClust 2"
# header[20,1]=paste0('bsub -w"done(DPPrep2_',tumourplatekey,')"',
# ' -J"DPClust2_',tumourplatekey,'"',
# # ' -R"select[mem>16000] rusage[mem=16000]" -M16000',
# ' -q medium -P ',project.code,
# ' -o ',sampledir,"/logs/DPClust2.%J.out",
# ' -e ',sampledir,"/logs/DPClust2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPClust2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[21,1]=""
# header[22,1]="# Assess PASS/FAIL of DPClust 2"
# header[23,1]=paste0('bsub -w"done(DPClust2_',tumourplatekey,')"',
# ' -J"AssessBBDPC2_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC2.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/AssessBBDPC2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[24,1]=""
# header[25,1]="# Assess PASS/FAIL status based on outcome of peak calling"
# header[26,1]=paste0('bsub -w"done(AssessBBDPC2_',tumourplatekey,')"',
# ' -J"AssessBBDPC_Peaks2_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_Peaks2.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_Peaks2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ComputePeaksVAF2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# write.table(header,paste0(sampledir,'/Run2.sh'),quote=F,col.names=F,row.names=F)
#
# # create script for third run if a rerun is needed (so Setup, FCN, CS, Convert, DPPrep, DPClust, Assess)
# header=matrix(nrow=26,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# header[4,1]="# Set up run 3 (rerun 2) parameters"
# header[5,1]=paste0('bsub -w"done(AssessBBDPC_Peaks2_',tumourplatekey,')"',
# ' -J"SetUpRun3_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/SetUpRun3.%J.out",
# ' -e ',sampledir,"/logs/SetUpRun3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/SetUpRun3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[6,1]=""
# header[7,1]="# Run BB FitCopyNumber 3"
# header[8,1]=paste0('bsub -w"done(SetUpRun3_',tumourplatekey,')"',
# ' -J"FitCopyNumber3_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/FitCopyNumber_run3.%J.out",
# ' -e ',sampledir,"/logs/FitCopyNumber_run3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/FitCopyNumber_run3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[9,1]=""
# header[10,1]="# Run BB CallSubclones 3"
# header[11,1]=paste0('bsub -w"done(FitCopyNumber3_',tumourplatekey,')"',
# ' -J"CallSubclones_run3_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/CallSubclones_run3.%J.out",
# ' -e ',sampledir,"/logs/CallSubclones_run3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones_run3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[12,1]=""
# header[13,1]="# Convert subclones from CallSubclones 3"
# header[14,1]=paste0('bsub -w"done(CallSubclones_run3_',tumourplatekey,')"',
# ' -J"ConvertSubclones3_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/ConvertSubclones3.%J.out",
# ' -e ',sampledir,"/logs/ConvertSubclones3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[15,1]=""
# header[16,1]="# Run DPPrep 3"
# header[17,1]=paste0('bsub -w"done(ConvertSubclones3_',tumourplatekey,')"',
# ' -J"DPPrep3_',tumourplatekey,'"',
# # ' -R"select[mem>8000] rusage[mem=8000]" -M8000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPPrep3.%J.out",
# ' -e ',sampledir,"/logs/DPPrep3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPPrep3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[18,1]=""
# header[19,1]="# Run DPClust 3"
# header[20,1]=paste0('bsub -w"done(DPPrep3_',tumourplatekey,')"',
# ' -J"DPClust3_',tumourplatekey,'"',
# # ' -R"select[mem>16000] rusage[mem=16000]" -M16000',
# ' -q medium -P ',project.code,
# ' -o ',sampledir,"/logs/DPClust3.%J.out",
# ' -e ',sampledir,"/logs/DPClust3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPClust3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[21,1]=""
# header[22,1]="# Assess PASS/FAIL of DPClust 3"
# header[23,1]=paste0('bsub -w"done(DPClust3_',tumourplatekey,')"',
# ' -J"AssessBBDPC3_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC3.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/AssessBBDPC3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[24,1]=""
# header[25,1]="# Assess PASS/FAIL status based on outcome of peak calling"
# header[26,1]=paste0('bsub -w"done(AssessBBDPC3_',tumourplatekey,')"',
# ' -J"AssessBBDPC_Peaks3_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_Peaks3.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_Peaks3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ComputePeaksVAF3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# write.table(header,paste0(sampledir,'/Run3.sh'),quote=F,col.names=F,row.names=F)
#
# # create script for fourth run if a rerun is needed (so Setup, FCN, CS, Convert, DPPrep, DPClust, Assess)
# header=matrix(nrow=26,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# header[4,1]="# Set up run 4 (rerun 3) parameters"
# header[5,1]=paste0('bsub -w"done(AssessBBDPC_Peaks3_',tumourplatekey,')"',
# ' -J"SetUpRun4_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/SetUpRun4.%J.out",
# ' -e ',sampledir,"/logs/SetUpRun4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/SetUpRun4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[6,1]=""
# header[7,1]="# Run BB FitCopyNumber 4"
# header[8,1]=paste0('bsub -w"done(SetUpRun4_',tumourplatekey,')"',
# ' -J"FitCopyNumber4_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/FitCopyNumber_run4.%J.out",
# ' -e ',sampledir,"/logs/FitCopyNumber_run4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/FitCopyNumber_run4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[9,1]=""
# header[10,1]="# Run BB CallSubclones 4"
# header[11,1]=paste0('bsub -w"done(FitCopyNumber4_',tumourplatekey,')"',
# ' -J"CallSubclones_run4_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/CallSubclones_run4.%J.out",
# ' -e ',sampledir,"/logs/CallSubclones_run4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones_run4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[12,1]=""
# header[13,1]="# Convert subclones from CallSubclones 4"
# header[14,1]=paste0('bsub -w"done(CallSubclones_run4_',tumourplatekey,')"',
# ' -J"ConvertSubclones4_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/ConvertSubclones4.%J.out",
# ' -e ',sampledir,"/logs/ConvertSubclones4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[15,1]=""
# header[16,1]="# Run DPPrep 4"
# header[17,1]=paste0('bsub -w"done(ConvertSubclones4_',tumourplatekey,')"',
# ' -J"DPPrep4_',tumourplatekey,'"',
# # ' -R"select[mem>8000] rusage[mem=8000]" -M8000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPPrep4.%J.out",
# ' -e ',sampledir,"/logs/DPPrep4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPPrep4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[18,1]=""
# header[19,1]="# Run DPClust 4"
# header[20,1]=paste0('bsub -w"done(DPPrep4_',tumourplatekey,')"',
# ' -J"DPClust4_',tumourplatekey,'"',
# # ' -R"select[mem>16000] rusage[mem=16000]" -M16000',
# ' -q medium -P ',project.code,
# ' -o ',sampledir,"/logs/DPClust4.%J.out",
# ' -e ',sampledir,"/logs/DPClust4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPClust4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[21,1]=""
# header[22,1]="# Assess PASS/FAIL of DPClust 4"
# header[23,1]=paste0('bsub -w"done(DPClust4_',tumourplatekey,')"',
# ' -J"AssessBBDPC4_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC4.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/AssessBBDPC4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[24,1]=""
# header[25,1]="# Assess PASS/FAIL status based on outcome of peak calling"
# header[26,1]=paste0('bsub -w"done(AssessBBDPC4_',tumourplatekey,')"',
# ' -J"AssessBBDPC_Peaks4_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_Peaks4.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_Peaks4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ComputePeaksVAF4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# write.table(header,paste0(sampledir,'/Run4.sh'),quote=F,col.names=F,row.names=F)
#
# # create overall script to submit whole sample with all (defined) rounds of recall
# # different for those which have first BB already
# if (bb1done==F) {
# header=matrix(nrow=17,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# header[4,1]="# First Battenberg run"
# header[5,1]=paste0('bsub -J"Submission_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Submission.%J.out",
# ' -e ',sampledir,"/logs/Submission.%J.err ",
# sampledir,'/',tumourplatekey,'_submission.sh')
# header[6,1]=""
# header[7,1]="# First DPPrep and DPClust run"
# header[8,1]=paste0('bsub -w"done(Submission_',tumourplatekey,')" -J"Run1_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run1.%J.out",
# ' -e ',sampledir,"/logs/Run1.%J.err ",
# sampledir,'/Run1.sh')
# header[9,1]=""
# header[10,1]="# Second Battenberg and DPClust run (new DPClust purity)"
# header[11,1]=paste0('bsub -w"done(Run1_',tumourplatekey,')" -J"Run2_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run2.%J.out",
# ' -e ',sampledir,"/logs/Run2.%J.err ",
# sampledir,'/Run2.sh')
# header[12,1]=""
# header[13,1]="# Third Battenberg and DPClust run (Ccube purity)"
# header[14,1]=paste0('bsub -w"done(Run2_',tumourplatekey,')" -J"Run3_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run3.%J.out",
# ' -e ',sampledir,"/logs/Run3.%J.err ",
# sampledir,'/Run3.sh')
# header[15,1]=""
# header[16,1]="# Fourth Battenberg and DPClust run (Peaks purity)"
# header[17,1]=paste0('bsub -w"done(Run3_',tumourplatekey,')" -J"Run4_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run4.%J.out",
# ' -e ',sampledir,"/logs/Run4.%J.err ",
# sampledir,'/Run4.sh')
# } else if (bb1done==T) {
# header=matrix(nrow=14,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
#
# header[4,1]="# First DPPrep and DPClust run"
# header[5,1]=paste0('bsub -J"Run1_',tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run1.%J.out",
# ' -e ',sampledir,"/logs/Run1.%J.err ",
# sampledir,'/Run1.sh')
# header[6,1]=""
# header[7,1]="# Second Battenberg and DPClust run (new DPClust purity)"
# header[8,1]=paste0('bsub -w"done(Run1_',tumourplatekey,')" -J"Run2_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run2.%J.out",
# ' -e ',sampledir,"/logs/Run2.%J.err ",
# sampledir,'/Run2.sh')
# header[9,1]=""
# header[10,1]="# Third Battenberg and DPClust run (Ccube purity)"
# header[11,1]=paste0('bsub -w"done(Run2_',tumourplatekey,')" -J"Run3_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run3.%J.out",
# ' -e ',sampledir,"/logs/Run3.%J.err ",
# sampledir,'/Run3.sh')
# header[12,1]=""
# header[13,1]="# Fourth Battenberg and DPClust run (Peaks purity)"
# header[14,1]=paste0('bsub -w"done(Run3_',tumourplatekey,')" -J"Run4_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run4.%J.out",
# ' -e ',sampledir,"/logs/Run4.%J.err ",
# sampledir,'/Run4.sh')
# }
# write.table(header,paste0(sampledir,'/Submit_sample.sh'),quote=F,col.names=F,row.names=F)
#
# system(paste0("chmod 750 ",sampledir,"/*.sh"))
# system(paste0("chmod 750 ",sampledir,"/*.txt"))
#
#
# }
#
#
# DPC1_Beag <- function(resultsdir,
# participantid,
# tumourplatekey,
# normalplatekey,
# tumourbam,
# normalbam,
# gender,
# project.code,
# bb1done,
# ccubeexists,
# vcfdir,
# ccubedir,
# ccubepurity,
# vcffilepath) {
#
# sampledir = paste0(resultsdir,"tumo",tumourplatekey,"_norm",normalplatekey)
#
# header=matrix(nrow=17,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
#
# header[4,1]=paste0('bsub -w"done(FitCopyNumber_',
# tumourplatekey,')" -J"CallSubclones_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/CallSubclones.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[5,1]=""
# header[6,1]=""
# header[7,1]="# RunDPPrep1"
# header[8,1]=paste0('bsub -w"done(CallSubclones_',tumourplatekey,')"',
# ' -J"DPPrep_B_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPPrep_B.%J.out",
# ' -e ',sampledir,"/logs/DPPrep_B.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPPrep_B.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[9,1]=""
# header[10,1]="# RunDPClust1"
# header[11,1]=paste0('bsub -w"done(DPPrep_B_',tumourplatekey,')"',
# ' -J"DPClust_',tumourplatekey,'"',
# # ' -R"select[mem>16000] rusage[mem=16000]" -M16000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPClust.%J.out",
# ' -e ',sampledir,"/logs/DPClust.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPClust.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[12,1]=""
# header[13,1]="# Assess PASS/FAIL status based on outcome of DPClust"
# header[14,1]=paste0('bsub -w"done(DPClust_',tumourplatekey,')"',
# ' -J"AssessBBDPC_B_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_B.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_B.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/AssessBBDPC1_B.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[15,1]=""
# header[16,1]="# Assess PASS/FAIL status based on outcome of peak calling"
# header[17,1]=paste0('bsub -w"done(AssessBBDPC_B_',tumourplatekey,')"',
# ' -J"AssessBBDPC_Peaks_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_Peaks_B.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_Peaks_B.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ComputePeaksVAF_B.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# write.table(header,paste0(sampledir,'/DPC1.sh'),quote=F,col.names=F,row.names=F)
# system(paste0("chmod 750 ",sampledir,"/DPC1.sh"))
#
# }
#
#
# SubmitSample_firsthalf <- function(resultsdir,
# participantid,
# tumourplatekey,
# normalplatekey,
# tumourbam,
# normalbam,
# gender,
# project.code,
# bb1done,
# ccubeexists,
# vcfdir,
# ccubedir,
# ccubepurity,
# vcffilepath) {
#
# sampledir = paste0(resultsdir,"tumo",tumourplatekey,"_norm",normalplatekey)
#
# header=matrix(nrow=17,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# header[4,1]="# First Battenberg run"
# header[5,1]=paste0('bsub -J"Submission_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Submission.%J.out",
# ' -e ',sampledir,"/logs/Submission.%J.err ",
# sampledir,'/',tumourplatekey,'_submission.sh')
# header[6,1]=""
# header[7,1]="# First DPPrep and DPClust run"
# header[8,1]=paste0('bsub -w"done(Submission_',tumourplatekey,')" -J"DPC1_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPC1.%J.out",
# ' -e ',sampledir,"/logs/DPC1.%J.err ",
# sampledir,'/DPC1.sh')
# # header[9,1]=""
# # header[10,1]="# Second Battenberg and DPClust run (new DPClust purity)"
# # header[11,1]=paste0('bsub -w"done(Run1_',tumourplatekey,')" -J"Run2_',
# # tumourplatekey,'"',
# # ' -q short -P ',project.code,
# # ' -o ',sampledir,"/logs/BBDPC2.%J.out",
# # ' -e ',sampledir,"/logs/BBDPC2.%J.err ",
# # sampledir,'/BBDPC2.sh')
# # header[12,1]=""
# # header[13,1]="# Third Battenberg and DPClust run (Ccube purity)"
# # header[14,1]=paste0('bsub -w"done(Run2_',tumourplatekey,')" -J"Run3_',
# # tumourplatekey,'"',
# # ' -q short -P ',project.code,
# # ' -o ',sampledir,"/logs/Run3.%J.out",
# # ' -e ',sampledir,"/logs/Run3.%J.err ",
# # sampledir,'/Run3.sh')
# # header[15,1]=""
# # header[16,1]="# Fourth Battenberg and DPClust run (Peaks purity)"
# # header[17,1]=paste0('bsub -w"done(Run3_',tumourplatekey,')" -J"Run4_',
# # tumourplatekey,'"',
# # ' -q short -P ',project.code,
# # ' -o ',sampledir,"/logs/Run4.%J.out",
# # ' -e ',sampledir,"/logs/Run4.%J.err ",
# # sampledir,'/Run4.sh')
#
# header[which(is.na(header)),1]=""
# write.table(header,paste0(sampledir,'/Submit_sample_firsthalf.sh'),quote=F,col.names=F,row.names=F)
# system(paste0("chmod 750 ",sampledir,"/Submit_sample_firsthalf.sh"))
#
# }
#
# # Using Beagle, rerun order (VAFpeaks,VAFpeaks,(Ccube?),DPC)
# CreateScriptsDirsBeagle <- function(resultsdir,
# participantid,
# tumourplatekey,
# normalplatekey,
# tumourbam,
# normalbam,
# gender,
# project.code,
# bb1done,
# ccubeexists,
# vcfdir,
# ccubedir,
# ccubepurity,
# vcffilepath) {
#
# # define gender true false
# if (gender=="Female") {gendertrue = "FALSE"}
# if (gender=="Male") {gendertrue = "TRUE"}
#
# # Make config file for peaks run (make this more manipulable later, just using standard for now)
# system(paste0("cp ",resultsdir,"peakconfigfile.R ",
# resultsdir,"tumo",tumourplatekey,"_norm",normalplatekey,"/",
# tumourplatekey,"_peakconfigfile.R"))
#
# # # if don't yet have a first BB run
# # if (bb1done==F) {
# # create overall sample dir
# sampledir = paste0(resultsdir,"tumo",tumourplatekey,"_norm",normalplatekey)
# dir.create(sampledir)
#
# # create subdirs & subsubdirs
# dir.create(paste0(sampledir,"/A-GetAlleleCounts"))
# dir.create(paste0(sampledir,"/B-RunBAFLogR"))
# dir.create(paste0(sampledir,"/C-RunGCcorrect"))
# dir.create(paste0(sampledir,"/D-GenerateImputeInputFromAlleleFrequencies"))
# dir.create(paste0(sampledir,"/E-RunBeagle5"))
# # dir.create(paste0(sampledir,"/E-RunImpute"))
# # dir.create(paste0(sampledir,"/F-CombineImputeOutputs"))
# dir.create(paste0(sampledir,"/G-GetHaplotypedBAFs"))
# # dir.create(paste0(sampledir,"/H-CleanUp"))
# dir.create(paste0(sampledir,"/I-PlotHaplotypedData"))
# dir.create(paste0(sampledir,"/J-CombineBAFfiles"))
# dir.create(paste0(sampledir,"/K-SegmentBAFphased"))
# dir.create(paste0(sampledir,"/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/N-wrapup"))
# # dir.create(paste0(sampledir,"/O-Postprocessing"))
# dir.create(paste0(sampledir,"/P-DPC1"))
# dir.create(paste0(sampledir,"/P-DPC1/DPPrep"))
# dir.create(paste0(sampledir,"/P-DPC1/DPClust"))
# dir.create(paste0(sampledir,"/Q-AssessBB1DPC1"))
# dir.create(paste0(sampledir,"/R-BB2"))
# dir.create(paste0(sampledir,"/R-BB2/L-FitCopyNumber"))
# dir.create(paste0(sampledir,"/R-BB2/M-CallSubclones"))
# dir.create(paste0(sampledir,"/R-BB2/O-Postprocessing"))
# dir.create(paste0(sampledir,"/S-DPC2"))
# dir.create(paste0(sampledir,"/S-DPC2/DPPrep"))
# dir.create(paste0(sampledir,"/S-DPC2/DPClust"))
# dir.create(paste0(sampledir,"/T-AssessBB2DPC2"))
# dir.create(paste0(sampledir,"/U-BB3"))
# dir.create(paste0(sampledir,"/U-BB3/L-FitCopyNumber"))
# dir.create(paste0(sampledir,"/U-BB3/M-CallSubclones"))
# dir.create(paste0(sampledir,"/U-BB3/O-Postprocessing"))
# dir.create(paste0(sampledir,"/V-DPC3"))
# dir.create(paste0(sampledir,"/V-DPC3/DPPrep"))
# dir.create(paste0(sampledir,"/V-DPC3/DPClust"))
# dir.create(paste0(sampledir,"/W-AssessBB3DPC3"))
# dir.create(paste0(sampledir,"/X-BB4"))
# dir.create(paste0(sampledir,"/X-BB4/L-FitCopyNumber"))
# dir.create(paste0(sampledir,"/X-BB4/M-CallSubclones"))
# dir.create(paste0(sampledir,"/X-BB4/O-Postprocessing"))
# dir.create(paste0(sampledir,"/Y-DPC4"))
# dir.create(paste0(sampledir,"/Y-DPC4/DPPrep"))
# dir.create(paste0(sampledir,"/Y-DPC4/DPClust"))
# dir.create(paste0(sampledir,"/Z-AssessBB4DPC4"))
# dir.create(paste0(sampledir,"/ZZ-BB_WGD"))
# dir.create(paste0(sampledir,"/ZZ-BB_WGD/L-FitCopyNumber"))
# dir.create(paste0(sampledir,"/ZZ-BB_WGD/M-CallSubclones"))
# dir.create(paste0(sampledir,"/ZZ-BB_WGD/O-Postprocessing"))
# dir.create(paste0(sampledir,"/ZZ-DPC_WGD"))
# dir.create(paste0(sampledir,"/ZZ-DPC_WGD/DPPrep"))
# dir.create(paste0(sampledir,"/ZZ-DPC_WGD/DPClust"))
# dir.create(paste0(sampledir,"/ZZ-AssessBBDPC_WGD"))
# dir.create(paste0(sampledir,"/logs"))
#
# # create basic config file (parameters will be added later if reruns are required)
# config=matrix(nrow=43,ncol=1)
# config[1,1]=paste0("RUN_DIR=",resultsdir)
# config[2,1]=paste0("LOG_DIR=",sampledir,"/logs/")
# config[3,1]=paste0("OUTPUT_DIR=",sampledir)
# config[4,1]=paste0("SAMPLE_PATH=",sampledir)
# config[5,1]="PIPELINE_DIR=/home/AFrangou/battenberg-lsf-pipeline"
# config[6,1]=paste0("TUMOURNAME=",tumourplatekey)
# config[7,1]=paste0("IS_MALE=",gendertrue)
# config[8,1]=paste0("NORMALNAME=",normalplatekey)
# config[9,1]=paste0("TUMOURBAM=",tumourbam)
# config[10,1]=paste0("NORMALBAM=",normalbam)
# config[11,1]="PLATFORM_GAMMA=1"
# config[12,1]="PHASING_GAMMA=1"
# config[13,1]="SEGMENTATION_GAMMA=10"
# config[14,1]="CLONALITY_DIST_METRIC=0"
# config[15,1]="ASCAT_DIST_METRIC=1"
# config[16,1]="MIN_PLOIDY=1.6"
# config[17,1]="MAX_PLOIDY=4.8"
# config[18,1]="MIN_RHO=0.13"
# config[19,1]="MAX_RHO=1.02"
# config[20,1]="MIN_GOODNESS_OF_FIT=0.63"
# config[21,1]="BALANCED_THRESHOLD=0.51"
# config[22,1]="IMPUTEINFOFILE=/home/AFrangou/ALL_100G_phase1integrated_v3_impute/impute_info.txt"
# config[23,1]="IMPUTE_EXE=/home/AFrangou/impute_v2.3.2_x86_64_static/impute2"
# config[24,1]=paste0("SEED=",as.integer(Sys.time()))
# config[25,1]="MAX_CN_STATE=250"
# config[26,1]="SV_BREAKPOINTS_FILE=NA"
# config[27,1]="PROBLEMLOCI=/home/AFrangou/probloci_270415.txt"
# config[28,1]="G1000_PREFIX_HG38=/home/AFrangou/battenberg_1000genomesloci2012_v3_hg38/hg38_alleleFiles_feb22_chr"
# config[29,1]="G1000_PREFIX_AC_HG38=/home/AFrangou/battenberg_1000genomesloci2012_v3_hg38/hg38_lociFiles_feb22_chr"
# config[30,1]="G1000_PREFIX=/home/AFrangou/battenberg_1000genomesloci2012_v3/1000genomesAlleles2012_chr"
# config[31,1]="G1000_PREFIX_AC=/home/AFrangou/runallelecounter/1000genomesloci2012/1000genomesloci2012_chr"
# config[32,1]="GCCORRECTPREFIX=/home/AFrangou/battenberg_wgs_gc_correction_1000g_v3/1000_genomes_GC_corr_filled_chr_"
# config[33,1]="MIN_NORMAL_DEPTH=10"
# config[34,1]="ALLELECOUNTER=/home/AFrangou/bin/alleleCounter-FixVAF"
# config[35,1]=paste0("PARTICIPANTID=",participantid)
# config[36,1]=paste0("VCFFILEPATH=",vcffilepath)
# config[37,1]=paste0("CCUBEDIR=",ccubedir)
# config[38,1]=paste0("CCUBEPURITY=",ccubepurity)
# config[39,1]="SHAPEIT_EXE=/home/AFrangou/bin/shapeit"
# config[40,1]="SHAPEITINFOFILE=/home/AFrangou/ALL_100G_phase1integrated_v3_impute/impute_info_shapeit.txt"
# config[41,1]="BEAGLE_JAR=/re_gecip/cancer_sarcoma/0.sharedResources/0.4.software/Beagle5.1/beagle.25Nov19.28d.jar"
# config[42,1]="BEAGLE_REF=/re_gecip/cancer_sarcoma/0.sharedResources/0.2.referenceFiles/Battenberg_hg38/beagle5/chrCHROMNAME.1kg.phase3.v5a_GRCh38nounref.vcf.gz"
# config[43,1]="BEAGLE_PLINK=/re_gecip/cancer_sarcoma/0.sharedResources/0.2.referenceFiles/Battenberg_hg38/beagle5/plink.chrCHROMNAME.GRCh38.map"
#
# write.table(config,paste0(sampledir,"/",tumourplatekey,"_configfile.txt"),
# quote=F,
# col.names=F,
# row.names=F)
#
# system(paste0("chmod 750 ",sampledir,"/",tumourplatekey,"_configfile.txt"))
#
# # create script for first Battenberg run
# header=matrix(nrow=51,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
#
# header[4,1]="# Get allele frequencies"
# header[5,1]="# Tumour"
# header[6,1]=paste0('bsub -J"GetAlleleFrequenciesTumour_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/GetAlleleFrequenciesTumour.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetAlleleCounts_tumour.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[7,1]="# Normal"
# header[8,1]=paste0('bsub -J"GetAlleleFrequenciesNormal_',
# normalplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/GetAlleleFrequenciesNormal.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetAlleleCounts_normal.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[10,1]="# Remove 'chr' from alleleCounter output, array"
# header[11,1]=paste0('bsub -w"done(GetAlleleFrequenciesTumour_',
# tumourplatekey,'[1-23]) && done(GetAlleleFrequenciesNormal_',
# normalplatekey,'[1-23])" -J"RunRemoveCHR_',tumourplatekey,'[1-23]"
# -q short -P ',project.code,
# ' -o ',sampledir,'/logs/RemoveCHR.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/RemoveCHR.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# # header[13,1]=paste0("# Convert alleleCounter output back to hg37")
# # header[14,1]=paste0('bsub -w"done(RunRemoveCHR_',tumourplatekey,')" -J"RunSwitchback_hg38_to_hg37_',
# # tumourplatekey,'[1-23]" -q short -P ',project.code,
# # ' -o ',sampledir,'/logs/Switchback_hg38_to_hg37.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/Switchback_hg38_to_hg37.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[16,1]="# Get BAF and logR"
# header[17,1]=paste0('bsub -w"done(RunRemoveCHR_',
# tumourplatekey,'[1-23])" -J"RunBAFLogR_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,'/logs/RunBAFLogR.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunBAFLogR.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[19,1]='# RunGCCorrect_wgs'
# header[20,1]=paste0('bsub -w "done(RunBAFLogR_',tumourplatekey,
# ')" -J"runGCcorrect_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,'/logs/runGCcorrect',tumourplatekey,
# '.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunGCcorrect_wgs.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[22,1]='# Perform phasing'
# header[23,1]='# GenerateImputeInputFromAlleleFrequencies'
# header[24,1]=paste0('bsub -w "done(RunRemoveCHR_',
# tumourplatekey,'[1-23])" -J"GenerateImputeInputs_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/GenerateImputeInputs.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GenerateImputeInputFromAlleleFrequencies.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[26,1]='# Convert Impute2 to Beagle5 input'
# header[27,1]=paste0('bsub -w "done(GenerateImputeInputs_',
# tumourplatekey,'[1-23])" -J"ConvertImputeInputToBeagleInput_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/ConvertImputeInputToBeagleInput.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertImputeInputToBeagleInput.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
#
# header[29,1]='# RunBeagle5'
# header[30,1]=paste0('bsub -w "done(ConvertImputeInputToBeagleInput_',
# tumourplatekey,'[*])" -J"RunBeagle5_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/RunBeagle5.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunBeagle5.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[32,1]='# Convert Beagle output to impute output'
# header[33,1]=paste0('bsub -w"done(RunBeagle5_',tumourplatekey,
# '[*])" -J"ConvertBeagleOutputToImputeOutput_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,' -o ',
# sampledir,'/logs/ConvertBeagleOutputToImputeOutput.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/WriteBeagleAsImpute.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[35,1]='# GetHaplotypeBAFs'
# header[36,1]=paste0('bsub -w"done(ConvertBeagleOutputToImputeOutput_',
# tumourplatekey,'[*])" -J"GetHaplotypedBAFs_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/GetHaplotypedBAFs.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetHaplotypedBAFs.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# # header[35,1]='# CleanUp'
# # header[36,1]=paste0('bsub -w"done(GetHaplotypedBAFs_',
# # tumourplatekey,'[*])" -J"CleanUp_',
# # tumourplatekey,'[1-23]" -q short -P ',project.code,
# # ' -o ',sampledir,
# # '/logs/CleanUp.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/CleanUp.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
# #
# header[38,1]='# PlotHaplotypedData'
# header[39,1]=paste0('bsub -w"done(GetHaplotypedBAFs_',
# tumourplatekey,'[*])" -J"PlotHaplotypedData_',
# tumourplatekey,'[1-23]" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/PlotHaplotypedData.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/PlotHaplotypedData.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[41,1]='# CombineBAFfiles'
# header[42,1]=paste0('bsub -w"done(PlotHaplotypedData_',
# tumourplatekey,')" -J"CombineBAFfiles_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,'/logs/CombineBAFfiles.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CombineBAFfiles.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[44,1]='# Segmentation and copy number calling'
# header[45,1]=paste0('bsub -w"done(CombineBAFfiles_',
# tumourplatekey,')" -J"SegmentBAFphased_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,'/logs/SegmentBAFphased.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/SegmentBAFphased.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[47,1]=paste0('bsub -w"done(SegmentBAFphased_',
# tumourplatekey,') && done(runGCcorrect_',
# tumourplatekey,')" -J"FitCopyNumber_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/FitCopyNumber.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/FitCopyNumber.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[49,1]=paste0('bsub -w"done(FitCopyNumber_',
# tumourplatekey,')" -J"CallSubclones_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/CallSubclones.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# # header[51,1]=paste0('bsub -w"done(CallSubclones_',
# # tumourplatekey,')" -J"wrapup_',
# # tumourplatekey,'" -q short -P ',project.code,
# # ' -o ',sampledir,'/logs/wrapup.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/wrapup.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[which(is.na(header[,1])),]=""
# write.table(header,paste0(sampledir,'/',tumourplatekey,"_submission.sh"),quote=F,col.names=F,row.names=F)
# system(paste0("chmod 750 ",sampledir,'/',tumourplatekey,"_submission.sh"))
#
# # } else if (bb1done==T) {
# #
# # sampledir = paste0(resultsdir,"tumo",tumourplatekey,"_norm",normalplatekey)
# #
# # # make additional directories for reruns
# # dir.create(paste0(sampledir,"/O-Postprocessing"))
# # dir.create(paste0(sampledir,"/P-DPC1"))
# # dir.create(paste0(sampledir,"/P-DPC1/DPPrep"))
# # dir.create(paste0(sampledir,"/P-DPC1/DPClust"))
# # dir.create(paste0(sampledir,"/Q-AssessBB1DPC1"))
# # dir.create(paste0(sampledir,"/R-BB2"))
# # dir.create(paste0(sampledir,"/R-BB2/L-FitCopyNumber"))
# # dir.create(paste0(sampledir,"/R-BB2/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/R-BB2/O-Postprocessing"))
# # dir.create(paste0(sampledir,"/S-DPC2"))
# # dir.create(paste0(sampledir,"/S-DPC2/DPPrep"))
# # dir.create(paste0(sampledir,"/S-DPC2/DPClust"))
# # dir.create(paste0(sampledir,"/T-AssessBB2DPC2"))
# # dir.create(paste0(sampledir,"/U-BB3"))
# # dir.create(paste0(sampledir,"/U-BB3/L-FitCopyNumber"))
# # dir.create(paste0(sampledir,"/U-BB3/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/U-BB3/O-Postprocessing"))
# # dir.create(paste0(sampledir,"/V-DPC3"))
# # dir.create(paste0(sampledir,"/V-DPC3/DPPrep"))
# # dir.create(paste0(sampledir,"/V-DPC3/DPClust"))
# # dir.create(paste0(sampledir,"/W-AssessBB3DPC3"))
# # dir.create(paste0(sampledir,"/X-BB4"))
# # dir.create(paste0(sampledir,"/X-BB4/L-FitCopyNumber"))
# # dir.create(paste0(sampledir,"/X-BB4/M-CallSubclones"))
# # dir.create(paste0(sampledir,"/X-BB4/O-Postprocessing"))
# # dir.create(paste0(sampledir,"/Y-DPC4"))
# # dir.create(paste0(sampledir,"/Y-DPC4/DPPrep"))
# # dir.create(paste0(sampledir,"/Y-DPC4/DPClust"))
# # dir.create(paste0(sampledir,"/Z-AssessBB4DPC4"))
# #
# # # add participant ID to the config file
# # system(paste0("echo PARTICIPANTID=",participantid,
# # " >> ",
# # sampledir,"/",
# # tumourplatekey,"_configfile.txt"))
# # # add vcffilepath to the config file
# # system(paste0("echo VCFFILEPATH=",vcffilepath,
# # " >> ",
# # sampledir,"/",
# # tumourplatekey,"_configfile.txt"))
# # # add ccubefilepath to the config file
# # system(paste0("echo CCUBEDIR=",ccubedir,
# # " >> ",
# # sampledir,"/",
# # tumourplatekey,"_configfile.txt"))
# # # add ccube purity to config file
# # system(paste0("echo CCUBEPURITY=",if(!is.na(ccubepurity)){ccubepurity/100}else{ccubepurity},
# # " >> ",
# # sampledir,"/",
# # tumourplatekey,"_configfile.txt"))
# #
# # }
#
# # create script for first DPClust run (does subclones conversion, DPPrep, DPClust)
# # this happens for all samples, whether first BB has run or not
# header=matrix(nrow=17,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# # header[4,1]="# Convert subclones file from BB1 to hg38"
# # if (bb1done==T) {
# # header[5,1]=paste0('bsub -J"ConvertSubclones1_',
# # tumourplatekey,'"',
# # # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# # ' -q short -P ',project.code,
# # ' -o ',sampledir,"/logs/ConvertSubclones1.%J.out",
# # ' -e ',sampledir,"/logs/ConvertSubclones1.%J.err",
# # ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
# # } else if (bb1done==F) {
# # header[5,1]=paste0('bsub -w"done(wrapup_',tumourplatekey,')"' ,
# # ' -J"ConvertSubclones1_',
# # tumourplatekey,'"',
# # # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# # ' -q short -P ',project.code,
# # ' -o ',sampledir,"/logs/ConvertSubclones1.%J.out",
# # ' -e ',sampledir,"/logs/ConvertSubclones1.%J.err",
# # ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones.sh ',
# # sampledir,'/',tumourplatekey,'_configfile.txt')
# # }
# header[4,1]=paste0('bsub -w"done(FitCopyNumber_',
# tumourplatekey,')" -J"CallSubclones_',
# tumourplatekey,'" -q short -P ',project.code,
# ' -o ',sampledir,
# '/logs/CallSubclones.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# header[6,1]=""
# header[7,1]="# RunDPPrep1"
# header[8,1]=paste0('bsub -w"done(CallSubclones_',tumourplatekey,')"',
# ' -J"DPPrep_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPPrep.%J.out",
# ' -e ',sampledir,"/logs/DPPrep.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPPrep.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[9,1]=""
# header[10,1]="# RunDPClust1"
# header[11,1]=paste0('bsub -w"done(DPPrep_',tumourplatekey,')"',
# ' -J"DPClust_',tumourplatekey,'"',
# # ' -R"select[mem>16000] rusage[mem=16000]" -M16000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPClust.%J.out",
# ' -e ',sampledir,"/logs/DPClust.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPClust.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[12,1]=""
# header[13,1]="# Assess PASS/FAIL status based on outcome of DPClust"
# header[14,1]=paste0('bsub -w"done(DPClust_',tumourplatekey,')"',
# ' -J"AssessBBDPC_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/AssessBBDPC1.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[15,1]=""
# header[16,1]="# Assess PASS/FAIL status based on outcome of peak calling"
# header[17,1]=paste0('bsub -w"done(AssessBBDPC_',tumourplatekey,')"',
# ' -J"AssessBBDPC_Peaks_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_Peaks.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_Peaks.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ComputePeaksVAF.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# write.table(header,paste0(sampledir,'/Run1.sh'),quote=F,col.names=F,row.names=F)
#
#
# # create script for second run if a rerun is needed (so Setup, FCN, CS, Convert, DPPrep, DPClust, Assess)
# header=matrix(nrow=26,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# header[4,1]="# Set up run 2 (rerun 1) parameters"
# header[5,1]=paste0('bsub -w"done(AssessBBDPC_Peaks_',tumourplatekey,')" -J"SetUpRun2_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/SetUpRun2.%J.out",
# ' -e ',sampledir,"/logs/SetUpRun2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/SetUpRun2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[6,1]=""
# header[7,1]="# Run BB FitCopyNumber 2"
# header[8,1]=paste0('bsub -w"done(SetUpRun2_',tumourplatekey,')"',
# ' -J"FitCopyNumber2_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/FitCopyNumber_run2.%J.out",
# ' -e ',sampledir,"/logs/FitCopyNumber_run2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/FitCopyNumber_run2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[9,1]=""
# header[10,1]="# Run BB CallSubclones 2"
# header[11,1]=paste0('bsub -w"done(FitCopyNumber2_',tumourplatekey,')"',
# ' -J"CallSubclones_run2_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/CallSubclones_run2.%J.out",
# ' -e ',sampledir,"/logs/CallSubclones_run2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones_run2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[12,1]=""
# header[13,1]="# Convert subclones from CallSubclones 2"
# header[14,1]=paste0('bsub -w"done(CallSubclones_run2_',tumourplatekey,')"',
# ' -J"ConvertSubclones2_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/ConvertSubclones2.%J.out",
# ' -e ',sampledir,"/logs/ConvertSubclones2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[15,1]=""
# header[16,1]="# Run DPPrep 2"
# header[17,1]=paste0('bsub -w"done(ConvertSubclones2_',tumourplatekey,')"',
# ' -J"DPPrep2_',tumourplatekey,'"',
# # ' -R"select[mem>8000] rusage[mem=8000]" -M8000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPPrep2.%J.out",
# ' -e ',sampledir,"/logs/DPPrep2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPPrep2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[18,1]=""
# header[19,1]="# Run DPClust 2"
# header[20,1]=paste0('bsub -w"done(DPPrep2_',tumourplatekey,')"',
# ' -J"DPClust2_',tumourplatekey,'"',
# # ' -R"select[mem>16000] rusage[mem=16000]" -M16000',
# ' -q medium -P ',project.code,
# ' -o ',sampledir,"/logs/DPClust2.%J.out",
# ' -e ',sampledir,"/logs/DPClust2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPClust2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[21,1]=""
# header[22,1]="# Assess PASS/FAIL of DPClust 2"
# header[23,1]=paste0('bsub -w"done(DPClust2_',tumourplatekey,')"',
# ' -J"AssessBBDPC2_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC2.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/AssessBBDPC2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[24,1]=""
# header[25,1]="# Assess PASS/FAIL status based on outcome of peak calling"
# header[26,1]=paste0('bsub -w"done(AssessBBDPC2_',tumourplatekey,')"',
# ' -J"AssessBBDPC_Peaks2_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_Peaks2.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_Peaks2.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ComputePeaksVAF2.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# write.table(header,paste0(sampledir,'/Run2.sh'),quote=F,col.names=F,row.names=F)
#
# # create script for third run if a rerun is needed (so Setup, FCN, CS, Convert, DPPrep, DPClust, Assess)
# header=matrix(nrow=26,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# header[4,1]="# Set up run 3 (rerun 2) parameters"
# header[5,1]=paste0('bsub -w"done(AssessBBDPC_Peaks2_',tumourplatekey,')"',
# ' -J"SetUpRun3_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/SetUpRun3.%J.out",
# ' -e ',sampledir,"/logs/SetUpRun3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/SetUpRun3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[6,1]=""
# header[7,1]="# Run BB FitCopyNumber 3"
# header[8,1]=paste0('bsub -w"done(SetUpRun3_',tumourplatekey,')"',
# ' -J"FitCopyNumber3_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/FitCopyNumber_run3.%J.out",
# ' -e ',sampledir,"/logs/FitCopyNumber_run3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/FitCopyNumber_run3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[9,1]=""
# header[10,1]="# Run BB CallSubclones 3"
# header[11,1]=paste0('bsub -w"done(FitCopyNumber3_',tumourplatekey,')"',
# ' -J"CallSubclones_run3_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/CallSubclones_run3.%J.out",
# ' -e ',sampledir,"/logs/CallSubclones_run3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones_run3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[12,1]=""
# header[13,1]="# Convert subclones from CallSubclones 3"
# header[14,1]=paste0('bsub -w"done(CallSubclones_run3_',tumourplatekey,')"',
# ' -J"ConvertSubclones3_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/ConvertSubclones3.%J.out",
# ' -e ',sampledir,"/logs/ConvertSubclones3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[15,1]=""
# header[16,1]="# Run DPPrep 3"
# header[17,1]=paste0('bsub -w"done(ConvertSubclones3_',tumourplatekey,')"',
# ' -J"DPPrep3_',tumourplatekey,'"',
# # ' -R"select[mem>8000] rusage[mem=8000]" -M8000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPPrep3.%J.out",
# ' -e ',sampledir,"/logs/DPPrep3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPPrep3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[18,1]=""
# header[19,1]="# Run DPClust 3"
# header[20,1]=paste0('bsub -w"done(DPPrep3_',tumourplatekey,')"',
# ' -J"DPClust3_',tumourplatekey,'"',
# # ' -R"select[mem>16000] rusage[mem=16000]" -M16000',
# ' -q medium -P ',project.code,
# ' -o ',sampledir,"/logs/DPClust3.%J.out",
# ' -e ',sampledir,"/logs/DPClust3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPClust3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[21,1]=""
# header[22,1]="# Assess PASS/FAIL of DPClust 3"
# header[23,1]=paste0('bsub -w"done(DPClust3_',tumourplatekey,')"',
# ' -J"AssessBBDPC3_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC3.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/AssessBBDPC3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[24,1]=""
# header[25,1]="# Assess PASS/FAIL status based on outcome of peak calling"
# header[26,1]=paste0('bsub -w"done(AssessBBDPC3_',tumourplatekey,')"',
# ' -J"AssessBBDPC_Peaks3_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_Peaks3.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_Peaks3.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ComputePeaksVAF3.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# write.table(header,paste0(sampledir,'/Run3.sh'),quote=F,col.names=F,row.names=F)
#
# # create script for fourth run if a rerun is needed (so Setup, FCN, CS, Convert, DPPrep, DPClust, Assess)
# header=matrix(nrow=26,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# header[4,1]="# Set up run 4 (rerun 3) parameters"
# header[5,1]=paste0('bsub -w"done(AssessBBDPC_Peaks3_',tumourplatekey,')"',
# ' -J"SetUpRun4_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/SetUpRun4.%J.out",
# ' -e ',sampledir,"/logs/SetUpRun4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/SetUpRun4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[6,1]=""
# header[7,1]="# Run BB FitCopyNumber 4"
# header[8,1]=paste0('bsub -w"done(SetUpRun4_',tumourplatekey,')"',
# ' -J"FitCopyNumber4_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/FitCopyNumber_run4.%J.out",
# ' -e ',sampledir,"/logs/FitCopyNumber_run4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/FitCopyNumber_run4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[9,1]=""
# header[10,1]="# Run BB CallSubclones 4"
# header[11,1]=paste0('bsub -w"done(FitCopyNumber4_',tumourplatekey,')"',
# ' -J"CallSubclones_run4_',tumourplatekey,'"',
# # ' -R"select[mem>15900] rusage[mem=15900]" -M15900',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/CallSubclones_run4.%J.out",
# ' -e ',sampledir,"/logs/CallSubclones_run4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones_run4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[12,1]=""
# header[13,1]="# Convert subclones from CallSubclones 4"
# header[14,1]=paste0('bsub -w"done(CallSubclones_run4_',tumourplatekey,')"',
# ' -J"ConvertSubclones4_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/ConvertSubclones4.%J.out",
# ' -e ',sampledir,"/logs/ConvertSubclones4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ConvertSubclones4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[15,1]=""
# header[16,1]="# Run DPPrep 4"
# header[17,1]=paste0('bsub -w"done(ConvertSubclones4_',tumourplatekey,')"',
# ' -J"DPPrep4_',tumourplatekey,'"',
# # ' -R"select[mem>8000] rusage[mem=8000]" -M8000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/DPPrep4.%J.out",
# ' -e ',sampledir,"/logs/DPPrep4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPPrep4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[18,1]=""
# header[19,1]="# Run DPClust 4"
# header[20,1]=paste0('bsub -w"done(DPPrep4_',tumourplatekey,')"',
# ' -J"DPClust4_',tumourplatekey,'"',
# # ' -R"select[mem>16000] rusage[mem=16000]" -M16000',
# ' -q medium -P ',project.code,
# ' -o ',sampledir,"/logs/DPClust4.%J.out",
# ' -e ',sampledir,"/logs/DPClust4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/DPClust4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[21,1]=""
# header[22,1]="# Assess PASS/FAIL of DPClust 4"
# header[23,1]=paste0('bsub -w"done(DPClust4_',tumourplatekey,')"',
# ' -J"AssessBBDPC4_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC4.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/AssessBBDPC4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
# header[24,1]=""
# header[25,1]="# Assess PASS/FAIL status based on outcome of peak calling"
# header[26,1]=paste0('bsub -w"done(AssessBBDPC4_',tumourplatekey,')"',
# ' -J"AssessBBDPC_Peaks4_',tumourplatekey,'"',
# # ' -R"select[mem>4000] rusage[mem=4000]" -M4000',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/AssessBBDPC_Peaks4.%J.out",
# ' -e ',sampledir,"/logs/AssessBBDPC_Peaks4.%J.err",
# ' /home/AFrangou/battenberg_lsf_pipeline/steps/ComputePeaksVAF4.sh ',
# sampledir,'/',tumourplatekey,'_configfile.txt')
#
# write.table(header,paste0(sampledir,'/Run4.sh'),quote=F,col.names=F,row.names=F)
#
# # create overall script to submit whole sample with all (defined) rounds of recall
# # different for those which have first BB already
# if (bb1done==F) {
# header=matrix(nrow=17,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
# header[4,1]="# First Battenberg run"
# header[5,1]=paste0('bsub -J"Submission_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Submission.%J.out",
# ' -e ',sampledir,"/logs/Submission.%J.err ",
# sampledir,'/',tumourplatekey,'_submission.sh')
# header[6,1]=""
# header[7,1]="# First DPPrep and DPClust run"
# header[8,1]=paste0('bsub -w"done(Submission_',tumourplatekey,')" -J"Run1_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run1.%J.out",
# ' -e ',sampledir,"/logs/Run1.%J.err ",
# sampledir,'/Run1.sh')
# header[9,1]=""
# header[10,1]="# Second Battenberg and DPClust run (new DPClust purity)"
# header[11,1]=paste0('bsub -w"done(Run1_',tumourplatekey,')" -J"Run2_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run2.%J.out",
# ' -e ',sampledir,"/logs/Run2.%J.err ",
# sampledir,'/Run2.sh')
# header[12,1]=""
# header[13,1]="# Third Battenberg and DPClust run (Ccube purity)"
# header[14,1]=paste0('bsub -w"done(Run2_',tumourplatekey,')" -J"Run3_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run3.%J.out",
# ' -e ',sampledir,"/logs/Run3.%J.err ",
# sampledir,'/Run3.sh')
# header[15,1]=""
# header[16,1]="# Fourth Battenberg and DPClust run (Peaks purity)"
# header[17,1]=paste0('bsub -w"done(Run3_',tumourplatekey,')" -J"Run4_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run4.%J.out",
# ' -e ',sampledir,"/logs/Run4.%J.err ",
# sampledir,'/Run4.sh')
# } else if (bb1done==T) {
# header=matrix(nrow=14,ncol=1)
# header[1,1]="#!/usr/bin/env bash"
# header[2,1]="CONFIG=$1"
# header[3.1]=""
#
# header[4,1]="# First DPPrep and DPClust run"
# header[5,1]=paste0('bsub -J"Run1_',tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run1.%J.out",
# ' -e ',sampledir,"/logs/Run1.%J.err ",
# sampledir,'/Run1.sh')
# header[6,1]=""
# header[7,1]="# Second Battenberg and DPClust run (new DPClust purity)"
# header[8,1]=paste0('bsub -w"done(Run1_',tumourplatekey,')" -J"Run2_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run2.%J.out",
# ' -e ',sampledir,"/logs/Run2.%J.err ",
# sampledir,'/Run2.sh')
# header[9,1]=""
# header[10,1]="# Third Battenberg and DPClust run (Ccube purity)"
# header[11,1]=paste0('bsub -w"done(Run2_',tumourplatekey,')" -J"Run3_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run3.%J.out",
# ' -e ',sampledir,"/logs/Run3.%J.err ",
# sampledir,'/Run3.sh')
# header[12,1]=""
# header[13,1]="# Fourth Battenberg and DPClust run (Peaks purity)"
# header[14,1]=paste0('bsub -w"done(Run3_',tumourplatekey,')" -J"Run4_',
# tumourplatekey,'"',
# ' -q short -P ',project.code,
# ' -o ',sampledir,"/logs/Run4.%J.out",
# ' -e ',sampledir,"/logs/Run4.%J.err ",
# sampledir,'/Run4.sh')
# }
# write.table(header,paste0(sampledir,'/Submit_sample.sh'),quote=F,col.names=F,row.names=F)
#
# }
#
#
#
#
#
#
#
