FirstBB: Make scripts for all Battenberg and DPClust runs with options...
In afrangou/CleanCNA: Calling and recalling subclonal copy number using SNP and SNV information to provide a high quality set of copy number profiles.
Usage
1
CreateScriptsDirs(resultsdir, participantid, tumourplatekey, normalplatekey, tumourbam, normalbam, gender, project.code)
Arguments
resultsdir
participantid
tumourplatekey
normalplatekey
tumourbam
normalbam
gender
project.code
bb1done
ccubeexists
Examples
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##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (resultsdir, participantid, tumourplatekey, normalplatekey,
tumourbam, normalbam, gender, project.code)
{
participantdir = paste0(resultsdir, participantid)
dir.create(participantdir)
sampledir = paste0(participantdir, "/tumo", tumourplatekey,
"_norm", normalplatekey)
dir.create(sampledir)
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-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, "/logs"))
config = matrix(nrow = 34, 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=", is.male)
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] = "SEED=123"
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"
write.table(config, paste0(sampledir, "/", tumourplatekey,
"_configfile.txt"), quote = F, col.names = F, row.names = F)
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 gecip -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 gecip -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,
"\" -q gecip -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 gecip -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(RunSwitchback_hg38_to_hg37_",
tumourplatekey, "[1-23])\" -R\"select[mem>28000] rusage[mem=28000]\" -M28000 -J\"RunBAFLogR_",
tumourplatekey, "\" -q gecip -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,
")\" -R\"select[mem>35000] rusage[mem=35000]\" -M35000 -J\"runGCcorrect_",
tumourplatekey, "\" -q gecip -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(RunSwitchback_hg38_to_hg37_",
tumourplatekey, "[1-23])\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"GenerateImputeInputs_",
tumourplatekey, "[1-23]\" -q gecip -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] = "# RunImpute"
header[27, 1] = paste0("bsub -w \"done(GenerateImputeInputs_",
tumourplatekey, "[*])\" -R\"select[mem>8000] rusage[mem=8000]\" -M8000 -J\"Impute_",
tumourplatekey, "[1-23]\" -q gecip -P ", project.code,
" -o ", sampledir, "/logs/Impute.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunImpute.sh ",
sampledir, "/", tumourplatekey, "_configfile.txt")
header[29, 1] = "# CombineImputeOutputs"
header[30, 1] = paste0("bsub -w\"done(Impute_", tumourplatekey,
"[*])\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"CombineImputeOutputs_",
tumourplatekey, "[1-23]\" -q gecip -P ", project.code,
" -o ", sampledir, "/logs/CombineImputeOutputs.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/CombineImputeOutputs.sh ",
sampledir, "/", tumourplatekey, "_configfile.txt")
header[32, 1] = "# GetHaplotypeBAFs"
header[33, 1] = paste("bsub -w\"done(CombineImputeOutputs_",
tumourplatekey, "[*])\" -R\"select[mem>2000] rusage[mem=2000]\" -M2000 -J\"GetHaplotypedBAFs_",
tumourplatekey, "[1-23]\" -q gecip -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 gecip -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, "[*])\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"PlotHaplotypedData_",
tumourplatekey, "[1-23]\" -q gecip -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(GetHaplotypedBAFs_",
tumourplatekey, ")\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"CombineBAFfiles_",
tumourplatekey, "\" -q gecip -P ", project.code, " -o ",
sampledir, "/logs/CombineBAFfiles.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CombineBAFfiles.sh ",
resultsdir, sampledir, "/", tumourplatekey, "_configfile.txt")
header[44, 1] = "# Segmentation and copy number calling"
header[45, 1] = paste0("bsub -w\"done(CombineBAFfiles_",
tumourplatekey, ")\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"SegmentBAFphased_",
tumourplatekey, "\" -q gecip -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,
")\" -R\"select[mem>15900] rusage[mem=15900]\" -M15900 -J\"FitCopyNumber_",
tumourplatekey, "\" -q gecip -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,
")\" -R\"select[mem>15900] rusage[mem=15900]\" -M15900 -J\"CallSubclones_",
tumourplatekey, "\" -q gecip -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,
")\" -R\"select[mem>500] rusage[mem=500]\" -M500 -J\"wrapup_",
tumourplatekey, "\" -q gecip -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, paste(sampledir, "/", tumourplatekey,
"_submission.sh", sep = ""), quote = F, col.names = F,
row.names = F)
}
afrangou/CleanCNA documentation built on Dec. 28, 2021, 8:21 p.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Usage
1 | CreateScriptsDirs(resultsdir, participantid, tumourplatekey, normalplatekey, tumourbam, normalbam, gender, project.code)
|
Arguments
resultsdir |
|
participantid |
|
tumourplatekey |
|
normalplatekey |
|
tumourbam |
|
normalbam |
|
gender |
|
project.code |
|
bb1done |
|
ccubeexists |
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (resultsdir, participantid, tumourplatekey, normalplatekey,
tumourbam, normalbam, gender, project.code)
{
participantdir = paste0(resultsdir, participantid)
dir.create(participantdir)
sampledir = paste0(participantdir, "/tumo", tumourplatekey,
"_norm", normalplatekey)
dir.create(sampledir)
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-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, "/logs"))
config = matrix(nrow = 34, 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=", is.male)
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] = "SEED=123"
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"
write.table(config, paste0(sampledir, "/", tumourplatekey,
"_configfile.txt"), quote = F, col.names = F, row.names = F)
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 gecip -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 gecip -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,
"\" -q gecip -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 gecip -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(RunSwitchback_hg38_to_hg37_",
tumourplatekey, "[1-23])\" -R\"select[mem>28000] rusage[mem=28000]\" -M28000 -J\"RunBAFLogR_",
tumourplatekey, "\" -q gecip -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,
")\" -R\"select[mem>35000] rusage[mem=35000]\" -M35000 -J\"runGCcorrect_",
tumourplatekey, "\" -q gecip -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(RunSwitchback_hg38_to_hg37_",
tumourplatekey, "[1-23])\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"GenerateImputeInputs_",
tumourplatekey, "[1-23]\" -q gecip -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] = "# RunImpute"
header[27, 1] = paste0("bsub -w \"done(GenerateImputeInputs_",
tumourplatekey, "[*])\" -R\"select[mem>8000] rusage[mem=8000]\" -M8000 -J\"Impute_",
tumourplatekey, "[1-23]\" -q gecip -P ", project.code,
" -o ", sampledir, "/logs/Impute.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunImpute.sh ",
sampledir, "/", tumourplatekey, "_configfile.txt")
header[29, 1] = "# CombineImputeOutputs"
header[30, 1] = paste0("bsub -w\"done(Impute_", tumourplatekey,
"[*])\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"CombineImputeOutputs_",
tumourplatekey, "[1-23]\" -q gecip -P ", project.code,
" -o ", sampledir, "/logs/CombineImputeOutputs.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/CombineImputeOutputs.sh ",
sampledir, "/", tumourplatekey, "_configfile.txt")
header[32, 1] = "# GetHaplotypeBAFs"
header[33, 1] = paste("bsub -w\"done(CombineImputeOutputs_",
tumourplatekey, "[*])\" -R\"select[mem>2000] rusage[mem=2000]\" -M2000 -J\"GetHaplotypedBAFs_",
tumourplatekey, "[1-23]\" -q gecip -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 gecip -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, "[*])\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"PlotHaplotypedData_",
tumourplatekey, "[1-23]\" -q gecip -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(GetHaplotypedBAFs_",
tumourplatekey, ")\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"CombineBAFfiles_",
tumourplatekey, "\" -q gecip -P ", project.code, " -o ",
sampledir, "/logs/CombineBAFfiles.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CombineBAFfiles.sh ",
resultsdir, sampledir, "/", tumourplatekey, "_configfile.txt")
header[44, 1] = "# Segmentation and copy number calling"
header[45, 1] = paste0("bsub -w\"done(CombineBAFfiles_",
tumourplatekey, ")\" -R\"select[mem>4000] rusage[mem=4000]\" -M4000 -J\"SegmentBAFphased_",
tumourplatekey, "\" -q gecip -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,
")\" -R\"select[mem>15900] rusage[mem=15900]\" -M15900 -J\"FitCopyNumber_",
tumourplatekey, "\" -q gecip -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,
")\" -R\"select[mem>15900] rusage[mem=15900]\" -M15900 -J\"CallSubclones_",
tumourplatekey, "\" -q gecip -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,
")\" -R\"select[mem>500] rusage[mem=500]\" -M500 -J\"wrapup_",
tumourplatekey, "\" -q gecip -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, paste(sampledir, "/", tumourplatekey,
"_submission.sh", sep = ""), quote = F, col.names = F,
row.names = F)
}
|
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