From 22f1e9a5c469e4349651f740902c4c1ee04af62a Mon Sep 17 00:00:00 2001 From: stellaning1120 Date: Tue, 4 Oct 2022 11:44:18 -0400 Subject: [PATCH 1/2] updated ichor step1 --- wdl/ichorCNA_step1.wdl | 518 +++++++++++++++++++++-------------------- 1 file changed, 268 insertions(+), 250 deletions(-) diff --git a/wdl/ichorCNA_step1.wdl b/wdl/ichorCNA_step1.wdl index 896aa1f..c2baa9f 100644 --- a/wdl/ichorCNA_step1.wdl +++ b/wdl/ichorCNA_step1.wdl @@ -1,280 +1,297 @@ -#upload commands -#docker run -it --rm -v "$HOME"/.config:/.config -v "$PWD":/working broadinstitute/firecloud-cli /bin/bash -#firecloud -m push -s chrislo -n ichorcna -t Workflow -y "ichorcna" ichorcna.wdl +workflow ichorCNA { + File bam_file + File bam_index + String sample_id + String genomeBuild + File? normalPanel + Int bin_size_kb + Int bin_size = bin_size_kb*1000 + File centromere + File gcWig + File mapWig + String genome_style + String chr_counter # All chromosomes for counting reads, as a list + String chrs # Autosomal and female chromosome for running ichor, as an R command + String chrTrain # Autosomal chromosomes to estimate ichor params, as an R command + Float maxFracCNASubclone + Float maxFracGenomeSubclone -#todo: -#put back NORMWIG, lambda etc. -#put back "X" + call read_counter { + input: bam_file = bam_file, + bam_index = bam_index, + sample_id = sample_id, + bin_size = bin_size, + chrs = chr_counter + } -workflow ichorCNA { - # Disk size parameter - Int disk_size + call ichorCNATask { + input: wig_file = read_counter.wig_file, + genomeBuild = genomeBuild, + sample_id = sample_id, + normalPanel = normalPanel, + bin_size_kb = bin_size_kb, + chrs = chrs, + chrTrain = chrTrain, + centromere = centromere, + genomeStyle = genome_style, + input_gcWig = gcWig, + input_mapWig = mapWig, + maxFracCNASubclone = maxFracCNASubclone, + maxFracGenomeSubclone = maxFracGenomeSubclone - # bamToWigTask - File bam_file - File bam_index_file - String sample_id + } + call extractIchorParams { + input: params = ichorCNATask.params, + maxFracCNASubclone = maxFracCNASubclone, + maxFracGenomeSubclone = maxFracGenomeSubclone + } + + call bundlePerChromosomePlots { + input: chrom_plots = ichorCNATask.perChromosomePlots, + sample_id = sample_id + } + + output { + File wig_file = read_counter.wig_file + + File allGenomeWidePlots = ichorCNATask.allGenomeWidePlots + File corrDepth = ichorCNATask.corrDepth + File cna = ichorCNATask.cna + File segTxt = ichorCNATask.segTxt + File seg = ichorCNATask.seg + File rdata = ichorCNATask.rdata - # readsCorrectionTask - Boolean normalizeMaleX - String chrs - String chrNormalize - File centromere - File normalPanel - #File targetedSequence - #File NORMWIG - Int rmCentromereFlankLength + Float tumor_fraction = extractIchorParams.tumor_fraction + Float ploidy = extractIchorParams.ploidy + String subclone_fraction = extractIchorParams.subclone_fraction + String fraction_genome_subclonal = extractIchorParams.fraction_genome_subclonal + String fraction_cna_subclonal = extractIchorParams.fraction_cna_subclonal + String gc_map_correction_mad = extractIchorParams.gc_map_correction_mad + Int top_solution_log_likelihood = extractIchorParams.top_solution_log_likelihood - # HMMTask - String ploidyParams - Boolean diploidChrX - String normal - Int maxCN - Boolean estimateNormal - Boolean estimatePloidy - Boolean includeHOMD - String chrTrain - Float txnE - Int txnStrength - String scStates - Boolean estimateScPrevalence - Float maxFracGenomeSubclone - Float maxFracCNASubclone - Int minSegmentBins - Float altFracThreshold - Int lambdaScaleHyperParam - Float mean_depth + File bias = ichorCNATask.bias + File tpdf = ichorCNATask.tpdf + File correct = ichorCNATask.correct + File params = ichorCNATask.params - call bamToWigTask { - input: disk_size = disk_size, - bam_file = bam_file, - bam_index_file = bam_index_file, - sample_id = sample_id - } + File optimalSolution = ichorCNATask.optimalSolution + File outSolutions = ichorCNATask.outSolutions + File perChromosomePlots = bundlePerChromosomePlots.output_plot + } +} - call readsCorrectionTask { - input: disk_size = disk_size, - wig_file = bamToWigTask.wig_file, - sample_id = sample_id, - normalizeMaleX = normalizeMaleX, - chrs = chrs, - chrNormalize = chrNormalize, - centromere = centromere, - normalPanel = normalPanel, - rmCentromereFlankLength = rmCentromereFlankLength - } +task read_counter { + File bam_file + File bam_index + String chrs + String sample_id + Int bin_size - call HMMTask { - input: disk_size = disk_size, - tumorCorrectedDepth_Rdata = readsCorrectionTask.tumorCorrectedDepthRdata, - sample_id = sample_id, - ploidyParams = ploidyParams, - diploidChrX = diploidChrX, - normal = normal, - maxCN = maxCN, - estimateNormal = estimateNormal, - estimatePloidy = estimatePloidy, - includeHOMD = includeHOMD, - chrs = chrs, - chrTrain = chrTrain, - txnE = txnE, - txnStrength = txnStrength, - scStates = scStates, - estimateScPrevalence = estimateScPrevalence, - maxFracGenomeSubclone = maxFracGenomeSubclone, - maxFracCNASubclone = maxFracCNASubclone, - minSegmentBins = minSegmentBins, - altFracThreshold = altFracThreshold, - lambdaScaleHyperParam = lambdaScaleHyperParam, - mean_depth = mean_depth - } + Int? min_qual = 20 + Int? memGB = 4 + Int? diskGB = 50 + Int? preemptible = 2 + + String? docker_override - call BundlePerChromosomePlots { - input: chrom_plots = HMMTask.perChromosomePlots, - sample_id = sample_id - } + command { + ln -vs ${bam_index} ${sample_id}.bam.bai + ln -vs ${bam_file} ${sample_id}.bam - output { - File allGenomeWidePlots = HMMTask.allGenomeWidePlots + /HMMcopy/bin/readCounter ${sample_id}.bam -c ${chrs} -w ${bin_size} \ + -q ${min_qual} > ${sample_id}.bin${bin_size}.wig + } - Float tumor_fraction = HMMTask.tumor_fraction - Float ploidy = HMMTask.ploidy - String subclone_fraction = HMMTask.subclone_fraction - String fraction_genome_subclonal = HMMTask.fraction_genome_subclonal - String fraction_cna_subclonal = HMMTask.fraction_cna_subclonal - String gc_map_correction_mad = HMMTask.gc_map_correction_mad + runtime { + docker: select_first([docker_override, "us.gcr.io/tag-team-160914/bloodbiopsy-hmmcopy:0.0.1"]) + disks: "local-disk ${diskGB} HDD" + memory: "${memGB}GB" + preemptible: "${preemptible}" + maxRetries: 1 + } - File bias = HMMTask.bias - File tpdf = HMMTask.tpdf - File correct = HMMTask.correct - File params = HMMTask.params - - File optimalSolution = HMMTask.optimalSolution - File outSolutions = HMMTask.outSolutions - File perChromosomePlots = BundlePerChromosomePlots.output_plot - } + output { + File wig_file = "${sample_id}.bin${bin_size}.wig" + } } +task ichorCNATask { + File wig_file + File? normalPanel + String genomeBuild + Int bin_size_kb + Float? mean_depth + String sample_id + String ploidy + String normal + Int maxCN + Boolean includeHOMD + String chrs + String chrTrain + String chrNormalize + String genomeStyle + Boolean estimateNormal + Boolean estimatePloidy + Boolean estimateClonality + String scStates + File centromere + File? exons + Float txnE + Int txnStrength + Int minSegmentBins + Float minMapScore + Float fracReadsChrYMale + Float maxFracCNASubclone + Float maxFracGenomeSubclone + Float altFracThreshold + Int lambdaScaleHyperParam + Int rmCentromereFlankLength + String? plotFileType = "pdf" + String plotYlim + File input_gcWig + File input_mapWig -task bamToWigTask { - Int disk_size - File bam_file - File bam_index_file - String sample_id + Int? memGB = 4 + Int? diskGB = 50 + Int? preemptible = 2 + Int? maxRetries = 1 + + String? docker_override - command <<< - ln -vs ${bam_index_file} ${sample_id}.bam.bai - ln -vs ${bam_file} ${sample_id}.bam + command <<< - /HMMcopy/bin/readCounter --window 1000000 \ - --quality 20 \ - --chromosome "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y" \ - ${sample_id}.bam > ${sample_id}.wig - >>> - output { - File wig_file = "${sample_id}.wig" - } - runtime { - docker: "us.gcr.io/tag-team-160914/bloodbiopsy-hmmcopy:0.0.1" - disks: "local-disk ${disk_size} HDD" - preemptible: 3 - } -} + Rscript /runIchorCNA.R --id ${sample_id} \ + --outDir ./ --libdir /ichorCNA \ + --WIG ${wig_file} \ + --gcWig ${input_gcWig} \ + --mapWig ${input_mapWig} \ + --normalPanel ${default="None" normalPanel} \ + --ploidy "${ploidy}" \ + --normal "${normal}" \ + ${"--coverage " + mean_depth} \ + --maxCN ${maxCN} \ + --includeHOMD ${includeHOMD} \ + --chrs "${chrs}" \ + --chrTrain "${chrTrain}" \ + --chrNormalize "${chrNormalize}" \ + --genomeStyle "${genomeStyle}" \ + --genomeBuild "${genomeBuild}" \ + --estimateNormal ${estimateNormal} \ + --estimatePloidy ${estimatePloidy} \ + --estimateScPrevalence ${estimateClonality} \ + --scStates "${scStates}" \ + --centromere ${centromere} \ + ${"--exons.bed " + exons} \ + --txnE ${txnE} \ + --txnStrength ${txnStrength} \ + --minSegmentBins ${minSegmentBins} \ + --minMapScore ${minMapScore} \ + --lambdaScaleHyperParam ${lambdaScaleHyperParam} \ + --fracReadsInChrYForMale ${fracReadsChrYMale} \ + --maxFracGenomeSubclone ${maxFracGenomeSubclone} \ + --altFracThreshold ${altFracThreshold} \ + --maxFracCNASubclone ${maxFracCNASubclone} \ + --rmCentromereFlankLength ${rmCentromereFlankLength} \ + --plotFileType ${plotFileType} \ + --plotYLim "${plotYlim}" + # Zip optimal solutions + mkdir ${sample_id}.optimalSolution + cp ${sample_id}/${sample_id}_genomeWide.pdf ${sample_id}.cna.seg ${sample_id}.seg.txt ${sample_id}.seg ${sample_id}.optimalSolution/ + zip -r ${sample_id}.optimalSolution.zip ${sample_id}.optimalSolution + + # Generate list of out solutions + Rscript /gatherOutSolutions.R --id ${sample_id} --rdata ${sample_id}.RData + >>> -task readsCorrectionTask { - Int disk_size - File wig_file - String sample_id - Boolean normalizeMaleX - String chrs - String chrNormalize - File centromere - File normalPanel - #File targetedSequence - #File NORMWIG - Int rmCentromereFlankLength + runtime { + docker: select_first([docker_override, "us.gcr.io/tag-team-160914/bloodbiopsy-ichorcna:0.2.1"]) + disks: "local-disk " + diskGB + " HDD" + memory: memGB + " GB" + preemptible: preemptible + maxRetries: maxRetries + } - command <<< - Rscript /readsCorrection.R --libdir /ichorCNA/R/ \ - --datadir /ichorCNA/inst/extdata/ \ - --id ${sample_id} \ - --WIG ${wig_file} \ - --normalizeMaleX ${normalizeMaleX} \ - --chrs "${chrs}" \ - --chrNormalize "${chrNormalize}" \ - --centromere ${centromere} \ - --normalPanel ${normalPanel} \ - --rmCentromereFlankLength ${rmCentromereFlankLength} \ - --outDir . - >>> - output { - File correctedDepth = "${sample_id}/${sample_id}.correctedDepth.txt" - File tumorCorrectedDepthRdata = "${sample_id}/${sample_id}.tumor_copy_correctedDepth.RData" - } - runtime { - docker: "us.gcr.io/tag-team-160914/bloodbiopsy-ichorcna:0.0.1" - disks: "local-disk ${disk_size} HDD" - preemptible: 3 - } -} + output { + File corrDepth = "${sample_id}.correctedDepth.txt" + File params = "${sample_id}.params.txt" + File cna = "${sample_id}.cna.seg" + File segTxt = "${sample_id}.seg.txt" + File seg = "${sample_id}.seg" + File rdata = "${sample_id}.RData" + File allGenomeWidePlots = "${sample_id}/${sample_id}_genomeWide_all_sols.pdf" + File bias = "${sample_id}/${sample_id}_bias.pdf" + File tpdf = "${sample_id}/${sample_id}_tpdf.pdf" + File correct = "${sample_id}/${sample_id}_correct.pdf" + Array[File] perChromosomePlots = glob("${sample_id}/${sample_id}_CNA*") -task HMMTask { - Int disk_size - File tumorCorrectedDepth_Rdata - String sample_id - String ploidyParams - Boolean diploidChrX - String normal - Int maxCN - Boolean estimateNormal - Boolean estimatePloidy - Boolean includeHOMD - String chrs - String chrTrain - Float txnE - Int txnStrength - String scStates - Boolean estimateScPrevalence - Float maxFracGenomeSubclone - Float maxFracCNASubclone - Int minSegmentBins - Float altFracThreshold - Int lambdaScaleHyperParam - Float mean_depth + File optimalSolution = "${sample_id}.optimalSolution.zip" + File outSolutions = "${sample_id}.outSolutions.zip" + } - command <<< - Rscript /HMM.R --libdir /ichorCNA/R/ \ - --id ${sample_id} \ - --tumourCopyCorrected ${tumorCorrectedDepth_Rdata} \ - --ploidy "${ploidyParams}" \ - --diploidChrX ${diploidChrX} \ - --normal "${normal}" \ - --maxCN ${maxCN} \ - --estimateNormal ${estimateNormal} \ - --estimatePloidy ${estimatePloidy} \ - --includeHOMD ${includeHOMD} \ - --chrs "${chrs}" \ - --chrTrain "${chrTrain}" \ - --txnE ${txnE} \ - --txnStrength ${txnStrength} \ - --scStates "${scStates}" \ - --estimateScPrevalence ${estimateScPrevalence} \ - --maxFracGenomeSubclone ${maxFracGenomeSubclone} \ - --maxFracCNASubclone ${maxFracCNASubclone} \ - --minSegmentBins ${minSegmentBins} \ - --altFracThreshold ${altFracThreshold} \ - --lambdaScaleHyperParam ${lambdaScaleHyperParam} \ - --coverage ${mean_depth} --outDir . +} - # Extract sample stats: though a bit ugly, grep'ing all the values - grep "^Tumor Fraction" ${sample_id}/${sample_id}.params.txt | cut -f2 > tumor_fraction - grep "^Ploidy" ${sample_id}/${sample_id}.params.txt | cut -f2 > ploidy - grep "^Subclone Fraction" ${sample_id}/${sample_id}.params.txt | cut -f2 > subclone_fraction - grep "^Fraction Genome Subclonal" ${sample_id}/${sample_id}.params.txt | cut -f2 > fraction_genome_subclonal - grep "^Fraction CNA Subclonal" ${sample_id}/${sample_id}.params.txt | cut -f2 > fraction_cna_subclonal - grep "^GC-Map correction MAD" ${sample_id}/${sample_id}.params.txt | cut -f2 > gc-map_correction_mad - # Zip optimal solutions - mkdir ${sample_id}.optimalSolution - mv ${sample_id}/optimalSolution/* ${sample_id}.optimalSolution - zip -r ${sample_id}.optimalSolution.zip ${sample_id}.optimalSolution - - # Zip the other solutions - mkdir ${sample_id}.outSolutions - mv ${sample_id}/n*/* ${sample_id}.outSolutions - zip -r ${sample_id}.outSolutions.zip ${sample_id}.outSolutions - >>> - output { - File allGenomeWidePlots = "${sample_id}/${sample_id}_genomeWide_all_sols.pdf" +task extractIchorParams { + File params + Float maxFracCNASubclone + Float maxFracGenomeSubclone - Float tumor_fraction = read_float("tumor_fraction") - Float ploidy = read_float("ploidy") - String subclone_fraction = read_string("subclone_fraction") - String fraction_genome_subclonal = read_string("fraction_genome_subclonal") - String fraction_cna_subclonal = read_string("fraction_cna_subclonal") - String gc_map_correction_mad = read_string("gc-map_correction_mad") + command <<< + cut -f1,2 ${params} | grep -v ^$ | tr "\t" " " > params_table.txt +python<log_lik and float(sol[4])<${maxFracGenomeSubclone} and float(sol[5])<${maxFracCNASubclone}: + log_lik=int(float(sol[6])) +params = open("params_table.txt","r").readlines() +params = [x.rstrip("\n").split(": ") for x in params if ":" in x] +param_dict = dict() +for a,b in params: + param_dict[a] = b +p=open("tumor_fraction","w"); p.write(param_dict["Tumor Fraction"]) +p=open("ploidy","w"); p.write(param_dict["Ploidy"]) +p=open("subclone_fraction","w"); p.write(param_dict["Subclone Fraction"]) +p=open("fraction_genome_subclonal","w"); p.write(param_dict["Fraction Genome Subclonal"]) +p=open("fraction_cna_subclonal","w"); p.write(param_dict["Fraction CNA Subclonal"]) +p=open("gc-map_correction_mad","w"); p.write(param_dict["GC-Map correction MAD"]) +p=open("top_solution_log_likelihood","w"); p.write(str(log_lik)) +p.close() +CODE + >>> - File bias = "${sample_id}/${sample_id}_bias.pdf" - File tpdf = "${sample_id}/${sample_id}_tpdf.pdf" - File correct = "${sample_id}/${sample_id}_correct.pdf" - File params = "${sample_id}/${sample_id}.params.txt" - - File optimalSolution = "${sample_id}.optimalSolution.zip" - File outSolutions = "${sample_id}.outSolutions.zip" - Array[File] perChromosomePlots = glob("${sample_id}/${sample_id}_CNA*") - } - runtime { - docker: "us.gcr.io/tag-team-160914/bloodbiopsy-ichorcna:0.0.1" - disks: "local-disk ${disk_size} HDD" - preemptible: 3 - } + runtime { + docker: "python:3" + memory: "2 GB" + disks: "local-disk 10 HDD" + preemptible: 1 + maxRetries: 1 + } + + output { + Float tumor_fraction = read_float("tumor_fraction") + Float ploidy = read_float("ploidy") + String subclone_fraction = read_string("subclone_fraction") + String fraction_genome_subclonal = read_string("fraction_genome_subclonal") + String fraction_cna_subclonal = read_string("fraction_cna_subclonal") + String gc_map_correction_mad = read_string("gc-map_correction_mad") + Int top_solution_log_likelihood = read_int("top_solution_log_likelihood") + } } -task BundlePerChromosomePlots { +task bundlePerChromosomePlots { Array[File] chrom_plots String sample_id + + Int? memGB = 2 + Int? diskGB = 10 + Int? preemptible = 3 + Int? maxRetries = 1 + + String? docker_override command <<< set -e @@ -288,9 +305,10 @@ task BundlePerChromosomePlots { File output_plot = "${sample_id}_OptimalSolutionPerChrom.pdf" } runtime { - docker: "us.gcr.io/tag-team-160914/tag-tools:0.0.4" - memory: "1 GB" - disks: "local-disk 2 HDD" - preemptible: 3 + docker: select_first([docker_override, "us.gcr.io/tag-team-160914/tag-tools:1.0.0"]) + memory: memGB + " GB" + disks: "local-disk " + diskGB + " HDD" + preemptible: preemptible + maxRetries: maxRetries } } From e45b546ebe18071e978f206442545e5d146a31e3 Mon Sep 17 00:00:00 2001 From: stellaning1120 Date: Tue, 4 Oct 2022 16:16:53 -0400 Subject: [PATCH 2/2] updated the input and output json files of iChor methods. --- input_json/ichorCNA_step1_pipeline_inputs.json | 2 +- input_json/ichorCNA_step1_pipeline_outputs.json | 1 + input_json/ichorCNA_step2_pipeline_inputs.json | 2 +- input_json/ichorCNA_step2_pipeline_outputs.json | 1 + 4 files changed, 4 insertions(+), 2 deletions(-) create mode 100644 input_json/ichorCNA_step1_pipeline_outputs.json create mode 100644 input_json/ichorCNA_step2_pipeline_outputs.json diff --git a/input_json/ichorCNA_step1_pipeline_inputs.json b/input_json/ichorCNA_step1_pipeline_inputs.json index 2d80062..9749542 100644 --- a/input_json/ichorCNA_step1_pipeline_inputs.json +++ b/input_json/ichorCNA_step1_pipeline_inputs.json @@ -1 +1 @@ -{"ichorCNA.altFracThreshold":"${0.7}","ichorCNA.bam_file":"${this.cram_or_bam_path}","ichorCNA.bam_index_file":"${this.crai_or_bai_path}","ichorCNA.centromere":"gs://gptag/somatic/aux/ichorCNA_filters/GRCh37.p13_centromere_UCSC-gapTable.txt","ichorCNA.chrNormalize":"c(1:22)","ichorCNA.chrTrain":"c(1:18, 20:22)","ichorCNA.chrs":"c(1:22)","ichorCNA.diploidChrX":"FALSE","ichorCNA.disk_size":"${25}","ichorCNA.estimateNormal":"TRUE","ichorCNA.estimatePloidy":"TRUE","ichorCNA.estimateScPrevalence":"TRUE","ichorCNA.includeHOMD":"FALSE","ichorCNA.lambdaScaleHyperParam":"${3}","ichorCNA.maxCN":"${7}","ichorCNA.maxFracCNASubclone":"${0.7}","ichorCNA.maxFracGenomeSubclone":"${0.5}","ichorCNA.mean_depth":"${this.mean_depth}","ichorCNA.minSegmentBins":"${25}","ichorCNA.normal":"c(0.35,0.45,0.55,0.65,0.75,0.85,0.95)","ichorCNA.normalPanel":"gs://gptag/somatic/aux/ichorCNA_filters/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds","ichorCNA.normalizeMaleX":"TRUE","ichorCNA.ploidyParams":"c(2,3,4)","ichorCNA.rmCentromereFlankLength":"${100000}","ichorCNA.sample_id":"${this.name}","ichorCNA.scStates":"c(1, 3)","ichorCNA.txnE":"${0.99999}","ichorCNA.txnStrength":"${100000}"} \ No newline at end of file +{"ichorCNA.bam_file":"${this.cram_or_bam_path}","ichorCNA.bam_index":"${this.crai_or_bai_path}","ichorCNA.bin_size_kb":"${1000}","ichorCNA.centromere":"gs://gptag/ichorCNA_resources/GRCh37.p13_centromere_UCSC-gapTable.txt","ichorCNA.chrTrain":"c(1:18, 20:22)","ichorCNA.chr_counter":"1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y","ichorCNA.chrs":"c(1:22)","ichorCNA.gcWig":"gs://gptag/ichorCNA_resources/gc_hg19_1000kb.wig","ichorCNA.genomeBuild":"hg19","ichorCNA.genome_style":"NCBI","ichorCNA.ichorCNATask.altFracThreshold":"${0.7}","ichorCNA.ichorCNATask.chrNormalize":"c(1:22)","ichorCNA.ichorCNATask.diskGB":"${}","ichorCNA.ichorCNATask.estimateClonality":"TRUE","ichorCNA.ichorCNATask.estimateNormal":"TRUE","ichorCNA.ichorCNATask.estimatePloidy":"TRUE","ichorCNA.ichorCNATask.exons":"${}","ichorCNA.ichorCNATask.fracReadsChrYMale":"${0.002}","ichorCNA.ichorCNATask.includeHOMD":"FALSE","ichorCNA.ichorCNATask.lambdaScaleHyperParam":"${3}","ichorCNA.ichorCNATask.maxCN":"${7}","ichorCNA.ichorCNATask.mean_depth":"${this.mean_depth}","ichorCNA.ichorCNATask.memGB":"${}","ichorCNA.ichorCNATask.minMapScore":"${0.9}","ichorCNA.ichorCNATask.minSegmentBins":"${25}","ichorCNA.ichorCNATask.normal":"c(0.35,0.45,0.55,0.65,0.75,0.85,0.95)","ichorCNA.ichorCNATask.ploidy":"c(2,3,4)","ichorCNA.ichorCNATask.plotFileType":"${}","ichorCNA.ichorCNATask.plotYlim":"c(-2,2)","ichorCNA.ichorCNATask.preemptible":"${}","ichorCNA.ichorCNATask.rmCentromereFlankLength":"${100000}","ichorCNA.ichorCNATask.scStates":"c(1,3)","ichorCNA.ichorCNATask.txnE":"${0.99999}","ichorCNA.ichorCNATask.txnStrength":"${100000}","ichorCNA.mapWig":"gs://gptag/ichorCNA_resources/map_hg19_1000kb.wig","ichorCNA.maxFracCNASubclone":"${0.7}","ichorCNA.maxFracGenomeSubclone":"${0.5}","ichorCNA.normalPanel":"gs://gptag/ichorCNA_resources/Stover_Lennon_UH2_20HD_PON_1X_ULP_median.rds","ichorCNA.read_counter.diskGB":"${}","ichorCNA.read_counter.memGB":"${}","ichorCNA.read_counter.min_qual":"${}","ichorCNA.read_counter.preemptible":"${}","ichorCNA.sample_id":"${this.sample_id}"} \ No newline at end of file diff --git a/input_json/ichorCNA_step1_pipeline_outputs.json b/input_json/ichorCNA_step1_pipeline_outputs.json new file mode 100644 index 0000000..140ed21 --- /dev/null +++ b/input_json/ichorCNA_step1_pipeline_outputs.json @@ -0,0 +1 @@ +{"ichorCNA.allGenomeWidePlots":"${this.allGenomeWidePlots}","ichorCNA.bias":"${this.bias}","ichorCNA.cna":"${this.cna}","ichorCNA.corrDepth":"${this.corrDepth}","ichorCNA.correct":"${this.correct}","ichorCNA.fraction_cna_subclonal":"${this.fraction_cna_subclonal}","ichorCNA.fraction_genome_subclonal":"${this.fraction_genome_subclonal}","ichorCNA.gc_map_correction_mad":"${this.gc_map_correction_mad}","ichorCNA.optimalSolution":"${this.optimalSolution}","ichorCNA.outSolutions":"${this.outSolutions}","ichorCNA.params":"${this.params}","ichorCNA.perChromosomePlots":"${this.perChromosomePlots}","ichorCNA.ploidy":"${this.ploidy}","ichorCNA.rdata":"${this.rdata}","ichorCNA.seg":"${this.seg}","ichorCNA.segTxt":"${this.segTxt}","ichorCNA.subclone_fraction":"${this.subclone_fraction}","ichorCNA.top_solution_log_likelihood":"${this.top_solution_log_likelihood}","ichorCNA.tpdf":"${this.tpdf}","ichorCNA.tumor_fraction":"${this.tumor_fraction}","ichorCNA.wig_file":"${this.wig_file}"} \ No newline at end of file diff --git a/input_json/ichorCNA_step2_pipeline_inputs.json b/input_json/ichorCNA_step2_pipeline_inputs.json index 61f40e0..c58deed 100644 --- a/input_json/ichorCNA_step2_pipeline_inputs.json +++ b/input_json/ichorCNA_step2_pipeline_inputs.json @@ -1 +1 @@ -{"ichorSummaryBundle.CNA_plots":"${this.samples.allGenomeWidePlots}","ichorSummaryBundle.sample_set_name":"${this.sample_set_id}","ichorSummaryBundle.summary_script":"${ \"gs://gptag/somatic/script/ichor_summary.py\"}"} \ No newline at end of file +{"ichorSummaryBundle.CNA_plots":"${this.samples.allGenomeWidePlots}","ichorSummaryBundle.sample_set_name":"${this.sample_set_id}","ichorSummaryBundle.summary_script":"gs://gptag-public/ichorcna/ichorcna_step2/summary_script/ichor_summary.py"} \ No newline at end of file diff --git a/input_json/ichorCNA_step2_pipeline_outputs.json b/input_json/ichorCNA_step2_pipeline_outputs.json new file mode 100644 index 0000000..140ed21 --- /dev/null +++ b/input_json/ichorCNA_step2_pipeline_outputs.json @@ -0,0 +1 @@ +{"ichorCNA.allGenomeWidePlots":"${this.allGenomeWidePlots}","ichorCNA.bias":"${this.bias}","ichorCNA.cna":"${this.cna}","ichorCNA.corrDepth":"${this.corrDepth}","ichorCNA.correct":"${this.correct}","ichorCNA.fraction_cna_subclonal":"${this.fraction_cna_subclonal}","ichorCNA.fraction_genome_subclonal":"${this.fraction_genome_subclonal}","ichorCNA.gc_map_correction_mad":"${this.gc_map_correction_mad}","ichorCNA.optimalSolution":"${this.optimalSolution}","ichorCNA.outSolutions":"${this.outSolutions}","ichorCNA.params":"${this.params}","ichorCNA.perChromosomePlots":"${this.perChromosomePlots}","ichorCNA.ploidy":"${this.ploidy}","ichorCNA.rdata":"${this.rdata}","ichorCNA.seg":"${this.seg}","ichorCNA.segTxt":"${this.segTxt}","ichorCNA.subclone_fraction":"${this.subclone_fraction}","ichorCNA.top_solution_log_likelihood":"${this.top_solution_log_likelihood}","ichorCNA.tpdf":"${this.tpdf}","ichorCNA.tumor_fraction":"${this.tumor_fraction}","ichorCNA.wig_file":"${this.wig_file}"} \ No newline at end of file