Merge pull request #3 from broadinstitute/sl_ichor_dockstore

Update wdl and json files for ichor.

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}"}
+{"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}"}

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}"}

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":"${ \"gs://gptag/somatic/script/ichor_summary.py\"}"}
+{"ichorSummaryBundle.CNA_plots":"${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"}

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}"}