{"CGA_Production_Analysis_Workflow.CrossCheckLaneFingerprints_Task.HaplotypeDBForCrossCheck":"${workspace.HAP_DB_FOR_CC}","CGA_Production_Analysis_Workflow.cosmicVCF":"${workspace.COSMIC_VCF}","CGA_Production_Analysis_Workflow.agilentMAFPonFilter.PONFile":"${workspace.AGILENT_TOKEN_PON}","CGA_Production_Analysis_Workflow.cga_pipeline_config":"${workspace.CGA_PIPELINE_CONFIG}","CGA_Production_Analysis_Workflow.VEP_Task.VEP_File":"${workspace.VEP_ZIP_FILE}","CGA_Production_Analysis_Workflow.Oncotate_Task.oncoDBTarBall":"${workspace.ONCO_TARBALL}","CGA_Production_Analysis_Workflow.Strelka.config":"${workspace.STRELKA_CONFIG}","CGA_Production_Analysis_Workflow.tumorBamIdx":"${this.case_sample.WXS_bai_path}","CGA_Production_Analysis_Workflow.DB_SNP_VCF_IDX":"${workspace.DB_SNP_VCF_IDX}","CGA_Production_Analysis_Workflow.ContEST_Task.SNP6Bed":"${workspace.SNP6BED}","CGA_Production_Analysis_Workflow.ctrlName":"${this.control_sample.name}","CGA_Production_Analysis_Workflow.GATK4_JAR":"${workspace.GATK4_JAR}","CGA_Production_Analysis_Workflow.gatk_acnv_only.gatk_protected":"${workspace.GATK_PROTECTED_JAR}","CGA_Production_Analysis_Workflow.pairName":"${this.name}","CGA_Production_Analysis_Workflow.iceMAFPonFilter.PONFile":"${workspace.ICE_TOKEN_PON}","CGA_Production_Analysis_Workflow.Gather_and_Compute_CopyNumberReportQC_Task.captureNormalsDBRCLZip":"${workspace.CAP_NORM_DB_ZIP}","CGA_Production_Analysis_Workflow.ContEST_Task.HapMapVCF":"${workspace.HAP_MAP_VCF}","CGA_Production_Analysis_Workflow.lego_plotter_task.mut_categs":"${workspace.MUT_CATEGORIES}","CGA_Production_Analysis_Workflow.cytoBandFile":"${workspace.CYTO_BAND}","CGA_Production_Analysis_Workflow.regionFile":"${workspace.REGION_FILE}","CGA_Production_Analysis_Workflow.GatherAndDeTiN_Task.exac_pickle":"${workspace.EXAC_PICKLE}","CGA_Production_Analysis_Workflow.refFastaDict":"${workspace.REF_FASTA_DICT}","CGA_Production_Analysis_Workflow.refFastaIdx":"${workspace.REF_FASTA_IDX}","CGA_Production_Analysis_Workflow.gatk_acnv_only.PoN":"${workspace.ACNV_PON}","CGA_Production_Analysis_Workflow.gatk_acnv_only.common_snp_list":"${workspace.GOOD_HETS}","CGA_Production_Analysis_Workflow.normalBamIdx":"${this.control_sample.WXS_bai_path}","CGA_Production_Analysis_Workflow.blat.hg19_bit":"${workspace.BLAT_REALIGNER_HG19_BIT}","CGA_Production_Analysis_Workflow.baitIntervals":"${workspace.AGILENT_BAIT_INTERVALS}","CGA_Production_Analysis_Workflow.normalBam":"${this.control_sample.WXS_bam_path}","CGA_Production_Analysis_Workflow.normalPanel":"${workspace.KGENOMES_NORMAL_PANEL_VCF}","CGA_Production_Analysis_Workflow.tumorBam":"${this.case_sample.WXS_bam_path}","CGA_Production_Analysis_Workflow.readGroupBlackList":"${workspace.READ_GROUP_BLACKLIST}","CGA_Production_Analysis_Workflow.MutectFC_Task.mutectIntervals":"${workspace.MUTECT_FC_INTERVALS}","CGA_Production_Analysis_Workflow.targetIntervals":"${workspace.AGILENT_TARGET_INTERVALS}","CGA_Production_Analysis_Workflow.caseName":"${this.case_sample.name}","CGA_Production_Analysis_Workflow.DB_SNP_VCF":"${workspace.DB_SNP_VCF}","CGA_Production_Analysis_Workflow.refFasta":"${workspace.REF_FASTA}"}