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[fillcolor=\"#94DDF4\",label=\"tumor_readgroups\"];\n    \"readcount_minimum_mapping_quality\" [fillcolor=\"#94DDF4\",label=\"readcount_minimum_mapping_quality\"];\n    \"custom_clinvar_vcf\" [fillcolor=\"#94DDF4\",label=\"custom_clinvar_vcf\"];\n    \"variants_to_table_genotype_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_genotype_fields\"];\n    \"rna_readgroups\" [fillcolor=\"#94DDF4\",label=\"rna_readgroups\"];\n    \"peptide_sequence_length\" [fillcolor=\"#94DDF4\",label=\"peptide_sequence_length\"];\n    \"trimming_adapters\" [fillcolor=\"#94DDF4\",label=\"trimming_adapters\"];\n    \"rna_bams\" [fillcolor=\"#94DDF4\",label=\"rna_bams\"];\n    \"readcount_minimum_base_quality\" [fillcolor=\"#94DDF4\",label=\"readcount_minimum_base_quality\"];\n    \"tdna_vaf\" [fillcolor=\"#94DDF4\",label=\"tdna_vaf\"];\n    \"manta_non_wgs\" [fillcolor=\"#94DDF4\",label=\"manta_non_wgs\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"normal_readgroups\" [fillcolor=\"#94DDF4\",label=\"normal_readgroups\"];\n    \"picard_metric_accumulation_level\" [fillcolor=\"#94DDF4\",label=\"picard_metric_accumulation_level\"];\n    \"varscan_min_coverage\" [fillcolor=\"#94DDF4\",label=\"varscan_min_coverage\"];\n    \"annotate_coding_only\" [fillcolor=\"#94DDF4\",label=\"annotate_coding_only\"];\n    \"mutect_artifact_detection_mode\" [fillcolor=\"#94DDF4\",label=\"mutect_artifact_detection_mode\"];\n    \"manta_call_regions\" [fillcolor=\"#94DDF4\",label=\"manta_call_regions\"];\n    \"downstream_sequence_length\" [fillcolor=\"#94DDF4\",label=\"downstream_sequence_length\"];\n    \"kallisto_index\" [fillcolor=\"#94DDF4\",label=\"kallisto_index\"];\n    \"normal_vaf\" [fillcolor=\"#94DDF4\",label=\"normal_vaf\"];\n    \"summary_intervals\" [fillcolor=\"#94DDF4\",label=\"summary_intervals\"];\n    \"omni_vcf\" [fillcolor=\"#94DDF4\",label=\"omni_vcf\"];\n    \"refFlat\" [fillcolor=\"#94DDF4\",label=\"refFlat\"];\n    \"somalier_vcf\" [fillcolor=\"#94DDF4\",label=\"somalier_vcf\"];\n    \"mutect_max_alt_alleles_in_normal_count\" [fillcolor=\"#94DDF4\",label=\"mutect_max_alt_alleles_in_normal_count\"];\n    \"mutect_scatter_count\" [fillcolor=\"#94DDF4\",label=\"mutect_scatter_count\"];\n    \"gene_transcript_lookup_table\" [fillcolor=\"#94DDF4\",label=\"gene_transcript_lookup_table\"];\n    \"exclude_nas\" [fillcolor=\"#94DDF4\",label=\"exclude_nas\"];\n    \"optitype_name\" [fillcolor=\"#94DDF4\",label=\"optitype_name\"];\n    \"trna_cov\" [fillcolor=\"#94DDF4\",label=\"trna_cov\"];\n    \"per_base_intervals\" [fillcolor=\"#94DDF4\",label=\"per_base_intervals\"];\n    \"vep_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"vep_to_table_fields\"];\n    \"phased_proximal_variants_vcf\" [fillcolor=\"#94DDF4\",label=\"phased_proximal_variants_vcf\"];\n    \"tumor_name\" [fillcolor=\"#94DDF4\",label=\"tumor_name\"];\n    \"interval_list\" [fillcolor=\"#94DDF4\",label=\"interval_list\"];\n    \"trna_vaf\" [fillcolor=\"#94DDF4\",label=\"trna_vaf\"];\n    \"expn_val\" [fillcolor=\"#94DDF4\",label=\"expn_val\"];\n    \"known_indels\" [fillcolor=\"#94DDF4\",label=\"known_indels\"];\n    \"normal_name\" [fillcolor=\"#94DDF4\",label=\"normal_name\"];\n    \"varscan_p_value\" [fillcolor=\"#94DDF4\",label=\"varscan_p_value\"];\n    \"vep_ensembl_species\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_species\"];\n    \"gatk_haplotypecaller_intervals\" [fillcolor=\"#94DDF4\",label=\"gatk_haplotypecaller_intervals\"];\n    \"binding_threshold\" [fillcolor=\"#94DDF4\",label=\"binding_threshold\"];\n    \"trimming_min_readlength\" [fillcolor=\"#94DDF4\",label=\"trimming_min_readlength\"];\n    \"gvcf_gq_bands\" [fillcolor=\"#94DDF4\",label=\"gvcf_gq_bands\"];\n    \"maximum_transcript_support_level\" [fillcolor=\"#94DDF4\",label=\"maximum_transcript_support_level\"];\n    \"net_chop_method\" [fillcolor=\"#94DDF4\",label=\"net_chop_method\"];\n    \"pindel_insert_size\" [fillcolor=\"#94DDF4\",label=\"pindel_insert_size\"];\n    \"per_target_intervals\" [fillcolor=\"#94DDF4\",label=\"per_target_intervals\"];\n    \"tdna_cov\" [fillcolor=\"#94DDF4\",label=\"tdna_cov\"];\n    \"trimming_adapter_min_overlap\" [fillcolor=\"#94DDF4\",label=\"trimming_adapter_min_overlap\"];\n    \"reference_annotation\" [fillcolor=\"#94DDF4\",label=\"reference_annotation\"];\n    \"ribosomal_intervals\" [fillcolor=\"#94DDF4\",label=\"ribosomal_intervals\"];\n    \"panel_of_normals_vcf\" [fillcolor=\"#94DDF4\",label=\"panel_of_normals_vcf\"];\n    \"sample_name\" [fillcolor=\"#94DDF4\",label=\"sample_name\"];\n    \"netmhc_stab\" [fillcolor=\"#94DDF4\",label=\"netmhc_stab\"];\n    \"bqsr_intervals\" [fillcolor=\"#94DDF4\",label=\"bqsr_intervals\"];\n    \"epitope_lengths\" [fillcolor=\"#94DDF4\",label=\"epitope_lengths\"];\n    \"normal_cov\" [fillcolor=\"#94DDF4\",label=\"normal_cov\"];\n    \"dbsnp_vcf\" [fillcolor=\"#94DDF4\",label=\"dbsnp_vcf\"];\n    \"vep_pick\" [fillcolor=\"#94DDF4\",label=\"vep_pick\"];\n    \"vep_ensembl_assembly\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_assembly\"];\n    \"strelka_cpu_reserved\" [fillcolor=\"#94DDF4\",label=\"strelka_cpu_reserved\"];\n    \"top_score_metric\" [fillcolor=\"#94DDF4\",label=\"top_score_metric\"];\n    \"varscan_max_normal_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_max_normal_freq\"];\n    \"reference_dict\" [fillcolor=\"#94DDF4\",label=\"reference_dict\"];\n    \"fasta_size\" [fillcolor=\"#94DDF4\",label=\"fasta_size\"];\n    \"strand\" [fillcolor=\"#94DDF4\",label=\"strand\"];\n    \"trimming_adapter_trim_end\" [fillcolor=\"#94DDF4\",label=\"trimming_adapter_trim_end\"];\n    \"read_group_fields\" [fillcolor=\"#94DDF4\",label=\"read_group_fields\"];\n    \"filter_docm_variants\" [fillcolor=\"#94DDF4\",label=\"filter_docm_variants\"];\n    \"manta_output_contigs\" [fillcolor=\"#94DDF4\",label=\"manta_output_contigs\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"normal_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_snv_bam_readcount_tsv\"];\n    \"normal_flagstats\" [fillcolor=\"#94DDF4\",label=\"normal_flagstats\"];\n    \"final_tsv\" [fillcolor=\"#94DDF4\",label=\"final_tsv\"];\n    \"somatic_final_vcf\" [fillcolor=\"#94DDF4\",label=\"somatic_final_vcf\"];\n    \"normal_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_hs_metrics\"];\n    \"insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"insert_size_metrics\"];\n    \"mhc_ii_filtered_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_ii_filtered_epitopes\"];\n    \"pindel_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_filtered_vcf\"];\n    \"normal_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"normal_antitarget_coverage\"];\n    \"normal_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_mark_duplicates_metrics\"];\n    \"final_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"final_filtered_vcf\"];\n    \"mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"mark_duplicates_metrics\"];\n    \"per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"per_base_coverage_metrics\"];\n    \"tumor_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_base_hs_metrics\"];\n    \"tumor_flagstats\" [fillcolor=\"#94DDF4\",label=\"tumor_flagstats\"];\n    \"combined_ranked_epitopes\" [fillcolor=\"#94DDF4\",label=\"combined_ranked_epitopes\"];\n    \"normal_per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_base_coverage_metrics\"];\n    \"tumor_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_mark_duplicates_metrics\"];\n    \"stringtie_gene_expression_tsv\" [fillcolor=\"#94DDF4\",label=\"stringtie_gene_expression_tsv\"];\n    \"somalier_concordance_metrics\" [fillcolor=\"#94DDF4\",label=\"somalier_concordance_metrics\"];\n    \"optitype_tsv\" [fillcolor=\"#94DDF4\",label=\"optitype_tsv\"];\n    \"germline_final_vcf\" [fillcolor=\"#94DDF4\",label=\"germline_final_vcf\"];\n    \"strelka_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_filtered_vcf\"];\n    \"small_candidates\" [fillcolor=\"#94DDF4\",label=\"small_candidates\"];\n    \"allele_string\" [fillcolor=\"#94DDF4\",label=\"allele_string\"];\n    \"final_bam\" [fillcolor=\"#94DDF4\",label=\"final_bam\"];\n    \"per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_base_hs_metrics\"];\n    \"transcript_abundance_tsv\" [fillcolor=\"#94DDF4\",label=\"transcript_abundance_tsv\"];\n    \"normal_per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_target_coverage_metrics\"];\n    \"annotated_vcf\" [fillcolor=\"#94DDF4\",label=\"annotated_vcf\"];\n    \"insert_size_histogram\" [fillcolor=\"#94DDF4\",label=\"insert_size_histogram\"];\n    \"normal_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_summary_hs_metrics\"];\n    \"per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"per_target_coverage_metrics\"];\n    \"tumor_verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_verify_bam_id_metrics\"];\n    \"normal_target_coverage\" [fillcolor=\"#94DDF4\",label=\"normal_target_coverage\"];\n    \"diploid_variants\" [fillcolor=\"#94DDF4\",label=\"diploid_variants\"];\n    \"normal_verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_verify_bam_id_metrics\"];\n    \"tumor_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_antitarget_coverage\"];\n    \"fusion_evidence\" [fillcolor=\"#94DDF4\",label=\"fusion_evidence\"];\n    \"summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"summary_hs_metrics\"];\n    \"optitype_plot\" [fillcolor=\"#94DDF4\",label=\"optitype_plot\"];\n    \"per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_target_hs_metrics\"];\n    \"metrics\" [fillcolor=\"#94DDF4\",label=\"metrics\"];\n    \"varscan_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_filtered_vcf\"];\n    \"combined_filtered_epitopes\" [fillcolor=\"#94DDF4\",label=\"combined_filtered_epitopes\"];\n    \"cn_scatter_plot\" [fillcolor=\"#94DDF4\",label=\"cn_scatter_plot\"];\n    \"strelka_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_unfiltered_vcf\"];\n    \"tumor_cram\" [fillcolor=\"#94DDF4\",label=\"tumor_cram\"];\n    \"normal_verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"normal_verify_bam_id_depth\"];\n    \"mutect_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_unfiltered_vcf\"];\n    \"gene_abundance\" [fillcolor=\"#94DDF4\",label=\"gene_abundance\"];\n    \"normal_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_insert_size_metrics\"];\n    \"pindel_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_unfiltered_vcf\"];\n    \"mhc_i_all_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_i_all_epitopes\"];\n    \"chart\" [fillcolor=\"#94DDF4\",label=\"chart\"];\n    \"mhc_i_filtered_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_i_filtered_epitopes\"];\n    \"tumor_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_indel_bam_readcount_tsv\"];\n    \"tumor_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_hs_metrics\"];\n    \"mhc_ii_all_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_ii_all_epitopes\"];\n    \"germline_vep_summary\" [fillcolor=\"#94DDF4\",label=\"germline_vep_summary\"];\n    \"mutect_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_filtered_vcf\"];\n    \"combined_all_epitopes\" [fillcolor=\"#94DDF4\",label=\"combined_all_epitopes\"];\n    \"somatic_vep_summary\" [fillcolor=\"#94DDF4\",label=\"somatic_vep_summary\"];\n    \"annotated_tsv\" [fillcolor=\"#94DDF4\",label=\"annotated_tsv\"];\n    \"normal_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_alignment_summary_metrics\"];\n    \"somalier_concordance_statistics\" [fillcolor=\"#94DDF4\",label=\"somalier_concordance_statistics\"];\n    \"varscan_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_unfiltered_vcf\"];\n    \"tumor_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_alignment_summary_metrics\"];\n    \"mhc_ii_ranked_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_ii_ranked_epitopes\"];\n    \"intervals_target\" [fillcolor=\"#94DDF4\",label=\"intervals_target\"];\n    \"flagstats\" [fillcolor=\"#94DDF4\",label=\"flagstats\"];\n    \"phased_vcf\" [fillcolor=\"#94DDF4\",label=\"phased_vcf\"];\n    \"all_candidates\" [fillcolor=\"#94DDF4\",label=\"all_candidates\"];\n    \"normal_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_indel_bam_readcount_tsv\"];\n    \"limited_vcf\" [fillcolor=\"#94DDF4\",label=\"limited_vcf\"];\n    \"tumor_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_snv_bam_readcount_tsv\"];\n    \"hs_metrics\" [fillcolor=\"#94DDF4\",label=\"hs_metrics\"];\n    \"normal_cram\" [fillcolor=\"#94DDF4\",label=\"normal_cram\"];\n    \"somatic_variants\" [fillcolor=\"#94DDF4\",label=\"somatic_variants\"];\n    \"coding_vcf\" [fillcolor=\"#94DDF4\",label=\"coding_vcf\"];\n    \"verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"verify_bam_id_metrics\"];\n    \"tumor_per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_base_coverage_metrics\"];\n    \"tumor_verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"tumor_verify_bam_id_depth\"];\n    \"tumor_per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_target_coverage_metrics\"];\n    \"tumor_bin_level_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_bin_level_ratios\"];\n    \"normal_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_base_hs_metrics\"];\n    \"cram\" [fillcolor=\"#94DDF4\",label=\"cram\"];\n    \"tumor_only_variants\" [fillcolor=\"#94DDF4\",label=\"tumor_only_variants\"];\n    \"reference_coverage\" [fillcolor=\"#94DDF4\",label=\"reference_coverage\"];\n    \"intervals_antitarget\" [fillcolor=\"#94DDF4\",label=\"intervals_antitarget\"];\n    \"gvcf\" [fillcolor=\"#94DDF4\",label=\"gvcf\"];\n    \"docm_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_filtered_vcf\"];\n    \"tumor_per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_target_hs_metrics\"];\n    \"cn_diagram\" [fillcolor=\"#94DDF4\",label=\"cn_diagram\"];\n    \"tumor_target_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_target_coverage\"];\n    \"normal_per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_target_hs_metrics\"];\n    \"tumor_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_summary_hs_metrics\"];\n    \"stringtie_transcript_gtf\" [fillcolor=\"#94DDF4\",label=\"stringtie_transcript_gtf\"];\n    \"verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"verify_bam_id_depth\"];\n    \"tumor_segmented_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_segmented_ratios\"];\n    \"alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"alignment_summary_metrics\"];\n    \"tumor_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_insert_size_metrics\"];\n    \"mhc_i_ranked_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_i_ranked_epitopes\"];\n    \"transcript_abundance_h5\" [fillcolor=\"#94DDF4\",label=\"transcript_abundance_h5\"];\n  }\n  \"rnaseq\" [label=\"RNA-Seq alignment and transcript/gene abundance workflow\", fillcolor=\"#F3CEA1\"];\n  \"extract_alleles\" [label=\"extract_alleles\"];\n  \"somatic\" [label=\"exome alignment and somatic variant detection\", fillcolor=\"#F3CEA1\"];\n  \"pvacseq\" [label=\"Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs\", fillcolor=\"#F3CEA1\"];\n  \"phase_vcf\" [label=\"phase VCF\", fillcolor=\"#F3CEA1\"];\n  \"germline\" [label=\"exome alignment and germline variant detection, with optitype for HLA typing\", fillcolor=\"#F3CEA1\"];\n  \"reference_index\" -> \"rnaseq\" [label=\"reference_index\"];\n  \"trimming_max_uncalled\" -> \"rnaseq\" [label=\"trimming_max_uncalled\"];\n  \"read_group_fields\" -> \"rnaseq\" [label=\"read_group_fields\"];\n  \"rna_readgroups\" -> \"rnaseq\" [label=\"read_group_id\"];\n  \"rna_bams\" -> \"rnaseq\" [label=\"instrument_data_bams\"];\n  \"refFlat\" -> \"rnaseq\" [label=\"refFlat\"];\n  \"ribosomal_intervals\" -> \"rnaseq\" [label=\"ribosomal_intervals\"];\n  \"reference_annotation\" -> \"rnaseq\" [label=\"reference_annotation\"];\n  \"kallisto_index\" -> \"rnaseq\" [label=\"kallisto_index\"];\n  \"trimming_adapters\" -> \"rnaseq\" [label=\"trimming_adapters\"];\n  \"strand\" -> \"rnaseq\" [label=\"strand\"];\n  \"gene_transcript_lookup_table\" -> \"rnaseq\" [label=\"gene_transcript_lookup_table\"];\n  \"trimming_min_readlength\" -> \"rnaseq\" [label=\"trimming_min_readlength\"];\n  \"trimming_adapter_min_overlap\" -> \"rnaseq\" [label=\"trimming_adapter_min_overlap\"];\n  \"sample_name\" -> \"rnaseq\" [label=\"sample_name\"];\n  \"trimming_adapter_trim_end\" -> \"rnaseq\" [label=\"trimming_adapter_trim_end\"];\n  \"germline\" -> \"extract_alleles\" [label=\"allele_file\"];\n  \"cosmic_vcf\" -> \"somatic\" [label=\"cosmic_vcf\"];\n  \"vep_ensembl_version\" -> \"somatic\" [label=\"vep_ensembl_version\"];\n  \"mills\" -> \"somatic\" [label=\"mills\"];\n  \"normal_bams\" -> \"somatic\" [label=\"normal_bams\"];\n  \"mutect_max_alt_allele_in_normal_fraction\" -> \"somatic\" [label=\"mutect_max_alt_allele_in_normal_fraction\"];\n  \"target_intervals\" -> \"somatic\" [label=\"target_intervals\"];\n  \"qc_minimum_mapping_quality\" -> \"somatic\" [label=\"qc_minimum_mapping_quality\"];\n  \"bait_intervals\" -> \"somatic\" [label=\"bait_intervals\"];\n  \"varscan_strand_filter\" -> \"somatic\" [label=\"varscan_strand_filter\"];\n  \"docm_vcf\" -> \"somatic\" [label=\"docm_vcf\"];\n  \"tumor_bams\" -> \"somatic\" [label=\"tumor_bams\"];\n  \"tumor_readgroups\" -> \"somatic\" [label=\"tumor_readgroups\"];\n  \"variants_to_table_genotype_fields\" -> \"somatic\" [label=\"variants_to_table_genotype_fields\"];\n  \"varscan_min_var_freq\" -> \"somatic\" [label=\"varscan_min_var_freq\"];\n  \"manta_non_wgs\" -> \"somatic\" [label=\"manta_non_wgs\"];\n  \"custom_gnomad_vcf\" -> \"somatic\" [label=\"custom_gnomad_vcf\"];\n  \"annotate_coding_only\" -> \"somatic\" [label=\"annotate_coding_only\"];\n  \"mutect_artifact_detection_mode\" -> \"somatic\" [label=\"mutect_artifact_detection_mode\"];\n  \"manta_call_regions\" -> \"somatic\" [label=\"manta_call_regions\"];\n  \"cle_vcf_filter\" -> \"somatic\" [label=\"cle_vcf_filter\"];\n  \"mutect_max_alt_alleles_in_normal_count\" -> \"somatic\" [label=\"mutect_max_alt_alleles_in_normal_count\"];\n  \"per_base_intervals\" -> \"somatic\" [label=\"per_base_intervals\"];\n  \"vep_cache_dir\" -> \"somatic\" [label=\"vep_cache_dir\"];\n  \"summary_intervals\" -> \"somatic\" [label=\"summary_intervals\"];\n  \"interval_list\" -> \"somatic\" [label=\"interval_list\"];\n  \"normal_readgroups\" -> \"somatic\" [label=\"normal_readgroups\"];\n  \"varscan_min_coverage\" -> \"somatic\" [label=\"varscan_min_coverage\"];\n  \"vep_to_table_fields\" -> \"somatic\" [label=\"vep_to_table_fields\"];\n  \"panel_of_normals_vcf\" -> \"somatic\" [label=\"panel_of_normals_vcf\"];\n  \"custom_clinvar_vcf\" -> \"somatic\" [label=\"custom_clinvar_vcf\"];\n  \"filter_docm_variants\" -> \"somatic\" [label=\"filter_docm_variants\"];\n  \"bqsr_intervals\" -> \"somatic\" [label=\"bqsr_intervals\"];\n  \"qc_minimum_base_quality\" -> \"somatic\" [label=\"qc_minimum_base_quality\"];\n  \"normal_name\" -> \"somatic\" [label=\"normal_name\"];\n  \"picard_metric_accumulation_level\" -> \"somatic\" [label=\"picard_metric_accumulation_level\"];\n  \"vep_ensembl_assembly\" -> \"somatic\" [label=\"vep_ensembl_assembly\"];\n  \"manta_output_contigs\" -> \"somatic\" [label=\"manta_output_contigs\"];\n  \"pindel_insert_size\" -> \"somatic\" [label=\"pindel_insert_size\"];\n  \"vep_ensembl_species\" -> \"somatic\" [label=\"vep_ensembl_species\"];\n  \"synonyms_file\" -> \"somatic\" [label=\"synonyms_file\"];\n  \"reference\" -> \"somatic\" [label=\"reference\"];\n  \"varscan_p_value\" -> \"somatic\" [label=\"varscan_p_value\"];\n  \"per_target_intervals\" -> \"somatic\" [label=\"per_target_intervals\"];\n  \"dbsnp_vcf\" -> \"somatic\" [label=\"dbsnp_vcf\"];\n  \"variants_to_table_fields\" -> \"somatic\" [label=\"variants_to_table_fields\"];\n  \"known_indels\" -> \"somatic\" [label=\"known_indels\"];\n  \"vep_pick\" -> \"somatic\" [label=\"vep_pick\"];\n  \"mutect_scatter_count\" -> \"somatic\" [label=\"mutect_scatter_count\"];\n  \"varscan_max_normal_freq\" -> \"somatic\" [label=\"varscan_max_normal_freq\"];\n  \"omni_vcf\" -> \"somatic\" [label=\"omni_vcf\"];\n  \"somalier_vcf\" -> \"somatic\" [label=\"somalier_vcf\"];\n  \"strelka_cpu_reserved\" -> \"somatic\" [label=\"strelka_cpu_reserved\"];\n  \"tumor_name\" -> \"somatic\" [label=\"tumor_name\"];\n  \"somatic\" -> \"pvacseq\" [label=\"detect_variants_vcf\"];\n  \"variants_to_table_fields\" -> \"pvacseq\" [label=\"variants_to_table_fields\"];\n  \"allele_specific_binding_thresholds\" -> \"pvacseq\" [label=\"allele_specific_binding_thresholds\"];\n  \"rnaseq\" -> \"pvacseq\" [label=\"gene_expression_file\"];\n  \"peptide_sequence_length\" -> \"pvacseq\" [label=\"peptide_sequence_length\"];\n  \"variants_to_table_genotype_fields\" -> \"pvacseq\" [label=\"variants_to_table_genotype_fields\"];\n  \"net_chop_threshold\" -> \"pvacseq\" [label=\"net_chop_threshold\"];\n  \"tdna_vaf\" -> \"pvacseq\" [label=\"tdna_vaf\"];\n  \"phase_vcf\" -> \"pvacseq\" [label=\"phased_proximal_variants_vcf\"];\n  \"normal_vaf\" -> \"pvacseq\" [label=\"normal_vaf\"];\n  \"downstream_sequence_length\" -> \"pvacseq\" [label=\"downstream_sequence_length\"];\n  \"trna_cov\" -> \"pvacseq\" [label=\"trna_cov\"];\n  \"vep_to_table_fields\" -> \"pvacseq\" [label=\"vep_to_table_fields\"];\n  \"rnaseq\" -> \"pvacseq\" [label=\"rnaseq_bam\"];\n  \"minimum_fold_change\" -> \"pvacseq\" [label=\"minimum_fold_change\"];\n  \"prediction_algorithms\" -> \"pvacseq\" [label=\"prediction_algorithms\"];\n  \"default1\" -> \"pvacseq\" [label=\"normal_sample_name\"];\n  \"default1\" [label=\"\\\"NORMAL\\\"\", fillcolor=\"#D5AEFC\"];\n  \"expn_val\" -> \"pvacseq\" [label=\"expn_val\"];\n  \"binding_threshold\" -> \"pvacseq\" [label=\"binding_threshold\"];\n  \"maximum_transcript_support_level\" -> \"pvacseq\" [label=\"maximum_transcript_support_level\"];\n  \"net_chop_method\" -> \"pvacseq\" [label=\"net_chop_method\"];\n  \"rnaseq\" -> \"pvacseq\" [label=\"transcript_expression_file\"];\n  \"trna_vaf\" -> \"pvacseq\" [label=\"trna_vaf\"];\n  \"normal_cov\" -> \"pvacseq\" [label=\"normal_cov\"];\n  \"extract_alleles\" -> \"pvacseq\" [label=\"alleles\"];\n  \"netmhc_stab\" -> \"pvacseq\" [label=\"netmhc_stab\"];\n  \"tdna_cov\" -> \"pvacseq\" [label=\"tdna_cov\"];\n  \"default2\" -> \"pvacseq\" [label=\"sample_name\"];\n  \"default2\" [label=\"\\\"TUMOR\\\"\", fillcolor=\"#D5AEFC\"];\n  \"readcount_minimum_mapping_quality\" -> \"pvacseq\" [label=\"readcount_minimum_mapping_quality\"];\n  \"exclude_nas\" -> \"pvacseq\" [label=\"exclude_nas\"];\n  \"epitope_lengths\" -> \"pvacseq\" [label=\"epitope_lengths\"];\n  \"readcount_minimum_base_quality\" -> \"pvacseq\" [label=\"readcount_minimum_base_quality\"];\n  \"additional_report_columns\" -> \"pvacseq\" [label=\"additional_report_columns\"];\n  \"pvacseq_threads\" -> \"pvacseq\" [label=\"n_threads\"];\n  \"reference\" -> \"pvacseq\" [label=\"reference_fasta\"];\n  \"top_score_metric\" -> \"pvacseq\" [label=\"top_score_metric\"];\n  \"fasta_size\" -> \"pvacseq\" [label=\"fasta_size\"];\n  \"reference\" -> \"phase_vcf\" [label=\"reference\"];\n  \"somatic\" -> \"phase_vcf\" [label=\"somatic_vcf\"];\n  \"somatic\" -> \"phase_vcf\" [label=\"bam\"];\n  \"reference_dict\" -> \"phase_vcf\" [label=\"reference_dict\"];\n  \"germline\" -> \"phase_vcf\" [label=\"germline_vcf\"];\n  \"mills\" -> \"germline\" [label=\"mills\"];\n  \"custom_gnomad_vcf\" -> \"germline\" [label=\"custom_gnomad_vcf\"];\n  \"qc_minimum_base_quality\" -> \"germline\" [label=\"qc_minimum_base_quality\"];\n  \"custom_clinvar_vcf\" -> \"germline\" [label=\"custom_clinvar_vcf\"];\n  \"emit_reference_confidence\" -> \"germline\" [label=\"emit_reference_confidence\"];\n  \"picard_metric_accumulation_level\" -> \"germline\" [label=\"picard_metric_accumulation_level\"];\n  \"vep_ensembl_version\" -> \"germline\" [label=\"vep_ensembl_version\"];\n  \"gatk_haplotypecaller_intervals\" -> \"germline\" [label=\"intervals\"];\n  \"summary_intervals\" -> \"germline\" [label=\"summary_intervals\"];\n  \"gvcf_gq_bands\" -> \"germline\" [label=\"gvcf_gq_bands\"];\n  \"normal_readgroups\" -> \"germline\" [label=\"readgroups\"];\n  \"qc_minimum_mapping_quality\" -> \"germline\" [label=\"qc_minimum_mapping_quality\"];\n  \"per_target_intervals\" -> \"germline\" [label=\"per_target_intervals\"];\n  \"target_intervals\" -> \"germline\" [label=\"target_intervals\"];\n  \"bqsr_intervals\" -> \"germline\" [label=\"bqsr_intervals\"];\n  \"vep_ensembl_assembly\" -> \"germline\" [label=\"vep_ensembl_assembly\"];\n  \"per_base_intervals\" -> \"germline\" [label=\"per_base_intervals\"];\n  \"normal_bams\" -> \"germline\" [label=\"bams\"];\n  \"known_indels\" -> \"germline\" [label=\"known_indels\"];\n  \"omni_vcf\" -> \"germline\" [label=\"omni_vcf\"];\n  \"synonyms_file\" -> \"germline\" [label=\"synonyms_file\"];\n  \"annotate_coding_only\" -> \"germline\" [label=\"annotate_coding_only\"];\n  \"reference\" -> \"germline\" [label=\"reference\"];\n  \"optitype_name\" -> \"germline\" [label=\"optitype_name\"];\n  \"dbsnp_vcf\" -> \"germline\" [label=\"dbsnp_vcf\"];\n  \"vep_ensembl_species\" -> \"germline\" [label=\"vep_ensembl_species\"];\n  \"bait_intervals\" -> \"germline\" [label=\"bait_intervals\"];\n  \"vep_cache_dir\" -> \"germline\" [label=\"vep_cache_dir\"];\n  \"somatic\" -> \"normal_snv_bam_readcount_tsv\";\n  \"somatic\" -> \"normal_flagstats\";\n  \"somatic\" -> \"final_tsv\";\n  \"somatic\" -> \"somatic_final_vcf\";\n  \"somatic\" -> \"normal_hs_metrics\";\n  \"germline\" -> \"insert_size_metrics\";\n  \"pvacseq\" -> \"mhc_ii_filtered_epitopes\";\n  \"somatic\" -> \"pindel_filtered_vcf\";\n  \"somatic\" -> \"normal_antitarget_coverage\";\n  \"somatic\" -> \"normal_mark_duplicates_metrics\";\n  \"somatic\" -> \"final_filtered_vcf\";\n  \"germline\" -> \"mark_duplicates_metrics\";\n  \"germline\" -> \"per_base_coverage_metrics\";\n  \"somatic\" -> \"tumor_per_base_hs_metrics\";\n  \"somatic\" -> \"tumor_flagstats\";\n  \"pvacseq\" -> \"combined_ranked_epitopes\";\n  \"somatic\" -> \"normal_per_base_coverage_metrics\";\n  \"somatic\" -> \"tumor_mark_duplicates_metrics\";\n  \"rnaseq\" -> \"stringtie_gene_expression_tsv\";\n  \"somatic\" -> \"somalier_concordance_metrics\";\n  \"germline\" -> \"optitype_tsv\";\n  \"germline\" -> \"germline_final_vcf\";\n  \"somatic\" -> \"strelka_filtered_vcf\";\n  \"somatic\" -> \"small_candidates\";\n  \"extract_alleles\" -> \"allele_string\";\n  \"rnaseq\" -> \"final_bam\";\n  \"germline\" -> \"per_base_hs_metrics\";\n  \"rnaseq\" -> \"transcript_abundance_tsv\";\n  \"somatic\" -> \"normal_per_target_coverage_metrics\";\n  \"pvacseq\" -> \"annotated_vcf\";\n  \"germline\" -> \"insert_size_histogram\";\n  \"somatic\" -> \"normal_summary_hs_metrics\";\n  \"germline\" -> \"per_target_coverage_metrics\";\n  \"somatic\" -> \"tumor_verify_bam_id_metrics\";\n  \"somatic\" -> \"normal_target_coverage\";\n  \"somatic\" -> \"diploid_variants\";\n  \"somatic\" -> \"normal_verify_bam_id_metrics\";\n  \"somatic\" -> \"tumor_antitarget_coverage\";\n  \"rnaseq\" -> \"fusion_evidence\";\n  \"germline\" -> \"summary_hs_metrics\";\n  \"germline\" -> \"optitype_plot\";\n  \"germline\" -> \"per_target_hs_metrics\";\n  \"rnaseq\" -> \"metrics\";\n  \"somatic\" -> \"varscan_filtered_vcf\";\n  \"pvacseq\" -> \"combined_filtered_epitopes\";\n  \"somatic\" -> \"cn_scatter_plot\";\n  \"somatic\" -> \"strelka_unfiltered_vcf\";\n  \"somatic\" -> \"tumor_cram\";\n  \"somatic\" -> \"normal_verify_bam_id_depth\";\n  \"somatic\" -> \"mutect_unfiltered_vcf\";\n  \"rnaseq\" -> \"gene_abundance\";\n  \"somatic\" -> \"normal_insert_size_metrics\";\n  \"somatic\" -> \"pindel_unfiltered_vcf\";\n  \"pvacseq\" -> \"mhc_i_all_epitopes\";\n  \"rnaseq\" -> \"chart\";\n  \"pvacseq\" -> \"mhc_i_filtered_epitopes\";\n  \"somatic\" -> \"tumor_indel_bam_readcount_tsv\";\n  \"somatic\" -> \"tumor_hs_metrics\";\n  \"pvacseq\" -> \"mhc_ii_all_epitopes\";\n  \"germline\" -> \"germline_vep_summary\";\n  \"somatic\" -> \"mutect_filtered_vcf\";\n  \"pvacseq\" -> \"combined_all_epitopes\";\n  \"somatic\" -> \"somatic_vep_summary\";\n  \"pvacseq\" -> \"annotated_tsv\";\n  \"somatic\" -> \"normal_alignment_summary_metrics\";\n  \"somatic\" -> \"somalier_concordance_statistics\";\n  \"somatic\" -> \"varscan_unfiltered_vcf\";\n  \"somatic\" -> \"tumor_alignment_summary_metrics\";\n  \"pvacseq\" -> \"mhc_ii_ranked_epitopes\";\n  \"somatic\" -> \"intervals_target\";\n  \"germline\" -> \"flagstats\";\n  \"phase_vcf\" -> \"phased_vcf\";\n  \"somatic\" -> \"all_candidates\";\n  \"somatic\" -> \"normal_indel_bam_readcount_tsv\";\n  \"germline\" -> \"limited_vcf\";\n  \"somatic\" -> \"tumor_snv_bam_readcount_tsv\";\n  \"germline\" -> \"hs_metrics\";\n  \"somatic\" -> \"normal_cram\";\n  \"somatic\" -> \"somatic_variants\";\n  \"germline\" -> \"coding_vcf\";\n  \"germline\" -> \"verify_bam_id_metrics\";\n  \"somatic\" -> \"tumor_per_base_coverage_metrics\";\n  \"somatic\" -> \"tumor_verify_bam_id_depth\";\n  \"somatic\" -> \"tumor_per_target_coverage_metrics\";\n  \"somatic\" -> \"tumor_bin_level_ratios\";\n  \"somatic\" -> \"normal_per_base_hs_metrics\";\n  \"germline\" -> \"cram\";\n  \"somatic\" -> \"tumor_only_variants\";\n  \"somatic\" -> \"reference_coverage\";\n  \"somatic\" -> \"intervals_antitarget\";\n  \"germline\" -> \"gvcf\";\n  \"somatic\" -> \"docm_filtered_vcf\";\n  \"somatic\" -> \"tumor_per_target_hs_metrics\";\n  \"somatic\" -> \"cn_diagram\";\n  \"somatic\" -> \"tumor_target_coverage\";\n  \"somatic\" -> \"normal_per_target_hs_metrics\";\n  \"somatic\" -> \"tumor_summary_hs_metrics\";\n  \"rnaseq\" -> \"stringtie_transcript_gtf\";\n  \"germline\" -> \"verify_bam_id_depth\";\n  \"somatic\" -> \"tumor_segmented_ratios\";\n  \"germline\" -> \"alignment_summary_metrics\";\n  \"somatic\" -> \"tumor_insert_size_metrics\";\n  \"pvacseq\" -> \"mhc_i_ranked_epitopes\";\n  \"rnaseq\" -> \"transcript_abundance_h5\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/immuno.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/immuno.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/immuno.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/immuno.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/immuno.cwl","licenseName":"MIT License"}