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  \"normal_cov\" [fillcolor=\"#94DDF4\",label=\"normal_cov\"];\n    \"detect_variants_vcf\" [fillcolor=\"#94DDF4\",label=\"detect_variants_vcf\"];\n    \"alleles\" [fillcolor=\"#94DDF4\",label=\"alleles\"];\n    \"transcript_expression_file\" [fillcolor=\"#94DDF4\",label=\"transcript_expression_file\"];\n    \"downstream_sequence_length\" [fillcolor=\"#94DDF4\",label=\"downstream_sequence_length\"];\n    \"expression_tool\" [fillcolor=\"#94DDF4\",label=\"expression_tool\"];\n    \"prediction_algorithms\" [fillcolor=\"#94DDF4\",label=\"prediction_algorithms\"];\n    \"trna_vaf\" [fillcolor=\"#94DDF4\",label=\"trna_vaf\"];\n    \"expn_val\" [fillcolor=\"#94DDF4\",label=\"expn_val\"];\n    \"readcount_minimum_base_quality\" [fillcolor=\"#94DDF4\",label=\"readcount_minimum_base_quality\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"mhc_i_ranked_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_i_ranked_epitopes\"];\n    \"combined_all_epitopes\" [fillcolor=\"#94DDF4\",label=\"combined_all_epitopes\"];\n    \"mhc_ii_filtered_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_ii_filtered_epitopes\"];\n    \"annotated_tsv\" [fillcolor=\"#94DDF4\",label=\"annotated_tsv\"];\n    \"mhc_i_all_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_i_all_epitopes\"];\n    \"combined_ranked_epitopes\" [fillcolor=\"#94DDF4\",label=\"combined_ranked_epitopes\"];\n    \"combined_filtered_epitopes\" [fillcolor=\"#94DDF4\",label=\"combined_filtered_epitopes\"];\n    \"mhc_ii_ranked_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_ii_ranked_epitopes\"];\n    \"mhc_i_filtered_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_i_filtered_epitopes\"];\n    \"mhc_ii_all_epitopes\" [fillcolor=\"#94DDF4\",label=\"mhc_ii_all_epitopes\"];\n    \"annotated_vcf\" [fillcolor=\"#94DDF4\",label=\"annotated_vcf\"];\n  }\n  \"add_tumor_rna_bam_readcount_to_vcf\" [label=\"Add snv and indel bam-readcount files to a vcf\", fillcolor=\"#F3CEA1\"];\n  \"index\" [label=\"vcf index\"];\n  \"variants_to_table\" [label=\"SelectVariants (GATK 3.6)\"];\n  \"add_vep_fields_to_table\" [label=\"add VEP annotation to report\"];\n  \"add_transcript_expression_data_to_vcf\" [label=\"add expression info to vcf\"];\n  \"tumor_rna_bam_readcount\" [label=\"bam_readcount workflow\", fillcolor=\"#F3CEA1\"];\n  \"pvacseq\" [label=\"run pVACseq\"];\n  \"add_gene_expression_data_to_vcf\" [label=\"add expression info to vcf\"];\n  \"sample_name\" -> \"add_tumor_rna_bam_readcount_to_vcf\" [label=\"sample_name\"];\n  \"tumor_rna_bam_readcount\" -> \"add_tumor_rna_bam_readcount_to_vcf\" [label=\"vcf\"];\n  \"tumor_rna_bam_readcount\" -> \"add_tumor_rna_bam_readcount_to_vcf\" [label=\"snv_bam_readcount_tsv\"];\n  \"tumor_rna_bam_readcount\" -> \"add_tumor_rna_bam_readcount_to_vcf\" [label=\"indel_bam_readcount_tsv\"];\n  \"default1\" -> \"add_tumor_rna_bam_readcount_to_vcf\" [label=\"data_type\"];\n  \"default1\" [label=\"\\\"RNA\\\"\", fillcolor=\"#D5AEFC\"];\n  \"add_transcript_expression_data_to_vcf\" -> \"index\" [label=\"vcf\"];\n  \"variants_to_table_genotype_fields\" -> \"variants_to_table\" [label=\"genotype_fields\"];\n  \"reference_fasta\" -> \"variants_to_table\" [label=\"reference\"];\n  \"index\" -> \"variants_to_table\" [label=\"vcf\"];\n  \"variants_to_table_fields\" -> \"variants_to_table\" [label=\"fields\"];\n  \"vep_to_table_fields\" -> \"add_vep_fields_to_table\" [label=\"vep_fields\"];\n  \"variants_to_table\" -> \"add_vep_fields_to_table\" [label=\"tsv\"];\n  \"index\" -> \"add_vep_fields_to_table\" [label=\"vcf\"];\n  \"default2\" -> \"add_transcript_expression_data_to_vcf\" [label=\"data_type\"];\n  \"default2\" [label=\"\\\"transcript\\\"\", fillcolor=\"#D5AEFC\"];\n  \"expression_tool\" -> \"add_transcript_expression_data_to_vcf\" [label=\"expression_tool\"];\n  \"add_gene_expression_data_to_vcf\" -> \"add_transcript_expression_data_to_vcf\" [label=\"vcf\"];\n  \"sample_name\" -> \"add_transcript_expression_data_to_vcf\" [label=\"sample_name\"];\n  \"transcript_expression_file\" -> \"add_transcript_expression_data_to_vcf\" [label=\"expression_file\"];\n  \"reference_fasta\" -> \"tumor_rna_bam_readcount\" [label=\"reference_fasta\"];\n  \"rnaseq_bam\" -> \"tumor_rna_bam_readcount\" [label=\"bam\"];\n  \"readcount_minimum_mapping_quality\" -> \"tumor_rna_bam_readcount\" [label=\"min_mapping_quality\"];\n  \"detect_variants_vcf\" -> \"tumor_rna_bam_readcount\" [label=\"vcf\"];\n  \"sample_name\" -> \"tumor_rna_bam_readcount\" [label=\"sample\"];\n  \"readcount_minimum_base_quality\" -> \"tumor_rna_bam_readcount\" [label=\"min_base_quality\"];\n  \"tdna_cov\" -> \"pvacseq\" [label=\"tdna_cov\"];\n  \"peptide_sequence_length\" -> \"pvacseq\" [label=\"peptide_sequence_length\"];\n  \"normal_vaf\" -> \"pvacseq\" [label=\"normal_vaf\"];\n  \"netmhc_stab\" -> \"pvacseq\" [label=\"netmhc_stab\"];\n  \"additional_report_columns\" -> \"pvacseq\" [label=\"additional_report_columns\"];\n  \"normal_sample_name\" -> \"pvacseq\" [label=\"normal_sample_name\"];\n  \"fasta_size\" -> \"pvacseq\" [label=\"fasta_size\"];\n  \"exclude_nas\" -> \"pvacseq\" [label=\"exclude_nas\"];\n  \"trna_vaf\" -> \"pvacseq\" [label=\"trna_vaf\"];\n  \"expn_val\" -> \"pvacseq\" [label=\"expn_val\"];\n  \"normal_cov\" -> \"pvacseq\" [label=\"normal_cov\"];\n  \"maximum_transcript_support_level\" -> \"pvacseq\" [label=\"maximum_transcript_support_level\"];\n  \"net_chop_method\" -> \"pvacseq\" [label=\"net_chop_method\"];\n  \"phased_proximal_variants_vcf\" -> \"pvacseq\" [label=\"phased_proximal_variants_vcf\"];\n  \"top_score_metric\" -> \"pvacseq\" [label=\"top_score_metric\"];\n  \"minimum_fold_change\" -> \"pvacseq\" [label=\"minimum_fold_change\"];\n  \"trna_cov\" -> \"pvacseq\" [label=\"trna_cov\"];\n  \"epitope_lengths\" -> \"pvacseq\" [label=\"epitope_lengths\"];\n  \"prediction_algorithms\" -> \"pvacseq\" [label=\"prediction_algorithms\"];\n  \"downstream_sequence_length\" -> \"pvacseq\" [label=\"downstream_sequence_length\"];\n  \"sample_name\" -> \"pvacseq\" [label=\"sample_name\"];\n  \"net_chop_threshold\" -> \"pvacseq\" [label=\"net_chop_threshold\"];\n  \"n_threads\" -> \"pvacseq\" [label=\"n_threads\"];\n  \"tdna_vaf\" -> \"pvacseq\" [label=\"tdna_vaf\"];\n  \"index\" -> \"pvacseq\" [label=\"input_vcf\"];\n  \"alleles\" -> \"pvacseq\" [label=\"alleles\"];\n  \"gene_expression_file\" -> \"add_gene_expression_data_to_vcf\" [label=\"expression_file\"];\n  \"sample_name\" -> \"add_gene_expression_data_to_vcf\" [label=\"sample_name\"];\n  \"default3\" -> \"add_gene_expression_data_to_vcf\" [label=\"data_type\"];\n  \"default3\" [label=\"\\\"gene\\\"\", fillcolor=\"#D5AEFC\"];\n  \"add_tumor_rna_bam_readcount_to_vcf\" -> \"add_gene_expression_data_to_vcf\" [label=\"vcf\"];\n  \"expression_tool\" -> \"add_gene_expression_data_to_vcf\" [label=\"expression_tool\"];\n  \"pvacseq\" -> \"mhc_i_ranked_epitopes\";\n  \"pvacseq\" -> \"combined_all_epitopes\";\n  \"pvacseq\" -> \"mhc_ii_filtered_epitopes\";\n  \"add_vep_fields_to_table\" -> \"annotated_tsv\";\n  \"pvacseq\" -> \"mhc_i_all_epitopes\";\n  \"pvacseq\" -> \"combined_ranked_epitopes\";\n  \"pvacseq\" -> \"combined_filtered_epitopes\";\n  \"pvacseq\" -> \"mhc_ii_ranked_epitopes\";\n  \"pvacseq\" -> \"mhc_i_filtered_epitopes\";\n  \"pvacseq\" -> \"mhc_ii_all_epitopes\";\n  \"add_transcript_expression_data_to_vcf\" -> \"annotated_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pvacseq.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pvacseq.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pvacseq.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pvacseq.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pvacseq.cwl","licenseName":"MIT License"}