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file\"];\n  \"index_disclaimer_filtered_vcf\" [label=\"vcf index\"];\n  \"index_disclaimer_final_vcf\" [label=\"vcf index\"];\n  \"bam_to_cram\" -> \"index_cram\" [label=\"cram\"];\n  \"omni_vcf\" -> \"alignment_and_qc\" [label=\"omni_vcf\"];\n  \"qc_intervals\" -> \"alignment_and_qc\" [label=\"intervals\"];\n  \"per_target_intervals\" -> \"alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"reference\" -> \"alignment_and_qc\" [label=\"reference\"];\n  \"bqsr_known_sites\" -> \"alignment_and_qc\" [label=\"bqsr_known_sites\"];\n  \"trimming\" -> \"alignment_and_qc\" [label=\"trimming\"];\n  \"minimum_base_quality\" -> \"alignment_and_qc\" [label=\"minimum_base_quality\"];\n  \"sequence\" -> \"alignment_and_qc\" [label=\"sequence\"];\n  \"summary_intervals\" -> \"alignment_and_qc\" [label=\"summary_intervals\"];\n  \"minimum_mapping_quality\" -> \"alignment_and_qc\" [label=\"minimum_mapping_quality\"];\n  \"picard_metric_accumulation_level\" -> \"alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"bqsr_intervals\" -> \"alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"per_base_intervals\" -> \"alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"reference\" -> \"bam_to_cram\" [label=\"reference\"];\n  \"alignment_and_qc\" -> \"bam_to_cram\" [label=\"bam\"];\n  \"cnvkit_scatter_plot\" -> \"sv_detect_variants\" [label=\"cnvkit_scatter_plot\"];\n  \"manta_non_wgs\" -> \"sv_detect_variants\" [label=\"manta_non_wgs\"];\n  \"sv_filter_split_count\" -> \"sv_detect_variants\" [label=\"sv_split_count\"];\n  \"smoove_exclude_regions\" -> \"sv_detect_variants\" [label=\"smoove_exclude_regions\"];\n  \"reference\" -> \"sv_detect_variants\" [label=\"reference\"];\n  \"blocklist_bedpe\" -> \"sv_detect_variants\" [label=\"blocklist_bedpe\"];\n  \"cnv_filter_duplication_depth\" -> \"sv_detect_variants\" [label=\"cnv_duplication_depth\"];\n  \"detect_variants\" -> \"sv_detect_variants\" [label=\"snps_vcf\"];\n  \"cnvkit_drop_low_coverage\" -> \"sv_detect_variants\" [label=\"cnvkit_drop_low_coverage\"];\n  \"merge_min_sv_size\" -> \"sv_detect_variants\" [label=\"merge_min_sv_size\"];\n  \"sv_filter_paired_count\" -> \"sv_detect_variants\" [label=\"sv_paired_count\"];\n  \"cnv_filter_deletion_depth\" -> \"sv_detect_variants\" [label=\"cnv_deletion_depth\"];\n  \"cnv_filter_min_size\" -> \"sv_detect_variants\" [label=\"cnv_filter_min_size\"];\n  \"sv_filter_alt_abundance_percentage\" -> \"sv_detect_variants\" [label=\"sv_alt_abundance_percentage\"];\n  \"alignment_and_qc\" -> \"sv_detect_variants\" [label=\"bam\"];\n  \"merge_same_strand\" -> \"sv_detect_variants\" [label=\"merge_same_strand\"];\n  \"merge_max_distance\" -> \"sv_detect_variants\" [label=\"merge_max_distance\"];\n  \"merge_same_type\" -> \"sv_detect_variants\" [label=\"merge_same_type\"];\n  \"cnvkit_diagram\" -> \"sv_detect_variants\" [label=\"cnvkit_diagram\"];\n  \"manta_output_contigs\" -> \"sv_detect_variants\" [label=\"manta_output_contigs\"];\n  \"merge_min_svs\" -> \"sv_detect_variants\" [label=\"merge_min_svs\"];\n  \"cnvkit_vcf_name\" -> \"sv_detect_variants\" [label=\"cnvkit_vcf_name\"];\n  \"vep_ensembl_assembly\" -> \"sv_detect_variants\" [label=\"genome_build\"];\n  \"cnvkit_male_reference\" -> \"sv_detect_variants\" [label=\"cnvkit_male_reference\"];\n  \"cnvkit_method\" -> \"sv_detect_variants\" [label=\"cnvkit_method\"];\n  \"cnvkit_reference_cnn\" -> \"sv_detect_variants\" [label=\"cnvkit_reference_cnn\"];\n  \"manta_call_regions\" -> \"sv_detect_variants\" [label=\"manta_call_regions\"];\n  \"merge_estimate_sv_distance\" -> \"sv_detect_variants\" [label=\"merge_estimate_sv_distance\"];\n  \"reference\" -> \"detect_variants\" [label=\"reference\"];\n  \"emit_reference_confidence\" -> \"detect_variants\" [label=\"emit_reference_confidence\"];\n  \"synonyms_file\" -> \"detect_variants\" [label=\"synonyms_file\"];\n  \"intervals\" -> \"detect_variants\" [label=\"intervals\"];\n  \"gvcf_gq_bands\" -> \"detect_variants\" [label=\"gvcf_gq_bands\"];\n  \"vep_ensembl_assembly\" -> \"detect_variants\" [label=\"vep_ensembl_assembly\"];\n  \"variant_reporting_intervals\" -> \"detect_variants\" [label=\"limit_variant_intervals\"];\n  \"vep_to_table_fields\" -> \"detect_variants\" [label=\"vep_to_table_fields\"];\n  \"vep_cache_dir\" -> \"detect_variants\" [label=\"vep_cache_dir\"];\n  \"variants_to_table_fields\" -> \"detect_variants\" [label=\"variants_to_table_fields\"];\n  \"vep_custom_annotations\" -> \"detect_variants\" [label=\"vep_custom_annotations\"];\n  \"vep_plugins\" -> \"detect_variants\" [label=\"vep_plugins\"];\n  \"vep_ensembl_species\" -> \"detect_variants\" [label=\"vep_ensembl_species\"];\n  \"extract_freemix\" -> \"detect_variants\" [label=\"contamination_fraction\"];\n  \"vep_ensembl_version\" -> \"detect_variants\" [label=\"vep_ensembl_version\"];\n  \"ploidy\" -> \"detect_variants\" [label=\"ploidy\"];\n  \"annotate_coding_only\" -> \"detect_variants\" [label=\"annotate_coding_only\"];\n  \"variants_to_table_genotype_fields\" -> \"detect_variants\" [label=\"variants_to_table_genotype_fields\"];\n  \"alignment_and_qc\" -> \"detect_variants\" [label=\"bam\"];\n  \"default1\" -> \"add_disclaimer_final_vcf\" [label=\"line_number\"];\n  \"default1\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"disclaimer_text\" -> \"add_disclaimer_final_vcf\" [label=\"some_text\"];\n  \"detect_variants\" -> \"add_disclaimer_final_vcf\" [label=\"output_name\"];\n  \"detect_variants\" -> \"add_disclaimer_final_vcf\" [label=\"input_file\"];\n  \"disclaimer_text\" -> \"add_disclaimer_bcftools_filtered_sv_tsv\" [label=\"some_text\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_bcftools_filtered_sv_tsv\" [label=\"output_name\"];\n  \"default2\" -> \"add_disclaimer_bcftools_filtered_sv_tsv\" [label=\"line_number\"];\n  \"default2\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_bcftools_filtered_sv_tsv\" [label=\"input_file\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_survivor_sv_tsv\" [label=\"input_file\"];\n  \"disclaimer_text\" -> \"add_disclaimer_survivor_sv_tsv\" [label=\"some_text\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_survivor_sv_tsv\" [label=\"output_name\"];\n  \"default3\" -> \"add_disclaimer_survivor_sv_tsv\" [label=\"line_number\"];\n  \"default3\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"default4\" -> \"add_disclaimer_filtered_vcf\" [label=\"line_number\"];\n  \"default4\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"disclaimer_text\" -> \"add_disclaimer_filtered_vcf\" [label=\"some_text\"];\n  \"detect_variants\" -> \"add_disclaimer_filtered_vcf\" [label=\"output_name\"];\n  \"detect_variants\" -> \"add_disclaimer_filtered_vcf\" [label=\"input_file\"];\n  \"detect_variants\" -> \"add_disclaimer_final_tsv\" [label=\"output_name\"];\n  \"disclaimer_text\" -> \"add_disclaimer_final_tsv\" [label=\"some_text\"];\n  \"detect_variants\" -> \"add_disclaimer_final_tsv\" [label=\"input_file\"];\n  \"default5\" -> \"add_disclaimer_final_tsv\" [label=\"line_number\"];\n  \"default5\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_bcftools_sv_vcf\" [label=\"input_file\"];\n  \"disclaimer_text\" -> \"add_disclaimer_bcftools_sv_vcf\" [label=\"some_text\"];\n  \"default6\" -> \"add_disclaimer_bcftools_sv_vcf\" [label=\"line_number\"];\n  \"default6\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_bcftools_sv_vcf\" [label=\"output_name\"];\n  \"disclaimer_text\" -> \"add_disclaimer_filtered_tsv\" [label=\"some_text\"];\n  \"detect_variants\" -> \"add_disclaimer_filtered_tsv\" [label=\"output_name\"];\n  \"default7\" -> \"add_disclaimer_filtered_tsv\" [label=\"line_number\"];\n  \"default7\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"detect_variants\" -> \"add_disclaimer_filtered_tsv\" [label=\"input_file\"];\n  \"alignment_and_qc\" -> \"extract_freemix\" [label=\"verify_bam_id_metrics\"];\n  \"disclaimer_text\" -> \"add_disclaimer_survivor_sv_vcf\" [label=\"some_text\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_survivor_sv_vcf\" [label=\"output_name\"];\n  \"default8\" -> \"add_disclaimer_survivor_sv_vcf\" [label=\"line_number\"];\n  \"default8\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_survivor_sv_vcf\" [label=\"input_file\"];\n  \"default9\" -> \"add_disclaimer_bcftools_sv_tsv\" [label=\"line_number\"];\n  \"default9\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_bcftools_sv_tsv\" [label=\"input_file\"];\n  \"disclaimer_text\" -> \"add_disclaimer_bcftools_sv_tsv\" [label=\"some_text\"];\n  \"sv_detect_variants\" -> \"add_disclaimer_bcftools_sv_tsv\" [label=\"output_name\"];\n  \"add_disclaimer_filtered_vcf\" -> \"index_disclaimer_filtered_vcf\" [label=\"vcf\"];\n  \"add_disclaimer_final_vcf\" -> \"index_disclaimer_final_vcf\" [label=\"vcf\"];\n  \"alignment_and_qc\" -> \"wgs_metrics\";\n  \"sv_detect_variants\" -> \"cnvkit_filtered_vcf\";\n  \"sv_detect_variants\" -> \"cnvnator_cn_file\";\n  \"index_cram\" -> \"cram\";\n  \"alignment_and_qc\" -> \"insert_size_histogram\";\n  \"sv_detect_variants\" -> \"cn_diagram\";\n  \"index_disclaimer_final_vcf\" -> \"final_vcf\";\n  \"sv_detect_variants\" -> \"cn_scatter_plot\";\n  \"sv_detect_variants\" -> \"manta_tumor_only_variants\";\n  \"sv_detect_variants\" -> \"cnvkit_vcf\";\n  \"add_disclaimer_bcftools_sv_vcf\" -> \"bcftools_merged_vcf\";\n  \"sv_detect_variants\" -> \"manta_somatic_variants\";\n  \"detect_variants\" -> \"raw_vcf\";\n  \"sv_detect_variants\" -> \"cnvnator_root\";\n  \"sv_detect_variants\" -> \"manta_small_candidates\";\n  \"alignment_and_qc\" -> \"per_target_hs_metrics\";\n  \"add_disclaimer_bcftools_sv_tsv\" -> \"bcftools_merged_annotated_tsv\";\n  \"sv_detect_variants\" -> \"manta_diploid_variants\";\n  \"detect_variants\" -> \"vep_summary\";\n  \"alignment_and_qc\" -> \"verify_bam_id_depth\";\n  \"alignment_and_qc\" -> \"flagstats\";\n  \"add_disclaimer_survivor_sv_tsv\" -> \"survivor_merged_annotated_tsv\";\n  \"alignment_and_qc\" -> \"gc_bias_metrics_summary\";\n  \"sv_detect_variants\" -> \"manta_filtered_vcf\";\n  \"alignment_and_qc\" -> \"per_target_coverage_metrics\";\n  \"alignment_and_qc\" -> \"gc_bias_metrics_chart\";\n  \"alignment_and_qc\" -> \"insert_size_metrics\";\n  \"sv_detect_variants\" -> \"tumor_target_coverage\";\n  \"alignment_and_qc\" -> \"alignment_summary_metrics\";\n  \"sv_detect_variants\" -> \"tumor_segmented_ratios\";\n  \"sv_detect_variants\" -> \"cnvnator_vcf\";\n  \"sv_detect_variants\" -> \"tumor_bin_level_ratios\";\n  \"add_disclaimer_filtered_tsv\" -> \"filtered_tsv\";\n  \"alignment_and_qc\" -> \"summary_hs_metrics\";\n  \"alignment_and_qc\" -> \"per_base_hs_metrics\";\n  \"alignment_and_qc\" -> \"gc_bias_metrics\";\n  \"add_disclaimer_final_tsv\" -> \"final_tsv\";\n  \"add_disclaimer_bcftools_filtered_sv_tsv\" -> \"bcftools_merged_filtered_annotated_tsv\";\n  \"alignment_and_qc\" -> \"verify_bam_id_metrics\";\n  \"alignment_and_qc\" -> \"per_base_coverage_metrics\";\n  \"sv_detect_variants\" -> \"smoove_filtered_vcf\";\n  \"sv_detect_variants\" -> \"manta_all_candidates\";\n  \"sv_detect_variants\" -> \"cnvnator_filtered_vcf\";\n  \"add_disclaimer_survivor_sv_vcf\" -> \"survivor_merged_vcf\";\n  \"sv_detect_variants\" -> \"smoove_output_variants\";\n  \"index_disclaimer_filtered_vcf\" -> \"filtered_vcf\";\n  \"alignment_and_qc\" -> \"mark_duplicates_metrics\";\n  \"sv_detect_variants\" -> \"tumor_antitarget_coverage\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/germline_wgs.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/germline_wgs.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/germline_wgs.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/germline_wgs.cwl","licenseName":"MIT License"}