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[fillcolor=\"#94DDF4\",label=\"vep_ensembl_species\"];\n    \"sv_filter_paired_count\" [fillcolor=\"#94DDF4\",label=\"sv_filter_paired_count\"];\n    \"intervals\" [fillcolor=\"#94DDF4\",label=\"intervals\"];\n    \"cnvkit_scatter_plot\" [fillcolor=\"#94DDF4\",label=\"cnvkit_scatter_plot\"];\n    \"merge_estimate_sv_distance\" [fillcolor=\"#94DDF4\",label=\"merge_estimate_sv_distance\"];\n    \"sv_filter_alt_abundance_percentage\" [fillcolor=\"#94DDF4\",label=\"sv_filter_alt_abundance_percentage\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"custom_clinvar_vcf\" [fillcolor=\"#94DDF4\",label=\"custom_clinvar_vcf\"];\n    \"cnvkit_reference_cnn\" [fillcolor=\"#94DDF4\",label=\"cnvkit_reference_cnn\"];\n    \"variant_reporting_intervals\" [fillcolor=\"#94DDF4\",label=\"variant_reporting_intervals\"];\n    \"cnvkit_diagram\" [fillcolor=\"#94DDF4\",label=\"cnvkit_diagram\"];\n    \"merge_min_svs\" [fillcolor=\"#94DDF4\",label=\"merge_min_svs\"];\n    \"cnvkit_method\" [fillcolor=\"#94DDF4\",label=\"cnvkit_method\"];\n    \"annotate_coding_only\" [fillcolor=\"#94DDF4\",label=\"annotate_coding_only\"];\n    \"manta_call_regions\" [fillcolor=\"#94DDF4\",label=\"manta_call_regions\"];\n    \"cnvkit_vcf_name\" [fillcolor=\"#94DDF4\",label=\"cnvkit_vcf_name\"];\n    \"cnv_filter_deletion_depth\" [fillcolor=\"#94DDF4\",label=\"cnv_filter_deletion_depth\"];\n    \"merge_min_sv_size\" [fillcolor=\"#94DDF4\",label=\"merge_min_sv_size\"];\n    \"omni_vcf\" [fillcolor=\"#94DDF4\",label=\"omni_vcf\"];\n    \"mills\" [fillcolor=\"#94DDF4\",label=\"mills\"];\n    \"vep_ensembl_assembly\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_assembly\"];\n    \"sequence\" [fillcolor=\"#94DDF4\",label=\"sequence\"];\n    \"variants_to_table_genotype_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_genotype_fields\"];\n    \"bqsr_intervals\" [fillcolor=\"#94DDF4\",label=\"bqsr_intervals\"];\n    \"cnvkit_male_reference\" [fillcolor=\"#94DDF4\",label=\"cnvkit_male_reference\"];\n    \"merge_same_type\" [fillcolor=\"#94DDF4\",label=\"merge_same_type\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"tumor_segmented_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_segmented_ratios\"];\n    \"per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_base_hs_metrics\"];\n    \"bcftools_merged_vcf\" [fillcolor=\"#94DDF4\",label=\"bcftools_merged_vcf\"];\n    \"summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"summary_hs_metrics\"];\n    \"alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"alignment_summary_metrics\"];\n    \"manta_diploid_variants\" [fillcolor=\"#94DDF4\",label=\"manta_diploid_variants\"];\n    \"final_vcf\" [fillcolor=\"#94DDF4\",label=\"final_vcf\"];\n    \"gc_bias_metrics\" [fillcolor=\"#94DDF4\",label=\"gc_bias_metrics\"];\n    \"flagstats\" [fillcolor=\"#94DDF4\",label=\"flagstats\"];\n    \"manta_somatic_variants\" [fillcolor=\"#94DDF4\",label=\"manta_somatic_variants\"];\n    \"survivor_merged_annotated_tsv\" [fillcolor=\"#94DDF4\",label=\"survivor_merged_annotated_tsv\"];\n    \"insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"insert_size_metrics\"];\n    \"cnvkit_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"cnvkit_filtered_vcf\"];\n    \"verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"verify_bam_id_depth\"];\n    \"manta_tumor_only_variants\" [fillcolor=\"#94DDF4\",label=\"manta_tumor_only_variants\"];\n    \"manta_small_candidates\" [fillcolor=\"#94DDF4\",label=\"manta_small_candidates\"];\n    \"gc_bias_metrics_chart\" [fillcolor=\"#94DDF4\",label=\"gc_bias_metrics_chart\"];\n    \"final_tsv\" [fillcolor=\"#94DDF4\",label=\"final_tsv\"];\n    \"cnvnator_root\" [fillcolor=\"#94DDF4\",label=\"cnvnator_root\"];\n    \"mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"mark_duplicates_metrics\"];\n    \"smoove_output_variants\" [fillcolor=\"#94DDF4\",label=\"smoove_output_variants\"];\n    \"manta_all_candidates\" [fillcolor=\"#94DDF4\",label=\"manta_all_candidates\"];\n    \"bcftools_merged_annotated_tsv\" [fillcolor=\"#94DDF4\",label=\"bcftools_merged_annotated_tsv\"];\n    \"coding_vcf\" [fillcolor=\"#94DDF4\",label=\"coding_vcf\"];\n    \"cram\" [fillcolor=\"#94DDF4\",label=\"cram\"];\n    \"gc_bias_metrics_summary\" [fillcolor=\"#94DDF4\",label=\"gc_bias_metrics_summary\"];\n    \"smoove_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"smoove_filtered_vcf\"];\n    \"survivor_merged_vcf\" [fillcolor=\"#94DDF4\",label=\"survivor_merged_vcf\"];\n    \"bcftools_merged_filtered_annotated_tsv\" [fillcolor=\"#94DDF4\",label=\"bcftools_merged_filtered_annotated_tsv\"];\n    \"manta_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"manta_filtered_vcf\"];\n    \"vep_summary\" [fillcolor=\"#94DDF4\",label=\"vep_summary\"];\n    \"cnvnator_vcf\" [fillcolor=\"#94DDF4\",label=\"cnvnator_vcf\"];\n    \"tumor_target_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_target_coverage\"];\n    \"cn_diagram\" [fillcolor=\"#94DDF4\",label=\"cn_diagram\"];\n    \"tumor_bin_level_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_bin_level_ratios\"];\n    \"per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_target_hs_metrics\"];\n    \"per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"per_target_coverage_metrics\"];\n    \"cnvkit_vcf\" [fillcolor=\"#94DDF4\",label=\"cnvkit_vcf\"];\n    \"insert_size_histogram\" [fillcolor=\"#94DDF4\",label=\"insert_size_histogram\"];\n    \"gvcf\" [fillcolor=\"#94DDF4\",label=\"gvcf\"];\n    \"cnvnator_cn_file\" [fillcolor=\"#94DDF4\",label=\"cnvnator_cn_file\"];\n    \"cnvnator_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"cnvnator_filtered_vcf\"];\n    \"tumor_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_antitarget_coverage\"];\n    \"per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"per_base_coverage_metrics\"];\n    \"wgs_metrics\" [fillcolor=\"#94DDF4\",label=\"wgs_metrics\"];\n    \"cn_scatter_plot\" [fillcolor=\"#94DDF4\",label=\"cn_scatter_plot\"];\n    \"limited_vcf\" [fillcolor=\"#94DDF4\",label=\"limited_vcf\"];\n    \"verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"verify_bam_id_metrics\"];\n  }\n  \"bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"extract_freemix\" [label=\"extract_freemix\"];\n  \"alignment_and_qc\" [label=\"wgs alignment with qc\", fillcolor=\"#F3CEA1\"];\n  \"index_cram\" [label=\"samtools index cram\"];\n  \"detect_variants\" [label=\"exome alignment and germline variant detection\", fillcolor=\"#F3CEA1\"];\n  \"sv_detect_variants\" [label=\"Subworkflow to allow calling different SV callers which require bam files as inputs\", fillcolor=\"#F3CEA1\"];\n  \"reference\" -> \"bam_to_cram\" [label=\"reference\"];\n  \"alignment_and_qc\" -> \"bam_to_cram\" [label=\"bam\"];\n  \"alignment_and_qc\" -> \"extract_freemix\" [label=\"verify_bam_id_metrics\"];\n  \"per_target_intervals\" -> \"alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"dbsnp_vcf\" -> \"alignment_and_qc\" [label=\"dbsnp_vcf\"];\n  \"minimum_mapping_quality\" -> \"alignment_and_qc\" [label=\"minimum_mapping_quality\"];\n  \"summary_intervals\" -> \"alignment_and_qc\" [label=\"summary_intervals\"];\n  \"minimum_base_quality\" -> \"alignment_and_qc\" [label=\"minimum_base_quality\"];\n  \"per_base_intervals\" -> \"alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"known_indels\" -> \"alignment_and_qc\" [label=\"known_indels\"];\n  \"qc_intervals\" -> \"alignment_and_qc\" [label=\"intervals\"];\n  \"mills\" -> \"alignment_and_qc\" [label=\"mills\"];\n  \"omni_vcf\" -> \"alignment_and_qc\" [label=\"omni_vcf\"];\n  \"sequence\" -> \"alignment_and_qc\" [label=\"sequence\"];\n  \"picard_metric_accumulation_level\" -> \"alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"bqsr_intervals\" -> \"alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"reference\" -> \"alignment_and_qc\" [label=\"reference\"];\n  \"bam_to_cram\" -> \"index_cram\" [label=\"cram\"];\n  \"extract_freemix\" -> \"detect_variants\" [label=\"contamination_fraction\"];\n  \"emit_reference_confidence\" -> \"detect_variants\" [label=\"emit_reference_confidence\"];\n  \"vep_plugins\" -> \"detect_variants\" [label=\"vep_plugins\"];\n  \"vep_ensembl_version\" -> \"detect_variants\" [label=\"vep_ensembl_version\"];\n  \"alignment_and_qc\" -> \"detect_variants\" [label=\"bam\"];\n  \"custom_gnomad_vcf\" -> \"detect_variants\" [label=\"custom_gnomad_vcf\"];\n  \"vep_ensembl_assembly\" -> \"detect_variants\" [label=\"vep_ensembl_assembly\"];\n  \"reference\" -> \"detect_variants\" [label=\"reference\"];\n  \"intervals\" -> \"detect_variants\" [label=\"intervals\"];\n  \"vep_to_table_fields\" -> \"detect_variants\" [label=\"vep_to_table_fields\"];\n  \"annotate_coding_only\" -> \"detect_variants\" [label=\"annotate_coding_only\"];\n  \"vep_ensembl_species\" -> \"detect_variants\" [label=\"vep_ensembl_species\"];\n  \"variant_reporting_intervals\" -> \"detect_variants\" [label=\"limit_variant_intervals\"];\n  \"custom_clinvar_vcf\" -> \"detect_variants\" [label=\"custom_clinvar_vcf\"];\n  \"vep_cache_dir\" -> \"detect_variants\" [label=\"vep_cache_dir\"];\n  \"synonyms_file\" -> \"detect_variants\" [label=\"synonyms_file\"];\n  \"variants_to_table_fields\" -> \"detect_variants\" [label=\"variants_to_table_fields\"];\n  \"gvcf_gq_bands\" -> \"detect_variants\" [label=\"gvcf_gq_bands\"];\n  \"variants_to_table_genotype_fields\" -> \"detect_variants\" [label=\"variants_to_table_genotype_fields\"];\n  \"cnv_filter_duplication_depth\" -> \"sv_detect_variants\" [label=\"cnv_duplication_depth\"];\n  \"cnvkit_reference_cnn\" -> \"sv_detect_variants\" [label=\"cnvkit_reference_cnn\"];\n  \"detect_variants\" -> \"sv_detect_variants\" [label=\"snps_vcf\"];\n  \"merge_min_svs\" -> \"sv_detect_variants\" [label=\"merge_min_svs\"];\n  \"merge_min_sv_size\" -> \"sv_detect_variants\" [label=\"merge_min_sv_size\"];\n  \"cnvkit_drop_low_coverage\" -> \"sv_detect_variants\" [label=\"cnvkit_drop_low_coverage\"];\n  \"cnvkit_diagram\" -> \"sv_detect_variants\" [label=\"cnvkit_diagram\"];\n  \"cnv_filter_min_size\" -> \"sv_detect_variants\" [label=\"cnv_filter_min_size\"];\n  \"merge_max_distance\" -> \"sv_detect_variants\" [label=\"merge_max_distance\"];\n  \"manta_output_contigs\" -> \"sv_detect_variants\" [label=\"manta_output_contigs\"];\n  \"merge_same_type\" -> \"sv_detect_variants\" [label=\"merge_same_type\"];\n  \"merge_same_strand\" -> \"sv_detect_variants\" [label=\"merge_same_strand\"];\n  \"cnvkit_vcf_name\" -> \"sv_detect_variants\" [label=\"cnvkit_vcf_name\"];\n  \"sv_filter_alt_abundance_percentage\" -> \"sv_detect_variants\" [label=\"sv_alt_abundance_percentage\"];\n  \"smoove_exclude_regions\" -> \"sv_detect_variants\" [label=\"smoove_exclude_regions\"];\n  \"sv_filter_paired_count\" -> \"sv_detect_variants\" [label=\"sv_paired_count\"];\n  \"cnvkit_scatter_plot\" -> \"sv_detect_variants\" [label=\"cnvkit_scatter_plot\"];\n  \"cnvkit_method\" -> \"sv_detect_variants\" [label=\"cnvkit_method\"];\n  \"reference\" -> \"sv_detect_variants\" [label=\"reference\"];\n  \"merge_estimate_sv_distance\" -> \"sv_detect_variants\" [label=\"merge_estimate_sv_distance\"];\n  \"cnvkit_male_reference\" -> \"sv_detect_variants\" [label=\"cnvkit_male_reference\"];\n  \"manta_call_regions\" -> \"sv_detect_variants\" [label=\"manta_call_regions\"];\n  \"sv_filter_split_count\" -> \"sv_detect_variants\" [label=\"sv_split_count\"];\n  \"alignment_and_qc\" -> \"sv_detect_variants\" [label=\"bam\"];\n  \"cnv_filter_deletion_depth\" -> \"sv_detect_variants\" [label=\"cnv_deletion_depth\"];\n  \"vep_ensembl_assembly\" -> \"sv_detect_variants\" [label=\"genome_build\"];\n  \"manta_non_wgs\" -> \"sv_detect_variants\" [label=\"manta_non_wgs\"];\n  \"sv_detect_variants\" -> \"tumor_segmented_ratios\";\n  \"alignment_and_qc\" -> \"per_base_hs_metrics\";\n  \"sv_detect_variants\" -> \"bcftools_merged_vcf\";\n  \"alignment_and_qc\" -> \"summary_hs_metrics\";\n  \"alignment_and_qc\" -> \"alignment_summary_metrics\";\n  \"sv_detect_variants\" -> \"manta_diploid_variants\";\n  \"detect_variants\" -> \"final_vcf\";\n  \"alignment_and_qc\" -> \"gc_bias_metrics\";\n  \"alignment_and_qc\" -> \"flagstats\";\n  \"sv_detect_variants\" -> \"manta_somatic_variants\";\n  \"sv_detect_variants\" -> \"survivor_merged_annotated_tsv\";\n  \"alignment_and_qc\" -> \"insert_size_metrics\";\n  \"sv_detect_variants\" -> \"cnvkit_filtered_vcf\";\n  \"alignment_and_qc\" -> \"verify_bam_id_depth\";\n  \"sv_detect_variants\" -> \"manta_tumor_only_variants\";\n  \"sv_detect_variants\" -> \"manta_small_candidates\";\n  \"alignment_and_qc\" -> \"gc_bias_metrics_chart\";\n  \"detect_variants\" -> \"final_tsv\";\n  \"sv_detect_variants\" -> \"cnvnator_root\";\n  \"alignment_and_qc\" -> \"mark_duplicates_metrics\";\n  \"sv_detect_variants\" -> \"smoove_output_variants\";\n  \"sv_detect_variants\" -> \"manta_all_candidates\";\n  \"sv_detect_variants\" -> \"bcftools_merged_annotated_tsv\";\n  \"detect_variants\" -> \"coding_vcf\";\n  \"index_cram\" -> \"cram\";\n  \"alignment_and_qc\" -> \"gc_bias_metrics_summary\";\n  \"sv_detect_variants\" -> \"smoove_filtered_vcf\";\n  \"sv_detect_variants\" -> \"survivor_merged_vcf\";\n  \"sv_detect_variants\" -> \"bcftools_merged_filtered_annotated_tsv\";\n  \"sv_detect_variants\" -> \"manta_filtered_vcf\";\n  \"detect_variants\" -> \"vep_summary\";\n  \"sv_detect_variants\" -> \"cnvnator_vcf\";\n  \"sv_detect_variants\" -> \"tumor_target_coverage\";\n  \"sv_detect_variants\" -> \"cn_diagram\";\n  \"sv_detect_variants\" -> \"tumor_bin_level_ratios\";\n  \"alignment_and_qc\" -> \"per_target_hs_metrics\";\n  \"alignment_and_qc\" -> \"per_target_coverage_metrics\";\n  \"sv_detect_variants\" -> \"cnvkit_vcf\";\n  \"alignment_and_qc\" -> \"insert_size_histogram\";\n  \"detect_variants\" -> \"gvcf\";\n  \"sv_detect_variants\" -> \"cnvnator_cn_file\";\n  \"sv_detect_variants\" -> \"cnvnator_filtered_vcf\";\n  \"sv_detect_variants\" -> \"tumor_antitarget_coverage\";\n  \"alignment_and_qc\" -> \"per_base_coverage_metrics\";\n  \"alignment_and_qc\" -> \"wgs_metrics\";\n  \"sv_detect_variants\" -> \"cn_scatter_plot\";\n  \"detect_variants\" -> \"limited_vcf\";\n  \"alignment_and_qc\" -> \"verify_bam_id_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/026bba9511561246ad65458f0f55c88cead26fbd/definitions/pipelines/germline_wgs.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/026bba9511561246ad65458f0f55c88cead26fbd/definitions/pipelines/germline_wgs.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/026bba9511561246ad65458f0f55c88cead26fbd/definitions/pipelines/germline_wgs.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/026bba9511561246ad65458f0f55c88cead26fbd/definitions/pipelines/germline_wgs.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/026bba9511561246ad65458f0f55c88cead26fbd/definitions/pipelines/germline_wgs.cwl","licenseName":"MIT License"}