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\"manta_somatic_variants\" [fillcolor=\"#94DDF4\",label=\"manta_somatic_variants\"];\n    \"alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"alignment_summary_metrics\"];\n    \"bamcoverage_bigwig\" [fillcolor=\"#94DDF4\",label=\"bamcoverage_bigwig\"];\n    \"final_vcf\" [fillcolor=\"#94DDF4\",label=\"final_vcf\"];\n    \"insert_size_histogram\" [fillcolor=\"#94DDF4\",label=\"insert_size_histogram\"];\n    \"limited_vcf\" [fillcolor=\"#94DDF4\",label=\"limited_vcf\"];\n    \"coding_vcf\" [fillcolor=\"#94DDF4\",label=\"coding_vcf\"];\n    \"summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"summary_hs_metrics\"];\n  }\n  \"index_cram\" [label=\"samtools index cram\"];\n  \"extract_freemix\" [label=\"extract_freemix\"];\n  \"bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"detect_variants\" [label=\"exome alignment and germline variant detection\", fillcolor=\"#F3CEA1\"];\n  \"variant_callers\" [label=\"Subworkflow to allow calling different SV callers which require bam files as inputs\", fillcolor=\"#F3CEA1\"];\n  \"alignment_and_qc\" [label=\"wgs alignment with qc\", fillcolor=\"#F3CEA1\"];\n  \"bam_to_cram\" -> \"index_cram\" [label=\"cram\"];\n  \"alignment_and_qc\" -> \"extract_freemix\" [label=\"verify_bam_id_metrics\"];\n  \"reference\" -> \"bam_to_cram\" [label=\"reference\"];\n  \"alignment_and_qc\" -> \"bam_to_cram\" [label=\"bam\"];\n  \"custom_gnomad_vcf\" -> \"detect_variants\" [label=\"custom_gnomad_vcf\"];\n  \"custom_clinvar_vcf\" -> \"detect_variants\" [label=\"custom_clinvar_vcf\"];\n  \"alignment_and_qc\" -> \"detect_variants\" [label=\"bam\"];\n  \"extract_freemix\" -> \"detect_variants\" [label=\"contamination_fraction\"];\n  \"vep_cache_dir\" -> \"detect_variants\" [label=\"vep_cache_dir\"];\n  \"reference\" -> \"detect_variants\" [label=\"reference\"];\n  \"variant_reporting_intervals\" -> \"detect_variants\" [label=\"limit_variant_intervals\"];\n  \"gvcf_gq_bands\" -> \"detect_variants\" [label=\"gvcf_gq_bands\"];\n  \"synonyms_file\" -> \"detect_variants\" [label=\"synonyms_file\"];\n  \"coding_only\" -> \"detect_variants\" [label=\"coding_only\"];\n  \"emit_reference_confidence\" -> \"detect_variants\" [label=\"emit_reference_confidence\"];\n  \"intervals\" -> \"detect_variants\" [label=\"intervals\"];\n  \"manta_call_regions\" -> \"variant_callers\" [label=\"manta_call_regions\"];\n  \"cnvkit_scatter_plot\" -> \"variant_callers\" [label=\"cnvkit_scatter_plot\"];\n  \"manta_output_contigs\" -> \"variant_callers\" [label=\"manta_output_contigs\"];\n  \"smoove_exclude_regions\" -> \"variant_callers\" [label=\"smoove_exclude_regions\"];\n  \"manta_non_wgs\" -> \"variant_callers\" [label=\"manta_non_wgs\"];\n  \"alignment_and_qc\" -> \"variant_callers\" [label=\"bam\"];\n  \"cnvkit_diagram\" -> \"variant_callers\" [label=\"cnvkit_diagram\"];\n  \"cnvkit_method\" -> \"variant_callers\" [label=\"cnvkit_method\"];\n  \"cnvkit_drop_low_coverage\" -> \"variant_callers\" [label=\"cnvkit_drop_low_coverage\"];\n  \"cnvkit_male_reference\" -> \"variant_callers\" [label=\"cnvkit_male_reference\"];\n  \"reference\" -> \"variant_callers\" [label=\"reference\"];\n  \"cnvkit_vcf_name\" -> \"variant_callers\" [label=\"cnvkit_vcf_name\"];\n  \"cnvkit_reference_cnn\" -> \"variant_callers\" [label=\"cnvkit_reference_cnn\"];\n  \"picard_metric_accumulation_level\" -> \"alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"bams\" -> \"alignment_and_qc\" [label=\"bams\"];\n  \"per_target_intervals\" -> \"alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"reference\" -> \"alignment_and_qc\" [label=\"reference\"];\n  \"readgroups\" -> \"alignment_and_qc\" [label=\"readgroups\"];\n  \"qc_intervals\" -> \"alignment_and_qc\" [label=\"intervals\"];\n  \"known_indels\" -> \"alignment_and_qc\" [label=\"known_indels\"];\n  \"omni_vcf\" -> \"alignment_and_qc\" [label=\"omni_vcf\"];\n  \"dbsnp_vcf\" -> \"alignment_and_qc\" [label=\"dbsnp_vcf\"];\n  \"mills\" -> \"alignment_and_qc\" [label=\"mills\"];\n  \"minimum_base_quality\" -> \"alignment_and_qc\" [label=\"minimum_base_quality\"];\n  \"minimum_mapping_quality\" -> \"alignment_and_qc\" [label=\"minimum_mapping_quality\"];\n  \"per_base_intervals\" -> \"alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"summary_intervals\" -> \"alignment_and_qc\" [label=\"summary_intervals\"];\n  \"bqsr_intervals\" -> \"alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"variant_callers\" -> \"manta_diploid_variants\";\n  \"variant_callers\" -> \"tumor_antitarget_coverage\";\n  \"index_cram\" -> \"cram\";\n  \"alignment_and_qc\" -> \"per_target_hs_metrics\";\n  \"variant_callers\" -> \"tumor_bin_level_ratios\";\n  \"variant_callers\" -> \"manta_small_candidates\";\n  \"variant_callers\" -> \"manta_all_candidates\";\n  \"variant_callers\" -> \"manta_tumor_only_variants\";\n  \"alignment_and_qc\" -> \"flagstats\";\n  \"variant_callers\" -> \"cn_scatter_plot\";\n  \"variant_callers\" -> \"smoove_output_variants\";\n  \"alignment_and_qc\" -> \"gc_bias_metrics_chart\";\n  \"detect_variants\" -> \"gvcf\";\n  \"alignment_and_qc\" -> \"per_base_coverage_metrics\";\n  \"alignment_and_qc\" -> \"verify_bam_id_depth\";\n  \"alignment_and_qc\" -> \"wgs_metrics\";\n  \"variant_callers\" -> \"cnvkit_vcf\";\n  \"variant_callers\" -> \"cn_diagram\";\n  \"alignment_and_qc\" -> \"verify_bam_id_metrics\";\n  \"variant_callers\" -> \"tumor_target_coverage\";\n  \"alignment_and_qc\" -> \"gc_bias_metrics_summary\";\n  \"variant_callers\" -> \"tumor_segmented_ratios\";\n  \"alignment_and_qc\" -> \"insert_size_metrics\";\n  \"detect_variants\" -> \"vep_summary\";\n  \"alignment_and_qc\" -> \"gc_bias_metrics\";\n  \"alignment_and_qc\" -> \"per_target_coverage_metrics\";\n  \"alignment_and_qc\" -> \"per_base_hs_metrics\";\n  \"alignment_and_qc\" -> \"mark_duplicates_metrics\";\n  \"variant_callers\" -> \"manta_somatic_variants\";\n  \"alignment_and_qc\" -> \"alignment_summary_metrics\";\n  \"alignment_and_qc\" -> \"bamcoverage_bigwig\";\n  \"detect_variants\" -> \"final_vcf\";\n  \"alignment_and_qc\" -> \"insert_size_histogram\";\n  \"detect_variants\" -> \"limited_vcf\";\n  \"detect_variants\" -> \"coding_vcf\";\n  \"alignment_and_qc\" -> \"summary_hs_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/5c4125344b1b9125ad04d7e768ecc99901570a7a/definitions/pipelines/germline_wgs.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/5c4125344b1b9125ad04d7e768ecc99901570a7a/definitions/pipelines/germline_wgs.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/5c4125344b1b9125ad04d7e768ecc99901570a7a/definitions/pipelines/germline_wgs.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/5c4125344b1b9125ad04d7e768ecc99901570a7a/definitions/pipelines/germline_wgs.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/5c4125344b1b9125ad04d7e768ecc99901570a7a/definitions/pipelines/germline_wgs.cwl","licenseName":"MIT License"}