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workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"omni_vcf\" [fillcolor=\"#94DDF4\",label=\"omni_vcf\"];\n    \"mills\" [fillcolor=\"#94DDF4\",label=\"mills\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"bqsr_intervals\" [fillcolor=\"#94DDF4\",label=\"bqsr_intervals\"];\n    \"summary_intervals\" 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\"limited_vcf\" [fillcolor=\"#94DDF4\",label=\"limited_vcf\"];\n    \"verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"verify_bam_id_depth\"];\n    \"cram\" [fillcolor=\"#94DDF4\",label=\"cram\"];\n    \"insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"insert_size_metrics\"];\n    \"per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_target_hs_metrics\"];\n    \"vep_summary\" [fillcolor=\"#94DDF4\",label=\"vep_summary\"];\n    \"insert_size_histogram\" [fillcolor=\"#94DDF4\",label=\"insert_size_histogram\"];\n    \"flagstats\" [fillcolor=\"#94DDF4\",label=\"flagstats\"];\n    \"gvcf\" [fillcolor=\"#94DDF4\",label=\"gvcf\"];\n    \"hs_metrics\" [fillcolor=\"#94DDF4\",label=\"hs_metrics\"];\n    \"alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"alignment_summary_metrics\"];\n    \"per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_base_hs_metrics\"];\n    \"coding_vcf\" [fillcolor=\"#94DDF4\",label=\"coding_vcf\"];\n    \"verify_bam_id_metrics\" 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\"summary_intervals\" -> \"alignment_and_qc\" [label=\"summary_intervals\"];\n  \"readgroups\" -> \"alignment_and_qc\" [label=\"readgroups\"];\n  \"per_base_intervals\" -> \"alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"bqsr_intervals\" -> \"alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"qc_minimum_mapping_quality\" -> \"alignment_and_qc\" [label=\"qc_minimum_mapping_quality\"];\n  \"picard_metric_accumulation_level\" -> \"alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"qc_minimum_base_quality\" -> \"alignment_and_qc\" [label=\"qc_minimum_base_quality\"];\n  \"bait_intervals\" -> \"alignment_and_qc\" [label=\"bait_intervals\"];\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  \"target_intervals\" -> \"alignment_and_qc\" [label=\"target_intervals\"];\n  \"dbsnp_vcf\" -> \"alignment_and_qc\" 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[label=\"custom_gnomad_vcf\"];\n  \"alignment_and_qc\" -> \"detect_variants\" [label=\"bam\"];\n  \"vep_cache_dir\" -> \"detect_variants\" [label=\"vep_cache_dir\"];\n  \"synonyms_file\" -> \"detect_variants\" [label=\"synonyms_file\"];\n  \"emit_reference_confidence\" -> \"detect_variants\" [label=\"emit_reference_confidence\"];\n  \"vep_ensembl_species\" -> \"detect_variants\" [label=\"vep_ensembl_species\"];\n  \"extract_freemix\" -> \"detect_variants\" [label=\"contamination_fraction\"];\n  \"detect_variants\" -> \"limited_vcf\";\n  \"alignment_and_qc\" -> \"verify_bam_id_depth\";\n  \"index_cram\" -> \"cram\";\n  \"alignment_and_qc\" -> \"insert_size_metrics\";\n  \"alignment_and_qc\" -> \"per_target_hs_metrics\";\n  \"detect_variants\" -> \"vep_summary\";\n  \"alignment_and_qc\" -> \"insert_size_histogram\";\n  \"alignment_and_qc\" -> \"flagstats\";\n  \"detect_variants\" -> \"gvcf\";\n  \"alignment_and_qc\" -> \"hs_metrics\";\n  \"alignment_and_qc\" -> \"alignment_summary_metrics\";\n  \"alignment_and_qc\" -> \"per_base_hs_metrics\";\n  \"detect_variants\" -> \"coding_vcf\";\n  \"alignment_and_qc\" -> \"verify_bam_id_metrics\";\n  \"alignment_and_qc\" -> \"mark_duplicates_metrics\";\n  \"alignment_and_qc\" -> \"per_base_coverage_metrics\";\n  \"alignment_and_qc\" -> \"summary_hs_metrics\";\n  \"alignment_and_qc\" -> \"per_target_coverage_metrics\";\n  \"detect_variants\" -> \"final_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/germline_exome.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/germline_exome.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/germline_exome.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/germline_exome.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9/definitions/pipelines/germline_exome.cwl","licenseName":"MIT License"}