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[fillcolor=\"#94DDF4\",label=\"emit_reference_confidence\"];\n    \"germline_coding_only\" [fillcolor=\"#94DDF4\",label=\"germline_coding_only\"];\n    \"annotate_coding_only\" [fillcolor=\"#94DDF4\",label=\"annotate_coding_only\"];\n    \"pindel_insert_size\" [fillcolor=\"#94DDF4\",label=\"pindel_insert_size\"];\n    \"germline_variants_to_table_genotype_fields\" [fillcolor=\"#94DDF4\",label=\"germline_variants_to_table_genotype_fields\"];\n    \"varscan_min_coverage\" [fillcolor=\"#94DDF4\",label=\"varscan_min_coverage\"];\n    \"varscan_strand_filter\" [fillcolor=\"#94DDF4\",label=\"varscan_strand_filter\"];\n    \"docm_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_vcf\"];\n    \"per_target_intervals\" [fillcolor=\"#94DDF4\",label=\"per_target_intervals\"];\n    \"target_intervals\" [fillcolor=\"#94DDF4\",label=\"target_intervals\"];\n    \"somalier_vcf\" [fillcolor=\"#94DDF4\",label=\"somalier_vcf\"];\n    \"filter_minimum_depth\" [fillcolor=\"#94DDF4\",label=\"filter_minimum_depth\"];\n    \"vep_ensembl_assembly\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_assembly\"];\n    \"vep_ensembl_species\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_species\"];\n    \"picard_metric_accumulation_level\" [fillcolor=\"#94DDF4\",label=\"picard_metric_accumulation_level\"];\n    \"tumor_sequence\" [fillcolor=\"#94DDF4\",label=\"tumor_sequence\"];\n    \"cle_vcf_filter\" [fillcolor=\"#94DDF4\",label=\"cle_vcf_filter\"];\n    \"bqsr_intervals\" [fillcolor=\"#94DDF4\",label=\"bqsr_intervals\"];\n    \"variants_to_table_genotype_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_genotype_fields\"];\n    \"qc_minimum_base_quality\" [fillcolor=\"#94DDF4\",label=\"qc_minimum_base_quality\"];\n    \"mutect_scatter_count\" [fillcolor=\"#94DDF4\",label=\"mutect_scatter_count\"];\n    \"varscan_max_normal_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_max_normal_freq\"];\n    \"germline_vep_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"germline_vep_to_table_fields\"];\n    \"interval_list\" [fillcolor=\"#94DDF4\",label=\"interval_list\"];\n    \"pindel_region_file\" [fillcolor=\"#94DDF4\",label=\"pindel_region_file\"];\n    \"variant_reporting_intervals\" [fillcolor=\"#94DDF4\",label=\"variant_reporting_intervals\"];\n    \"filter_docm_variants\" [fillcolor=\"#94DDF4\",label=\"filter_docm_variants\"];\n    \"bait_intervals\" [fillcolor=\"#94DDF4\",label=\"bait_intervals\"];\n    \"germline_tsv_prefix\" [fillcolor=\"#94DDF4\",label=\"germline_tsv_prefix\"];\n    \"tumor_name\" [fillcolor=\"#94DDF4\",label=\"tumor_name\"];\n    \"qc_minimum_mapping_quality\" [fillcolor=\"#94DDF4\",label=\"qc_minimum_mapping_quality\"];\n    \"dbsnp_vcf\" [fillcolor=\"#94DDF4\",label=\"dbsnp_vcf\"];\n    \"disclaimer_version\" [fillcolor=\"#94DDF4\",label=\"disclaimer_version\"];\n    \"followup_sequence\" [fillcolor=\"#94DDF4\",label=\"followup_sequence\"];\n    \"variants_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_fields\"];\n    \"vep_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"vep_to_table_fields\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"full_variant_report\" [fillcolor=\"#94DDF4\",label=\"full_variant_report\"];\n    \"tumor_verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"tumor_verify_bam_id_depth\"];\n    \"followup_cram\" [fillcolor=\"#94DDF4\",label=\"followup_cram\"];\n    \"followup_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"followup_insert_size_metrics\"];\n    \"pindel_region_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_region_vcf\"];\n    \"followup_flagstats\" [fillcolor=\"#94DDF4\",label=\"followup_flagstats\"];\n    \"strelka_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_filtered_vcf\"];\n    \"coverage_stat_report\" [fillcolor=\"#94DDF4\",label=\"coverage_stat_report\"];\n    \"germline_final_tsv\" [fillcolor=\"#94DDF4\",label=\"germline_final_tsv\"];\n    \"normal_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_alignment_summary_metrics\"];\n    \"tumor_vep_summary\" [fillcolor=\"#94DDF4\",label=\"tumor_vep_summary\"];\n    \"strelka_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_unfiltered_vcf\"];\n    \"tumor_final_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_final_tsv\"];\n    \"followup_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"followup_snv_bam_readcount_tsv\"];\n    \"germline_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"germline_filtered_vcf\"];\n    \"tumor_cram\" [fillcolor=\"#94DDF4\",label=\"tumor_cram\"];\n    \"normal_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_insert_size_metrics\"];\n    \"pindel_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_unfiltered_vcf\"];\n    \"normal_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_snv_bam_readcount_tsv\"];\n    \"normal_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_indel_bam_readcount_tsv\"];\n    \"followup_verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"followup_verify_bam_id_depth\"];\n    \"docm_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_filtered_vcf\"];\n    \"tumor_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_summary_hs_metrics\"];\n    \"tumor_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_alignment_summary_metrics\"];\n    \"normal_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_hs_metrics\"];\n    \"mutect_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_unfiltered_vcf\"];\n    \"normal_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_mark_duplicates_metrics\"];\n    \"germline_final_vcf\" [fillcolor=\"#94DDF4\",label=\"germline_final_vcf\"];\n    \"tumor_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_indel_bam_readcount_tsv\"];\n    \"normal_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_summary_hs_metrics\"];\n    \"tumor_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_snv_bam_readcount_tsv\"];\n    \"followup_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"followup_summary_hs_metrics\"];\n    \"varscan_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_filtered_vcf\"];\n    \"normal_cram\" [fillcolor=\"#94DDF4\",label=\"normal_cram\"];\n    \"tumor_final_vcf\" [fillcolor=\"#94DDF4\",label=\"tumor_final_vcf\"];\n    \"followup_verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"followup_verify_bam_id_metrics\"];\n    \"tumor_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_hs_metrics\"];\n    \"mutect_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_filtered_vcf\"];\n    \"normal_verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_verify_bam_id_metrics\"];\n    \"tumor_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_mark_duplicates_metrics\"];\n    \"tumor_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_insert_size_metrics\"];\n    \"pindel_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_filtered_vcf\"];\n    \"somalier_concordance_statistics\" [fillcolor=\"#94DDF4\",label=\"somalier_concordance_statistics\"];\n    \"normal_flagstats\" [fillcolor=\"#94DDF4\",label=\"normal_flagstats\"];\n    \"tumor_flagstats\" [fillcolor=\"#94DDF4\",label=\"tumor_flagstats\"];\n    \"varscan_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_unfiltered_vcf\"];\n    \"alignment_stat_report\" [fillcolor=\"#94DDF4\",label=\"alignment_stat_report\"];\n    \"followup_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"followup_indel_bam_readcount_tsv\"];\n    \"germline_filtered_tsv\" [fillcolor=\"#94DDF4\",label=\"germline_filtered_tsv\"];\n    \"tumor_final_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"tumor_final_filtered_vcf\"];\n    \"followup_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"followup_alignment_summary_metrics\"];\n    \"tumor_verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_verify_bam_id_metrics\"];\n    \"normal_verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"normal_verify_bam_id_depth\"];\n    \"followup_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"followup_mark_duplicates_metrics\"];\n    \"followup_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"followup_hs_metrics\"];\n    \"somalier_concordance_metrics\" [fillcolor=\"#94DDF4\",label=\"somalier_concordance_metrics\"];\n  }\n  \"tumor_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"full_variant_report\" [label=\"cle aml_trio full variants report\"];\n  \"pindel_region\" [label=\"Run pindel on provided region\", fillcolor=\"#F3CEA1\"];\n  \"followup_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"normal_index_cram\" [label=\"samtools index cram\"];\n  \"coverage_stat_report\" [label=\"cle aml_trio hs_metrics coverage_stat report\"];\n  \"tumor_alignment_and_qc\" [label=\"exome alignment with qc\", fillcolor=\"#F3CEA1\"];\n  \"followup_alignment_and_qc\" [label=\"exome alignment with qc\", fillcolor=\"#F3CEA1\"];\n  \"concordance\" [label=\"Concordance checking between Tumor and Normal BAM\"];\n  \"normal_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"germline_detect_variants\" [label=\"exome alignment and germline variant detection\", fillcolor=\"#F3CEA1\"];\n  \"add_disclaimer_to_tumor_final_tsv\" [label=\"Insert an arbitrary string at a specific line of a file\"];\n  \"add_disclaimer_version_to_full_variant_report\" [label=\"Insert an arbitrary string at a specific line of a file\"];\n  \"tumor_index_cram\" [label=\"samtools index cram\"];\n  \"add_disclaimer_to_full_variant_report\" [label=\"Insert an arbitrary string at a specific line of a file\"];\n  \"followup_index_cram\" [label=\"samtools index cram\"];\n  \"add_disclaimer_version_to_tumor_final_tsv\" [label=\"Insert an arbitrary string at a specific line of a file\"];\n  \"followup_bam_readcount\" [label=\"run bam-readcount\"];\n  \"alignment_stat_report\" [label=\"cle aml_trio alignment_stat report\"];\n  \"extract_freemix\" [label=\"extract_freemix\"];\n  \"add_disclaimer_version_to_germline_final_tsv\" [label=\"Insert an arbitrary string at a specific line of a file\"];\n  \"add_disclaimer_to_germline_final_tsv\" [label=\"Insert an arbitrary string at a specific line of a file\"];\n  \"normal_alignment_and_qc\" [label=\"exome alignment with qc\", fillcolor=\"#F3CEA1\"];\n  \"tumor_detect_variants\" [label=\"Detect Variants workflow\", fillcolor=\"#F3CEA1\"];\n  \"reference\" -> \"tumor_bam_to_cram\" [label=\"reference\"];\n  \"tumor_alignment_and_qc\" -> \"tumor_bam_to_cram\" [label=\"bam\"];\n  \"tumor_detect_variants\" -> \"full_variant_report\" [label=\"variant_tsv\"];\n  \"pindel_region\" -> \"full_variant_report\" [label=\"pindel_region_vcf\"];\n  \"followup_bam_readcount\" -> \"full_variant_report\" [label=\"followup_snv_bam_readcount\"];\n  \"followup_bam_readcount\" -> \"full_variant_report\" [label=\"followup_indel_bam_readcount\"];\n  \"reference\" -> \"pindel_region\" [label=\"reference\"];\n  \"tumor_alignment_and_qc\" -> \"pindel_region\" [label=\"tumor_bam\"];\n  \"pindel_region_file\" -> \"pindel_region\" [label=\"region_file\"];\n  \"normal_alignment_and_qc\" -> \"pindel_region\" [label=\"normal_bam\"];\n  \"pindel_insert_size\" -> \"pindel_region\" [label=\"insert_size\"];\n  \"reference\" -> \"followup_bam_to_cram\" [label=\"reference\"];\n  \"followup_alignment_and_qc\" -> \"followup_bam_to_cram\" [label=\"bam\"];\n  \"normal_bam_to_cram\" -> \"normal_index_cram\" [label=\"cram\"];\n  \"followup_alignment_and_qc\" -> \"coverage_stat_report\" [label=\"followup_roi_hs_metrics\"];\n  \"followup_alignment_and_qc\" -> \"coverage_stat_report\" [label=\"followup_summary_hs_metrics\"];\n  \"tumor_alignment_and_qc\" -> \"coverage_stat_report\" [label=\"tumor_summary_hs_metrics\"];\n  \"normal_alignment_and_qc\" -> \"coverage_stat_report\" [label=\"normal_summary_hs_metrics\"];\n  \"normal_alignment_and_qc\" -> \"coverage_stat_report\" [label=\"normal_roi_hs_metrics\"];\n  \"tumor_alignment_and_qc\" -> \"coverage_stat_report\" [label=\"tumor_roi_hs_metrics\"];\n  \"reference\" -> \"tumor_alignment_and_qc\" [label=\"reference\"];\n  \"dbsnp_vcf\" -> \"tumor_alignment_and_qc\" [label=\"dbsnp_vcf\"];\n  \"tumor_name\" -> \"tumor_alignment_and_qc\" [label=\"final_name\"];\n  \"bait_intervals\" -> \"tumor_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"bqsr_intervals\" -> \"tumor_alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"target_intervals\"];\n  \"picard_metric_accumulation_level\" -> \"tumor_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"qc_minimum_base_quality\" -> \"tumor_alignment_and_qc\" [label=\"minimum_base_quality\"];\n  \"tumor_sequence\" -> \"tumor_alignment_and_qc\" [label=\"sequence\"];\n  \"per_base_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"mills\" -> \"tumor_alignment_and_qc\" [label=\"mills\"];\n  \"omni_vcf\" -> \"tumor_alignment_and_qc\" [label=\"omni_vcf\"];\n  \"summary_intervals\" -> \"tumor_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"per_target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"known_indels\" -> \"tumor_alignment_and_qc\" [label=\"known_indels\"];\n  \"qc_minimum_mapping_quality\" -> \"tumor_alignment_and_qc\" [label=\"minimum_mapping_quality\"];\n  \"per_base_intervals\" -> \"followup_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"followup_name\" -> \"followup_alignment_and_qc\" [label=\"final_name\"];\n  \"picard_metric_accumulation_level\" -> \"followup_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"summary_intervals\" -> \"followup_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"per_target_intervals\" -> \"followup_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"followup_sequence\" -> \"followup_alignment_and_qc\" [label=\"sequence\"];\n  \"qc_minimum_base_quality\" -> \"followup_alignment_and_qc\" [label=\"minimum_base_quality\"];\n  \"qc_minimum_mapping_quality\" -> \"followup_alignment_and_qc\" [label=\"minimum_mapping_quality\"];\n  \"known_indels\" -> \"followup_alignment_and_qc\" [label=\"known_indels\"];\n  \"bait_intervals\" -> \"followup_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"bqsr_intervals\" -> \"followup_alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"mills\" -> \"followup_alignment_and_qc\" [label=\"mills\"];\n  \"dbsnp_vcf\" -> \"followup_alignment_and_qc\" [label=\"dbsnp_vcf\"];\n  \"reference\" -> \"followup_alignment_and_qc\" [label=\"reference\"];\n  \"target_intervals\" -> \"followup_alignment_and_qc\" [label=\"target_intervals\"];\n  \"omni_vcf\" -> \"followup_alignment_and_qc\" [label=\"omni_vcf\"];\n  \"tumor_alignment_and_qc\" -> \"concordance\" [label=\"bam_1\"];\n  \"somalier_vcf\" -> \"concordance\" [label=\"vcf\"];\n  \"reference\" -> \"concordance\" [label=\"reference\"];\n  \"followup_alignment_and_qc\" -> \"concordance\" [label=\"bam_3\"];\n  \"normal_alignment_and_qc\" -> \"concordance\" [label=\"bam_2\"];\n  \"reference\" -> \"normal_bam_to_cram\" [label=\"reference\"];\n  \"normal_alignment_and_qc\" -> \"normal_bam_to_cram\" [label=\"bam\"];\n  \"intervals\" -> \"germline_detect_variants\" [label=\"intervals\"];\n  \"synonyms_file\" -> \"germline_detect_variants\" [label=\"synonyms_file\"];\n  \"vep_cache_dir\" -> \"germline_detect_variants\" [label=\"vep_cache_dir\"];\n  \"emit_reference_confidence\" -> \"germline_detect_variants\" [label=\"emit_reference_confidence\"];\n  \"germline_coding_only\" -> \"germline_detect_variants\" [label=\"annotate_coding_only\"];\n  \"germline_variants_to_table_genotype_fields\" -> \"germline_detect_variants\" [label=\"variants_to_table_genotype_fields\"];\n  \"vep_ensembl_assembly\" -> \"germline_detect_variants\" [label=\"vep_ensembl_assembly\"];\n  \"germline_variants_to_table_fields\" -> \"germline_detect_variants\" [label=\"variants_to_table_fields\"];\n  \"normal_alignment_and_qc\" -> \"germline_detect_variants\" [label=\"bam\"];\n  \"germline_vep_to_table_fields\" -> \"germline_detect_variants\" [label=\"vep_to_table_fields\"];\n  \"reference\" -> \"germline_detect_variants\" [label=\"reference\"];\n  \"vep_ensembl_species\" -> \"germline_detect_variants\" [label=\"vep_ensembl_species\"];\n  \"gvcf_gq_bands\" -> \"germline_detect_variants\" [label=\"gvcf_gq_bands\"];\n  \"vep_ensembl_version\" -> \"germline_detect_variants\" [label=\"vep_ensembl_version\"];\n  \"germline_tsv_prefix\" -> \"germline_detect_variants\" [label=\"final_tsv_prefix\"];\n  \"extract_freemix\" -> \"germline_detect_variants\" [label=\"contamination_fraction\"];\n  \"variant_reporting_intervals\" -> \"germline_detect_variants\" [label=\"limit_variant_intervals\"];\n  \"vep_custom_annotations\" -> \"germline_detect_variants\" [label=\"vep_custom_annotations\"];\n  \"default1\" -> \"add_disclaimer_to_tumor_final_tsv\" [label=\"line_number\"];\n  \"default1\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"disclaimer_text\" -> \"add_disclaimer_to_tumor_final_tsv\" [label=\"some_text\"];\n  \"tumor_detect_variants\" -> \"add_disclaimer_to_tumor_final_tsv\" [label=\"input_file\"];\n  \"disclaimer_version\" -> \"add_disclaimer_version_to_full_variant_report\" [label=\"some_text\"];\n  \"default2\" -> \"add_disclaimer_version_to_full_variant_report\" [label=\"line_number\"];\n  \"default2\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"add_disclaimer_to_full_variant_report\" -> \"add_disclaimer_version_to_full_variant_report\" [label=\"input_file\"];\n  \"tumor_bam_to_cram\" -> \"tumor_index_cram\" [label=\"cram\"];\n  \"disclaimer_text\" -> \"add_disclaimer_to_full_variant_report\" [label=\"some_text\"];\n  \"default3\" -> \"add_disclaimer_to_full_variant_report\" [label=\"line_number\"];\n  \"default3\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"full_variant_report\" -> \"add_disclaimer_to_full_variant_report\" [label=\"input_file\"];\n  \"followup_bam_to_cram\" -> \"followup_index_cram\" [label=\"cram\"];\n  \"add_disclaimer_to_tumor_final_tsv\" -> \"add_disclaimer_version_to_tumor_final_tsv\" [label=\"input_file\"];\n  \"default4\" -> \"add_disclaimer_version_to_tumor_final_tsv\" [label=\"line_number\"];\n  \"default4\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"disclaimer_version\" -> \"add_disclaimer_version_to_tumor_final_tsv\" [label=\"some_text\"];\n  \"default5\" -> \"followup_bam_readcount\" [label=\"sample\"];\n  \"default5\" [label=\"\\\"TUMOR\\\"\", fillcolor=\"#D5AEFC\"];\n  \"tumor_detect_variants\" -> \"followup_bam_readcount\" [label=\"vcf\"];\n  \"followup_name\" -> \"followup_bam_readcount\" [label=\"prefix\"];\n  \"followup_alignment_and_qc\" -> \"followup_bam_readcount\" [label=\"bam\"];\n  \"reference\" -> \"followup_bam_readcount\" [label=\"reference_fasta\"];\n  \"normal_alignment_and_qc\" -> \"alignment_stat_report\" [label=\"normal_alignment_summary_metrics\"];\n  \"followup_alignment_and_qc\" -> \"alignment_stat_report\" [label=\"followup_alignment_summary_metrics\"];\n  \"tumor_alignment_and_qc\" -> \"alignment_stat_report\" [label=\"tumor_alignment_summary_metrics\"];\n  \"normal_alignment_and_qc\" -> \"extract_freemix\" [label=\"verify_bam_id_metrics\"];\n  \"default6\" -> \"add_disclaimer_version_to_germline_final_tsv\" [label=\"line_number\"];\n  \"default6\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"add_disclaimer_to_germline_final_tsv\" -> \"add_disclaimer_version_to_germline_final_tsv\" [label=\"input_file\"];\n  \"disclaimer_version\" -> \"add_disclaimer_version_to_germline_final_tsv\" [label=\"some_text\"];\n  \"disclaimer_text\" -> \"add_disclaimer_to_germline_final_tsv\" [label=\"some_text\"];\n  \"germline_detect_variants\" -> \"add_disclaimer_to_germline_final_tsv\" [label=\"input_file\"];\n  \"default7\" -> \"add_disclaimer_to_germline_final_tsv\" [label=\"line_number\"];\n  \"default7\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"normal_sequence\" -> \"normal_alignment_and_qc\" [label=\"sequence\"];\n  \"known_indels\" -> \"normal_alignment_and_qc\" [label=\"known_indels\"];\n  \"normal_name\" -> \"normal_alignment_and_qc\" [label=\"final_name\"];\n  \"summary_intervals\" -> \"normal_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"omni_vcf\" -> \"normal_alignment_and_qc\" [label=\"omni_vcf\"];\n  \"target_intervals\" -> \"normal_alignment_and_qc\" [label=\"target_intervals\"];\n  \"bqsr_intervals\" -> \"normal_alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"mills\" -> \"normal_alignment_and_qc\" [label=\"mills\"];\n  \"bait_intervals\" -> \"normal_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"per_base_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"qc_minimum_mapping_quality\" -> \"normal_alignment_and_qc\" [label=\"minimum_mapping_quality\"];\n  \"dbsnp_vcf\" -> \"normal_alignment_and_qc\" [label=\"dbsnp_vcf\"];\n  \"per_target_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"picard_metric_accumulation_level\" -> \"normal_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"reference\" -> \"normal_alignment_and_qc\" [label=\"reference\"];\n  \"qc_minimum_base_quality\" -> \"normal_alignment_and_qc\" [label=\"minimum_base_quality\"];\n  \"vep_custom_annotations\" -> \"tumor_detect_variants\" [label=\"vep_custom_annotations\"];\n  \"varscan_p_value\" -> \"tumor_detect_variants\" [label=\"varscan_p_value\"];\n  \"tumor_alignment_and_qc\" -> \"tumor_detect_variants\" [label=\"tumor_bam\"];\n  \"pindel_insert_size\" -> \"tumor_detect_variants\" [label=\"pindel_insert_size\"];\n  \"varscan_min_coverage\" -> \"tumor_detect_variants\" [label=\"varscan_min_coverage\"];\n  \"docm_vcf\" -> \"tumor_detect_variants\" [label=\"docm_vcf\"];\n  \"filter_minimum_depth\" -> \"tumor_detect_variants\" [label=\"filter_minimum_depth\"];\n  \"vep_ensembl_assembly\" -> \"tumor_detect_variants\" [label=\"vep_ensembl_assembly\"];\n  \"vep_ensembl_species\" -> \"tumor_detect_variants\" [label=\"vep_ensembl_species\"];\n  \"cle_vcf_filter\" -> \"tumor_detect_variants\" [label=\"cle_vcf_filter\"];\n  \"variants_to_table_genotype_fields\" -> \"tumor_detect_variants\" [label=\"variants_to_table_genotype_fields\"];\n  \"reference\" -> \"tumor_detect_variants\" [label=\"reference\"];\n  \"synonyms_file\" -> \"tumor_detect_variants\" [label=\"synonyms_file\"];\n  \"vep_cache_dir\" -> \"tumor_detect_variants\" [label=\"vep_cache_dir\"];\n  \"interval_list\" -> \"tumor_detect_variants\" [label=\"interval_list\"];\n  \"vep_pick\" -> \"tumor_detect_variants\" [label=\"vep_pick\"];\n  \"varscan_max_normal_freq\" -> \"tumor_detect_variants\" [label=\"varscan_max_normal_freq\"];\n  \"varscan_min_var_freq\" -> \"tumor_detect_variants\" [label=\"varscan_min_var_freq\"];\n  \"vep_ensembl_version\" -> \"tumor_detect_variants\" [label=\"vep_ensembl_version\"];\n  \"normal_alignment_and_qc\" -> \"tumor_detect_variants\" [label=\"normal_bam\"];\n  \"mutect_scatter_count\" -> \"tumor_detect_variants\" [label=\"mutect_scatter_count\"];\n  \"varscan_strand_filter\" -> \"tumor_detect_variants\" [label=\"varscan_strand_filter\"];\n  \"vep_to_table_fields\" -> \"tumor_detect_variants\" [label=\"vep_to_table_fields\"];\n  \"filter_docm_variants\" -> \"tumor_detect_variants\" [label=\"filter_docm_variants\"];\n  \"variants_to_table_fields\" -> \"tumor_detect_variants\" [label=\"variants_to_table_fields\"];\n  \"annotate_coding_only\" -> \"tumor_detect_variants\" [label=\"annotate_coding_only\"];\n  \"strelka_cpu_reserved\" -> \"tumor_detect_variants\" [label=\"strelka_cpu_reserved\"];\n  \"default8\" -> \"tumor_detect_variants\" [label=\"strelka_exome_mode\"];\n  \"default8\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"add_disclaimer_version_to_full_variant_report\" -> \"full_variant_report\";\n  \"tumor_alignment_and_qc\" -> \"tumor_verify_bam_id_depth\";\n  \"followup_index_cram\" -> \"followup_cram\";\n  \"followup_alignment_and_qc\" -> \"followup_insert_size_metrics\";\n  \"pindel_region\" -> \"pindel_region_vcf\";\n  \"followup_alignment_and_qc\" -> \"followup_flagstats\";\n  \"tumor_detect_variants\" -> \"strelka_filtered_vcf\";\n  \"coverage_stat_report\" -> \"coverage_stat_report\";\n  \"add_disclaimer_version_to_germline_final_tsv\" -> \"germline_final_tsv\";\n  \"normal_alignment_and_qc\" -> \"normal_alignment_summary_metrics\";\n  \"tumor_detect_variants\" -> \"tumor_vep_summary\";\n  \"tumor_detect_variants\" -> \"strelka_unfiltered_vcf\";\n  \"add_disclaimer_version_to_tumor_final_tsv\" -> \"tumor_final_tsv\";\n  \"followup_bam_readcount\" -> \"followup_snv_bam_readcount_tsv\";\n  \"germline_detect_variants\" -> \"germline_filtered_vcf\";\n  \"tumor_index_cram\" -> \"tumor_cram\";\n  \"normal_alignment_and_qc\" -> \"normal_insert_size_metrics\";\n  \"tumor_detect_variants\" -> \"pindel_unfiltered_vcf\";\n  \"tumor_detect_variants\" -> \"normal_snv_bam_readcount_tsv\";\n  \"tumor_detect_variants\" -> \"normal_indel_bam_readcount_tsv\";\n  \"followup_alignment_and_qc\" -> \"followup_verify_bam_id_depth\";\n  \"tumor_detect_variants\" -> \"docm_filtered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_summary_hs_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_alignment_summary_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_hs_metrics\";\n  \"tumor_detect_variants\" -> \"mutect_unfiltered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_mark_duplicates_metrics\";\n  \"germline_detect_variants\" -> \"germline_final_vcf\";\n  \"tumor_detect_variants\" -> \"tumor_indel_bam_readcount_tsv\";\n  \"normal_alignment_and_qc\" -> \"normal_summary_hs_metrics\";\n  \"tumor_detect_variants\" -> \"tumor_snv_bam_readcount_tsv\";\n  \"followup_alignment_and_qc\" -> \"followup_summary_hs_metrics\";\n  \"tumor_detect_variants\" -> \"varscan_filtered_vcf\";\n  \"normal_index_cram\" -> \"normal_cram\";\n  \"tumor_detect_variants\" -> \"tumor_final_vcf\";\n  \"followup_alignment_and_qc\" -> \"followup_verify_bam_id_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_hs_metrics\";\n  \"tumor_detect_variants\" -> \"mutect_filtered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_verify_bam_id_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_mark_duplicates_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_insert_size_metrics\";\n  \"tumor_detect_variants\" -> \"pindel_filtered_vcf\";\n  \"concordance\" -> \"somalier_concordance_statistics\";\n  \"normal_alignment_and_qc\" -> \"normal_flagstats\";\n  \"tumor_alignment_and_qc\" -> \"tumor_flagstats\";\n  \"tumor_detect_variants\" -> \"varscan_unfiltered_vcf\";\n  \"alignment_stat_report\" -> \"alignment_stat_report\";\n  \"followup_bam_readcount\" -> \"followup_indel_bam_readcount_tsv\";\n  \"germline_detect_variants\" -> \"germline_filtered_tsv\";\n  \"tumor_detect_variants\" -> \"tumor_final_filtered_vcf\";\n  \"followup_alignment_and_qc\" -> \"followup_alignment_summary_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_verify_bam_id_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_verify_bam_id_depth\";\n  \"followup_alignment_and_qc\" -> \"followup_mark_duplicates_metrics\";\n  \"followup_alignment_and_qc\" -> \"followup_hs_metrics\";\n  \"concordance\" -> \"somalier_concordance_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/aml_trio_cle.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/aml_trio_cle.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/aml_trio_cle.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/aml_trio_cle.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/aml_trio_cle.cwl","licenseName":"MIT License"}