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\"mutect_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_unfiltered_vcf\"];\n    \"varscan_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_unfiltered_vcf\"];\n    \"normal_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_base_hs_metrics\"];\n    \"mutect_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_filtered_vcf\"];\n    \"normal_per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_target_coverage_metrics\"];\n    \"final_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"final_filtered_vcf\"];\n    \"normal_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_insert_size_metrics\"];\n    \"normal_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_hs_metrics\"];\n    \"normal_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_alignment_summary_metrics\"];\n    \"tumor_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_indel_bam_readcount_tsv\"];\n    \"normal_per_base_coverage_metrics\" 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[fillcolor=\"#94DDF4\",label=\"docm_filtered_vcf\"];\n    \"normal_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_mark_duplicates_metrics\"];\n    \"tumor_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_mark_duplicates_metrics\"];\n    \"tumor_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_base_hs_metrics\"];\n    \"tumor_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_insert_size_metrics\"];\n  }\n  \"normal_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"tumor_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"add_disclaimer_version_to_final_tsv\" [label=\"Insert an arbitrary string at a specific line of a file\"];\n  \"normal_index_cram\" [label=\"samtools index cram\"];\n  \"concordance\" [label=\"Concordance checking between Tumor and Normal BAM\"];\n  \"tumor_alignment_and_qc\" [label=\"exome alignment with qc\", fillcolor=\"#F3CEA1\"];\n  \"detect_variants\" [label=\"Detect Variants workflow\", 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[label=\"vcf\"];\n  \"normal_alignment_and_qc\" -> \"concordance\" [label=\"bam_2\"];\n  \"reference\" -> \"concordance\" [label=\"reference\"];\n  \"tumor_alignment_and_qc\" -> \"concordance\" [label=\"bam_1\"];\n  \"per_base_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"bait_intervals\" -> \"tumor_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"tumor_name\" -> \"tumor_alignment_and_qc\" [label=\"final_name\"];\n  \"picard_metric_accumulation_level\" -> \"tumor_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"dbsnp_vcf\" -> \"tumor_alignment_and_qc\" [label=\"dbsnp_vcf\"];\n  \"reference\" -> \"tumor_alignment_and_qc\" [label=\"reference\"];\n  \"target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"target_intervals\"];\n  \"per_target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"qc_minimum_base_quality\" -> \"tumor_alignment_and_qc\" [label=\"minimum_base_quality\"];\n  \"qc_minimum_mapping_quality\" -> \"tumor_alignment_and_qc\" [label=\"minimum_mapping_quality\"];\n  \"summary_intervals\" -> \"tumor_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"tumor_sequence\" -> \"tumor_alignment_and_qc\" [label=\"sequence\"];\n  \"known_indels\" -> \"tumor_alignment_and_qc\" [label=\"known_indels\"];\n  \"omni_vcf\" -> \"tumor_alignment_and_qc\" [label=\"omni_vcf\"];\n  \"mills\" -> \"tumor_alignment_and_qc\" [label=\"mills\"];\n  \"bqsr_intervals\" -> \"tumor_alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"vep_ensembl_species\" -> \"detect_variants\" [label=\"vep_ensembl_species\"];\n  \"tumor_alignment_and_qc\" -> \"detect_variants\" [label=\"tumor_bam\"];\n  \"mutect_scatter_count\" -> \"detect_variants\" [label=\"mutect_scatter_count\"];\n  \"interval_list\" -> \"detect_variants\" [label=\"interval_list\"];\n  \"strelka_cpu_reserved\" -> \"detect_variants\" [label=\"strelka_cpu_reserved\"];\n  \"filter_docm_variants\" -> \"detect_variants\" [label=\"filter_docm_variants\"];\n  \"annotate_coding_only\" -> \"detect_variants\" [label=\"annotate_coding_only\"];\n  \"vep_pick\" -> \"detect_variants\" [label=\"vep_pick\"];\n  \"default2\" -> \"detect_variants\" [label=\"strelka_exome_mode\"];\n  \"default2\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"synonyms_file\" -> \"detect_variants\" [label=\"synonyms_file\"];\n  \"varscan_max_normal_freq\" -> \"detect_variants\" [label=\"varscan_max_normal_freq\"];\n  \"reference\" -> \"detect_variants\" [label=\"reference\"];\n  \"vep_cache_dir\" -> \"detect_variants\" [label=\"vep_cache_dir\"];\n  \"custom_clinvar_vcf\" -> \"detect_variants\" [label=\"custom_clinvar_vcf\"];\n  \"variants_to_table_genotype_fields\" -> \"detect_variants\" [label=\"variants_to_table_genotype_fields\"];\n  \"varscan_min_coverage\" -> \"detect_variants\" [label=\"varscan_min_coverage\"];\n  \"filter_minimum_depth\" -> \"detect_variants\" [label=\"filter_minimum_depth\"];\n  \"vep_ensembl_assembly\" -> \"detect_variants\" [label=\"vep_ensembl_assembly\"];\n  \"vep_ensembl_version\" -> \"detect_variants\" [label=\"vep_ensembl_version\"];\n  \"custom_gnomad_vcf\" -> \"detect_variants\" [label=\"custom_gnomad_vcf\"];\n  \"cle_vcf_filter\" -> \"detect_variants\" [label=\"cle_vcf_filter\"];\n  \"variants_to_table_fields\" -> \"detect_variants\" [label=\"variants_to_table_fields\"];\n  \"pindel_insert_size\" -> \"detect_variants\" [label=\"pindel_insert_size\"];\n  \"varscan_p_value\" -> \"detect_variants\" [label=\"varscan_p_value\"];\n  \"varscan_min_var_freq\" -> \"detect_variants\" [label=\"varscan_min_var_freq\"];\n  \"varscan_strand_filter\" -> \"detect_variants\" [label=\"varscan_strand_filter\"];\n  \"normal_alignment_and_qc\" -> \"detect_variants\" [label=\"normal_bam\"];\n  \"docm_vcf\" -> \"detect_variants\" [label=\"docm_vcf\"];\n  \"vep_to_table_fields\" -> \"detect_variants\" [label=\"vep_to_table_fields\"];\n  \"tumor_bam_to_cram\" -> \"tumor_index_cram\" [label=\"cram\"];\n  \"bqsr_intervals\" -> \"normal_alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"qc_minimum_mapping_quality\" -> \"normal_alignment_and_qc\" [label=\"minimum_mapping_quality\"];\n  \"picard_metric_accumulation_level\" -> \"normal_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"bait_intervals\" -> \"normal_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"normal_name\" -> \"normal_alignment_and_qc\" [label=\"final_name\"];\n  \"target_intervals\" -> \"normal_alignment_and_qc\" [label=\"target_intervals\"];\n  \"normal_sequence\" -> \"normal_alignment_and_qc\" [label=\"sequence\"];\n  \"mills\" -> \"normal_alignment_and_qc\" [label=\"mills\"];\n  \"per_base_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"per_target_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"omni_vcf\" -> \"normal_alignment_and_qc\" [label=\"omni_vcf\"];\n  \"summary_intervals\" -> \"normal_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"known_indels\" -> \"normal_alignment_and_qc\" [label=\"known_indels\"];\n  \"reference\" -> \"normal_alignment_and_qc\" [label=\"reference\"];\n  \"dbsnp_vcf\" -> \"normal_alignment_and_qc\" [label=\"dbsnp_vcf\"];\n  \"qc_minimum_base_quality\" -> \"normal_alignment_and_qc\" [label=\"minimum_base_quality\"];\n  \"disclaimer_text\" -> \"add_disclaimer_to_final_tsv\" [label=\"some_text\"];\n  \"detect_variants\" -> \"add_disclaimer_to_final_tsv\" [label=\"input_file\"];\n  \"default3\" -> \"add_disclaimer_to_final_tsv\" [label=\"line_number\"];\n  \"default3\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"normal_alignment_and_qc\" -> \"normal_verify_bam_id_depth\";\n  \"tumor_alignment_and_qc\" -> \"tumor_hs_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_flagstats\";\n  \"normal_alignment_and_qc\" -> \"normal_flagstats\";\n  \"detect_variants\" -> \"pindel_filtered_vcf\";\n  \"detect_variants\" -> \"tumor_snv_bam_readcount_tsv\";\n  \"detect_variants\" -> \"pindel_unfiltered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_target_hs_metrics\";\n  \"concordance\" -> \"somalier_concordance_statistics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_base_coverage_metrics\";\n  \"detect_variants\" -> \"final_vcf\";\n  \"detect_variants\" -> \"strelka_filtered_vcf\";\n  \"detect_variants\" -> \"normal_snv_bam_readcount_tsv\";\n  \"detect_variants\" -> \"vep_summary\";\n  \"normal_alignment_and_qc\" -> \"normal_per_target_hs_metrics\";\n  \"detect_variants\" -> \"normal_indel_bam_readcount_tsv\";\n  \"normal_index_cram\" -> \"normal_cram\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_target_coverage_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_verify_bam_id_metrics\";\n  \"detect_variants\" -> \"mutect_unfiltered_vcf\";\n  \"detect_variants\" -> \"varscan_unfiltered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_per_base_hs_metrics\";\n  \"detect_variants\" -> \"mutect_filtered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_per_target_coverage_metrics\";\n  \"detect_variants\" -> \"final_filtered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_insert_size_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_hs_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_alignment_summary_metrics\";\n  \"detect_variants\" -> \"tumor_indel_bam_readcount_tsv\";\n  \"normal_alignment_and_qc\" -> \"normal_per_base_coverage_metrics\";\n  \"detect_variants\" -> \"strelka_unfiltered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_verify_bam_id_metrics\";\n  \"detect_variants\" -> \"varscan_filtered_vcf\";\n  \"add_disclaimer_version_to_final_tsv\" -> \"final_tsv\";\n  \"normal_alignment_and_qc\" -> \"normal_summary_hs_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_verify_bam_id_depth\";\n  \"tumor_index_cram\" -> \"tumor_cram\";\n  \"tumor_alignment_and_qc\" -> \"tumor_alignment_summary_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_summary_hs_metrics\";\n  \"concordance\" -> \"somalier_concordance_metrics\";\n  \"detect_variants\" -> \"docm_filtered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_mark_duplicates_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_mark_duplicates_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_base_hs_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_insert_size_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/efbbe5ed51f6ac583e87a348785c72818a33f56e/definitions/pipelines/somatic_exome_cle.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/efbbe5ed51f6ac583e87a348785c72818a33f56e/definitions/pipelines/somatic_exome_cle.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/efbbe5ed51f6ac583e87a348785c72818a33f56e/definitions/pipelines/somatic_exome_cle.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/efbbe5ed51f6ac583e87a348785c72818a33f56e/definitions/pipelines/somatic_exome_cle.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/efbbe5ed51f6ac583e87a348785c72818a33f56e/definitions/pipelines/somatic_exome_cle.cwl","licenseName":"MIT License"}