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[fillcolor=\"#94DDF4\",label=\"annotate_coding_only\"];\n    \"normal_readgroups\" [fillcolor=\"#94DDF4\",label=\"normal_readgroups\"];\n    \"per_base_intervals\" [fillcolor=\"#94DDF4\",label=\"per_base_intervals\"];\n    \"filter_somatic_llr_threshold\" [fillcolor=\"#94DDF4\",label=\"filter_somatic_llr_threshold\"];\n    \"tumor_bams\" [fillcolor=\"#94DDF4\",label=\"tumor_bams\"];\n    \"per_target_intervals\" [fillcolor=\"#94DDF4\",label=\"per_target_intervals\"];\n    \"normal_sample_name\" [fillcolor=\"#94DDF4\",label=\"normal_sample_name\"];\n    \"cle_vcf_filter\" [fillcolor=\"#94DDF4\",label=\"cle_vcf_filter\"];\n    \"varscan_max_normal_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_max_normal_freq\"];\n    \"tumor_name\" [fillcolor=\"#94DDF4\",label=\"tumor_name\"];\n    \"variants_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_fields\"];\n    \"varscan_min_var_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_min_var_freq\"];\n    \"picard_metric_accumulation_level\" [fillcolor=\"#94DDF4\",label=\"picard_metric_accumulation_level\"];\n    \"varscan_strand_filter\" [fillcolor=\"#94DDF4\",label=\"varscan_strand_filter\"];\n    \"target_interval_padding\" [fillcolor=\"#94DDF4\",label=\"target_interval_padding: number of bp flanking each target region in which to allow variant calls\"];\n    \"vep_ensembl_version\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_version\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"strelka_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_unfiltered_vcf\"];\n    \"tumor_cram\" [fillcolor=\"#94DDF4\",label=\"tumor_cram\"];\n    \"final_tsv\" [fillcolor=\"#94DDF4\",label=\"final_tsv\"];\n    \"tumor_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_hs_metrics\"];\n    \"varscan_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_filtered_vcf\"];\n    \"tumor_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_base_hs_metrics\"];\n    \"normal_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_base_hs_metrics\"];\n    \"normal_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_alignment_summary_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    \"varscan_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_unfiltered_vcf\"];\n    \"tumor_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_insert_size_metrics\"];\n    \"tumor_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_snv_bam_readcount_tsv\"];\n    \"pindel_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_filtered_vcf\"];\n    \"normal_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_insert_size_metrics\"];\n    \"tumor_per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_target_hs_metrics\"];\n    \"normal_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_summary_hs_metrics\"];\n    \"normal_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_indel_bam_readcount_tsv\"];\n    \"tumor_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_summary_hs_metrics\"];\n    \"final_vcf\" [fillcolor=\"#94DDF4\",label=\"final_vcf\"];\n    \"tumor_per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_base_coverage_metrics\"];\n    \"normal_flagstats\" [fillcolor=\"#94DDF4\",label=\"normal_flagstats\"];\n    \"tumor_flagstats\" [fillcolor=\"#94DDF4\",label=\"tumor_flagstats\"];\n    \"normal_cram\" [fillcolor=\"#94DDF4\",label=\"normal_cram\"];\n    \"tumor_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_indel_bam_readcount_tsv\"];\n    \"strelka_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_filtered_vcf\"];\n    \"final_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"final_filtered_vcf\"];\n    \"tumor_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_mark_duplicates_metrics\"];\n    \"pindel_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_unfiltered_vcf\"];\n    \"normal_per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_base_coverage_metrics\"];\n    \"normal_per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_target_hs_metrics\"];\n    \"tumor_per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_target_coverage_metrics\"];\n    \"normal_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_mark_duplicates_metrics\"];\n    \"mutect_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_unfiltered_vcf\"];\n    \"normal_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_hs_metrics\"];\n    \"normal_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_snv_bam_readcount_tsv\"];\n    \"vep_summary\" [fillcolor=\"#94DDF4\",label=\"vep_summary\"];\n    \"tumor_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_alignment_summary_metrics\"];\n  }\n  \"pad_target_intervals\" [label=\"expand interval list regions by a given number of basepairs\"];\n  \"normal_index_cram\" [label=\"samtools index cram\"];\n  \"tumor_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"detect_variants\" [label=\"Detect Variants workflow\", fillcolor=\"#F3CEA1\"];\n  \"normal_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"tumor_index_cram\" [label=\"samtools index cram\"];\n  \"normal_alignment_and_qc\" [label=\"exome alignment with qc, no bqsr, no verify_bam_id\", fillcolor=\"#F3CEA1\"];\n  \"tumor_alignment_and_qc\" [label=\"exome alignment with qc, no bqsr, no verify_bam_id\", fillcolor=\"#F3CEA1\"];\n  \"target_interval_padding\" -> \"pad_target_intervals\" [label=\"roi_padding\"];\n  \"target_intervals\" -> \"pad_target_intervals\" [label=\"interval_list\"];\n  \"normal_bam_to_cram\" -> \"normal_index_cram\" [label=\"cram\"];\n  \"reference\" -> \"tumor_bam_to_cram\" [label=\"reference\"];\n  \"tumor_alignment_and_qc\" -> \"tumor_bam_to_cram\" [label=\"bam\"];\n  \"vep_to_table_fields\" -> \"detect_variants\" [label=\"vep_to_table_fields\"];\n  \"default1\" -> \"detect_variants\" [label=\"strelka_exome_mode\"];\n  \"default1\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"strelka_cpu_reserved\" -> \"detect_variants\" [label=\"strelka_cpu_reserved\"];\n  \"synonyms_file\" -> \"detect_variants\" [label=\"synonyms_file\"];\n  \"vep_cache_dir\" -> \"detect_variants\" [label=\"vep_cache_dir\"];\n  \"vep_pick\" -> \"detect_variants\" [label=\"vep_pick\"];\n  \"varscan_p_value\" -> \"detect_variants\" [label=\"varscan_p_value\"];\n  \"varscan_max_normal_freq\" -> \"detect_variants\" [label=\"varscan_max_normal_freq\"];\n  \"annotate_coding_only\" -> \"detect_variants\" [label=\"annotate_coding_only\"];\n  \"varscan_min_coverage\" -> \"detect_variants\" [label=\"varscan_min_coverage\"];\n  \"normal_sample_name\" -> \"detect_variants\" [label=\"normal_sample_name\"];\n  \"vep_ensembl_version\" -> \"detect_variants\" [label=\"vep_ensembl_version\"];\n  \"tumor_sample_name\" -> \"detect_variants\" [label=\"tumor_sample_name\"];\n  \"varscan_strand_filter\" -> \"detect_variants\" [label=\"varscan_strand_filter\"];\n  \"normal_alignment_and_qc\" -> \"detect_variants\" [label=\"normal_bam\"];\n  \"reference\" -> \"detect_variants\" [label=\"reference\"];\n  \"vep_ensembl_species\" -> \"detect_variants\" [label=\"vep_ensembl_species\"];\n  \"filter_somatic_llr_normal_contamination_rate\" -> \"detect_variants\" [label=\"filter_somatic_llr_normal_contamination_rate\"];\n  \"cle_vcf_filter\" -> \"detect_variants\" [label=\"cle_vcf_filter\"];\n  \"scatter_count\" -> \"detect_variants\" [label=\"scatter_count\"];\n  \"varscan_min_var_freq\" -> \"detect_variants\" [label=\"varscan_min_var_freq\"];\n  \"filter_somatic_llr_threshold\" -> \"detect_variants\" [label=\"filter_somatic_llr_threshold\"];\n  \"variants_to_table_genotype_fields\" -> \"detect_variants\" [label=\"variants_to_table_genotype_fields\"];\n  \"pindel_insert_size\" -> \"detect_variants\" [label=\"pindel_insert_size\"];\n  \"variants_to_table_fields\" -> \"detect_variants\" [label=\"variants_to_table_fields\"];\n  \"tumor_alignment_and_qc\" -> \"detect_variants\" [label=\"tumor_bam\"];\n  \"filter_somatic_llr_tumor_purity\" -> \"detect_variants\" [label=\"filter_somatic_llr_tumor_purity\"];\n  \"pad_target_intervals\" -> \"detect_variants\" [label=\"roi_intervals\"];\n  \"vep_ensembl_assembly\" -> \"detect_variants\" [label=\"vep_ensembl_assembly\"];\n  \"reference\" -> \"normal_bam_to_cram\" [label=\"reference\"];\n  \"normal_alignment_and_qc\" -> \"normal_bam_to_cram\" [label=\"bam\"];\n  \"tumor_bam_to_cram\" -> \"tumor_index_cram\" [label=\"cram\"];\n  \"normal_name\" -> \"normal_alignment_and_qc\" [label=\"final_name\"];\n  \"normal_bams\" -> \"normal_alignment_and_qc\" [label=\"bams\"];\n  \"summary_intervals\" -> \"normal_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"reference\" -> \"normal_alignment_and_qc\" [label=\"reference\"];\n  \"normal_readgroups\" -> \"normal_alignment_and_qc\" [label=\"readgroups\"];\n  \"qc_minimum_base_quality\" -> \"normal_alignment_and_qc\" [label=\"qc_minimum_base_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  \"per_base_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"target_intervals\" -> \"normal_alignment_and_qc\" [label=\"target_intervals\"];\n  \"qc_minimum_mapping_quality\" -> \"normal_alignment_and_qc\" [label=\"qc_minimum_mapping_quality\"];\n  \"per_target_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"qc_minimum_mapping_quality\" -> \"tumor_alignment_and_qc\" [label=\"qc_minimum_mapping_quality\"];\n  \"summary_intervals\" -> \"tumor_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"bait_intervals\" -> \"tumor_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"tumor_readgroups\" -> \"tumor_alignment_and_qc\" [label=\"readgroups\"];\n  \"qc_minimum_base_quality\" -> \"tumor_alignment_and_qc\" [label=\"qc_minimum_base_quality\"];\n  \"per_base_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"per_target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"tumor_bams\" -> \"tumor_alignment_and_qc\" [label=\"bams\"];\n  \"target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"target_intervals\"];\n  \"tumor_name\" -> \"tumor_alignment_and_qc\" [label=\"final_name\"];\n  \"reference\" -> \"tumor_alignment_and_qc\" [label=\"reference\"];\n  \"picard_metric_accumulation_level\" -> \"tumor_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"detect_variants\" -> \"strelka_unfiltered_vcf\";\n  \"tumor_index_cram\" -> \"tumor_cram\";\n  \"detect_variants\" -> \"final_tsv\";\n  \"tumor_alignment_and_qc\" -> \"tumor_hs_metrics\";\n  \"detect_variants\" -> \"varscan_filtered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_base_hs_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_per_base_hs_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_alignment_summary_metrics\";\n  \"detect_variants\" -> \"mutect_filtered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_per_target_coverage_metrics\";\n  \"detect_variants\" -> \"varscan_unfiltered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_insert_size_metrics\";\n  \"detect_variants\" -> \"tumor_snv_bam_readcount_tsv\";\n  \"detect_variants\" -> \"pindel_filtered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_insert_size_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_target_hs_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_summary_hs_metrics\";\n  \"detect_variants\" -> \"normal_indel_bam_readcount_tsv\";\n  \"tumor_alignment_and_qc\" -> \"tumor_summary_hs_metrics\";\n  \"detect_variants\" -> \"final_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_base_coverage_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_flagstats\";\n  \"tumor_alignment_and_qc\" -> \"tumor_flagstats\";\n  \"normal_index_cram\" -> \"normal_cram\";\n  \"detect_variants\" -> \"tumor_indel_bam_readcount_tsv\";\n  \"detect_variants\" -> \"strelka_filtered_vcf\";\n  \"detect_variants\" -> \"final_filtered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_mark_duplicates_metrics\";\n  \"detect_variants\" -> \"pindel_unfiltered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_per_base_coverage_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_per_target_hs_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_target_coverage_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_mark_duplicates_metrics\";\n  \"detect_variants\" -> \"mutect_unfiltered_vcf\";\n  \"normal_alignment_and_qc\" -> \"normal_hs_metrics\";\n  \"detect_variants\" -> \"normal_snv_bam_readcount_tsv\";\n  \"detect_variants\" -> \"vep_summary\";\n  \"tumor_alignment_and_qc\" -> \"tumor_alignment_summary_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/b465f0da2806ddb6df481409541d13288ccb40ec/definitions/pipelines/somatic_exome_nonhuman.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/b465f0da2806ddb6df481409541d13288ccb40ec/definitions/pipelines/somatic_exome_nonhuman.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/b465f0da2806ddb6df481409541d13288ccb40ec/definitions/pipelines/somatic_exome_nonhuman.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/b465f0da2806ddb6df481409541d13288ccb40ec/definitions/pipelines/somatic_exome_nonhuman.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/b465f0da2806ddb6df481409541d13288ccb40ec/definitions/pipelines/somatic_exome_nonhuman.cwl","licenseName":"MIT License"}