{"@id":"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"93656ed6582073e434eab168c610625a835dce37","path":"definitions/pipelines/somatic_exome_gathered.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl","url":"https://github.com/genome/analysis-workflows/blob/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl"},"retrievedOn":"2026-09-21T15:18:12.980+00:00","lastCommit":"93656ed6582073e434eab168c610625a835dce37","label":"gathered exome alignment and somatic variant detection","inputs":{"docm_vcf":{"doc":"Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)","type":"File"},"omni_vcf":{"type":"File"},"vep_pick":{},"reference":{"type":"File"},"output_dir":{"type":"String"},"somalier_vcf":{"type":"File"},"scatter_count":{"doc":"scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs","type":"Integer"},"synonyms_file":{"type":"File (Optional)"},"vep_cache_dir":{"type":"Directory"},"bait_intervals":{"type":"File"},"bqsr_intervals":{"type":"String[]"},"cle_vcf_filter":{"type":"Boolean"},"tumor_sequence":{"label":"tumor_sequence: MT sequencing data and readgroup information","doc":"tumor_sequence represents the sequencing data for the MT sample as either FASTQs or BAMs with\naccompanying readgroup information. Note that in the @RG field ID and SM are required.\n","type":"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/sequence_data.yml#sequence_data[]"},"hgvs_annotation":{"type":"Boolean (Optional)"},"normal_sequence":{"label":"normal_sequence: WT sequencing data and readgroup information","doc":"normal_sequence represents the sequencing data for the WT sample as either FASTQs or BAMs with\naccompanying readgroup information. Note that in the @RG field ID and SM are required.\n","type":"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/sequence_data.yml#sequence_data[]"},"tumor_cram_name":{"type":"String (Optional)"},"varscan_p_value":{"type":"Float (Optional)"},"bqsr_known_sites":{"doc":"One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.","type":"File[]"},"normal_cram_name":{"type":"String (Optional)"},"target_intervals":{"label":"target_intervals: interval_list file of targets used in the sequencing experiment","doc":"target_intervals is an interval_list corresponding to the targets for the capture reagent.\nBed files with this information can be converted to interval_lists with Picard BedToIntervalList.\nIn general for a WES exome reagent bait_intervals and target_intervals are the same.\n","type":"File"},"summary_intervals":{"type":"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/labelled_file.yml#labelled_file[]"},"tumor_sample_name":{"type":"String"},"normal_sample_name":{"type":"String"},"per_base_intervals":{"type":"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/labelled_file.yml#labelled_file[]"},"pindel_insert_size":{"type":"Integer"},"validated_variants":{"doc":"An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF","type":"File (Optional)"},"vep_ensembl_species":{"doc":"ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus","type":"String"},"vep_ensembl_version":{"doc":"ensembl version - Must be present in the cache directory. Example: 95","type":"String"},"vep_to_table_fields":{"type":"String[]"},"annotate_coding_only":{"type":"Boolean (Optional)"},"filter_docm_variants":{"doc":"Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls","type":"Boolean (Optional)"},"per_target_intervals":{"type":"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/labelled_file.yml#labelled_file[]"},"strelka_cpu_reserved":{"type":"Integer (Optional)"},"varscan_min_coverage":{"type":"Integer (Optional)"},"varscan_min_var_freq":{"type":"Float (Optional)"},"vep_ensembl_assembly":{"doc":"genome assembly to use in vep. Examples: GRCh38 or GRCm38","type":"String"},"varscan_strand_filter":{"type":"Integer (Optional)"},"vep_custom_annotations":{"doc":"custom type, check types directory for input format","type":"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[]"},"qc_minimum_base_quality":{"type":"Integer (Optional)"},"target_interval_padding":{"label":"target_interval_padding","doc":"The effective coverage of capture products generally extends out beyond the actual regions\ntargeted. This parameter allows variants to be called in these wingspan regions, extending\nthis many base pairs from each side of the target regions.\n","type":"Integer"},"varscan_max_normal_freq":{"type":"Float (Optional)"},"variants_to_table_fields":{"type":"String[]"},"qc_minimum_mapping_quality":{"type":"Integer (Optional)"},"filter_somatic_llr_threshold":{"doc":"Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants.  Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure.","type":"Float"},"mutect_artifact_detection_mode":{"type":"Boolean"},"filter_somatic_llr_tumor_purity":{"doc":"Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%).  Range is 0 to 1","type":"Float"},"picard_metric_accumulation_level":{"type":"String"},"variants_to_table_genotype_fields":{"type":"String[]"},"mutect_max_alt_alleles_in_normal_count":{"type":"Integer (Optional)"},"mutect_max_alt_allele_in_normal_fraction":{"type":"Float (Optional)"},"filter_somatic_llr_normal_contamination_rate":{"doc":"Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1","type":"Float"}},"outputs":{"final_outputs":{"type":"String[]"}},"steps":{"gatherer":{"run":"../tools/gatherer.cwl","runType":"COMMANDLINETOOL","sources":{"gatherer":{"sourceIDs":["output_dir"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#gatherer/all_files":{"sourceIDs":["somatic_exome"]}}},"somatic_exome":{"label":"somatic_exome: exome alignment and somatic variant detection","doc":"somatic_exome is designed to perform processing of mutant/wildtype H.sapiens\nexome sequencing data. It features BQSR corrected alignments, 4 caller variant\ndetection, and vep style annotations. Structural variants are detected via\nmanta and cnvkit. In addition QC metrics are run, including\nsomalier concordance metrics.\n\nexample input file = analysis_workflows/example_data/somatic_exome.yaml\n","run":"somatic_exome.cwl","runType":"WORKFLOW","sources":{"somatic_exome":{"sourceIDs":["qc_minimum_base_quality"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/docm_vcf":{"sourceIDs":["docm_vcf"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/omni_vcf":{"sourceIDs":["omni_vcf"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/vep_pick":{"sourceIDs":["vep_pick"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/somalier_vcf":{"sourceIDs":["somalier_vcf"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/scatter_count":{"sourceIDs":["scatter_count"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/synonyms_file":{"sourceIDs":["synonyms_file"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/vep_cache_dir":{"sourceIDs":["vep_cache_dir"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/bait_intervals":{"sourceIDs":["bait_intervals"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/bqsr_intervals":{"sourceIDs":["bqsr_intervals"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/cle_vcf_filter":{"sourceIDs":["cle_vcf_filter"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/tumor_sequence":{"sourceIDs":["tumor_sequence"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/hgvs_annotation":{"sourceIDs":["hgvs_annotation"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/normal_sequence":{"sourceIDs":["normal_sequence"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/tumor_cram_name":{"sourceIDs":["tumor_cram_name"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/varscan_p_value":{"sourceIDs":["varscan_p_value"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/bqsr_known_sites":{"sourceIDs":["bqsr_known_sites"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/normal_cram_name":{"sourceIDs":["normal_cram_name"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/target_intervals":{"sourceIDs":["target_intervals"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/summary_intervals":{"sourceIDs":["summary_intervals"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/tumor_sample_name":{"sourceIDs":["tumor_sample_name"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/normal_sample_name":{"sourceIDs":["normal_sample_name"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/per_base_intervals":{"sourceIDs":["per_base_intervals"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/pindel_insert_size":{"sourceIDs":["pindel_insert_size"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/validated_variants":{"sourceIDs":["validated_variants"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/vep_ensembl_species":{"sourceIDs":["vep_ensembl_species"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/vep_ensembl_version":{"sourceIDs":["vep_ensembl_version"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/vep_to_table_fields":{"sourceIDs":["vep_to_table_fields"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/annotate_coding_only":{"sourceIDs":["annotate_coding_only"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/per_target_intervals":{"sourceIDs":["per_target_intervals"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/strelka_cpu_reserved":{"sourceIDs":["strelka_cpu_reserved"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/varscan_min_coverage":{"sourceIDs":["varscan_min_coverage"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/varscan_min_var_freq":{"sourceIDs":["varscan_min_var_freq"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/vep_ensembl_assembly":{"sourceIDs":["vep_ensembl_assembly"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/varscan_strand_filter":{"sourceIDs":["varscan_strand_filter"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/vep_custom_annotations":{"sourceIDs":["vep_custom_annotations"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/target_interval_padding":{"sourceIDs":["target_interval_padding"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/varscan_max_normal_freq":{"sourceIDs":["varscan_max_normal_freq"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/variants_to_table_fields":{"sourceIDs":["variants_to_table_fields"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/qc_minimum_mapping_quality":{"sourceIDs":["qc_minimum_mapping_quality"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/filter_somatic_llr_threshold":{"sourceIDs":["filter_somatic_llr_threshold"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/mutect_artifact_detection_mode":{"sourceIDs":["mutect_artifact_detection_mode"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/filter_somatic_llr_tumor_purity":{"sourceIDs":["filter_somatic_llr_tumor_purity"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/picard_metric_accumulation_level":{"sourceIDs":["picard_metric_accumulation_level"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/variants_to_table_genotype_fields":{"sourceIDs":["variants_to_table_genotype_fields"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/mutect_max_alt_alleles_in_normal_count":{"sourceIDs":["mutect_max_alt_alleles_in_normal_count"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/mutect_max_alt_allele_in_normal_fraction":{"sourceIDs":["mutect_max_alt_allele_in_normal_fraction"]},"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl#somatic_exome/filter_somatic_llr_normal_contamination_rate":{"sourceIDs":["filter_somatic_llr_normal_contamination_rate"]}}}},"cwltoolVersion":"3.1.20230201224320","visualisationDot":"digraph 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    \"varscan_min_var_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_min_var_freq\"];\n    \"qc_minimum_base_quality\" [fillcolor=\"#94DDF4\",label=\"qc_minimum_base_quality\"];\n    \"varscan_strand_filter\" [fillcolor=\"#94DDF4\",label=\"varscan_strand_filter\"];\n    \"per_target_intervals\" [fillcolor=\"#94DDF4\",label=\"per_target_intervals\"];\n    \"scatter_count\" [fillcolor=\"#94DDF4\",label=\"scatter_count\"];\n    \"normal_sequence\" [fillcolor=\"#94DDF4\",label=\"normal_sequence: WT sequencing data and readgroup information\"];\n    \"filter_somatic_llr_tumor_purity\" [fillcolor=\"#94DDF4\",label=\"filter_somatic_llr_tumor_purity\"];\n    \"vep_ensembl_species\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_species\"];\n    \"mutect_max_alt_alleles_in_normal_count\" [fillcolor=\"#94DDF4\",label=\"mutect_max_alt_alleles_in_normal_count\"];\n    \"per_base_intervals\" [fillcolor=\"#94DDF4\",label=\"per_base_intervals\"];\n    \"strelka_cpu_reserved\" [fillcolor=\"#94DDF4\",label=\"strelka_cpu_reserved\"];\n    \"bqsr_known_sites\" [fillcolor=\"#94DDF4\",label=\"bqsr_known_sites\"];\n    \"picard_metric_accumulation_level\" [fillcolor=\"#94DDF4\",label=\"picard_metric_accumulation_level\"];\n    \"cle_vcf_filter\" [fillcolor=\"#94DDF4\",label=\"cle_vcf_filter\"];\n    \"pindel_insert_size\" [fillcolor=\"#94DDF4\",label=\"pindel_insert_size\"];\n    \"annotate_coding_only\" [fillcolor=\"#94DDF4\",label=\"annotate_coding_only\"];\n    \"omni_vcf\" [fillcolor=\"#94DDF4\",label=\"omni_vcf\"];\n    \"varscan_max_normal_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_max_normal_freq\"];\n    \"mutect_max_alt_allele_in_normal_fraction\" [fillcolor=\"#94DDF4\",label=\"mutect_max_alt_allele_in_normal_fraction\"];\n    \"mutect_artifact_detection_mode\" [fillcolor=\"#94DDF4\",label=\"mutect_artifact_detection_mode\"];\n    \"qc_minimum_mapping_quality\" [fillcolor=\"#94DDF4\",label=\"qc_minimum_mapping_quality\"];\n    \"vep_pick\" [fillcolor=\"#94DDF4\",label=\"vep_pick\"];\n    \"varscan_min_coverage\" [fillcolor=\"#94DDF4\",label=\"varscan_min_coverage\"];\n    \"bqsr_intervals\" [fillcolor=\"#94DDF4\",label=\"bqsr_intervals\"];\n    \"tumor_sample_name\" [fillcolor=\"#94DDF4\",label=\"tumor_sample_name\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"target_interval_padding\" [fillcolor=\"#94DDF4\",label=\"target_interval_padding\"];\n    \"vep_ensembl_version\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_version\"];\n    \"vep_ensembl_assembly\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_assembly\"];\n    \"tumor_sequence\" [fillcolor=\"#94DDF4\",label=\"tumor_sequence: MT sequencing data and readgroup information\"];\n    \"normal_cram_name\" [fillcolor=\"#94DDF4\",label=\"normal_cram_name\"];\n    \"somalier_vcf\" [fillcolor=\"#94DDF4\",label=\"somalier_vcf\"];\n    \"synonyms_file\" [fillcolor=\"#94DDF4\",label=\"synonyms_file\"];\n    \"bait_intervals\" [fillcolor=\"#94DDF4\",label=\"bait_intervals\"];\n    \"filter_docm_variants\" [fillcolor=\"#94DDF4\",label=\"filter_docm_variants\"];\n    \"output_dir\" [fillcolor=\"#94DDF4\",label=\"output_dir\"];\n    \"target_intervals\" [fillcolor=\"#94DDF4\",label=\"target_intervals: interval_list file of targets used in the sequencing experiment\"];\n    \"summary_intervals\" [fillcolor=\"#94DDF4\",label=\"summary_intervals\"];\n    \"vep_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"vep_to_table_fields\"];\n    \"variants_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_fields\"];\n    \"vep_cache_dir\" [fillcolor=\"#94DDF4\",label=\"vep_cache_dir\"];\n    \"vep_cache_dir\" [fillcolor=\"#94DDF4\",label=\"vep_cache_dir\"];\n    \"docm_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_vcf\"];\n    \"tumor_cram_name\" [fillcolor=\"#94DDF4\",label=\"tumor_cram_name\"];\n    \"varscan_p_value\" [fillcolor=\"#94DDF4\",label=\"varscan_p_value\"];\n    \"filter_somatic_llr_normal_contamination_rate\" [fillcolor=\"#94DDF4\",label=\"filter_somatic_llr_normal_contamination_rate\"];\n    \"hgvs_annotation\" [fillcolor=\"#94DDF4\",label=\"hgvs_annotation\"];\n    \"filter_somatic_llr_threshold\" [fillcolor=\"#94DDF4\",label=\"filter_somatic_llr_threshold\"];\n    \"vep_custom_annotations\" [fillcolor=\"#94DDF4\",label=\"vep_custom_annotations\"];\n    \"validated_variants\" [fillcolor=\"#94DDF4\",label=\"validated_variants\"];\n    \"variants_to_table_genotype_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_genotype_fields\"];\n    \"normal_sample_name\" [fillcolor=\"#94DDF4\",label=\"normal_sample_name\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"final_outputs\" [fillcolor=\"#94DDF4\",label=\"final_outputs\"];\n  }\n  \"gatherer\" [label=\"gatherer\"];\n  \"somatic_exome\" [label=\"somatic_exome: exome alignment and somatic variant detection\", fillcolor=\"#F3CEA1\"];\n  \"output_dir\" -> \"gatherer\" [label=\"output_dir\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"somatic_exome\" -> \"gatherer\" [label=\"all_files\"];\n  \"qc_minimum_base_quality\" -> \"somatic_exome\" [label=\"qc_minimum_base_quality\"];\n  \"per_target_intervals\" -> \"somatic_exome\" [label=\"per_target_intervals\"];\n  \"scatter_count\" -> \"somatic_exome\" [label=\"scatter_count\"];\n  \"normal_sequence\" -> \"somatic_exome\" [label=\"normal_sequence\"];\n  \"picard_metric_accumulation_level\" -> \"somatic_exome\" [label=\"picard_metric_accumulation_level\"];\n  \"bqsr_known_sites\" -> \"somatic_exome\" [label=\"bqsr_known_sites\"];\n  \"pindel_insert_size\" -> \"somatic_exome\" [label=\"pindel_insert_size\"];\n  \"omni_vcf\" -> \"somatic_exome\" [label=\"omni_vcf\"];\n  \"filter_somatic_llr_tumor_purity\" -> \"somatic_exome\" [label=\"filter_somatic_llr_tumor_purity\"];\n  \"varscan_max_normal_freq\" -> \"somatic_exome\" [label=\"varscan_max_normal_freq\"];\n  \"mutect_max_alt_allele_in_normal_fraction\" -> \"somatic_exome\" [label=\"mutect_max_alt_allele_in_normal_fraction\"];\n  \"qc_minimum_mapping_quality\" -> \"somatic_exome\" [label=\"qc_minimum_mapping_quality\"];\n  \"vep_pick\" -> \"somatic_exome\" [label=\"vep_pick\"];\n  \"varscan_min_coverage\" -> \"somatic_exome\" [label=\"varscan_min_coverage\"];\n  \"bqsr_intervals\" -> \"somatic_exome\" [label=\"bqsr_intervals\"];\n  \"target_interval_padding\" -> \"somatic_exome\" [label=\"target_interval_padding\"];\n  \"vep_ensembl_assembly\" -> \"somatic_exome\" [label=\"vep_ensembl_assembly\"];\n  \"tumor_sequence\" -> \"somatic_exome\" [label=\"tumor_sequence\"];\n  \"mutect_max_alt_alleles_in_normal_count\" -> \"somatic_exome\" [label=\"mutect_max_alt_alleles_in_normal_count\"];\n  \"normal_cram_name\" -> \"somatic_exome\" [label=\"normal_cram_name\"];\n  \"bait_intervals\" -> \"somatic_exome\" [label=\"bait_intervals\"];\n  \"reference\" -> \"somatic_exome\" [label=\"reference\"];\n  \"mutect_artifact_detection_mode\" -> \"somatic_exome\" [label=\"mutect_artifact_detection_mode\"];\n  \"variants_to_table_fields\" -> \"somatic_exome\" [label=\"variants_to_table_fields\"];\n  \"somalier_vcf\" -> \"somatic_exome\" [label=\"somalier_vcf\"];\n  \"target_intervals\" -> \"somatic_exome\" [label=\"target_intervals\"];\n  \"synonyms_file\" -> \"somatic_exome\" [label=\"synonyms_file\"];\n  \"vep_ensembl_species\" -> \"somatic_exome\" [label=\"vep_ensembl_species\"];\n  \"varscan_min_var_freq\" -> \"somatic_exome\" [label=\"varscan_min_var_freq\"];\n  \"tumor_cram_name\" -> \"somatic_exome\" [label=\"tumor_cram_name\"];\n  \"filter_somatic_llr_normal_contamination_rate\" -> \"somatic_exome\" [label=\"filter_somatic_llr_normal_contamination_rate\"];\n  \"vep_cache_dir\" -> \"somatic_exome\" [label=\"vep_cache_dir\"];\n  \"hgvs_annotation\" -> \"somatic_exome\" [label=\"hgvs_annotation\"];\n  \"varscan_p_value\" -> \"somatic_exome\" [label=\"varscan_p_value\"];\n  \"strelka_cpu_reserved\" -> \"somatic_exome\" [label=\"strelka_cpu_reserved\"];\n  \"per_base_intervals\" -> \"somatic_exome\" [label=\"per_base_intervals\"];\n  \"varscan_strand_filter\" -> \"somatic_exome\" [label=\"varscan_strand_filter\"];\n  \"tumor_sample_name\" -> \"somatic_exome\" [label=\"tumor_sample_name\"];\n  \"annotate_coding_only\" -> \"somatic_exome\" [label=\"annotate_coding_only\"];\n  \"normal_sample_name\" -> \"somatic_exome\" [label=\"normal_sample_name\"];\n  \"validated_variants\" -> \"somatic_exome\" [label=\"validated_variants\"];\n  \"vep_ensembl_version\" -> \"somatic_exome\" [label=\"vep_ensembl_version\"];\n  \"docm_vcf\" -> \"somatic_exome\" [label=\"docm_vcf\"];\n  \"vep_custom_annotations\" -> \"somatic_exome\" [label=\"vep_custom_annotations\"];\n  \"cle_vcf_filter\" -> \"somatic_exome\" [label=\"cle_vcf_filter\"];\n  \"summary_intervals\" -> \"somatic_exome\" [label=\"summary_intervals\"];\n  \"vep_to_table_fields\" -> \"somatic_exome\" [label=\"vep_to_table_fields\"];\n  \"filter_somatic_llr_threshold\" -> \"somatic_exome\" [label=\"filter_somatic_llr_threshold\"];\n  \"variants_to_table_genotype_fields\" -> \"somatic_exome\" [label=\"variants_to_table_genotype_fields\"];\n  \"gatherer\" -> \"final_outputs\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/somatic_exome_gathered.cwl","licenseName":"MIT License"}