{"@id":"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f","path":"definitions/pipelines/somatic_exome.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl","url":"https://github.com/genome/analysis-workflows/blob/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl"},"retrievedOn":"2026-10-26T21:36:26.880+00:00","lastCommit":"ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f","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","inputs":{"docm_vcf":{"doc":"The set of alleles that gatk haplotype caller will use to force-call regardless of evidence","type":"File"},"omni_vcf":{"type":"File"},"trimming":{"type":"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/types/trimming_options.yml#trimming_options (Optional)"},"vep_pick":{"doc":"configures how vep will annotate genomic features that each variant overlaps; for a detailed description of each option see https://useast.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick_allele_gene_eg"},"reference":{"label":"reference: Reference fasta file for a desired assembly","doc":"reference contains the nucleotide sequence for a given assembly (hg37, hg38, etc.)\nin fasta format for the entire genome. This is what reads will be aligned to.\nAppropriate files can be found on ensembl at https://ensembl.org/info/data/ftp/index.html\nWhen providing the reference secondary files corresponding to reference indices must be\nlocated in the same directory as the reference itself. These files can be created with\nsamtools index, bwa index, and picard CreateSequenceDictionary.\n","type":"File"},"tumor_name":{"label":"tumor_name: String specifying the name of the MT sample","doc":"tumor_name provides a string for what the MT sample will be referred to in the various\noutputs, for example the VCF files.\n","type":"String (Optional)"},"normal_name":{"label":"normal_name: String specifying the name of the WT sample","doc":"normal_name provides a string for what the WT sample will be referred to in the various\noutputs, for example the VCF files.\n","type":"String (Optional)"},"somalier_vcf":{"doc":"a vcf file of known polymorphic sites for somalier to compare normal and tumor samples for identity; sites files can be found at: https://github.com/brentp/somalier/releases","type":"File"},"manta_non_wgs":{"doc":"toggles on or off manta settings for WES vs. WGS mode for structural variant detection","type":"Boolean (Optional)"},"scatter_count":{"doc":"scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs","type":"Integer"},"synonyms_file":{"doc":"synonyms_file allows the use of different chromosome identifiers in vep inputs or annotation files (cache, database, GFF, custom file, fasta). File should be tab-delimited with the primary identifier in column 1 and the synonym in column 2.","type":"File (Optional)"},"vep_cache_dir":{"doc":"path to the vep cache directory, available at: https://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html#pre","type":"Directory"},"bait_intervals":{"label":"bait_intervals: interval_list file of baits used in the sequencing experiment","doc":"bait_intervals is an interval_list corresponding to the baits used in sequencing reagent.\nThese are essentially coordinates for regions you were able to design probes for in the reagent.\nTypically the reagent provider has this information available in bed format and it can be\nconverted to an interval_list with Picard BedToIntervalList. Astrazeneca also maintains a repo\nof baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data\n","type":"File"},"bqsr_intervals":{"label":"bqsr_intervals: Array of strings specifying regions for base quality score recalibration","doc":"bqsr_intervals provides an array of genomic intervals for which to apply\nGATK base quality score recalibrations. Typically intervals are given\nfor the entire chromosome (chr1, chr2, etc.), these names should match\nthe format in the reference file.\n","type":"String[]"},"cle_vcf_filter":{"type":"Boolean"},"known_variants":{"doc":"Previously discovered variants to be flagged in this pipelines's output vcf","type":"File (Optional)"},"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/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/types/sequence_data.yml#sequence_data[]"},"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/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/types/sequence_data.yml#sequence_data[]"},"varscan_p_value":{"type":"Float (Optional)"},"bqsr_known_sites":{"label":"bqsr_known_sites: One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.","doc":"Known polymorphic indels recommended by GATK for a variety of\ntools including the BaseRecalibrator. This is part of the GATK resource\nbundle available at http://www.broadinstitute.org/gatk/guide/article?id=1213\nFile should be in vcf format, and tabix indexed.\n","type":"File[]"},"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/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/types/labelled_file.yml#labelled_file[]"},"tumor_sample_name":{"type":"String"},"manta_call_regions":{"doc":"bgzip-compressed, tabix-indexed BED file specifiying regions to which manta structural variant analysis is limited","type":"File (Optional)"},"normal_sample_name":{"type":"String"},"per_base_intervals":{"label":"per_base_intervals: additional intervals over which to summarize coverage/QC at a per-base resolution","doc":"per_base_intervals is a list of regions (in interval_list format) over which to summarize coverage/QC at a per-base resolution.","type":"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/types/labelled_file.yml#labelled_file[]"},"pindel_insert_size":{"type":"Integer"},"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":{"doc":"VEP fields in final output","type":"String[]"},"annotate_coding_only":{"doc":"if set to true, vep only returns consequences that fall in the coding regions of transcripts","type":"Boolean (Optional)"},"filter_docm_variants":{"type":"Boolean (Optional)"},"manta_output_contigs":{"doc":"if set to true configures manta to output assembled contig sequences in the final VCF files","type":"Boolean (Optional)"},"per_target_intervals":{"label":"per_target_intervals: additional intervals over which to summarize coverage/QC at a per-target resolution","doc":"per_target_intervals list of regions (in interval_list format) over which to summarize coverage/QC at a per-target resolution.","type":"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/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/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[]"},"qc_minimum_base_quality":{"type":"Integer (Optional)"},"target_interval_padding":{"label":"target_interval_padding: number of bp flanking each target region in which to allow variant calls","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":{"doc":"The names of one or more standard VCF fields or INFO fields to include in the output table","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":{"doc":"The name of a genotype field to include in the output table","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_tsv":{"type":"File"},"final_vcf":{"type":"File"},"cn_diagram":{"type":"File (Optional)"},"tumor_cram":{"type":"File"},"normal_cram":{"type":"File"},"vep_summary":{"type":"File"},"all_candidates":{"type":"File"},"cn_scatter_plot":{"type":"File (Optional)"},"tumor_flagstats":{"type":"File"},"diploid_variants":{"type":"File (Optional)"},"intervals_target":{"type":"File (Optional)"},"normal_flagstats":{"type":"File"},"small_candidates":{"type":"File"},"somatic_variants":{"type":"File (Optional)"},"tumor_hs_metrics":{"type":"File"},"docm_filtered_vcf":{"type":"File"},"normal_hs_metrics":{"type":"File"},"final_filtered_vcf":{"type":"File"},"reference_coverage":{"type":"File (Optional)"},"mutect_filtered_vcf":{"type":"File"},"pindel_filtered_vcf":{"type":"File"},"tumor_only_variants":{"type":"File (Optional)"},"intervals_antitarget":{"type":"File (Optional)"},"strelka_filtered_vcf":{"type":"File"},"varscan_filtered_vcf":{"type":"File"},"mutect_unfiltered_vcf":{"type":"File"},"pindel_unfiltered_vcf":{"type":"File"},"tumor_target_coverage":{"type":"File"},"normal_target_coverage":{"type":"File"},"strelka_unfiltered_vcf":{"type":"File"},"tumor_bin_level_ratios":{"type":"File"},"tumor_segmented_ratios":{"type":"File"},"varscan_unfiltered_vcf":{"type":"File"},"tumor_summary_hs_metrics":{"type":"File[]"},"normal_summary_hs_metrics":{"type":"File[]"},"tumor_antitarget_coverage":{"type":"File"},"tumor_insert_size_metrics":{"type":"File"},"tumor_per_base_hs_metrics":{"type":"File[]"},"tumor_verify_bam_id_depth":{"type":"File"},"normal_antitarget_coverage":{"type":"File"},"normal_insert_size_metrics":{"type":"File"},"normal_per_base_hs_metrics":{"type":"File[]"},"normal_verify_bam_id_depth":{"type":"File"},"tumor_per_target_hs_metrics":{"type":"File[]"},"tumor_snv_bam_readcount_tsv":{"type":"File"},"tumor_verify_bam_id_metrics":{"type":"File"},"normal_per_target_hs_metrics":{"type":"File[]"},"normal_snv_bam_readcount_tsv":{"type":"File"},"normal_verify_bam_id_metrics":{"type":"File"},"somalier_concordance_metrics":{"type":"File"},"tumor_indel_bam_readcount_tsv":{"type":"File"},"tumor_mark_duplicates_metrics":{"type":"File"},"normal_indel_bam_readcount_tsv":{"type":"File"},"normal_mark_duplicates_metrics":{"type":"File"},"somalier_concordance_statistics":{"type":"File"},"tumor_alignment_summary_metrics":{"type":"File"},"tumor_per_base_coverage_metrics":{"type":"File[]"},"normal_alignment_summary_metrics":{"type":"File"},"normal_per_base_coverage_metrics":{"type":"File[]"},"tumor_per_target_coverage_metrics":{"type":"File[]"},"normal_per_target_coverage_metrics":{"type":"File[]"}},"steps":{"manta":{"label":"Set up and execute manta","run":"../tools/manta_somatic.cwl","runType":"COMMANDLINETOOL","sources":{"manta":{"sourceIDs":["manta_output_contigs"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#manta/non_wgs":{"sourceIDs":["manta_non_wgs"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#manta/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#manta/tumor_bam":{"sourceIDs":["tumor_alignment_and_qc"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#manta/normal_bam":{"sourceIDs":["normal_alignment_and_qc"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#manta/call_regions":{"sourceIDs":["manta_call_regions"]}}},"cnvkit":{"run":"../tools/cnvkit_batch.cwl","runType":"COMMANDLINETOOL","sources":{"cnvkit":{"sourceIDs":["bait_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#cnvkit/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_bam":{"sourceIDs":["tumor_alignment_and_qc"]}}},"concordance":{"label":"Concordance checking between Tumor and Normal BAM","run":"../tools/concordance.cwl","runType":"COMMANDLINETOOL","sources":{"concordance":{"sourceIDs":["tumor_alignment_and_qc"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#concordance/vcf":{"sourceIDs":["somalier_vcf"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#concordance/bam_2":{"sourceIDs":["normal_alignment_and_qc"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#concordance/reference":{"sourceIDs":["reference"]}}},"detect_variants":{"label":"Detect Variants workflow","run":"detect_variants.cwl","runType":"WORKFLOW","sources":{"detect_variants":{"sourceIDs":["docm_vcf"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_pick":{"sourceIDs":["vep_pick"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/tumor_bam":{"sourceIDs":["tumor_alignment_and_qc"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/normal_bam":{"sourceIDs":["normal_alignment_and_qc"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/roi_intervals":{"sourceIDs":["pad_target_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/scatter_count":{"sourceIDs":["scatter_count"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/synonyms_file":{"sourceIDs":["synonyms_file"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_cache_dir":{"sourceIDs":["vep_cache_dir"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/cle_vcf_filter":{"sourceIDs":["cle_vcf_filter"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/known_variants":{"sourceIDs":["known_variants"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_p_value":{"sourceIDs":["varscan_p_value"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/tumor_sample_name":{"sourceIDs":["tumor_sample_name"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/normal_sample_name":{"sourceIDs":["normal_sample_name"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/pindel_insert_size":{"sourceIDs":["pindel_insert_size"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_exome_mode":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_ensembl_species":{"sourceIDs":["vep_ensembl_species"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_ensembl_version":{"sourceIDs":["vep_ensembl_version"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_to_table_fields":{"sourceIDs":["vep_to_table_fields"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/annotate_coding_only":{"sourceIDs":["annotate_coding_only"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/filter_docm_variants":{"sourceIDs":["filter_docm_variants"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_cpu_reserved":{"sourceIDs":["strelka_cpu_reserved"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_min_coverage":{"sourceIDs":["varscan_min_coverage"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_min_var_freq":{"sourceIDs":["varscan_min_var_freq"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_ensembl_assembly":{"sourceIDs":["vep_ensembl_assembly"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_strand_filter":{"sourceIDs":["varscan_strand_filter"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_custom_annotations":{"sourceIDs":["vep_custom_annotations"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_max_normal_freq":{"sourceIDs":["varscan_max_normal_freq"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/variants_to_table_fields":{"sourceIDs":["variants_to_table_fields"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/filter_somatic_llr_threshold":{"sourceIDs":["filter_somatic_llr_threshold"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/filter_somatic_llr_tumor_purity":{"sourceIDs":["filter_somatic_llr_tumor_purity"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/variants_to_table_genotype_fields":{"sourceIDs":["variants_to_table_genotype_fields"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#detect_variants/filter_somatic_llr_normal_contamination_rate":{"sourceIDs":["filter_somatic_llr_normal_contamination_rate"]}}},"tumor_index_cram":{"label":"samtools index cram","run":"../tools/index_cram.cwl","runType":"COMMANDLINETOOL","sources":{"tumor_index_cram":{"sourceIDs":["tumor_bam_to_cram"]}}},"normal_index_cram":{"label":"samtools index cram","run":"../tools/index_cram.cwl","runType":"COMMANDLINETOOL","sources":{"normal_index_cram":{"sourceIDs":["normal_bam_to_cram"]}}},"tumor_bam_to_cram":{"label":"BAM to CRAM conversion","run":"../tools/bam_to_cram.cwl","runType":"COMMANDLINETOOL","sources":{"tumor_bam_to_cram":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_bam_to_cram/bam":{"sourceIDs":["tumor_alignment_and_qc"]}}},"normal_bam_to_cram":{"label":"BAM to CRAM conversion","run":"../tools/bam_to_cram.cwl","runType":"COMMANDLINETOOL","sources":{"normal_bam_to_cram":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_bam_to_cram/bam":{"sourceIDs":["normal_alignment_and_qc"]}}},"pad_target_intervals":{"label":"expand interval list regions by a given number of basepairs","run":"../tools/interval_list_expand.cwl","runType":"COMMANDLINETOOL","sources":{"pad_target_intervals":{"sourceIDs":["target_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#pad_target_intervals/roi_padding":{"sourceIDs":["target_interval_padding"]}}},"tumor_alignment_and_qc":{"label":"exome alignment with qc","run":"alignment_exome.cwl","runType":"WORKFLOW","sources":{"tumor_alignment_and_qc":{"sourceIDs":["per_base_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/omni_vcf":{"sourceIDs":["omni_vcf"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/sequence":{"sourceIDs":["tumor_sequence"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/trimming":{"sourceIDs":["trimming"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/final_name":{"sourceIDs":["tumor_name"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bait_intervals":{"sourceIDs":["bait_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bqsr_intervals":{"sourceIDs":["bqsr_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bqsr_known_sites":{"sourceIDs":["bqsr_known_sites"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/target_intervals":{"sourceIDs":["target_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/summary_intervals":{"sourceIDs":["summary_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_target_intervals":{"sourceIDs":["per_target_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/qc_minimum_base_quality":{"sourceIDs":["qc_minimum_base_quality"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/qc_minimum_mapping_quality":{"sourceIDs":["qc_minimum_mapping_quality"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/picard_metric_accumulation_level":{"sourceIDs":["picard_metric_accumulation_level"]}}},"normal_alignment_and_qc":{"label":"exome alignment with qc","run":"alignment_exome.cwl","runType":"WORKFLOW","sources":{"normal_alignment_and_qc":{"sourceIDs":["normal_name"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/omni_vcf":{"sourceIDs":["omni_vcf"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/sequence":{"sourceIDs":["normal_sequence"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/trimming":{"sourceIDs":["trimming"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bait_intervals":{"sourceIDs":["bait_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bqsr_intervals":{"sourceIDs":["bqsr_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bqsr_known_sites":{"sourceIDs":["bqsr_known_sites"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/target_intervals":{"sourceIDs":["target_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/summary_intervals":{"sourceIDs":["summary_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_base_intervals":{"sourceIDs":["per_base_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_target_intervals":{"sourceIDs":["per_target_intervals"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/qc_minimum_base_quality":{"sourceIDs":["qc_minimum_base_quality"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/qc_minimum_mapping_quality":{"sourceIDs":["qc_minimum_mapping_quality"]},"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/picard_metric_accumulation_level":{"sourceIDs":["picard_metric_accumulation_level"]}}}},"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    \"normal_sequence\" [fillcolor=\"#94DDF4\",label=\"normal_sequence: WT sequencing data and readgroup information\"];\n    \"bait_intervals\" [fillcolor=\"#94DDF4\",label=\"bait_intervals: interval_list file of baits used in the sequencing experiment\"];\n    \"docm_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_vcf\"];\n    \"target_interval_padding\" [fillcolor=\"#94DDF4\",label=\"target_interval_padding: number of bp flanking each target region in which to allow variant calls\"];\n    \"varscan_min_var_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_min_var_freq\"];\n    \"known_variants\" [fillcolor=\"#94DDF4\",label=\"known_variants\"];\n    \"varscan_min_coverage\" [fillcolor=\"#94DDF4\",label=\"varscan_min_coverage\"];\n    \"filter_somatic_llr_tumor_purity\" [fillcolor=\"#94DDF4\",label=\"filter_somatic_llr_tumor_purity\"];\n    \"manta_output_contigs\" [fillcolor=\"#94DDF4\",label=\"manta_output_contigs\"];\n    \"bqsr_intervals\" [fillcolor=\"#94DDF4\",label=\"bqsr_intervals: Array of strings specifying regions for base quality score recalibration\"];\n    \"normal_name\" [fillcolor=\"#94DDF4\",label=\"normal_name: String specifying the name of the WT sample\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference: Reference fasta file for a desired assembly\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference: Reference fasta file for a desired assembly\"];\n    \"somalier_vcf\" [fillcolor=\"#94DDF4\",label=\"somalier_vcf\"];\n    \"trimming\" [fillcolor=\"#94DDF4\",label=\"trimming\"];\n    \"per_base_intervals\" [fillcolor=\"#94DDF4\",label=\"per_base_intervals: additional intervals over which to summarize coverage/QC at a per-base resolution\"];\n    \"vep_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"vep_to_table_fields\"];\n    \"per_target_intervals\" [fillcolor=\"#94DDF4\",label=\"per_target_intervals: additional intervals over which to summarize coverage/QC at a per-target resolution\"];\n    \"filter_somatic_llr_normal_contamination_rate\" [fillcolor=\"#94DDF4\",label=\"filter_somatic_llr_normal_contamination_rate\"];\n    \"vep_ensembl_assembly\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_assembly\"];\n    \"manta_call_regions\" [fillcolor=\"#94DDF4\",label=\"manta_call_regions\"];\n    \"variants_to_table_genotype_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_genotype_fields\"];\n    \"filter_somatic_llr_threshold\" [fillcolor=\"#94DDF4\",label=\"filter_somatic_llr_threshold\"];\n    \"mutect_max_alt_allele_in_normal_fraction\" [fillcolor=\"#94DDF4\",label=\"mutect_max_alt_allele_in_normal_fraction\"];\n    \"bqsr_known_sites\" [fillcolor=\"#94DDF4\",label=\"bqsr_known_sites: One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.\"];\n    \"vep_cache_dir\" [fillcolor=\"#94DDF4\",label=\"vep_cache_dir\"];\n    \"vep_cache_dir\" [fillcolor=\"#94DDF4\",label=\"vep_cache_dir\"];\n    \"pindel_insert_size\" [fillcolor=\"#94DDF4\",label=\"pindel_insert_size\"];\n    \"filter_docm_variants\" [fillcolor=\"#94DDF4\",label=\"filter_docm_variants\"];\n    \"qc_minimum_base_quality\" [fillcolor=\"#94DDF4\",label=\"qc_minimum_base_quality\"];\n    \"vep_pick\" [fillcolor=\"#94DDF4\",label=\"vep_pick\"];\n    \"strelka_cpu_reserved\" [fillcolor=\"#94DDF4\",label=\"strelka_cpu_reserved\"];\n    \"manta_non_wgs\" [fillcolor=\"#94DDF4\",label=\"manta_non_wgs\"];\n    \"varscan_strand_filter\" [fillcolor=\"#94DDF4\",label=\"varscan_strand_filter\"];\n    \"mutect_max_alt_alleles_in_normal_count\" [fillcolor=\"#94DDF4\",label=\"mutect_max_alt_alleles_in_normal_count\"];\n    \"tumor_sequence\" [fillcolor=\"#94DDF4\",label=\"tumor_sequence: MT sequencing data and readgroup information\"];\n    \"picard_metric_accumulation_level\" [fillcolor=\"#94DDF4\",label=\"picard_metric_accumulation_level\"];\n    \"annotate_coding_only\" [fillcolor=\"#94DDF4\",label=\"annotate_coding_only\"];\n    \"normal_sample_name\" [fillcolor=\"#94DDF4\",label=\"normal_sample_name\"];\n    \"vep_custom_annotations\" [fillcolor=\"#94DDF4\",label=\"vep_custom_annotations\"];\n    \"varscan_max_normal_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_max_normal_freq\"];\n    \"summary_intervals\" [fillcolor=\"#94DDF4\",label=\"summary_intervals\"];\n    \"synonyms_file\" [fillcolor=\"#94DDF4\",label=\"synonyms_file\"];\n    \"tumor_name\" [fillcolor=\"#94DDF4\",label=\"tumor_name: String specifying the name of the MT sample\"];\n    \"scatter_count\" [fillcolor=\"#94DDF4\",label=\"scatter_count\"];\n    \"mutect_artifact_detection_mode\" [fillcolor=\"#94DDF4\",label=\"mutect_artifact_detection_mode\"];\n    \"variants_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_fields\"];\n    \"varscan_p_value\" [fillcolor=\"#94DDF4\",label=\"varscan_p_value\"];\n    \"tumor_sample_name\" [fillcolor=\"#94DDF4\",label=\"tumor_sample_name\"];\n    \"omni_vcf\" [fillcolor=\"#94DDF4\",label=\"omni_vcf\"];\n    \"vep_ensembl_version\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_version\"];\n    \"cle_vcf_filter\" [fillcolor=\"#94DDF4\",label=\"cle_vcf_filter\"];\n    \"vep_ensembl_species\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_species\"];\n    \"target_intervals\" [fillcolor=\"#94DDF4\",label=\"target_intervals: interval_list file of targets used in the sequencing experiment\"];\n    \"qc_minimum_mapping_quality\" [fillcolor=\"#94DDF4\",label=\"qc_minimum_mapping_quality\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"pindel_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_unfiltered_vcf\"];\n    \"tumor_cram\" [fillcolor=\"#94DDF4\",label=\"tumor_cram\"];\n    \"normal_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_base_hs_metrics\"];\n    \"tumor_per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_target_hs_metrics\"];\n    \"tumor_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_mark_duplicates_metrics\"];\n    \"varscan_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_filtered_vcf\"];\n    \"normal_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"normal_antitarget_coverage\"];\n    \"pindel_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_filtered_vcf\"];\n    \"tumor_only_variants\" [fillcolor=\"#94DDF4\",label=\"tumor_only_variants\"];\n    \"tumor_per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_target_coverage_metrics\"];\n    \"tumor_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_summary_hs_metrics\"];\n    \"vep_summary\" [fillcolor=\"#94DDF4\",label=\"vep_summary\"];\n    \"final_vcf\" [fillcolor=\"#94DDF4\",label=\"final_vcf\"];\n    \"docm_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_filtered_vcf\"];\n    \"cn_diagram\" [fillcolor=\"#94DDF4\",label=\"cn_diagram\"];\n    \"somatic_variants\" [fillcolor=\"#94DDF4\",label=\"somatic_variants\"];\n    \"normal_verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_verify_bam_id_metrics\"];\n    \"tumor_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_indel_bam_readcount_tsv\"];\n    \"normal_per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_target_coverage_metrics\"];\n    \"normal_target_coverage\" [fillcolor=\"#94DDF4\",label=\"normal_target_coverage\"];\n    \"tumor_verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"tumor_verify_bam_id_depth\"];\n    \"normal_summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_summary_hs_metrics\"];\n    \"normal_per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_base_coverage_metrics\"];\n    \"somalier_concordance_statistics\" [fillcolor=\"#94DDF4\",label=\"somalier_concordance_statistics\"];\n    \"reference_coverage\" [fillcolor=\"#94DDF4\",label=\"reference_coverage\"];\n    \"normal_flagstats\" [fillcolor=\"#94DDF4\",label=\"normal_flagstats\"];\n    \"tumor_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_snv_bam_readcount_tsv\"];\n    \"tumor_target_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_target_coverage\"];\n    \"varscan_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_unfiltered_vcf\"];\n    \"normal_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_snv_bam_readcount_tsv\"];\n    \"intervals_target\" [fillcolor=\"#94DDF4\",label=\"intervals_target\"];\n    \"tumor_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_insert_size_metrics\"];\n    \"tumor_bin_level_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_bin_level_ratios\"];\n    \"tumor_per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_base_coverage_metrics\"];\n    \"strelka_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_filtered_vcf\"];\n    \"tumor_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_alignment_summary_metrics\"];\n    \"final_tsv\" [fillcolor=\"#94DDF4\",label=\"final_tsv\"];\n    \"mutect_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_unfiltered_vcf\"];\n    \"tumor_segmented_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_segmented_ratios\"];\n    \"normal_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_hs_metrics\"];\n    \"intervals_antitarget\" [fillcolor=\"#94DDF4\",label=\"intervals_antitarget\"];\n    \"normal_mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_mark_duplicates_metrics\"];\n    \"normal_per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_per_target_hs_metrics\"];\n    \"diploid_variants\" [fillcolor=\"#94DDF4\",label=\"diploid_variants\"];\n    \"normal_cram\" [fillcolor=\"#94DDF4\",label=\"normal_cram\"];\n    \"normal_alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_alignment_summary_metrics\"];\n    \"small_candidates\" [fillcolor=\"#94DDF4\",label=\"small_candidates\"];\n    \"normal_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_indel_bam_readcount_tsv\"];\n    \"tumor_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_hs_metrics\"];\n    \"tumor_flagstats\" [fillcolor=\"#94DDF4\",label=\"tumor_flagstats\"];\n    \"normal_verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"normal_verify_bam_id_depth\"];\n    \"mutect_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_filtered_vcf\"];\n    \"tumor_per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_per_base_hs_metrics\"];\n    \"strelka_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_unfiltered_vcf\"];\n    \"somalier_concordance_metrics\" [fillcolor=\"#94DDF4\",label=\"somalier_concordance_metrics\"];\n    \"tumor_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_antitarget_coverage\"];\n    \"final_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"final_filtered_vcf\"];\n    \"cn_scatter_plot\" [fillcolor=\"#94DDF4\",label=\"cn_scatter_plot\"];\n    \"normal_insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"normal_insert_size_metrics\"];\n    \"all_candidates\" [fillcolor=\"#94DDF4\",label=\"all_candidates\"];\n    \"tumor_verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"tumor_verify_bam_id_metrics\"];\n  }\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  \"tumor_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"detect_variants\" [label=\"Detect Variants workflow\", fillcolor=\"#F3CEA1\"];\n  \"cnvkit\" [label=\"cnvkit\"];\n  \"tumor_index_cram\" [label=\"samtools index cram\"];\n  \"normal_bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"manta\" [label=\"Set up and execute manta\"];\n  \"normal_alignment_and_qc\" [label=\"exome alignment with qc\", fillcolor=\"#F3CEA1\"];\n  \"pad_target_intervals\" [label=\"expand interval list regions by a given number of basepairs\"];\n  \"normal_bam_to_cram\" -> \"normal_index_cram\" [label=\"cram\"];\n  \"tumor_alignment_and_qc\" -> \"concordance\" [label=\"bam_1\"];\n  \"normal_alignment_and_qc\" -> \"concordance\" [label=\"bam_2\"];\n  \"somalier_vcf\" -> \"concordance\" [label=\"vcf\"];\n  \"reference\" -> \"concordance\" [label=\"reference\"];\n  \"per_base_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"omni_vcf\" -> \"tumor_alignment_and_qc\" [label=\"omni_vcf\"];\n  \"tumor_sequence\" -> \"tumor_alignment_and_qc\" [label=\"sequence\"];\n  \"reference\" -> \"tumor_alignment_and_qc\" [label=\"reference\"];\n  \"target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"target_intervals\"];\n  \"qc_minimum_base_quality\" -> \"tumor_alignment_and_qc\" [label=\"qc_minimum_base_quality\"];\n  \"qc_minimum_mapping_quality\" -> \"tumor_alignment_and_qc\" [label=\"qc_minimum_mapping_quality\"];\n  \"trimming\" -> \"tumor_alignment_and_qc\" [label=\"trimming\"];\n  \"summary_intervals\" -> \"tumor_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"picard_metric_accumulation_level\" -> \"tumor_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"bait_intervals\" -> \"tumor_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"bqsr_intervals\" -> \"tumor_alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"tumor_name\" -> \"tumor_alignment_and_qc\" [label=\"final_name\"];\n  \"bqsr_known_sites\" -> \"tumor_alignment_and_qc\" [label=\"bqsr_known_sites\"];\n  \"per_target_intervals\" -> \"tumor_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"reference\" -> \"tumor_bam_to_cram\" [label=\"reference\"];\n  \"tumor_alignment_and_qc\" -> \"tumor_bam_to_cram\" [label=\"bam\"];\n  \"docm_vcf\" -> \"detect_variants\" [label=\"docm_vcf\"];\n  \"varscan_min_var_freq\" -> \"detect_variants\" [label=\"varscan_min_var_freq\"];\n  \"filter_somatic_llr_tumor_purity\" -> \"detect_variants\" [label=\"filter_somatic_llr_tumor_purity\"];\n  \"normal_sample_name\" -> \"detect_variants\" [label=\"normal_sample_name\"];\n  \"vep_ensembl_version\" -> \"detect_variants\" [label=\"vep_ensembl_version\"];\n  \"varscan_min_coverage\" -> \"detect_variants\" [label=\"varscan_min_coverage\"];\n  \"variants_to_table_genotype_fields\" -> \"detect_variants\" [label=\"variants_to_table_genotype_fields\"];\n  \"vep_pick\" -> \"detect_variants\" [label=\"vep_pick\"];\n  \"vep_custom_annotations\" -> \"detect_variants\" [label=\"vep_custom_annotations\"];\n  \"normal_alignment_and_qc\" -> \"detect_variants\" [label=\"normal_bam\"];\n  \"default1\" -> \"detect_variants\" [label=\"strelka_exome_mode\"];\n  \"default1\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"annotate_coding_only\" -> \"detect_variants\" [label=\"annotate_coding_only\"];\n  \"tumor_alignment_and_qc\" -> \"detect_variants\" [label=\"tumor_bam\"];\n  \"synonyms_file\" -> \"detect_variants\" [label=\"synonyms_file\"];\n  \"pindel_insert_size\" -> \"detect_variants\" [label=\"pindel_insert_size\"];\n  \"pad_target_intervals\" -> \"detect_variants\" [label=\"roi_intervals\"];\n  \"vep_cache_dir\" -> \"detect_variants\" [label=\"vep_cache_dir\"];\n  \"varscan_p_value\" -> \"detect_variants\" [label=\"varscan_p_value\"];\n  \"varscan_strand_filter\" -> \"detect_variants\" [label=\"varscan_strand_filter\"];\n  \"filter_docm_variants\" -> \"detect_variants\" [label=\"filter_docm_variants\"];\n  \"varscan_max_normal_freq\" -> \"detect_variants\" [label=\"varscan_max_normal_freq\"];\n  \"variants_to_table_fields\" -> \"detect_variants\" [label=\"variants_to_table_fields\"];\n  \"known_variants\" -> \"detect_variants\" [label=\"known_variants\"];\n  \"filter_somatic_llr_normal_contamination_rate\" -> \"detect_variants\" [label=\"filter_somatic_llr_normal_contamination_rate\"];\n  \"vep_ensembl_species\" -> \"detect_variants\" [label=\"vep_ensembl_species\"];\n  \"vep_to_table_fields\" -> \"detect_variants\" [label=\"vep_to_table_fields\"];\n  \"tumor_sample_name\" -> \"detect_variants\" [label=\"tumor_sample_name\"];\n  \"filter_somatic_llr_threshold\" -> \"detect_variants\" [label=\"filter_somatic_llr_threshold\"];\n  \"vep_ensembl_assembly\" -> \"detect_variants\" [label=\"vep_ensembl_assembly\"];\n  \"cle_vcf_filter\" -> \"detect_variants\" [label=\"cle_vcf_filter\"];\n  \"reference\" -> \"detect_variants\" [label=\"reference\"];\n  \"scatter_count\" -> \"detect_variants\" [label=\"scatter_count\"];\n  \"strelka_cpu_reserved\" -> \"detect_variants\" [label=\"strelka_cpu_reserved\"];\n  \"bait_intervals\" -> \"cnvkit\" [label=\"bait_intervals\"];\n  \"tumor_alignment_and_qc\" -> \"cnvkit\" [label=\"tumor_bam\"];\n  \"normal_alignment_and_qc\" -> \"cnvkit\" [label=\"reference\"];\n  \"reference\" -> \"cnvkit\" [label=\"reference\"];\n  \"tumor_bam_to_cram\" -> \"tumor_index_cram\" [label=\"cram\"];\n  \"reference\" -> \"normal_bam_to_cram\" [label=\"reference\"];\n  \"normal_alignment_and_qc\" -> \"normal_bam_to_cram\" [label=\"bam\"];\n  \"manta_output_contigs\" -> \"manta\" [label=\"output_contigs\"];\n  \"normal_alignment_and_qc\" -> \"manta\" [label=\"normal_bam\"];\n  \"reference\" -> \"manta\" [label=\"reference\"];\n  \"manta_call_regions\" -> \"manta\" [label=\"call_regions\"];\n  \"manta_non_wgs\" -> \"manta\" [label=\"non_wgs\"];\n  \"tumor_alignment_and_qc\" -> \"manta\" [label=\"tumor_bam\"];\n  \"normal_name\" -> \"normal_alignment_and_qc\" [label=\"final_name\"];\n  \"trimming\" -> \"normal_alignment_and_qc\" [label=\"trimming\"];\n  \"qc_minimum_base_quality\" -> \"normal_alignment_and_qc\" [label=\"qc_minimum_base_quality\"];\n  \"normal_sequence\" -> \"normal_alignment_and_qc\" [label=\"sequence\"];\n  \"target_intervals\" -> \"normal_alignment_and_qc\" [label=\"target_intervals\"];\n  \"reference\" -> \"normal_alignment_and_qc\" [label=\"reference\"];\n  \"bait_intervals\" -> \"normal_alignment_and_qc\" [label=\"bait_intervals\"];\n  \"per_target_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_target_intervals\"];\n  \"qc_minimum_mapping_quality\" -> \"normal_alignment_and_qc\" [label=\"qc_minimum_mapping_quality\"];\n  \"per_base_intervals\" -> \"normal_alignment_and_qc\" [label=\"per_base_intervals\"];\n  \"omni_vcf\" -> \"normal_alignment_and_qc\" [label=\"omni_vcf\"];\n  \"summary_intervals\" -> \"normal_alignment_and_qc\" [label=\"summary_intervals\"];\n  \"bqsr_intervals\" -> \"normal_alignment_and_qc\" [label=\"bqsr_intervals\"];\n  \"bqsr_known_sites\" -> \"normal_alignment_and_qc\" [label=\"bqsr_known_sites\"];\n  \"picard_metric_accumulation_level\" -> \"normal_alignment_and_qc\" [label=\"picard_metric_accumulation_level\"];\n  \"target_intervals\" -> \"pad_target_intervals\" [label=\"interval_list\"];\n  \"target_interval_padding\" -> \"pad_target_intervals\" [label=\"roi_padding\"];\n  \"detect_variants\" -> \"pindel_unfiltered_vcf\";\n  \"tumor_index_cram\" -> \"tumor_cram\";\n  \"normal_alignment_and_qc\" -> \"normal_per_base_hs_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_target_hs_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_mark_duplicates_metrics\";\n  \"detect_variants\" -> \"varscan_filtered_vcf\";\n  \"cnvkit\" -> \"normal_antitarget_coverage\";\n  \"detect_variants\" -> \"pindel_filtered_vcf\";\n  \"manta\" -> \"tumor_only_variants\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_target_coverage_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_summary_hs_metrics\";\n  \"detect_variants\" -> \"vep_summary\";\n  \"detect_variants\" -> \"final_vcf\";\n  \"detect_variants\" -> \"docm_filtered_vcf\";\n  \"cnvkit\" -> \"cn_diagram\";\n  \"manta\" -> \"somatic_variants\";\n  \"normal_alignment_and_qc\" -> \"normal_verify_bam_id_metrics\";\n  \"detect_variants\" -> \"tumor_indel_bam_readcount_tsv\";\n  \"normal_alignment_and_qc\" -> \"normal_per_target_coverage_metrics\";\n  \"cnvkit\" -> \"normal_target_coverage\";\n  \"tumor_alignment_and_qc\" -> \"tumor_verify_bam_id_depth\";\n  \"normal_alignment_and_qc\" -> \"normal_summary_hs_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_per_base_coverage_metrics\";\n  \"concordance\" -> \"somalier_concordance_statistics\";\n  \"cnvkit\" -> \"reference_coverage\";\n  \"normal_alignment_and_qc\" -> \"normal_flagstats\";\n  \"detect_variants\" -> \"tumor_snv_bam_readcount_tsv\";\n  \"cnvkit\" -> \"tumor_target_coverage\";\n  \"detect_variants\" -> \"varscan_unfiltered_vcf\";\n  \"detect_variants\" -> \"normal_snv_bam_readcount_tsv\";\n  \"cnvkit\" -> \"intervals_target\";\n  \"tumor_alignment_and_qc\" -> \"tumor_insert_size_metrics\";\n  \"cnvkit\" -> \"tumor_bin_level_ratios\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_base_coverage_metrics\";\n  \"detect_variants\" -> \"strelka_filtered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_alignment_summary_metrics\";\n  \"detect_variants\" -> \"final_tsv\";\n  \"detect_variants\" -> \"mutect_unfiltered_vcf\";\n  \"cnvkit\" -> \"tumor_segmented_ratios\";\n  \"normal_alignment_and_qc\" -> \"normal_hs_metrics\";\n  \"cnvkit\" -> \"intervals_antitarget\";\n  \"normal_alignment_and_qc\" -> \"normal_mark_duplicates_metrics\";\n  \"normal_alignment_and_qc\" -> \"normal_per_target_hs_metrics\";\n  \"manta\" -> \"diploid_variants\";\n  \"normal_index_cram\" -> \"normal_cram\";\n  \"normal_alignment_and_qc\" -> \"normal_alignment_summary_metrics\";\n  \"manta\" -> \"small_candidates\";\n  \"detect_variants\" -> \"normal_indel_bam_readcount_tsv\";\n  \"tumor_alignment_and_qc\" -> \"tumor_hs_metrics\";\n  \"tumor_alignment_and_qc\" -> \"tumor_flagstats\";\n  \"normal_alignment_and_qc\" -> \"normal_verify_bam_id_depth\";\n  \"detect_variants\" -> \"mutect_filtered_vcf\";\n  \"tumor_alignment_and_qc\" -> \"tumor_per_base_hs_metrics\";\n  \"detect_variants\" -> \"strelka_unfiltered_vcf\";\n  \"concordance\" -> \"somalier_concordance_metrics\";\n  \"cnvkit\" -> \"tumor_antitarget_coverage\";\n  \"detect_variants\" -> \"final_filtered_vcf\";\n  \"cnvkit\" -> \"cn_scatter_plot\";\n  \"normal_alignment_and_qc\" -> \"normal_insert_size_metrics\";\n  \"manta\" -> \"all_candidates\";\n  \"tumor_alignment_and_qc\" -> \"tumor_verify_bam_id_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/pipelines/somatic_exome.cwl","licenseName":"MIT License"}