{"@id":"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"6bfb64375e7ebb6eb40f463ede86d8deccdb9eff","path":"definitions/pipelines/detect_variants_wgs.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl","url":"https://github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl"},"retrievedOn":"2026-09-10T15:15:46.731+00:00","lastCommit":"6bfb64375e7ebb6eb40f463ede86d8deccdb9eff","label":"Detect Variants workflow for WGS pipeline","inputs":{"docm_vcf":{"type":"File"},"vep_pick":{},"reference":{"type":"String"},"tumor_bam":{"type":"File"},"normal_bam":{"type":"File"},"vep_plugins":{"type":"String[] (Optional)"},"interval_list":{"type":"File"},"synonyms_file":{"type":"File (Optional)"},"vep_cache_dir":{"type":"String"},"cle_vcf_filter":{"type":"Boolean (Optional)"},"known_variants":{"doc":"Previously discovered variants to be flagged in this pipelines's output vcf","type":"File (Optional)"},"varscan_p_value":{"type":"Float (Optional)"},"tumor_sample_name":{"type":"String"},"normal_sample_name":{"type":"String"},"pindel_insert_size":{"type":"Integer"},"strelka_exome_mode":{"type":"Boolean"},"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[] (Optional)"},"annotate_coding_only":{"type":"Boolean (Optional)"},"filter_docm_variants":{"type":"Boolean (Optional)"},"filter_minimum_depth":{"type":"Integer (Optional)"},"mutect_scatter_count":{"type":"Integer (Optional)"},"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)"},"filter_mapq0_threshold":{"type":"Float (Optional)"},"vep_custom_annotations":{"doc":"custom type, check types directory for input format","type":"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[]"},"varscan_max_normal_freq":{"type":"Float (Optional)"},"variants_to_table_fields":{"type":"String[] (Optional)"},"filter_somatic_llr_threshold":{"type":"Float (Optional)"},"readcount_minimum_base_quality":{"type":"Integer (Optional)"},"readcount_minimum_mapping_quality":{"type":"Integer (Optional)"},"variants_to_table_genotype_fields":{"type":"String[] (Optional)"},"filter_gnomADe_maximum_population_allele_frequency":{"type":"Float (Optional)"}},"outputs":{"final_tsv":{"type":"File"},"final_vcf":{"type":"File"},"vep_summary":{"type":"File"},"docm_filtered_vcf":{"type":"File"},"final_filtered_vcf":{"type":"File"},"mutect_filtered_vcf":{"type":"File"},"strelka_filtered_vcf":{"type":"File"},"varscan_filtered_vcf":{"type":"File"},"mutect_unfiltered_vcf":{"type":"File"},"strelka_unfiltered_vcf":{"type":"File"},"varscan_unfiltered_vcf":{"type":"File"},"tumor_snv_bam_readcount_tsv":{"type":"File"},"normal_snv_bam_readcount_tsv":{"type":"File"},"tumor_indel_bam_readcount_tsv":{"type":"File"},"normal_indel_bam_readcount_tsv":{"type":"File"}},"steps":{"docm":{"label":"Detect Docm variants","run":"../subworkflows/docm_cle.cwl","runType":"WORKFLOW","sources":{"docm":{"sourceIDs":["filter_docm_variants"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#docm/docm_vcf":{"sourceIDs":["docm_vcf"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#docm/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#docm/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#docm/normal_bam":{"sourceIDs":["normal_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#docm/interval_list":{"sourceIDs":["interval_list"]}}},"index":{"label":"vcf index","run":"../tools/index_vcf.cwl","runType":"COMMANDLINETOOL","sources":{"index":{"sourceIDs":["add_normal_bam_readcount_to_vcf"]}}},"mutect":{"label":"mutect parallel workflow","run":"../subworkflows/mutect.cwl","runType":"WORKFLOW","sources":{"mutect":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#mutect/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#mutect/normal_bam":{"sourceIDs":["normal_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#mutect/interval_list":{"sourceIDs":["interval_list"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#mutect/scatter_count":{"sourceIDs":["mutect_scatter_count"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#mutect/tumor_sample_name":{"sourceIDs":["tumor_sample_name"]}}},"combine":{"label":"CombineVariants (GATK 3.6)","run":"../tools/combine_variants_wgs.cwl","runType":"COMMANDLINETOOL","sources":{"combine":{"sourceIDs":["strelka"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#combine/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#combine/mutect_vcf":{"sourceIDs":["mutect"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#combine/varscan_vcf":{"sourceIDs":["varscan"]}}},"strelka":{"label":"strelka workflow","run":"../subworkflows/strelka_and_post_processing.cwl","runType":"WORKFLOW","sources":{"strelka":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#strelka/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#strelka/exome_mode":{"sourceIDs":["strelka_exome_mode"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#strelka/normal_bam":{"sourceIDs":["normal_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#strelka/cpu_reserved":{"sourceIDs":["strelka_cpu_reserved"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#strelka/interval_list":{"sourceIDs":["interval_list"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#strelka/tumor_sample_name":{"sourceIDs":["tumor_sample_name"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#strelka/normal_sample_name":{"sourceIDs":["normal_sample_name"]}}},"varscan":{"label":"Varscan Workflow","run":"../subworkflows/varscan_pre_and_post_processing.cwl","runType":"WORKFLOW","sources":{"varscan":{"sourceIDs":["varscan_min_var_freq"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/p_value":{"sourceIDs":["varscan_p_value"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/normal_bam":{"sourceIDs":["normal_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/min_coverage":{"sourceIDs":["varscan_min_coverage"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/interval_list":{"sourceIDs":["interval_list"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/strand_filter":{"sourceIDs":["varscan_strand_filter"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/max_normal_freq":{"sourceIDs":["varscan_max_normal_freq"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/tumor_sample_name":{"sourceIDs":["tumor_sample_name"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#varscan/normal_sample_name":{"sourceIDs":["normal_sample_name"]}}},"decompose":{"label":"run vt decompose","run":"../tools/vt_decompose.cwl","runType":"COMMANDLINETOOL","sources":{"decompose":{"sourceIDs":["add_docm_variants"]}}},"filter_vcf":{"label":"Apply filters to VCF file","run":"../subworkflows/filter_vcf.cwl","runType":"WORKFLOW","sources":{"filter_vcf":{"sourceIDs":["vep_custom_annotations"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/vcf":{"sourceIDs":["index"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/known_variants":{"sourceIDs":["known_variants"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/do_cle_vcf_filter":{"sourceIDs":["cle_vcf_filter"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/tumor_sample_name":{"sourceIDs":["tumor_sample_name"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/normal_sample_name":{"sourceIDs":["normal_sample_name"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/filter_minimum_depth":{"sourceIDs":["filter_minimum_depth"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/filter_mapq0_threshold":{"sourceIDs":["filter_mapq0_threshold"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/filter_somatic_llr_threshold":{"sourceIDs":["filter_somatic_llr_threshold"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#filter_vcf/filter_gnomADe_maximum_population_allele_frequency":{"sourceIDs":["filter_gnomADe_maximum_population_allele_frequency"]}}},"decompose_index":{"label":"vcf index","run":"../tools/index_vcf.cwl","runType":"COMMANDLINETOOL","sources":{"decompose_index":{"sourceIDs":["decompose"]}}},"add_docm_variants":{"label":"CombineVariants (GATK 3.6)","run":"../tools/docm_add_variants.cwl","runType":"COMMANDLINETOOL","sources":{"add_docm_variants":{"sourceIDs":["docm"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_docm_variants/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_docm_variants/callers_vcf":{"sourceIDs":["combine"]}}},"annotate_variants":{"label":"Ensembl Variant Effect Predictor","run":"../tools/vep.cwl","runType":"COMMANDLINETOOL","sources":{"annotate_variants":{"sourceIDs":["annotate_coding_only"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/vcf":{"sourceIDs":["decompose_index"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/pick":{"sourceIDs":["vep_pick"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/plugins":{"sourceIDs":["vep_plugins"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/cache_dir":{"sourceIDs":["vep_cache_dir"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/synonyms_file":{"sourceIDs":["synonyms_file"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/ensembl_species":{"sourceIDs":["vep_ensembl_species"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/ensembl_version":{"sourceIDs":["vep_ensembl_version"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/ensembl_assembly":{"sourceIDs":["vep_ensembl_assembly"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#annotate_variants/custom_annotations":{"sourceIDs":["vep_custom_annotations"]}}},"variants_to_table":{"label":"SelectVariants (GATK 3.6)","run":"../tools/variants_to_table.cwl","runType":"COMMANDLINETOOL","sources":{"variants_to_table":{"sourceIDs":["variants_to_table_genotype_fields"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#variants_to_table/vcf":{"sourceIDs":["annotated_filter_index"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#variants_to_table/fields":{"sourceIDs":["variants_to_table_fields"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#variants_to_table/reference":{"sourceIDs":["reference"]}}},"tumor_bam_readcount":{"label":"run bam-readcount","run":"../tools/bam_readcount.cwl","runType":"COMMANDLINETOOL","sources":{"tumor_bam_readcount":{"sourceIDs":["readcount_minimum_base_quality"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#tumor_bam_readcount/bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#tumor_bam_readcount/vcf":{"sourceIDs":["annotate_variants"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#tumor_bam_readcount/sample":{"defaultVal":"\\\"TUMOR\\\""},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#tumor_bam_readcount/reference_fasta":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#tumor_bam_readcount/min_mapping_quality":{"sourceIDs":["readcount_minimum_mapping_quality"]}}},"normal_bam_readcount":{"label":"run bam-readcount","run":"../tools/bam_readcount.cwl","runType":"COMMANDLINETOOL","sources":{"normal_bam_readcount":{"sourceIDs":["annotate_variants"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#normal_bam_readcount/bam":{"sourceIDs":["normal_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#normal_bam_readcount/sample":{"defaultVal":"\\\"NORMAL\\\""},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#normal_bam_readcount/reference_fasta":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#normal_bam_readcount/min_base_quality":{"sourceIDs":["readcount_minimum_base_quality"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#normal_bam_readcount/min_mapping_quality":{"sourceIDs":["readcount_minimum_mapping_quality"]}}},"annotated_filter_bgzip":{"label":"bgzip VCF","run":"../tools/bgzip.cwl","runType":"COMMANDLINETOOL","sources":{"annotated_filter_bgzip":{"sourceIDs":["filter_vcf"]}}},"annotated_filter_index":{"label":"vcf index","run":"../tools/index_vcf.cwl","runType":"COMMANDLINETOOL","sources":{"annotated_filter_index":{"sourceIDs":["annotated_filter_bgzip"]}}},"add_vep_fields_to_table":{"label":"add VEP annotation to report","run":"../tools/add_vep_fields_to_table.cwl","runType":"COMMANDLINETOOL","sources":{"add_vep_fields_to_table":{"sourceIDs":["variants_to_table"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_vep_fields_to_table/vcf":{"sourceIDs":["annotated_filter_index"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_vep_fields_to_table/vep_fields":{"sourceIDs":["vep_to_table_fields"]}}},"add_tumor_bam_readcount_to_vcf":{"label":"Add snv and indel bam-readcount files to a vcf","run":"../subworkflows/vcf_readcount_annotator.cwl","runType":"WORKFLOW","sources":{"add_tumor_bam_readcount_to_vcf":{"sourceIDs":["tumor_bam_readcount"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_tumor_bam_readcount_to_vcf/vcf":{"sourceIDs":["annotate_variants"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_tumor_bam_readcount_to_vcf/data_type":{"defaultVal":"\\\"DNA\\\""},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_tumor_bam_readcount_to_vcf/sample_name":{"defaultVal":"\\\"TUMOR\\\""},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_tumor_bam_readcount_to_vcf/indel_bam_readcount_tsv":{"sourceIDs":["tumor_bam_readcount"]}}},"add_normal_bam_readcount_to_vcf":{"label":"Add snv and indel bam-readcount files to a vcf","run":"../subworkflows/vcf_readcount_annotator.cwl","runType":"WORKFLOW","sources":{"add_normal_bam_readcount_to_vcf":{"sourceIDs":["add_tumor_bam_readcount_to_vcf"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_normal_bam_readcount_to_vcf/data_type":{"defaultVal":"\\\"DNA\\\""},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_normal_bam_readcount_to_vcf/sample_name":{"defaultVal":"\\\"NORMAL\\\""},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_normal_bam_readcount_to_vcf/snv_bam_readcount_tsv":{"sourceIDs":["normal_bam_readcount"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl#add_normal_bam_readcount_to_vcf/indel_bam_readcount_tsv":{"sourceIDs":["normal_bam_readcount"]}}}},"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    \"vep_custom_annotations\" [fillcolor=\"#94DDF4\",label=\"vep_custom_annotations\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"annotate_coding_only\" [fillcolor=\"#94DDF4\",label=\"annotate_coding_only\"];\n    \"varscan_min_var_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_min_var_freq\"];\n    \"readcount_minimum_base_quality\" [fillcolor=\"#94DDF4\",label=\"readcount_minimum_base_quality\"];\n    \"tumor_bam\" [fillcolor=\"#94DDF4\",label=\"tumor_bam\"];\n    \"filter_somatic_llr_threshold\" [fillcolor=\"#94DDF4\",label=\"filter_somatic_llr_threshold\"];\n    \"filter_gnomADe_maximum_population_allele_frequency\" [fillcolor=\"#94DDF4\",label=\"filter_gnomADe_maximum_population_allele_frequency\"];\n    \"variants_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_fields\"];\n    \"normal_sample_name\" [fillcolor=\"#94DDF4\",label=\"normal_sample_name\"];\n    \"cle_vcf_filter\" [fillcolor=\"#94DDF4\",label=\"cle_vcf_filter\"];\n    \"filter_minimum_depth\" [fillcolor=\"#94DDF4\",label=\"filter_minimum_depth\"];\n    \"varscan_max_normal_freq\" [fillcolor=\"#94DDF4\",label=\"varscan_max_normal_freq\"];\n    \"vep_pick\" [fillcolor=\"#94DDF4\",label=\"vep_pick\"];\n    \"synonyms_file\" [fillcolor=\"#94DDF4\",label=\"synonyms_file\"];\n    \"readcount_minimum_mapping_quality\" [fillcolor=\"#94DDF4\",label=\"readcount_minimum_mapping_quality\"];\n    \"mutect_scatter_count\" [fillcolor=\"#94DDF4\",label=\"mutect_scatter_count\"];\n    \"vep_plugins\" [fillcolor=\"#94DDF4\",label=\"vep_plugins\"];\n    \"known_variants\" [fillcolor=\"#94DDF4\",label=\"known_variants\"];\n    \"tumor_sample_name\" [fillcolor=\"#94DDF4\",label=\"tumor_sample_name\"];\n    \"pindel_insert_size\" [fillcolor=\"#94DDF4\",label=\"pindel_insert_size\"];\n    \"strelka_cpu_reserved\" [fillcolor=\"#94DDF4\",label=\"strelka_cpu_reserved\"];\n    \"filter_mapq0_threshold\" [fillcolor=\"#94DDF4\",label=\"filter_mapq0_threshold\"];\n    \"variants_to_table_genotype_fields\" [fillcolor=\"#94DDF4\",label=\"variants_to_table_genotype_fields\"];\n    \"filter_docm_variants\" [fillcolor=\"#94DDF4\",label=\"filter_docm_variants\"];\n    \"interval_list\" [fillcolor=\"#94DDF4\",label=\"interval_list\"];\n    \"vep_ensembl_species\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_species\"];\n    \"strelka_exome_mode\" [fillcolor=\"#94DDF4\",label=\"strelka_exome_mode\"];\n    \"vep_to_table_fields\" [fillcolor=\"#94DDF4\",label=\"vep_to_table_fields\"];\n    \"varscan_p_value\" [fillcolor=\"#94DDF4\",label=\"varscan_p_value\"];\n    \"varscan_strand_filter\" [fillcolor=\"#94DDF4\",label=\"varscan_strand_filter\"];\n    \"vep_cache_dir\" [fillcolor=\"#94DDF4\",label=\"vep_cache_dir\"];\n    \"vep_ensembl_version\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_version\"];\n    \"vep_ensembl_assembly\" [fillcolor=\"#94DDF4\",label=\"vep_ensembl_assembly\"];\n    \"docm_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_vcf\"];\n    \"normal_bam\" [fillcolor=\"#94DDF4\",label=\"normal_bam\"];\n    \"varscan_min_coverage\" [fillcolor=\"#94DDF4\",label=\"varscan_min_coverage\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"final_tsv\" [fillcolor=\"#94DDF4\",label=\"final_tsv\"];\n    \"tumor_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_snv_bam_readcount_tsv\"];\n    \"vep_summary\" [fillcolor=\"#94DDF4\",label=\"vep_summary\"];\n    \"varscan_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_filtered_vcf\"];\n    \"varscan_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"varscan_unfiltered_vcf\"];\n    \"mutect_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_filtered_vcf\"];\n    \"tumor_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"tumor_indel_bam_readcount_tsv\"];\n    \"strelka_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_unfiltered_vcf\"];\n    \"final_vcf\" [fillcolor=\"#94DDF4\",label=\"final_vcf\"];\n    \"final_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"final_filtered_vcf\"];\n    \"normal_indel_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_indel_bam_readcount_tsv\"];\n    \"docm_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_filtered_vcf\"];\n    \"normal_snv_bam_readcount_tsv\" [fillcolor=\"#94DDF4\",label=\"normal_snv_bam_readcount_tsv\"];\n    \"mutect_unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"mutect_unfiltered_vcf\"];\n    \"strelka_filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"strelka_filtered_vcf\"];\n  }\n  \"normal_bam_readcount\" [label=\"run bam-readcount\"];\n  \"decompose\" [label=\"run vt decompose\"];\n  \"annotated_filter_bgzip\" [label=\"bgzip VCF\"];\n  \"add_tumor_bam_readcount_to_vcf\" [label=\"Add snv and indel bam-readcount files to a vcf\", fillcolor=\"#F3CEA1\"];\n  \"add_vep_fields_to_table\" [label=\"add VEP annotation to report\"];\n  \"add_normal_bam_readcount_to_vcf\" [label=\"Add snv and indel bam-readcount files to a vcf\", fillcolor=\"#F3CEA1\"];\n  \"variants_to_table\" [label=\"SelectVariants (GATK 3.6)\"];\n  \"decompose_index\" [label=\"vcf index\"];\n  \"annotated_filter_index\" [label=\"vcf index\"];\n  \"mutect\" [label=\"mutect parallel workflow\", fillcolor=\"#F3CEA1\"];\n  \"docm\" [label=\"Detect Docm variants\", fillcolor=\"#F3CEA1\"];\n  \"strelka\" [label=\"strelka workflow\", fillcolor=\"#F3CEA1\"];\n  \"tumor_bam_readcount\" [label=\"run bam-readcount\"];\n  \"combine\" [label=\"CombineVariants (GATK 3.6)\"];\n  \"annotate_variants\" [label=\"Ensembl Variant Effect Predictor\"];\n  \"index\" [label=\"vcf index\"];\n  \"varscan\" [label=\"Varscan Workflow\", fillcolor=\"#F3CEA1\"];\n  \"filter_vcf\" [label=\"Apply filters to VCF file\", fillcolor=\"#F3CEA1\"];\n  \"add_docm_variants\" [label=\"CombineVariants (GATK 3.6)\"];\n  \"annotate_variants\" -> \"normal_bam_readcount\" [label=\"vcf\"];\n  \"default1\" -> \"normal_bam_readcount\" [label=\"sample\"];\n  \"default1\" [label=\"\\\"NORMAL\\\"\", fillcolor=\"#D5AEFC\"];\n  \"reference\" -> \"normal_bam_readcount\" [label=\"reference_fasta\"];\n  \"readcount_minimum_mapping_quality\" -> \"normal_bam_readcount\" [label=\"min_mapping_quality\"];\n  \"readcount_minimum_base_quality\" -> \"normal_bam_readcount\" [label=\"min_base_quality\"];\n  \"normal_bam\" -> \"normal_bam_readcount\" [label=\"bam\"];\n  \"add_docm_variants\" -> \"decompose\" [label=\"vcf\"];\n  \"filter_vcf\" -> \"annotated_filter_bgzip\" [label=\"file\"];\n  \"tumor_bam_readcount\" -> \"add_tumor_bam_readcount_to_vcf\" [label=\"snv_bam_readcount_tsv\"];\n  \"annotate_variants\" -> \"add_tumor_bam_readcount_to_vcf\" [label=\"vcf\"];\n  \"default2\" -> \"add_tumor_bam_readcount_to_vcf\" [label=\"data_type\"];\n  \"default2\" [label=\"\\\"DNA\\\"\", fillcolor=\"#D5AEFC\"];\n  \"tumor_bam_readcount\" -> \"add_tumor_bam_readcount_to_vcf\" [label=\"indel_bam_readcount_tsv\"];\n  \"default3\" -> \"add_tumor_bam_readcount_to_vcf\" [label=\"sample_name\"];\n  \"default3\" [label=\"\\\"TUMOR\\\"\", fillcolor=\"#D5AEFC\"];\n  \"variants_to_table\" -> \"add_vep_fields_to_table\" [label=\"tsv\"];\n  \"vep_to_table_fields\" -> \"add_vep_fields_to_table\" [label=\"vep_fields\"];\n  \"annotated_filter_index\" -> \"add_vep_fields_to_table\" [label=\"vcf\"];\n  \"add_tumor_bam_readcount_to_vcf\" -> \"add_normal_bam_readcount_to_vcf\" [label=\"vcf\"];\n  \"default4\" -> \"add_normal_bam_readcount_to_vcf\" [label=\"sample_name\"];\n  \"default4\" [label=\"\\\"NORMAL\\\"\", fillcolor=\"#D5AEFC\"];\n  \"normal_bam_readcount\" -> \"add_normal_bam_readcount_to_vcf\" [label=\"snv_bam_readcount_tsv\"];\n  \"normal_bam_readcount\" -> \"add_normal_bam_readcount_to_vcf\" [label=\"indel_bam_readcount_tsv\"];\n  \"default5\" -> \"add_normal_bam_readcount_to_vcf\" [label=\"data_type\"];\n  \"default5\" [label=\"\\\"DNA\\\"\", fillcolor=\"#D5AEFC\"];\n  \"variants_to_table_genotype_fields\" -> \"variants_to_table\" [label=\"genotype_fields\"];\n  \"reference\" -> \"variants_to_table\" [label=\"reference\"];\n  \"variants_to_table_fields\" -> \"variants_to_table\" [label=\"fields\"];\n  \"annotated_filter_index\" -> \"variants_to_table\" [label=\"vcf\"];\n  \"decompose\" -> \"decompose_index\" [label=\"vcf\"];\n  \"annotated_filter_bgzip\" -> \"annotated_filter_index\" [label=\"vcf\"];\n  \"reference\" -> \"mutect\" [label=\"reference\"];\n  \"tumor_bam\" -> \"mutect\" [label=\"tumor_bam\"];\n  \"interval_list\" -> \"mutect\" [label=\"interval_list\"];\n  \"tumor_sample_name\" -> \"mutect\" [label=\"tumor_sample_name\"];\n  \"normal_bam\" -> \"mutect\" [label=\"normal_bam\"];\n  \"mutect_scatter_count\" -> \"mutect\" [label=\"scatter_count\"];\n  \"filter_docm_variants\" -> \"docm\" [label=\"filter_docm_variants\"];\n  \"docm_vcf\" -> \"docm\" [label=\"docm_vcf\"];\n  \"tumor_bam\" -> \"docm\" [label=\"tumor_bam\"];\n  \"interval_list\" -> \"docm\" [label=\"interval_list\"];\n  \"normal_bam\" -> \"docm\" [label=\"normal_bam\"];\n  \"reference\" -> \"docm\" [label=\"reference\"];\n  \"reference\" -> \"strelka\" [label=\"reference\"];\n  \"tumor_sample_name\" -> \"strelka\" [label=\"tumor_sample_name\"];\n  \"strelka_cpu_reserved\" -> \"strelka\" [label=\"cpu_reserved\"];\n  \"normal_bam\" -> \"strelka\" [label=\"normal_bam\"];\n  \"interval_list\" -> \"strelka\" [label=\"interval_list\"];\n  \"tumor_bam\" -> \"strelka\" [label=\"tumor_bam\"];\n  \"normal_sample_name\" -> \"strelka\" [label=\"normal_sample_name\"];\n  \"strelka_exome_mode\" -> \"strelka\" [label=\"exome_mode\"];\n  \"readcount_minimum_base_quality\" -> \"tumor_bam_readcount\" [label=\"min_base_quality\"];\n  \"annotate_variants\" -> \"tumor_bam_readcount\" [label=\"vcf\"];\n  \"default6\" -> \"tumor_bam_readcount\" [label=\"sample\"];\n  \"default6\" [label=\"\\\"TUMOR\\\"\", fillcolor=\"#D5AEFC\"];\n  \"reference\" -> \"tumor_bam_readcount\" [label=\"reference_fasta\"];\n  \"readcount_minimum_mapping_quality\" -> \"tumor_bam_readcount\" [label=\"min_mapping_quality\"];\n  \"tumor_bam\" -> \"tumor_bam_readcount\" [label=\"bam\"];\n  \"strelka\" -> \"combine\" [label=\"strelka_vcf\"];\n  \"mutect\" -> \"combine\" [label=\"mutect_vcf\"];\n  \"reference\" -> \"combine\" [label=\"reference\"];\n  \"varscan\" -> \"combine\" [label=\"varscan_vcf\"];\n  \"annotate_coding_only\" -> \"annotate_variants\" [label=\"coding_only\"];\n  \"reference\" -> \"annotate_variants\" [label=\"reference\"];\n  \"vep_pick\" -> \"annotate_variants\" [label=\"pick\"];\n  \"vep_ensembl_species\" -> \"annotate_variants\" [label=\"ensembl_species\"];\n  \"vep_ensembl_version\" -> \"annotate_variants\" [label=\"ensembl_version\"];\n  \"vep_custom_annotations\" -> \"annotate_variants\" [label=\"custom_annotations\"];\n  \"synonyms_file\" -> \"annotate_variants\" [label=\"synonyms_file\"];\n  \"vep_ensembl_assembly\" -> \"annotate_variants\" [label=\"ensembl_assembly\"];\n  \"decompose_index\" -> \"annotate_variants\" [label=\"vcf\"];\n  \"vep_cache_dir\" -> \"annotate_variants\" [label=\"cache_dir\"];\n  \"vep_plugins\" -> \"annotate_variants\" [label=\"plugins\"];\n  \"add_normal_bam_readcount_to_vcf\" -> \"index\" [label=\"vcf\"];\n  \"varscan_min_var_freq\" -> \"varscan\" [label=\"min_var_freq\"];\n  \"varscan_max_normal_freq\" -> \"varscan\" [label=\"max_normal_freq\"];\n  \"varscan_strand_filter\" -> \"varscan\" [label=\"strand_filter\"];\n  \"normal_bam\" -> \"varscan\" [label=\"normal_bam\"];\n  \"varscan_min_coverage\" -> \"varscan\" [label=\"min_coverage\"];\n  \"varscan_p_value\" -> \"varscan\" [label=\"p_value\"];\n  \"tumor_sample_name\" -> \"varscan\" [label=\"tumor_sample_name\"];\n  \"reference\" -> \"varscan\" [label=\"reference\"];\n  \"tumor_bam\" -> \"varscan\" [label=\"tumor_bam\"];\n  \"normal_sample_name\" -> \"varscan\" [label=\"normal_sample_name\"];\n  \"interval_list\" -> \"varscan\" [label=\"interval_list\"];\n  \"vep_custom_annotations\" -> \"filter_vcf\" [label=\"gnomad_field_name\"];\n  \"reference\" -> \"filter_vcf\" [label=\"reference\"];\n  \"filter_somatic_llr_threshold\" -> \"filter_vcf\" [label=\"filter_somatic_llr_threshold\"];\n  \"normal_sample_name\" -> \"filter_vcf\" [label=\"normal_sample_name\"];\n  \"known_variants\" -> \"filter_vcf\" [label=\"known_variants\"];\n  \"cle_vcf_filter\" -> \"filter_vcf\" [label=\"do_cle_vcf_filter\"];\n  \"filter_mapq0_threshold\" -> \"filter_vcf\" [label=\"filter_mapq0_threshold\"];\n  \"filter_minimum_depth\" -> \"filter_vcf\" [label=\"filter_minimum_depth\"];\n  \"tumor_bam\" -> \"filter_vcf\" [label=\"tumor_bam\"];\n  \"filter_gnomADe_maximum_population_allele_frequency\" -> \"filter_vcf\" [label=\"filter_gnomADe_maximum_population_allele_frequency\"];\n  \"index\" -> \"filter_vcf\" [label=\"vcf\"];\n  \"tumor_sample_name\" -> \"filter_vcf\" [label=\"tumor_sample_name\"];\n  \"docm\" -> \"add_docm_variants\" [label=\"docm_vcf\"];\n  \"combine\" -> \"add_docm_variants\" [label=\"callers_vcf\"];\n  \"reference\" -> \"add_docm_variants\" [label=\"reference\"];\n  \"add_vep_fields_to_table\" -> \"final_tsv\";\n  \"tumor_bam_readcount\" -> \"tumor_snv_bam_readcount_tsv\";\n  \"annotate_variants\" -> \"vep_summary\";\n  \"varscan\" -> \"varscan_filtered_vcf\";\n  \"varscan\" -> \"varscan_unfiltered_vcf\";\n  \"mutect\" -> \"mutect_filtered_vcf\";\n  \"tumor_bam_readcount\" -> \"tumor_indel_bam_readcount_tsv\";\n  \"strelka\" -> \"strelka_unfiltered_vcf\";\n  \"index\" -> \"final_vcf\";\n  \"annotated_filter_index\" -> \"final_filtered_vcf\";\n  \"normal_bam_readcount\" -> \"normal_indel_bam_readcount_tsv\";\n  \"docm\" -> \"docm_filtered_vcf\";\n  \"normal_bam_readcount\" -> \"normal_snv_bam_readcount_tsv\";\n  \"mutect\" -> \"mutect_unfiltered_vcf\";\n  \"strelka\" -> \"strelka_filtered_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/pipelines/detect_variants_wgs.cwl","licenseName":"MIT License"}