{"@id":"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/germline_detect_variants.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"f7ac3eff79128831c9f7a565d5b187882f39aa58","path":"definitions/subworkflows/germline_detect_variants.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/germline_detect_variants.cwl","url":"https://github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/germline_detect_variants.cwl"},"retrievedOn":"2026-09-25T02:37:25.476+00:00","lastCommit":"f7ac3eff79128831c9f7a565d5b187882f39aa58","label":"exome alignment and germline variant detection","inputs":{"bam":{"type":"File"},"intervals":{"type":"adc04d674c5e9478f4595a05bd031f49[]"},"reference":{"type":"String"},"vep_plugins":{"type":"String[] (Optional)"},"gvcf_gq_bands":{"type":"String[]"},"synonyms_file":{"type":"File (Optional)"},"vep_cache_dir":{"type":"String"},"final_tsv_prefix":{"type":"String (Optional)"},"custom_gnomad_vcf":{"type":"File (Optional)"},"custom_clinvar_vcf":{"type":"File (Optional)"},"vep_ensembl_species":{"doc":"ensembl species - Must be present in the cache directory. 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