{"@id":"https://w3id.org/cwl/view/git/10870aefd20469e728969269ff3c54b3b8339a18/definitions/subworkflows/germline_detect_variants.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"10870aefd20469e728969269ff3c54b3b8339a18","path":"definitions/subworkflows/germline_detect_variants.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/10870aefd20469e728969269ff3c54b3b8339a18/definitions/subworkflows/germline_detect_variants.cwl","url":"https://github.com/genome/analysis-workflows/blob/10870aefd20469e728969269ff3c54b3b8339a18/definitions/subworkflows/germline_detect_variants.cwl"},"retrievedOn":"2026-09-22T05:11:55.353+00:00","lastCommit":"10870aefd20469e728969269ff3c54b3b8339a18","label":"exome alignment and germline variant detection","inputs":{"bam":{"type":"File"},"ploidy":{"type":"Integer (Optional)"},"intervals":{"type":"9f545f1b7d07e82dfae9000633e17cbd[]"},"reference":{"type":"File"},"vep_plugins":{"type":"String[]"},"gvcf_gq_bands":{"type":"String[]"},"synonyms_file":{"type":"File (Optional)"},"vep_cache_dir":{"type":"Directory"},"final_tsv_prefix":{"type":"String (Optional)"},"vep_ensembl_species":{"doc":"ensembl species - Must be present in the cache directory. 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A workaround for workflow engines that don't support rename.cwl.  If running in cwltool, use the other one instead.","run":"../tools/staged_rename.cwl","runType":"COMMANDLINETOOL","sources":{"set_final_tsv_name":{"sourceIDs":["final_add_vep_fields_to_table"]}}},"bgzip_annotated_vcf":{"label":"bgzip VCF","run":"../tools/bgzip.cwl","runType":"COMMANDLINETOOL","sources":{"bgzip_annotated_vcf":{"sourceIDs":["annotate_variants"]}}},"index_annotated_vcf":{"label":"vcf index","run":"../tools/index_vcf.cwl","runType":"COMMANDLINETOOL","sources":{"index_annotated_vcf":{"sourceIDs":["bgzip_annotated_vcf"]}}},"set_filtered_tsv_name":{"label":"Staged Renamer","doc":"Renames a file by staging and then `mv`ing it.  A workaround for workflow engines that don't support rename.cwl.  If running in cwltool, use the other one instead.","run":"../tools/staged_rename.cwl","runType":"COMMANDLINETOOL","sources":{"set_filtered_tsv_name":{"sourceIDs":["filtered_add_vep_fields_to_table"]}}},"final_variants_to_table":{"label":"SelectVariants (GATK 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\"filtered_variants_to_table\" -> \"filtered_add_vep_fields_to_table\" [label=\"tsv\"];\n  \"vep_custom_annotations\" -> \"filter_vcf\" [label=\"gnomad_field_name\"];\n  \"limit_variant_intervals\" -> \"filter_vcf\" [label=\"limit_variant_intervals\"];\n  \"filter_gnomAD_maximum_population_allele_frequency\" -> \"filter_vcf\" [label=\"filter_gnomAD_maximum_population_allele_frequency\"];\n  \"annotate_variants\" -> \"filter_vcf\" [label=\"annotated_vcf\"];\n  \"reference\" -> \"filter_vcf\" [label=\"reference\"];\n  \"vep_plugins\" -> \"annotate_variants\" [label=\"plugins\"];\n  \"annotate_coding_only\" -> \"annotate_variants\" [label=\"coding_only\"];\n  \"synonyms_file\" -> \"annotate_variants\" [label=\"synonyms_file\"];\n  \"vep_ensembl_assembly\" -> \"annotate_variants\" [label=\"ensembl_assembly\"];\n  \"vep_cache_dir\" -> \"annotate_variants\" [label=\"cache_dir\"];\n  \"reference\" -> \"annotate_variants\" [label=\"reference\"];\n  \"vep_ensembl_version\" -> 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