{"@id":"https://w3id.org/cwl/view/git/60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2/definitions/pipelines/wgs.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2","path":"definitions/pipelines/wgs.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2/definitions/pipelines/wgs.cwl","url":"https://github.com/genome/analysis-workflows/blob/60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2/definitions/pipelines/wgs.cwl"},"retrievedOn":"2026-09-23T14:17:06.108+00:00","lastCommit":"60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2","label":"wgs alignment and tumor-only variant detection","inputs":{"mills":{"type":"File"},"docm_vcf":{"type":"File"},"omni_vcf":{"type":"File"},"sequence":{"type":"https://w3id.org/cwl/view/git/60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2/definitions/types/sequence_data.yml#sequence_data[]"},"vep_pick":{},"dbsnp_vcf":{"type":"File"},"reference":{"type":"String"},"sample_name":{"type":"String"},"known_indels":{"type":"File"},"qc_intervals":{"type":"File"},"synonyms_file":{"type":"File (Optional)"},"vep_cache_dir":{"type":"String"},"custom_gnomad_vcf":{"type":"File (Optional)"},"summary_intervals":{"type":"https://w3id.org/cwl/view/git/60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2/definitions/types/labelled_file.yml#labelled_file[]"},"per_base_intervals":{"type":"https://w3id.org/cwl/view/git/60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2/definitions/types/labelled_file.yml#labelled_file[]"},"vep_ensembl_species":{"doc":"ensembl species - Must be present in the cache directory. 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