{"@id":"https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/varscan/germline_workflow.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/cancer-genomics-workflow.git","branch":"d1ee6a2a323cee7e4af00c7e0b926c2192038e1d","path":"varscan/germline_workflow.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/cancer-genomics-workflow/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/varscan/germline_workflow.cwl","url":"https://github.com/genome/cancer-genomics-workflow/blob/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/varscan/germline_workflow.cwl"},"retrievedOn":"2023-01-12T05:57:02.750+00:00","lastCommit":"d1ee6a2a323cee7e4af00c7e0b926c2192038e1d","label":"Varscan Workflow","inputs":{"cram":{"type":"File"},"p_value":{"type":"Float (Optional)"},"min_reads":{"type":"Integer (Optional)"},"reference":{"type":"String"},"sample_name":{"type":"String"},"min_coverage":{"type":"Integer (Optional)"},"min_var_freq":{"type":"Float 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= \"Workflow Inputs\";\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"sample_name\" [fillcolor=\"#94DDF4\",label=\"sample_name\"];\n    \"interval_list\" [fillcolor=\"#94DDF4\",label=\"interval_list\"];\n    \"cram\" [fillcolor=\"#94DDF4\",label=\"cram\"];\n    \"min_reads\" [fillcolor=\"#94DDF4\",label=\"min_reads\"];\n    \"strand_filter\" [fillcolor=\"#94DDF4\",label=\"strand_filter\"];\n    \"max_normal_freq\" [fillcolor=\"#94DDF4\",label=\"max_normal_freq\"];\n    \"p_value\" [fillcolor=\"#94DDF4\",label=\"p_value\"];\n    \"min_var_freq\" [fillcolor=\"#94DDF4\",label=\"min_var_freq\"];\n    \"min_coverage\" [fillcolor=\"#94DDF4\",label=\"min_coverage\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"filtered_vcf\"];\n    \"unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"unfiltered_vcf\"];\n  }\n  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\"bgzip_and_index\" -> \"filter\" [label=\"vcf\"];\n  \"sample_name\" -> \"filter\" [label=\"sample_name\"];\n  \"reference\" -> \"filter\" [label=\"reference\"];\n  \"filter\" -> \"filtered_vcf\";\n  \"filter\" -> \"unfiltered_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/varscan/germline_workflow.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/cancer-genomics-workflow/blob/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/varscan/germline_workflow.cwl","visualisationPng":"/graph/png/github.com/genome/cancer-genomics-workflow/blob/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/varscan/germline_workflow.cwl","visualisationSvg":"/graph/svg/github.com/genome/cancer-genomics-workflow/blob/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/varscan/germline_workflow.cwl","roBundle":"/robundle/github.com/genome/cancer-genomics-workflow/blob/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/varscan/germline_workflow.cwl","licenseName":"MIT License"}