{"@id":"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"88f1e02b261bf9ce882eba306b6245c64328632b","path":"definitions/subworkflows/cnvkit_single_sample.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl","url":"https://github.com/genome/analysis-workflows/blob/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl"},"retrievedOn":"2026-09-10T21:59:41.402+00:00","lastCommit":"88f1e02b261bf9ce882eba306b6245c64328632b","label":"Subworkflow that runs cnvkit in single sample mode and returns a vcf file","inputs":{"method":{"type":"String (Optional)"},"diagram":{"type":"Boolean (Optional)"},"tumor_bam":{"type":"File"},"scatter_plot":{"type":"Boolean (Optional)"},"reference_cnn":{"type":"File"},"male_reference":{"type":"Boolean (Optional)"},"cnvkit_vcf_name":{"type":"String (Optional)"},"drop_low_coverage":{"type":"Boolean (Optional)"}},"outputs":{"cn_diagram":{"type":"File (Optional)"},"cnvkit_vcf":{"type":"File"},"cn_scatter_plot":{"type":"File (Optional)"},"tumor_target_coverage":{"type":"File"},"tumor_bin_level_ratios":{"type":"File"},"tumor_segmented_ratios":{"type":"File"},"tumor_antitarget_coverage":{"type":"File"}},"steps":{"cns_to_vcf":{"label":"Convert default cnvkit .cns output to standard vcf format","run":"../tools/cnvkit_vcf_export.cwl","runType":"COMMANDLINETOOL","sources":{"cns_to_vcf":{"sourceIDs":["cnvkit_main"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cns_to_vcf/cnr_file":{"sourceIDs":["cnvkit_main"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cns_to_vcf/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cns_to_vcf/output_name":{"sourceIDs":["cnvkit_vcf_name"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cns_to_vcf/male_reference":{"sourceIDs":["male_reference"]}}},"cnvkit_main":{"run":"../tools/cnvkit_batch.cwl","runType":"COMMANDLINETOOL","sources":{"cnvkit_main":{"sourceIDs":["reference_cnn"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cnvkit_main/method":{"sourceIDs":["method"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cnvkit_main/diagram":{"sourceIDs":["diagram"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cnvkit_main/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cnvkit_main/scatter_plot":{"sourceIDs":["scatter_plot"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cnvkit_main/male_reference":{"sourceIDs":["male_reference"]},"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl#cnvkit_main/drop_low_coverage":{"sourceIDs":["drop_low_coverage"]}}}},"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    \"reference_cnn\" [fillcolor=\"#94DDF4\",label=\"reference_cnn\"];\n    \"male_reference\" [fillcolor=\"#94DDF4\",label=\"male_reference\"];\n    \"tumor_bam\" [fillcolor=\"#94DDF4\",label=\"tumor_bam\"];\n    \"cnvkit_vcf_name\" [fillcolor=\"#94DDF4\",label=\"cnvkit_vcf_name\"];\n    \"diagram\" [fillcolor=\"#94DDF4\",label=\"diagram\"];\n    \"method\" [fillcolor=\"#94DDF4\",label=\"method\"];\n    \"scatter_plot\" [fillcolor=\"#94DDF4\",label=\"scatter_plot\"];\n    \"drop_low_coverage\" [fillcolor=\"#94DDF4\",label=\"drop_low_coverage\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"tumor_target_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_target_coverage\"];\n    \"tumor_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_antitarget_coverage\"];\n    \"cn_scatter_plot\" [fillcolor=\"#94DDF4\",label=\"cn_scatter_plot\"];\n    \"tumor_bin_level_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_bin_level_ratios\"];\n    \"cnvkit_vcf\" [fillcolor=\"#94DDF4\",label=\"cnvkit_vcf\"];\n    \"tumor_segmented_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_segmented_ratios\"];\n    \"cn_diagram\" [fillcolor=\"#94DDF4\",label=\"cn_diagram\"];\n  }\n  \"cns_to_vcf\" [label=\"Convert default cnvkit .cns output to standard vcf format\"];\n  \"cnvkit_main\" [label=\"cnvkit_main\"];\n  \"cnvkit_main\" -> \"cns_to_vcf\" [label=\"cns_file\"];\n  \"tumor_bam\" -> \"cns_to_vcf\" [label=\"tumor_bam\"];\n  \"cnvkit_vcf_name\" -> \"cns_to_vcf\" [label=\"output_name\"];\n  \"male_reference\" -> \"cns_to_vcf\" [label=\"male_reference\"];\n  \"cnvkit_main\" -> \"cns_to_vcf\" [label=\"cnr_file\"];\n  \"reference_cnn\" -> \"cnvkit_main\" [label=\"reference_cnn\"];\n  \"diagram\" -> \"cnvkit_main\" [label=\"diagram\"];\n  \"scatter_plot\" -> \"cnvkit_main\" [label=\"scatter_plot\"];\n  \"method\" -> \"cnvkit_main\" [label=\"method\"];\n  \"drop_low_coverage\" -> \"cnvkit_main\" [label=\"drop_low_coverage\"];\n  \"tumor_bam\" -> \"cnvkit_main\" [label=\"tumor_bam\"];\n  \"male_reference\" -> \"cnvkit_main\" [label=\"male_reference\"];\n  \"cnvkit_main\" -> \"tumor_target_coverage\";\n  \"cnvkit_main\" -> \"tumor_antitarget_coverage\";\n  \"cnvkit_main\" -> \"cn_scatter_plot\";\n  \"cnvkit_main\" -> \"tumor_bin_level_ratios\";\n  \"cns_to_vcf\" -> \"cnvkit_vcf\";\n  \"cnvkit_main\" -> \"tumor_segmented_ratios\";\n  \"cnvkit_main\" -> \"cn_diagram\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/88f1e02b261bf9ce882eba306b6245c64328632b/definitions/subworkflows/cnvkit_single_sample.cwl","licenseName":"MIT License"}