{"@id":"https://w3id.org/cwl/view/git/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"5677d6df78453e62d2e78ab485f216feaef91681","path":"definitions/subworkflows/varscan.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl","url":"https://github.com/genome/analysis-workflows/blob/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl"},"retrievedOn":"2026-09-21T00:00:24.933+00:00","lastCommit":"5677d6df78453e62d2e78ab485f216feaef91681","label":"varscan somatic workflow","inputs":{"p_value":{"type":"Float (Optional)"},"roi_bed":{"type":"File (Optional)"},"reference":{"type":"String"},"tumor_bam":{"type":"File"},"normal_bam":{"type":"File"},"min_coverage":{"type":"Integer (Optional)"},"min_var_freq":{"type":"Float 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v2.4.2 processSomatic","run":"../tools/varscan_process_somatic.cwl","runType":"COMMANDLINETOOL","sources":{"process_somatic_snvs":{"sourceIDs":["max_normal_freq"]},"https://w3id.org/cwl/view/git/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl#process_somatic_snvs/variants":{"sourceIDs":["somatic"]}}},"process_somatic_indels":{"label":"varscan v2.4.2 processSomatic","run":"../tools/varscan_process_somatic.cwl","runType":"COMMANDLINETOOL","sources":{"process_somatic_indels":{"sourceIDs":["somatic"]},"https://w3id.org/cwl/view/git/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl#process_somatic_indels/max_normal_freq":{"sourceIDs":["max_normal_freq"]}}}},"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    \"tumor_bam\" [fillcolor=\"#94DDF4\",label=\"tumor_bam\"];\n    \"roi_bed\" [fillcolor=\"#94DDF4\",label=\"roi_bed\"];\n    \"normal_bam\" [fillcolor=\"#94DDF4\",label=\"normal_bam\"];\n    \"strand_filter\" [fillcolor=\"#94DDF4\",label=\"strand_filter\"];\n    \"p_value\" [fillcolor=\"#94DDF4\",label=\"p_value\"];\n    \"min_var_freq\" [fillcolor=\"#94DDF4\",label=\"min_var_freq\"];\n    \"max_normal_freq\" [fillcolor=\"#94DDF4\",label=\"max_normal_freq\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\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    \"loh_snvs\" [fillcolor=\"#94DDF4\",label=\"loh_snvs\"];\n    \"germline_snvs\" [fillcolor=\"#94DDF4\",label=\"germline_snvs\"];\n    \"germline_indels\" [fillcolor=\"#94DDF4\",label=\"germline_indels\"];\n    \"somatic_snvs\" [fillcolor=\"#94DDF4\",label=\"somatic_snvs\"];\n    \"somatic_hc_indels\" [fillcolor=\"#94DDF4\",label=\"somatic_hc_indels\"];\n    \"germline_hc_indels\" [fillcolor=\"#94DDF4\",label=\"germline_hc_indels\"];\n    \"germline_hc_snvs\" [fillcolor=\"#94DDF4\",label=\"germline_hc_snvs\"];\n    \"snvs\" [fillcolor=\"#94DDF4\",label=\"snvs\"];\n    \"loh_hc_snvs\" [fillcolor=\"#94DDF4\",label=\"loh_hc_snvs\"];\n    \"loh_indels\" [fillcolor=\"#94DDF4\",label=\"loh_indels\"];\n    \"indels\" [fillcolor=\"#94DDF4\",label=\"indels\"];\n    \"somatic_hc_snvs\" [fillcolor=\"#94DDF4\",label=\"somatic_hc_snvs\"];\n    \"somatic_indels\" [fillcolor=\"#94DDF4\",label=\"somatic_indels\"];\n    \"loh_hc_indels\" [fillcolor=\"#94DDF4\",label=\"loh_hc_indels\"];\n  }\n  \"process_somatic_snvs\" [label=\"varscan v2.4.2 processSomatic\"];\n  \"process_somatic_indels\" [label=\"varscan v2.4.2 processSomatic\"];\n  \"somatic\" [label=\"varscan v2.4.2 somatic\"];\n  \"max_normal_freq\" -> \"process_somatic_snvs\" [label=\"max_normal_freq\"];\n  \"somatic\" -> \"process_somatic_snvs\" [label=\"variants\"];\n  \"somatic\" -> \"process_somatic_indels\" [label=\"variants\"];\n  \"max_normal_freq\" -> \"process_somatic_indels\" [label=\"max_normal_freq\"];\n  \"tumor_bam\" -> \"somatic\" [label=\"tumor_bam\"];\n  \"p_value\" -> \"somatic\" [label=\"p_value\"];\n  \"roi_bed\" -> \"somatic\" [label=\"roi_bed\"];\n  \"strand_filter\" -> \"somatic\" [label=\"strand_filter\"];\n  \"normal_bam\" -> \"somatic\" [label=\"normal_bam\"];\n  \"reference\" -> \"somatic\" [label=\"reference\"];\n  \"min_coverage\" -> \"somatic\" [label=\"min_coverage\"];\n  \"min_var_freq\" -> \"somatic\" [label=\"min_var_freq\"];\n  \"process_somatic_snvs\" -> \"loh_snvs\";\n  \"process_somatic_snvs\" -> \"germline_snvs\";\n  \"process_somatic_indels\" -> \"germline_indels\";\n  \"process_somatic_snvs\" -> \"somatic_snvs\";\n  \"process_somatic_indels\" -> \"somatic_hc_indels\";\n  \"process_somatic_indels\" -> \"germline_hc_indels\";\n  \"process_somatic_snvs\" -> \"germline_hc_snvs\";\n  \"somatic\" -> \"snvs\";\n  \"process_somatic_snvs\" -> \"loh_hc_snvs\";\n  \"process_somatic_indels\" -> \"loh_indels\";\n  \"somatic\" -> \"indels\";\n  \"process_somatic_snvs\" -> \"somatic_hc_snvs\";\n  \"process_somatic_indels\" -> \"somatic_indels\";\n  \"process_somatic_indels\" -> \"loh_hc_indels\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/5677d6df78453e62d2e78ab485f216feaef91681/definitions/subworkflows/varscan.cwl","licenseName":"MIT License"}