{"@id":"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"195b4ab487c939eb32a55d9f78bc1befd100caae","path":"definitions/pipelines/panel_of_normals.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl","url":"https://github.com/genome/analysis-workflows/blob/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl"},"retrievedOn":"2026-09-26T11:46:44.392+00:00","lastCommit":"195b4ab487c939eb32a55d9f78bc1befd100caae","label":"mutect panel-of-normals workflow","inputs":{"dbsnp_vcf":{"type":"File (Optional)"},"reference":{"type":"String"},"cosmic_vcf":{"type":"File (Optional)"},"normal_bams":{"type":"File[]"},"interval_list":{"type":"File"},"scatter_count":{"type":"Integer"}},"outputs":{"pon_vcf":{"type":"File"}},"steps":{"mutect":{"label":"mutect parallel workflow","run":"../subworkflows/mutect.cwl","runType":"WORKFLOW","sources":{"mutect":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl#mutect/dbsnp_vcf":{"sourceIDs":["dbsnp_vcf"]},"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl#mutect/tumor_bam":{"sourceIDs":["normal_bams"]},"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl#mutect/cosmic_vcf":{"sourceIDs":["cosmic_vcf"]},"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl#mutect/interval_list":{"sourceIDs":["interval_list"]},"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl#mutect/scatter_count":{"sourceIDs":["scatter_count"]},"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl#mutect/artifact_detection_mode":{"defaultVal":"true"}}},"combine":{"label":"CombineVariants for Panel of Normals","run":"../tools/pon_combine_variants.cwl","runType":"COMMANDLINETOOL","sources":{"combine":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl#combine/normal_vcfs":{"sourceIDs":["mutect"]},"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl#combine/interval_list":{"sourceIDs":["interval_list"]}}}},"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\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"normal_bams\" [fillcolor=\"#94DDF4\",label=\"normal_bams\"];\n    \"cosmic_vcf\" [fillcolor=\"#94DDF4\",label=\"cosmic_vcf\"];\n    \"dbsnp_vcf\" [fillcolor=\"#94DDF4\",label=\"dbsnp_vcf\"];\n    \"interval_list\" [fillcolor=\"#94DDF4\",label=\"interval_list\"];\n    \"scatter_count\" [fillcolor=\"#94DDF4\",label=\"scatter_count\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"pon_vcf\" [fillcolor=\"#94DDF4\",label=\"pon_vcf\"];\n  }\n  \"mutect\" [label=\"mutect parallel workflow\", fillcolor=\"#F3CEA1\"];\n  \"combine\" [label=\"CombineVariants for Panel of Normals\"];\n  \"reference\" -> \"mutect\" [label=\"reference\"];\n  \"scatter_count\" -> \"mutect\" [label=\"scatter_count\"];\n  \"dbsnp_vcf\" -> \"mutect\" [label=\"dbsnp_vcf\"];\n  \"normal_bams\" -> \"mutect\" [label=\"tumor_bam\"];\n  \"default1\" -> \"mutect\" [label=\"artifact_detection_mode\"];\n  \"default1\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"cosmic_vcf\" -> \"mutect\" [label=\"cosmic_vcf\"];\n  \"interval_list\" -> \"mutect\" [label=\"interval_list\"];\n  \"reference\" -> \"combine\" [label=\"reference\"];\n  \"mutect\" -> \"combine\" [label=\"normal_vcfs\"];\n  \"interval_list\" -> \"combine\" [label=\"interval_list\"];\n  \"combine\" -> \"pon_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/panel_of_normals.cwl","licenseName":"MIT License"}