{"@id":"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl","retrievedFrom":{"repoUrl":"https://github.com/tmooney/cancer-genomics-workflow.git","branch":"233f026ffce240071edda526391be0c03186fce8","path":"definitions/subworkflows/varscan_germline.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/tmooney/cancer-genomics-workflow/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl","url":"https://github.com/tmooney/cancer-genomics-workflow/blob/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl"},"retrievedOn":"2023-01-10T10:07:23.018+00:00","lastCommit":"233f026ffce240071edda526391be0c03186fce8","label":"Varscan Workflow","inputs":{"bam":{"type":"File"},"p_value":{"type":"Float (Optional)"},"min_reads":{"type":"Integer (Optional)"},"reference":{"type":"File"},"sample_name":{"type":"String"},"min_coverage":{"type":"Integer (Optional)"},"min_var_freq":{"type":"Float (Optional)"},"interval_list":{"type":"File"},"strand_filter":{"type":"Integer (Optional)"},"max_normal_freq":{"type":"Float (Optional)"}},"outputs":{"filtered_vcf":{"type":"File"},"unfiltered_vcf":{"type":"File"}},"steps":{"filter":{"label":"fp_filter workflow","run":"fp_filter.cwl","runType":"WORKFLOW","sources":{"filter":{"sourceIDs":["bam"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#filter/vcf":{"sourceIDs":["bgzip_and_index"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#filter/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#filter/sample_name":{"sourceIDs":["sample_name"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#filter/min_var_freq":{"sourceIDs":["min_var_freq"]}}},"varscan":{"label":"varscan v2.4.2 germline","run":"../tools/varscan_germline.cwl","runType":"COMMANDLINETOOL","sources":{"varscan":{"sourceIDs":["min_reads"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#varscan/bam":{"sourceIDs":["bam"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#varscan/p_value":{"sourceIDs":["p_value"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#varscan/roi_bed":{"sourceIDs":["intervals_to_bed"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#varscan/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#varscan/sample_name":{"sourceIDs":["sample_name"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#varscan/min_coverage":{"sourceIDs":["min_coverage"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#varscan/min_var_freq":{"sourceIDs":["min_var_freq"]},"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl#varscan/strand_filter":{"sourceIDs":["strand_filter"]}}},"bgzip_and_index":{"label":"bgzip and index VCF","run":"bgzip_and_index.cwl","runType":"WORKFLOW","sources":{"bgzip_and_index":{"sourceIDs":["varscan"]}}},"intervals_to_bed":{"run":"../tools/intervals_to_bed.cwl","runType":"COMMANDLINETOOL","sources":{"intervals_to_bed":{"sourceIDs":["interval_list"]}}}},"cwltoolVersion":"3.1.20221201130942","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    \"strand_filter\" [fillcolor=\"#94DDF4\",label=\"strand_filter\"];\n    \"bam\" [fillcolor=\"#94DDF4\",label=\"bam\"];\n    \"min_var_freq\" [fillcolor=\"#94DDF4\",label=\"min_var_freq\"];\n    \"interval_list\" [fillcolor=\"#94DDF4\",label=\"interval_list\"];\n    \"sample_name\" [fillcolor=\"#94DDF4\",label=\"sample_name\"];\n    \"p_value\" [fillcolor=\"#94DDF4\",label=\"p_value\"];\n    \"min_coverage\" [fillcolor=\"#94DDF4\",label=\"min_coverage\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"max_normal_freq\" [fillcolor=\"#94DDF4\",label=\"max_normal_freq\"];\n    \"min_reads\" [fillcolor=\"#94DDF4\",label=\"min_reads\"];\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  \"intervals_to_bed\" [label=\"intervals_to_bed\"];\n  \"varscan\" [label=\"varscan v2.4.2 germline\"];\n  \"filter\" [label=\"fp_filter workflow\", fillcolor=\"#F3CEA1\"];\n  \"bgzip_and_index\" [label=\"bgzip and index VCF\", fillcolor=\"#F3CEA1\"];\n  \"interval_list\" -> \"intervals_to_bed\" [label=\"interval_list\"];\n  \"min_reads\" -> \"varscan\" [label=\"min_reads\"];\n  \"intervals_to_bed\" -> \"varscan\" [label=\"roi_bed\"];\n  \"strand_filter\" -> \"varscan\" [label=\"strand_filter\"];\n  \"sample_name\" -> \"varscan\" [label=\"sample_name\"];\n  \"reference\" -> \"varscan\" [label=\"reference\"];\n  \"min_var_freq\" -> \"varscan\" [label=\"min_var_freq\"];\n  \"min_coverage\" -> \"varscan\" [label=\"min_coverage\"];\n  \"bam\" -> \"varscan\" [label=\"bam\"];\n  \"p_value\" -> \"varscan\" [label=\"p_value\"];\n  \"bam\" -> \"filter\" [label=\"bam\"];\n  \"min_var_freq\" -> \"filter\" [label=\"min_var_freq\"];\n  \"sample_name\" -> \"filter\" [label=\"sample_name\"];\n  \"bgzip_and_index\" -> \"filter\" [label=\"vcf\"];\n  \"reference\" -> \"filter\" [label=\"reference\"];\n  \"varscan\" -> \"bgzip_and_index\" [label=\"vcf\"];\n  \"filter\" -> \"filtered_vcf\";\n  \"filter\" -> \"unfiltered_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","packed":false,"permalink":"https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl","visualisationXdot":"/graph/xdot/github.com/tmooney/cancer-genomics-workflow/blob/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl","roBundle":"/robundle/github.com/tmooney/cancer-genomics-workflow/blob/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl","licenseName":"MIT License","visualisationPng":"/graph/png/github.com/tmooney/cancer-genomics-workflow/blob/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl","visualisationSvg":"/graph/svg/github.com/tmooney/cancer-genomics-workflow/blob/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl"}