{"@id":"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"f7ac3eff79128831c9f7a565d5b187882f39aa58","path":"definitions/subworkflows/docm_cle.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl","url":"https://github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl"},"retrievedOn":"2026-09-23T19:35:50.078+00:00","lastCommit":"f7ac3eff79128831c9f7a565d5b187882f39aa58","label":"Detect Docm variants","inputs":{"docm_vcf":{"type":"File"},"reference":{"type":"String"},"tumor_bam":{"type":"File"},"normal_bam":{"type":"File"},"interval_list":{"type":"File"},"filter_docm_variants":{"type":"Boolean"}},"outputs":{"docm_variants_vcf":{"type":"File"}},"steps":{"bgzip":{"label":"bgzip VCF","run":"../tools/bgzip.cwl","runType":"COMMANDLINETOOL","sources":{"bgzip":{"sourceIDs":["GATK_haplotype_caller"]}}},"index":{"label":"vcf index","run":"../tools/index_vcf.cwl","runType":"COMMANDLINETOOL","sources":{"index":{"sourceIDs":["bgzip"]}}},"bgzip2":{"label":"bgzip VCF","run":"../tools/bgzip.cwl","runType":"COMMANDLINETOOL","sources":{"bgzip2":{"sourceIDs":["docm_filter"]}}},"index2":{"label":"vcf index","run":"../tools/index_vcf.cwl","runType":"COMMANDLINETOOL","sources":{"index2":{"sourceIDs":["bgzip2"]}}},"decompose":{"label":"run vt decompose","run":"../tools/vt_decompose.cwl","runType":"COMMANDLINETOOL","sources":{"decompose":{"sourceIDs":["index"]}}},"docm_filter":{"label":"Filter variants from the DoCM detector","run":"../tools/filter_vcf_docm.cwl","runType":"COMMANDLINETOOL","sources":{"docm_filter":{"sourceIDs":["decompose"]},"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl#docm_filter/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl#docm_filter/normal_bam":{"sourceIDs":["normal_bam"]},"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl#docm_filter/filter_docm_variants":{"sourceIDs":["filter_docm_variants"]}}},"GATK_haplotype_caller":{"label":"HaplotypeCaller (GATK 3.6)","run":"../tools/docm_gatk_haplotype_caller.cwl","runType":"COMMANDLINETOOL","sources":{"GATK_haplotype_caller":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/docm_vcf":{"sourceIDs":["docm_vcf"]},"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/normal_bam":{"sourceIDs":["normal_bam"]},"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/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    \"interval_list\" [fillcolor=\"#94DDF4\",label=\"interval_list\"];\n    \"docm_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_vcf\"];\n    \"filter_docm_variants\" [fillcolor=\"#94DDF4\",label=\"filter_docm_variants\"];\n    \"tumor_bam\" [fillcolor=\"#94DDF4\",label=\"tumor_bam\"];\n    \"normal_bam\" [fillcolor=\"#94DDF4\",label=\"normal_bam\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"docm_variants_vcf\" [fillcolor=\"#94DDF4\",label=\"docm_variants_vcf\"];\n  }\n  \"decompose\" [label=\"run vt decompose\"];\n  \"docm_filter\" [label=\"Filter variants from the DoCM detector\"];\n  \"bgzip2\" [label=\"bgzip VCF\"];\n  \"bgzip\" [label=\"bgzip VCF\"];\n  \"index2\" [label=\"vcf index\"];\n  \"index\" [label=\"vcf index\"];\n  \"GATK_haplotype_caller\" [label=\"HaplotypeCaller (GATK 3.6)\"];\n  \"index\" -> \"decompose\" [label=\"vcf\"];\n  \"decompose\" -> \"docm_filter\" [label=\"docm_raw_variants\"];\n  \"filter_docm_variants\" -> \"docm_filter\" [label=\"filter_docm_variants\"];\n  \"normal_bam\" -> \"docm_filter\" [label=\"normal_bam\"];\n  \"tumor_bam\" -> \"docm_filter\" [label=\"tumor_bam\"];\n  \"docm_filter\" -> \"bgzip2\" [label=\"file\"];\n  \"GATK_haplotype_caller\" -> \"bgzip\" [label=\"file\"];\n  \"bgzip2\" -> \"index2\" [label=\"vcf\"];\n  \"bgzip\" -> \"index\" [label=\"vcf\"];\n  \"reference\" -> \"GATK_haplotype_caller\" [label=\"reference\"];\n  \"normal_bam\" -> \"GATK_haplotype_caller\" [label=\"normal_bam\"];\n  \"interval_list\" -> \"GATK_haplotype_caller\" [label=\"interval_list\"];\n  \"docm_vcf\" -> \"GATK_haplotype_caller\" [label=\"docm_vcf\"];\n  \"tumor_bam\" -> \"GATK_haplotype_caller\" [label=\"bam\"];\n  \"index2\" -> \"docm_variants_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/docm_cle.cwl","licenseName":"MIT License"}