{"@id":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/merge_svs.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"1585504ccffafac53b1594349ed934f45206ee2b","path":"definitions/subworkflows/merge_svs.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/merge_svs.cwl","url":"https://github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/merge_svs.cwl"},"retrievedOn":"2026-08-29T15:27:07.368+00:00","lastCommit":"1585504ccffafac53b1594349ed934f45206ee2b","label":"Merge, annotate, and generate a TSV for SVs","inputs":{"sv_vcfs":{"type":"File[]"},"snps_vcf":{"type":"File (Optional)"},"same_type":{"type":"Boolean"},"cohort_name":{"type":"String 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AnnotSV tsv output generated from a bcftools merged 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VCF","run":"../tools/bgzip.cwl","runType":"COMMANDLINETOOL","sources":{"bcftools_bgzip_merged_sv_vcf":{"sourceIDs":["bcftools_merge_sv_vcfs"]}}},"survivor_bgzip_merged_sv_vcf":{"label":"bgzip VCF","run":"../tools/bgzip.cwl","runType":"COMMANDLINETOOL","sources":{"survivor_bgzip_merged_sv_vcf":{"sourceIDs":["survivor_merge_sv_vcfs"]}}}},"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    \"minimum_sv_size\" [fillcolor=\"#94DDF4\",label=\"minimum_sv_size\"];\n    \"same_type\" [fillcolor=\"#94DDF4\",label=\"same_type\"];\n    \"same_strand\" [fillcolor=\"#94DDF4\",label=\"same_strand\"];\n    \"genome_build\" [fillcolor=\"#94DDF4\",label=\"genome_build\"];\n    \"snps_vcf\" [fillcolor=\"#94DDF4\",label=\"snps_vcf\"];\n    \"sv_vcfs\" [fillcolor=\"#94DDF4\",label=\"sv_vcfs\"];\n    \"cohort_name\" [fillcolor=\"#94DDF4\",label=\"cohort_name\"];\n    \"minimum_sv_calls\" [fillcolor=\"#94DDF4\",label=\"minimum_sv_calls\"];\n    \"estimate_sv_distance\" [fillcolor=\"#94DDF4\",label=\"estimate_sv_distance\"];\n    \"max_distance_to_merge\" [fillcolor=\"#94DDF4\",label=\"max_distance_to_merge\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"survivor_merged_annotated_tsv\" [fillcolor=\"#94DDF4\",label=\"survivor_merged_annotated_tsv\"];\n    \"bcftools_merged_sv_vcf\" [fillcolor=\"#94DDF4\",label=\"bcftools_merged_sv_vcf\"];\n    \"bcftools_merged_annotated_tsv\" [fillcolor=\"#94DDF4\",label=\"bcftools_merged_annotated_tsv\"];\n    \"bcftools_merged_filtered_annotated_tsv\" [fillcolor=\"#94DDF4\",label=\"bcftools_merged_filtered_annotated_tsv\"];\n    \"survivor_merged_sv_vcf\" [fillcolor=\"#94DDF4\",label=\"survivor_merged_sv_vcf\"];\n  }\n  \"survivor_annotate_variants\" [label=\"survivor_annotate_variants\"];\n  \"bcftools_bgzip_merged_sv_vcf\" [label=\"bgzip VCF\"];\n  \"survivor_bgzip_merged_sv_vcf\" [label=\"bgzip VCF\"];\n  \"bcftools_merge_sv_vcfs\" [label=\"bcftools_merge_sv_vcfs\"];\n  \"survivor_merge_sv_vcfs\" [label=\"Run SURVIVOR to merge SV calls\"];\n  \"bcftools_annotate_variants\" [label=\"bcftools_annotate_variants\"];\n  \"bcftools_annotsv_filter\" [label=\"filter AnnotSV tsv output generated from a bcftools merged vcf\"];\n  \"genome_build\" -> \"survivor_annotate_variants\" [label=\"genome_build\"];\n  \"snps_vcf\" -> \"survivor_annotate_variants\" [label=\"snps_vcf\"];\n  \"default1\" -> \"survivor_annotate_variants\" [label=\"output_tsv_name\"];\n  \"default1\" [label=\"\\\"SURVIVOR-merged-AnnotSV.tsv\\\"\", fillcolor=\"#D5AEFC\"];\n  \"survivor_merge_sv_vcfs\" -> \"survivor_annotate_variants\" [label=\"input_vcf\"];\n  \"bcftools_merge_sv_vcfs\" -> \"bcftools_bgzip_merged_sv_vcf\" [label=\"file\"];\n  \"survivor_merge_sv_vcfs\" -> \"survivor_bgzip_merged_sv_vcf\" [label=\"file\"];\n  \"default2\" -> \"bcftools_merge_sv_vcfs\" [label=\"output_type\"];\n  \"default2\" [label=\"\\\"v\\\"\", fillcolor=\"#D5AEFC\"];\n  \"sv_vcfs\" -> \"bcftools_merge_sv_vcfs\" [label=\"vcfs\"];\n  \"default3\" -> \"bcftools_merge_sv_vcfs\" [label=\"output_vcf_name\"];\n  \"default3\" [label=\"\\\"bcftools-sv-merged.vcf\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default4\" -> \"bcftools_merge_sv_vcfs\" [label=\"merge_method\"];\n  \"default4\" [label=\"\\\"none\\\"\", fillcolor=\"#D5AEFC\"];\n  \"same_type\" -> \"survivor_merge_sv_vcfs\" [label=\"same_type\"];\n  \"default5\" -> \"survivor_merge_sv_vcfs\" [label=\"cohort_name\"];\n  \"default5\" [label=\"\\\"SURVIVOR-sv-merged.vcf\\\"\", fillcolor=\"#D5AEFC\"];\n  \"sv_vcfs\" -> \"survivor_merge_sv_vcfs\" [label=\"vcfs\"];\n  \"minimum_sv_size\" -> \"survivor_merge_sv_vcfs\" [label=\"minimum_sv_size\"];\n  \"same_strand\" -> \"survivor_merge_sv_vcfs\" [label=\"same_strand\"];\n  \"minimum_sv_calls\" -> \"survivor_merge_sv_vcfs\" [label=\"minimum_sv_calls\"];\n  \"estimate_sv_distance\" -> \"survivor_merge_sv_vcfs\" [label=\"estimate_sv_distance\"];\n  \"max_distance_to_merge\" -> \"survivor_merge_sv_vcfs\" [label=\"max_distance_to_merge\"];\n  \"snps_vcf\" -> \"bcftools_annotate_variants\" [label=\"snps_vcf\"];\n  \"bcftools_merge_sv_vcfs\" -> \"bcftools_annotate_variants\" [label=\"input_vcf\"];\n  \"genome_build\" -> \"bcftools_annotate_variants\" [label=\"genome_build\"];\n  \"default6\" -> \"bcftools_annotate_variants\" [label=\"output_tsv_name\"];\n  \"default6\" [label=\"\\\"bcftools-merged-AnnotSV.tsv\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default7\" -> \"bcftools_annotsv_filter\" [label=\"filtering_frequency\"];\n  \"default7\" [label=\"\\\"0.05\\\"\", fillcolor=\"#D5AEFC\"];\n  \"bcftools_annotate_variants\" -> \"bcftools_annotsv_filter\" [label=\"annotsv_tsv\"];\n  \"survivor_annotate_variants\" -> \"survivor_merged_annotated_tsv\";\n  \"bcftools_bgzip_merged_sv_vcf\" -> \"bcftools_merged_sv_vcf\";\n  \"bcftools_annotate_variants\" -> \"bcftools_merged_annotated_tsv\";\n  \"bcftools_annotsv_filter\" -> \"bcftools_merged_filtered_annotated_tsv\";\n  \"survivor_bgzip_merged_sv_vcf\" -> \"survivor_merged_sv_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/merge_svs.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/merge_svs.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/merge_svs.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/merge_svs.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/merge_svs.cwl","licenseName":"MIT License"}