{"@id":"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"70e05adeda8b3b4c77b8947266684ce4305db6ac","path":"definitions/subworkflows/merge_svs.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl","url":"https://github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl"},"retrievedOn":"2026-08-31T06:40:40.692+00:00","lastCommit":"70e05adeda8b3b4c77b8947266684ce4305db6ac","label":"merge and annotate svs with population allele freq","inputs":{"vcfs":{"type":"File[]"},"sv_db":{"type":"File"},"same_type":{"type":"Boolean"},"cohort_name":{"type":"String (Optional)"},"same_strand":{"type":"Boolean"},"minimum_sv_size":{"type":"Integer"},"minimum_sv_calls":{"type":"Integer"},"estimate_sv_distance":{"type":"Boolean"},"max_distance_to_merge":{"type":"Integer"}},"outputs":{"merged_annotated_vcf":{"type":"File"}},"steps":{"merge_vcfs":{"label":"Run SURVIVOR to merge SV calls","run":"../tools/survivor.cwl","runType":"COMMANDLINETOOL","sources":{"merge_vcfs":{"sourceIDs":["cohort_name"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl#merge_vcfs/vcfs":{"sourceIDs":["vcfs"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl#merge_vcfs/same_type":{"sourceIDs":["same_type"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl#merge_vcfs/same_strand":{"sourceIDs":["same_strand"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl#merge_vcfs/minimum_sv_size":{"sourceIDs":["minimum_sv_size"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl#merge_vcfs/minimum_sv_calls":{"sourceIDs":["minimum_sv_calls"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl#merge_vcfs/estimate_sv_distance":{"sourceIDs":["estimate_sv_distance"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl#merge_vcfs/max_distance_to_merge":{"sourceIDs":["max_distance_to_merge"]}}},"add_population_frequency":{"label":"add population allele frequencies to a vcf","run":"../tools/add_sv_population_frequency.cwl","runType":"COMMANDLINETOOL","sources":{"add_population_frequency":{"sourceIDs":["merge_vcfs"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl#add_population_frequency/sv_db":{"sourceIDs":["sv_db"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl#add_population_frequency/cohort_name":{"sourceIDs":["cohort_name"]}}}},"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    \"sv_db\" [fillcolor=\"#94DDF4\",label=\"sv_db\"];\n    \"estimate_sv_distance\" [fillcolor=\"#94DDF4\",label=\"estimate_sv_distance\"];\n    \"same_type\" [fillcolor=\"#94DDF4\",label=\"same_type\"];\n    \"max_distance_to_merge\" [fillcolor=\"#94DDF4\",label=\"max_distance_to_merge\"];\n    \"minimum_sv_size\" [fillcolor=\"#94DDF4\",label=\"minimum_sv_size\"];\n    \"same_strand\" [fillcolor=\"#94DDF4\",label=\"same_strand\"];\n    \"minimum_sv_calls\" [fillcolor=\"#94DDF4\",label=\"minimum_sv_calls\"];\n    \"cohort_name\" [fillcolor=\"#94DDF4\",label=\"cohort_name\"];\n    \"vcfs\" [fillcolor=\"#94DDF4\",label=\"vcfs\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"merged_annotated_vcf\" [fillcolor=\"#94DDF4\",label=\"merged_annotated_vcf\"];\n  }\n  \"merge_vcfs\" [label=\"Run SURVIVOR to merge SV calls\"];\n  \"add_population_frequency\" [label=\"add population allele frequencies to a vcf\"];\n  \"cohort_name\" -> \"merge_vcfs\" [label=\"cohort_name\"];\n  \"same_type\" -> \"merge_vcfs\" [label=\"same_type\"];\n  \"vcfs\" -> \"merge_vcfs\" [label=\"vcfs\"];\n  \"max_distance_to_merge\" -> \"merge_vcfs\" [label=\"max_distance_to_merge\"];\n  \"minimum_sv_calls\" -> \"merge_vcfs\" [label=\"minimum_sv_calls\"];\n  \"same_strand\" -> \"merge_vcfs\" [label=\"same_strand\"];\n  \"estimate_sv_distance\" -> \"merge_vcfs\" [label=\"estimate_sv_distance\"];\n  \"minimum_sv_size\" -> \"merge_vcfs\" [label=\"minimum_sv_size\"];\n  \"merge_vcfs\" -> \"add_population_frequency\" [label=\"vcf\"];\n  \"sv_db\" -> \"add_population_frequency\" [label=\"sv_db\"];\n  \"cohort_name\" -> \"add_population_frequency\" [label=\"cohort_name\"];\n  \"add_population_frequency\" -> \"merged_annotated_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/merge_svs.cwl","licenseName":"MIT License"}