{"@id":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"1585504ccffafac53b1594349ed934f45206ee2b","path":"definitions/subworkflows/pindel_region.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl","url":"https://github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl"},"retrievedOn":"2026-09-12T19:39:14.643+00:00","lastCommit":"1585504ccffafac53b1594349ed934f45206ee2b","label":"Run pindel on provided region","inputs":{"ref_name":{"type":"String (Optional)"},"reference":{"type":"String"},"tumor_bam":{"type":"File"},"normal_bam":{"type":"File"},"insert_size":{"type":"Integer"},"output_name":{"type":"String (Optional)"},"region_file":{"type":"File"}},"outputs":{"pindel_region_vcf":{"type":"File"}},"steps":{"cat":{"run":"../tools/cat_out.cwl","runType":"COMMANDLINETOOL","sources":{"cat":{"sourceIDs":["pindel_region"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl#cat/pindel_outs":{"sourceIDs":["pindel_region"]}}},"index":{"label":"vcf index","run":"../tools/index_vcf.cwl","runType":"COMMANDLINETOOL","sources":{"index":{"sourceIDs":["remove_end_tags"]}}},"pindel2vcf":{"label":"pindel v0.2.5b8","run":"../tools/pindel2vcf.cwl","runType":"COMMANDLINETOOL","sources":{"pindel2vcf":{"sourceIDs":["output_name"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl#pindel2vcf/ref_name":{"sourceIDs":["ref_name"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl#pindel2vcf/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl#pindel2vcf/pindel_out":{"sourceIDs":["cat"]}}},"pindel_region":{"label":"pindel v0.2.5b8","run":"../tools/pindel.cwl","runType":"COMMANDLINETOOL","sources":{"pindel_region":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl#pindel_region/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl#pindel_region/normal_bam":{"sourceIDs":["normal_bam"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl#pindel_region/insert_size":{"sourceIDs":["insert_size"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl#pindel_region/region_file":{"sourceIDs":["region_file"]}}},"fix_vcf_header":{"label":"fix vcf header","run":"../tools/fix_vcf_header.cwl","runType":"COMMANDLINETOOL","sources":{"fix_vcf_header":{"sourceIDs":["pindel2vcf"]}}},"remove_end_tags":{"label":"remove END INFO tags","run":"../tools/remove_end_tags.cwl","runType":"COMMANDLINETOOL","sources":{"remove_end_tags":{"sourceIDs":["fix_vcf_header"]}}}},"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    \"output_name\" [fillcolor=\"#94DDF4\",label=\"output_name\"];\n    \"region_file\" [fillcolor=\"#94DDF4\",label=\"region_file\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"insert_size\" [fillcolor=\"#94DDF4\",label=\"insert_size\"];\n    \"ref_name\" [fillcolor=\"#94DDF4\",label=\"ref_name\"];\n    \"normal_bam\" [fillcolor=\"#94DDF4\",label=\"normal_bam\"];\n    \"tumor_bam\" [fillcolor=\"#94DDF4\",label=\"tumor_bam\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"pindel_region_vcf\" [fillcolor=\"#94DDF4\",label=\"pindel_region_vcf\"];\n  }\n  \"cat\" [label=\"cat\"];\n  \"index\" [label=\"vcf index\"];\n  \"fix_vcf_header\" [label=\"fix vcf header\"];\n  \"pindel_region\" [label=\"pindel v0.2.5b8\"];\n  \"remove_end_tags\" [label=\"remove END INFO tags\"];\n  \"pindel2vcf\" [label=\"pindel v0.2.5b8\"];\n  \"pindel_region\" -> \"cat\" [label=\"pindel_outs\"];\n  \"pindel_region\" -> \"cat\" [label=\"pindel_outs\"];\n  \"pindel_region\" -> \"cat\" [label=\"pindel_outs\"];\n  \"pindel_region\" -> \"cat\" [label=\"pindel_outs\"];\n  \"pindel_region\" -> \"cat\" [label=\"pindel_outs\"];\n  \"remove_end_tags\" -> \"index\" [label=\"vcf\"];\n  \"pindel2vcf\" -> \"fix_vcf_header\" [label=\"vcf\"];\n  \"reference\" -> \"pindel_region\" [label=\"reference\"];\n  \"region_file\" -> \"pindel_region\" [label=\"region_file\"];\n  \"insert_size\" -> \"pindel_region\" [label=\"insert_size\"];\n  \"normal_bam\" -> \"pindel_region\" [label=\"normal_bam\"];\n  \"tumor_bam\" -> \"pindel_region\" [label=\"tumor_bam\"];\n  \"fix_vcf_header\" -> \"remove_end_tags\" [label=\"vcf\"];\n  \"output_name\" -> \"pindel2vcf\" [label=\"output_name\"];\n  \"reference\" -> \"pindel2vcf\" [label=\"reference\"];\n  \"ref_name\" -> \"pindel2vcf\" [label=\"ref_name\"];\n  \"cat\" -> \"pindel2vcf\" [label=\"pindel_out\"];\n  \"index\" -> \"pindel_region_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/subworkflows/pindel_region.cwl","licenseName":"MIT License"}