{"@id":"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pindel.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"f7ac3eff79128831c9f7a565d5b187882f39aa58","path":"definitions/subworkflows/pindel.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pindel.cwl","url":"https://github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pindel.cwl"},"retrievedOn":"2026-09-11T17:27:11.425+00:00","lastCommit":"f7ac3eff79128831c9f7a565d5b187882f39aa58","label":"pindel parallel 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 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    \"tumor_bam\" [fillcolor=\"#94DDF4\",label=\"tumor_bam\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"insert_size\" [fillcolor=\"#94DDF4\",label=\"insert_size\"];\n    \"scatter_count\" [fillcolor=\"#94DDF4\",label=\"scatter_count\"];\n    \"interval_list\" [fillcolor=\"#94DDF4\",label=\"interval_list\"];\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    \"unfiltered_vcf\" [fillcolor=\"#94DDF4\",label=\"unfiltered_vcf\"];\n    \"filtered_vcf\" [fillcolor=\"#94DDF4\",label=\"filtered_vcf\"];\n  }\n  \"somaticfilter\" [label=\"pindel somatic filter v1\"];\n  \"pindel_cat\" [label=\"Per-region pindel\", fillcolor=\"#F3CEA1\"];\n  \"cat_all\" [label=\"cat_all\"];\n  \"remove_end_tags\" [label=\"remove END INFO tags\"];\n  \"bgzip\" [label=\"bgzip VCF\"];\n  \"reindex\" [label=\"vcf index\"];\n  \"filter\" [label=\"fp_filter workflow\", fillcolor=\"#F3CEA1\"];\n  \"index\" [label=\"vcf index\"];\n  \"split_interval_list_to_bed\" [label=\"split_interval_list_to_bed\"];\n  \"reference\" -> \"somaticfilter\" [label=\"reference\"];\n  \"cat_all\" -> \"somaticfilter\" [label=\"pindel_output_summary\"];\n  \"reference\" -> \"pindel_cat\" [label=\"reference\"];\n  \"tumor_bam\" -> \"pindel_cat\" [label=\"tumor_bam\"];\n  \"split_interval_list_to_bed\" -> \"pindel_cat\" [label=\"region_file\"];\n  \"normal_bam\" -> \"pindel_cat\" [label=\"normal_bam\"];\n  \"insert_size\" -> \"pindel_cat\" [label=\"insert_size\"];\n  \"pindel_cat\" -> \"cat_all\" [label=\"region_pindel_outs\"];\n  \"index\" -> \"remove_end_tags\" [label=\"vcf\"];\n  \"somaticfilter\" -> \"bgzip\" [label=\"file\"];\n  \"remove_end_tags\" -> \"reindex\" [label=\"vcf\"];\n  \"reindex\" -> \"filter\" [label=\"vcf\"];\n  \"reference\" -> \"filter\" [label=\"reference\"];\n  \"tumor_bam\" -> \"filter\" [label=\"bam\"];\n  \"bgzip\" -> \"index\" [label=\"vcf\"];\n  \"interval_list\" -> \"split_interval_list_to_bed\" [label=\"interval_list\"];\n  \"scatter_count\" -> \"split_interval_list_to_bed\" [label=\"scatter_count\"];\n  \"filter\" -> \"unfiltered_vcf\";\n  \"filter\" -> \"filtered_vcf\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pindel.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pindel.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pindel.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pindel.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/f7ac3eff79128831c9f7a565d5b187882f39aa58/definitions/subworkflows/pindel.cwl","licenseName":"MIT License"}