{"@id":"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"f90b39e1b05e9bb37079b09f337f7e7ba5027f99","path":"definitions/subworkflows/pindel_cat.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl","url":"https://github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl"},"retrievedOn":"2026-09-24T04:39:51.588+00:00","lastCommit":"f90b39e1b05e9bb37079b09f337f7e7ba5027f99","label":"Per-chromosome pindel","inputs":{"reference":{"type":"String"},"tumor_bam":{"type":"File"},"chromosome":{"type":"String"},"normal_bam":{"type":"File"},"insert_size":{"type":"Integer"}},"outputs":{"per_chromosome_pindel_out":{"type":"File"}},"steps":{"cat":{"run":"../tools/cat_out.cwl","runType":"COMMANDLINETOOL","sources":{"cat":{"sourceIDs":["pindel"]},"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl#cat/pindel_outs":{"sourceIDs":["pindel"]}}},"pindel":{"label":"pindel v0.2.5b8","run":"../tools/pindel.cwl","runType":"COMMANDLINETOOL","sources":{"pindel":{"sourceIDs":["normal_bam"]},"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl#pindel/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl#pindel/tumor_bam":{"sourceIDs":["tumor_bam"]},"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl#pindel/chromosome":{"sourceIDs":["chromosome"]},"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl#pindel/insert_size":{"sourceIDs":["insert_size"]}}}},"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    \"normal_bam\" [fillcolor=\"#94DDF4\",label=\"normal_bam\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"tumor_bam\" [fillcolor=\"#94DDF4\",label=\"tumor_bam\"];\n    \"chromosome\" [fillcolor=\"#94DDF4\",label=\"chromosome\"];\n    \"insert_size\" [fillcolor=\"#94DDF4\",label=\"insert_size\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"per_chromosome_pindel_out\" [fillcolor=\"#94DDF4\",label=\"per_chromosome_pindel_out\"];\n  }\n  \"pindel\" [label=\"pindel v0.2.5b8\"];\n  \"cat\" [label=\"cat\"];\n  \"normal_bam\" -> \"pindel\" [label=\"normal_bam\"];\n  \"insert_size\" -> \"pindel\" [label=\"insert_size\"];\n  \"tumor_bam\" -> \"pindel\" [label=\"tumor_bam\"];\n  \"reference\" -> \"pindel\" [label=\"reference\"];\n  \"chromosome\" -> \"pindel\" [label=\"chromosome\"];\n  \"pindel\" -> \"cat\" [label=\"pindel_outs\"];\n  \"pindel\" -> \"cat\" [label=\"pindel_outs\"];\n  \"pindel\" -> \"cat\" [label=\"pindel_outs\"];\n  \"pindel\" -> \"cat\" [label=\"pindel_outs\"];\n  \"pindel\" -> \"cat\" [label=\"pindel_outs\"];\n  \"cat\" -> \"per_chromosome_pindel_out\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/pindel_cat.cwl","licenseName":"MIT License"}