{"@id":"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"f90b39e1b05e9bb37079b09f337f7e7ba5027f99","path":"definitions/subworkflows/align.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl","url":"https://github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl"},"retrievedOn":"2026-09-05T14:19:09.220+00:00","lastCommit":"f90b39e1b05e9bb37079b09f337f7e7ba5027f99","label":"Unaligned to aligned BAM","inputs":{"bam":{"type":"File"},"readgroup":{"type":"String"},"reference":{"type":"String"}},"outputs":{"tagged_bam":{"type":"File"}},"steps":{"align_and_tag":{"label":"align with bwa_mem and tag","run":"../tools/align_and_tag.cwl","runType":"COMMANDLINETOOL","sources":{"align_and_tag":{"sourceIDs":["bam"]},"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl#align_and_tag/readgroup":{"sourceIDs":["readgroup"]},"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl#align_and_tag/reference":{"sourceIDs":["reference"]}}}},"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    \"bam\" [fillcolor=\"#94DDF4\",label=\"bam\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"readgroup\" [fillcolor=\"#94DDF4\",label=\"readgroup\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"tagged_bam\" [fillcolor=\"#94DDF4\",label=\"tagged_bam\"];\n  }\n  \"align_and_tag\" [label=\"align with bwa_mem and tag\"];\n  \"bam\" -> \"align_and_tag\" [label=\"bam\"];\n  \"reference\" -> \"align_and_tag\" [label=\"reference\"];\n  \"readgroup\" -> \"align_and_tag\" [label=\"readgroup\"];\n  \"align_and_tag\" -> \"tagged_bam\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/f90b39e1b05e9bb37079b09f337f7e7ba5027f99/definitions/subworkflows/align.cwl","licenseName":"MIT License"}