{"@id":"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"70e05adeda8b3b4c77b8947266684ce4305db6ac","path":"definitions/subworkflows/umi_alignment.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl","url":"https://github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl"},"retrievedOn":"2026-09-09T13:27:08.308+00:00","lastCommit":"70e05adeda8b3b4c77b8947266684ce4305db6ac","label":"umi per-lane alignment subworkflow","inputs":{"bam":{"type":"File"},"reference":{"type":"String"},"read_structure":{"type":"String[]"}},"outputs":{"aligned_bam":{"type":"File"},"adapter_metrics":{"type":"File"}},"steps":{"align":{"label":"umi alignment","run":"../tools/umi_align.cwl","runType":"COMMANDLINETOOL","sources":{"align":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl#align/bam":{"sourceIDs":["mark_illumina_adapters"]}}},"extract_umis":{"label":"extract umis from bam","run":"../tools/extract_umis.cwl","runType":"COMMANDLINETOOL","sources":{"extract_umis":{"sourceIDs":["bam"]},"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl#extract_umis/read_structure":{"sourceIDs":["read_structure"]}}},"mark_illumina_adapters":{"label":"fastq to bam","run":"../tools/mark_illumina_adapters.cwl","runType":"COMMANDLINETOOL","sources":{"mark_illumina_adapters":{"sourceIDs":["extract_umis"]}}}},"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    \"read_structure\" [fillcolor=\"#94DDF4\",label=\"read_structure\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"aligned_bam\" [fillcolor=\"#94DDF4\",label=\"aligned_bam\"];\n    \"adapter_metrics\" [fillcolor=\"#94DDF4\",label=\"adapter_metrics\"];\n  }\n  \"align\" [label=\"umi alignment\"];\n  \"mark_illumina_adapters\" [label=\"fastq to bam\"];\n  \"extract_umis\" [label=\"extract umis from bam\"];\n  \"reference\" -> \"align\" [label=\"reference\"];\n  \"mark_illumina_adapters\" -> \"align\" [label=\"bam\"];\n  \"extract_umis\" -> \"mark_illumina_adapters\" [label=\"bam\"];\n  \"bam\" -> \"extract_umis\" [label=\"bam\"];\n  \"read_structure\" -> \"extract_umis\" [label=\"read_structure\"];\n  \"align\" -> \"aligned_bam\";\n  \"mark_illumina_adapters\" -> \"adapter_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/umi_alignment.cwl","licenseName":"MIT License"}