{"@id":"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"526df6d2937f92ecd00c3029748958faa692ac55","path":"definitions/subworkflows/molecular_alignment.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl","url":"https://github.com/genome/analysis-workflows/blob/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl"},"retrievedOn":"2026-10-31T02:23:22.303+00:00","lastCommit":"526df6d2937f92ecd00c3029748958faa692ac55","label":"umi molecular alignment workflow","inputs":{"bam":{"type":"File[]"},"reference":{"type":"String"},"sample_name":{"type":"String"},"read_structure":{"type":"String[]"},"target_intervals":{"type":"File (Optional)"}},"outputs":{"aligned_cram":{"type":"File"},"adapter_histogram":{"type":"File[]"},"duplex_seq_metrics":{"type":"File[]"}},"steps":{"align":{"label":"umi per-lane alignment subworkflow","run":"umi_alignment.cwl","runType":"WORKFLOW","sources":{"align":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl#align/bam":{"sourceIDs":["bam"]},"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl#align/read_structure":{"sourceIDs":["read_structure"]}}},"merge":{"label":"Sambamba: merge","run":"../tools/merge_bams.cwl","runType":"COMMANDLINETOOL","sources":{"merge":{"sourceIDs":["align"]}}},"index_cram":{"label":"samtools index cram","run":"../tools/index_cram.cwl","runType":"COMMANDLINETOOL","sources":{"index_cram":{"sourceIDs":["bam_to_cram"]}}},"bam_to_cram":{"label":"BAM to CRAM conversion","run":"../tools/bam_to_cram.cwl","runType":"COMMANDLINETOOL","sources":{"bam_to_cram":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl#bam_to_cram/bam":{"sourceIDs":["clip_overlap"]}}},"clip_overlap":{"label":"clip overlapping reads","run":"../tools/clip_overlap.cwl","runType":"COMMANDLINETOOL","sources":{"clip_overlap":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl#clip_overlap/bam":{"sourceIDs":["filter_consensus"]}}},"align_consensus":{"label":"umi realignment","run":"../tools/realign.cwl","runType":"COMMANDLINETOOL","sources":{"align_consensus":{"sourceIDs":["call_molecular_consensus"]},"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl#align_consensus/reference":{"sourceIDs":["reference"]}}},"filter_consensus":{"label":"filter consensus reads","run":"../tools/filter_consensus.cwl","runType":"COMMANDLINETOOL","sources":{"filter_consensus":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl#filter_consensus/bam":{"sourceIDs":["align_consensus"]}}},"group_reads_by_umi":{"label":"group reads by umi","run":"../tools/group_reads.cwl","runType":"COMMANDLINETOOL","sources":{"group_reads_by_umi":{"sourceIDs":["merge"]}}},"call_molecular_consensus":{"label":"call molecular consensus","run":"../tools/call_molecular_consensus.cwl","runType":"COMMANDLINETOOL","sources":{"call_molecular_consensus":{"sourceIDs":["group_reads_by_umi"]}}},"collect_duplex_seq_metrics":{"label":"collect duplex seq metrics","run":"../tools/duplex_seq_metrics.cwl","runType":"COMMANDLINETOOL","sources":{"collect_duplex_seq_metrics":{"sourceIDs":["target_intervals"]},"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl#collect_duplex_seq_metrics/bam":{"sourceIDs":["group_reads_by_umi"]},"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl#collect_duplex_seq_metrics/description":{"sourceIDs":["sample_name"]}}}},"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    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"target_intervals\" [fillcolor=\"#94DDF4\",label=\"target_intervals\"];\n    \"sample_name\" [fillcolor=\"#94DDF4\",label=\"sample_name\"];\n    \"read_structure\" [fillcolor=\"#94DDF4\",label=\"read_structure\"];\n    \"bam\" [fillcolor=\"#94DDF4\",label=\"bam\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"duplex_seq_metrics\" [fillcolor=\"#94DDF4\",label=\"duplex_seq_metrics\"];\n    \"adapter_histogram\" [fillcolor=\"#94DDF4\",label=\"adapter_histogram\"];\n    \"aligned_cram\" [fillcolor=\"#94DDF4\",label=\"aligned_cram\"];\n  }\n  \"clip_overlap\" [label=\"clip overlapping reads\"];\n  \"group_reads_by_umi\" [label=\"group reads by umi\"];\n  \"index_cram\" [label=\"samtools index cram\"];\n  \"bam_to_cram\" [label=\"BAM to CRAM conversion\"];\n  \"merge\" [label=\"Sambamba: merge\"];\n  \"align\" [label=\"umi per-lane alignment subworkflow\", fillcolor=\"#F3CEA1\"];\n  \"call_molecular_consensus\" [label=\"call molecular consensus\"];\n  \"collect_duplex_seq_metrics\" [label=\"collect duplex seq metrics\"];\n  \"filter_consensus\" [label=\"filter consensus reads\"];\n  \"align_consensus\" [label=\"umi realignment\"];\n  \"reference\" -> \"clip_overlap\" [label=\"reference\"];\n  \"filter_consensus\" -> \"clip_overlap\" [label=\"bam\"];\n  \"merge\" -> \"group_reads_by_umi\" [label=\"bam\"];\n  \"bam_to_cram\" -> \"index_cram\" [label=\"cram\"];\n  \"reference\" -> \"bam_to_cram\" [label=\"reference\"];\n  \"clip_overlap\" -> \"bam_to_cram\" [label=\"bam\"];\n  \"align\" -> \"merge\" [label=\"bams\"];\n  \"reference\" -> \"align\" [label=\"reference\"];\n  \"read_structure\" -> \"align\" [label=\"read_structure\"];\n  \"bam\" -> \"align\" [label=\"bam\"];\n  \"group_reads_by_umi\" -> \"call_molecular_consensus\" [label=\"bam\"];\n  \"target_intervals\" -> \"collect_duplex_seq_metrics\" [label=\"intervals\"];\n  \"group_reads_by_umi\" -> \"collect_duplex_seq_metrics\" [label=\"bam\"];\n  \"sample_name\" -> \"collect_duplex_seq_metrics\" [label=\"description\"];\n  \"reference\" -> \"filter_consensus\" [label=\"reference\"];\n  \"align_consensus\" -> \"filter_consensus\" [label=\"bam\"];\n  \"call_molecular_consensus\" -> \"align_consensus\" [label=\"bam\"];\n  \"reference\" -> \"align_consensus\" [label=\"reference\"];\n  \"collect_duplex_seq_metrics\" -> \"duplex_seq_metrics\";\n  \"align\" -> \"adapter_histogram\";\n  \"index_cram\" -> \"aligned_cram\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/526df6d2937f92ecd00c3029748958faa692ac55/definitions/subworkflows/molecular_alignment.cwl","licenseName":"MIT License"}