{"@id":"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"6bfb64375e7ebb6eb40f463ede86d8deccdb9eff","path":"definitions/subworkflows/cram_to_cnvkit.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl","url":"https://github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl"},"retrievedOn":"2026-09-23T08:56:51.197+00:00","lastCommit":"6bfb64375e7ebb6eb40f463ede86d8deccdb9eff","label":"Subworkflow to allow calling cnvkit with cram instead of bam files","inputs":{"access":{"type":"File (Optional)"},"method":{"type":"String (Optional)"},"diagram":{"type":"Boolean (Optional)"},"reference":{"type":"String"},"tumor_cram":{"type":"File"},"normal_cram":{"type":"File"},"scatter_plot":{"type":"Boolean (Optional)"},"bait_intervals":{"type":"File"},"drop_low_coverage":{"type":"Boolean (Optional)"}},"outputs":{"cn_diagram":{"type":"File (Optional)"},"cn_scatter_plot":{"type":"File (Optional)"},"intervals_target":{"type":"File (Optional)"},"reference_coverage":{"type":"File (Optional)"},"intervals_antitarget":{"type":"File (Optional)"},"tumor_target_coverage":{"type":"File"},"normal_target_coverage":{"type":"File"},"tumor_bin_level_ratios":{"type":"File"},"tumor_segmented_ratios":{"type":"File"},"tumor_antitarget_coverage":{"type":"File"},"normal_antitarget_coverage":{"type":"File"}},"steps":{"run_cnvkit":{"run":"../tools/cnvkit_batch.cwl","runType":"COMMANDLINETOOL","sources":{"run_cnvkit":{"sourceIDs":["bait_intervals"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/access":{"sourceIDs":["access"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/method":{"sourceIDs":["method"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/diagram":{"sourceIDs":["diagram"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_bam":{"sourceIDs":["tumor_cram_to_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/normal_bam":{"sourceIDs":["normal_cram_to_bam"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/scatter_plot":{"sourceIDs":["scatter_plot"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/drop_low_coverage":{"sourceIDs":["drop_low_coverage"]}}},"tumor_cram_to_bam":{"label":"samtools view cram to bam","run":"../tools/cram_to_bam.cwl","runType":"COMMANDLINETOOL","sources":{"tumor_cram_to_bam":{"sourceIDs":["tumor_cram"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram_to_bam/reference":{"sourceIDs":["reference"]}}},"normal_cram_to_bam":{"label":"samtools view cram to bam","run":"../tools/cram_to_bam.cwl","runType":"COMMANDLINETOOL","sources":{"normal_cram_to_bam":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram_to_bam/cram":{"sourceIDs":["normal_cram"]}}}},"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    \"tumor_cram\" [fillcolor=\"#94DDF4\",label=\"tumor_cram\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"normal_cram\" [fillcolor=\"#94DDF4\",label=\"normal_cram\"];\n    \"bait_intervals\" [fillcolor=\"#94DDF4\",label=\"bait_intervals\"];\n    \"drop_low_coverage\" [fillcolor=\"#94DDF4\",label=\"drop_low_coverage\"];\n    \"method\" [fillcolor=\"#94DDF4\",label=\"method\"];\n    \"scatter_plot\" [fillcolor=\"#94DDF4\",label=\"scatter_plot\"];\n    \"access\" [fillcolor=\"#94DDF4\",label=\"access\"];\n    \"diagram\" [fillcolor=\"#94DDF4\",label=\"diagram\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"cn_diagram\" [fillcolor=\"#94DDF4\",label=\"cn_diagram\"];\n    \"normal_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"normal_antitarget_coverage\"];\n    \"tumor_bin_level_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_bin_level_ratios\"];\n    \"tumor_target_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_target_coverage\"];\n    \"intervals_antitarget\" [fillcolor=\"#94DDF4\",label=\"intervals_antitarget\"];\n    \"normal_target_coverage\" [fillcolor=\"#94DDF4\",label=\"normal_target_coverage\"];\n    \"tumor_segmented_ratios\" [fillcolor=\"#94DDF4\",label=\"tumor_segmented_ratios\"];\n    \"cn_scatter_plot\" [fillcolor=\"#94DDF4\",label=\"cn_scatter_plot\"];\n    \"tumor_antitarget_coverage\" [fillcolor=\"#94DDF4\",label=\"tumor_antitarget_coverage\"];\n    \"reference_coverage\" [fillcolor=\"#94DDF4\",label=\"reference_coverage\"];\n    \"intervals_target\" [fillcolor=\"#94DDF4\",label=\"intervals_target\"];\n  }\n  \"normal_cram_to_bam\" [label=\"samtools view cram to bam\"];\n  \"tumor_cram_to_bam\" [label=\"samtools view cram to bam\"];\n  \"run_cnvkit\" [label=\"run_cnvkit\"];\n  \"reference\" -> \"normal_cram_to_bam\" [label=\"reference\"];\n  \"normal_cram\" -> \"normal_cram_to_bam\" [label=\"cram\"];\n  \"tumor_cram\" -> \"tumor_cram_to_bam\" [label=\"cram\"];\n  \"reference\" -> \"tumor_cram_to_bam\" [label=\"reference\"];\n  \"bait_intervals\" -> \"run_cnvkit\" [label=\"bait_intervals\"];\n  \"method\" -> \"run_cnvkit\" [label=\"method\"];\n  \"tumor_cram_to_bam\" -> \"run_cnvkit\" [label=\"tumor_bam\"];\n  \"scatter_plot\" -> \"run_cnvkit\" [label=\"scatter_plot\"];\n  \"reference\" -> \"run_cnvkit\" [label=\"reference\"];\n  \"drop_low_coverage\" -> \"run_cnvkit\" [label=\"drop_low_coverage\"];\n  \"access\" -> \"run_cnvkit\" [label=\"access\"];\n  \"normal_cram_to_bam\" -> \"run_cnvkit\" [label=\"normal_bam\"];\n  \"diagram\" -> \"run_cnvkit\" [label=\"diagram\"];\n  \"run_cnvkit\" -> \"cn_diagram\";\n  \"run_cnvkit\" -> \"normal_antitarget_coverage\";\n  \"run_cnvkit\" -> \"tumor_bin_level_ratios\";\n  \"run_cnvkit\" -> \"tumor_target_coverage\";\n  \"run_cnvkit\" -> \"intervals_antitarget\";\n  \"run_cnvkit\" -> \"normal_target_coverage\";\n  \"run_cnvkit\" -> \"tumor_segmented_ratios\";\n  \"run_cnvkit\" -> \"cn_scatter_plot\";\n  \"run_cnvkit\" -> \"tumor_antitarget_coverage\";\n  \"run_cnvkit\" -> \"reference_coverage\";\n  \"run_cnvkit\" -> \"intervals_target\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/6bfb64375e7ebb6eb40f463ede86d8deccdb9eff/definitions/subworkflows/cram_to_cnvkit.cwl","licenseName":"MIT License"}