{"@id":"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl","retrievedFrom":{"repoUrl":"https://github.com/adamscharlotte/CWL-workflow.git","branch":"fad08b1bff0ae38dca3a39907b25a248d069e514","path":"CompPASS-Plus_workflow.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/adamscharlotte/CWL-workflow/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl","url":"https://github.com/adamscharlotte/CWL-workflow/blob/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl"},"retrievedOn":"2026-10-28T23:40:49.612+00:00","lastCommit":"fad08b1bff0ae38dca3a39907b25a248d069e514","label":"CompPASS-Plus_workflow.cwl","inputs":{"to":{"type":"String"},"from":{"type":"String"},"email":{"type":"String"},"fileType":{"type":"String"},"CompPASS_R":{"type":"File"},"CompPASS_pre_R":{"type":"File"},"id_remapper_py":{"type":"File"},"remapped_identifiers":{"type":"String"},"protein_directory_path":{"type":"String"}},"outputs":{"CompPASS_csv":{"type":"File"}},"steps":{"CompPASS":{"run":"Tools/CompPASS.cwl","runType":"COMMANDLINETOOL","sources":{"CompPASS":{"sourceIDs":["protein_directory_path"]},"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl#CompPASS/CompPASS_R":{"sourceIDs":["CompPASS_R"]},"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl#CompPASS/gene_names":{"sourceIDs":["id_remapper"]}}},"id_remapper":{"run":"Tools/id_remapper.cwl","runType":"COMMANDLINETOOL","sources":{"id_remapper":{"sourceIDs":["email"]},"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl#id_remapper/to":{"sourceIDs":["to"]},"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl#id_remapper/from":{"sourceIDs":["from"]},"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl#id_remapper/fileType":{"sourceIDs":["fileType"]},"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl#id_remapper/id_remapper_py":{"sourceIDs":["id_remapper_py"]},"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl#id_remapper/remapped_identifiers":{"sourceIDs":["remapped_identifiers"]},"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl#id_remapper/protein_accessions_csv":{"sourceIDs":["CompPASS_pre"]}}},"CompPASS_pre":{"run":"Tools/CompPASS_pre.cwl","runType":"COMMANDLINETOOL","sources":{"CompPASS_pre":{"sourceIDs":["protein_directory_path"]},"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl#CompPASS_pre/CompPASS_pre_R":{"sourceIDs":["CompPASS_pre_R"]}}}},"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    \"email\" [fillcolor=\"#94DDF4\",label=\"email\"];\n    \"from\" [fillcolor=\"#94DDF4\",label=\"from\"];\n    \"id_remapper_py\" [fillcolor=\"#94DDF4\",label=\"id_remapper_py\"];\n    \"fileType\" [fillcolor=\"#94DDF4\",label=\"fileType\"];\n    \"remapped_identifiers\" [fillcolor=\"#94DDF4\",label=\"remapped_identifiers\"];\n    \"CompPASS_R\" [fillcolor=\"#94DDF4\",label=\"CompPASS_R\"];\n    \"CompPASS_pre_R\" [fillcolor=\"#94DDF4\",label=\"CompPASS_pre_R\"];\n    \"to\" [fillcolor=\"#94DDF4\",label=\"to\"];\n    \"protein_directory_path\" [fillcolor=\"#94DDF4\",label=\"protein_directory_path\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"CompPASS_csv\" [fillcolor=\"#94DDF4\",label=\"CompPASS_csv\"];\n  }\n  \"CompPASS\" [label=\"CompPASS\"];\n  \"CompPASS_pre\" [label=\"CompPASS_pre\"];\n  \"id_remapper\" [label=\"id_remapper\"];\n  \"protein_directory_path\" -> \"CompPASS\" [label=\"protein_directory_path\"];\n  \"id_remapper\" -> \"CompPASS\" [label=\"gene_names\"];\n  \"CompPASS_R\" -> \"CompPASS\" [label=\"CompPASS_R\"];\n  \"protein_directory_path\" -> \"CompPASS_pre\" [label=\"protein_directory_path\"];\n  \"CompPASS_pre_R\" -> \"CompPASS_pre\" [label=\"CompPASS_pre_R\"];\n  \"email\" -> \"id_remapper\" [label=\"email\"];\n  \"from\" -> \"id_remapper\" [label=\"from\"];\n  \"fileType\" -> \"id_remapper\" [label=\"fileType\"];\n  \"remapped_identifiers\" -> \"id_remapper\" [label=\"remapped_identifiers\"];\n  \"CompPASS_pre\" -> \"id_remapper\" [label=\"protein_accessions_csv\"];\n  \"id_remapper_py\" -> \"id_remapper\" [label=\"id_remapper_py\"];\n  \"to\" -> \"id_remapper\" [label=\"to\"];\n  \"CompPASS\" -> \"CompPASS_csv\";\n}\n","permalink":"https://w3id.org/cwl/view/git/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/adamscharlotte/CWL-workflow/blob/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl","visualisationPng":"/graph/png/github.com/adamscharlotte/CWL-workflow/blob/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl","visualisationSvg":"/graph/svg/github.com/adamscharlotte/CWL-workflow/blob/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl","roBundle":"/robundle/github.com/adamscharlotte/CWL-workflow/blob/fad08b1bff0ae38dca3a39907b25a248d069e514/CompPASS-Plus_workflow.cwl"}