{"@id":"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl","retrievedFrom":{"repoUrl":"https://github.com/MG-RAST/pipeline.git","branch":"8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8","path":"CWL/Workflows/contig-lca.workflow.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/MG-RAST/pipeline/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl","url":"https://github.com/MG-RAST/pipeline/blob/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl"},"retrievedOn":"2026-10-26T08:39:40.582+00:00","lastCommit":"8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8","label":"contig LCA","doc":"create LCA consistant across input contigs contigs\norder of precedence - rRNA, single copy gene, LCA of genes\n","inputs":{"jobid":{"type":"String"},"m5nrSCG":{"type":"File"},"coverage":{"type":"File (Optional)"},"rnaClustMap":{"type":"File"},"protClustMap":{"type":"File"},"rnaExpandLca":{"type":"File"},"protExpandLca":{"type":"File"}},"outputs":{"contigLCA":{"type":"File"}},"steps":{"sortRna":{"label":"GNU sort","doc":"sort text file base on given field(s)","run":"../Tools/sort.tool.cwl","runType":"COMMANDLINETOOL","sources":{"sortRna":{"sourceIDs":["unclusterRna"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#sortRna/outName":{"sourceIDs":["unclusterRna"]}}},"sortProt":{"label":"GNU sort","doc":"sort text file base on given field(s)","run":"../Tools/sort.tool.cwl","runType":"COMMANDLINETOOL","sources":{"sortProt":{"sourceIDs":["unclusterProt"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#sortProt/outName":{"sourceIDs":["unclusterProt"]}}},"expandLca":{"label":"contig LCA","doc":"create contig LCA from rRNA and Protein LCAs\n>find_contig_lca.py --rna <rnaLCA> --prot <protLCA> --scg <scgs> --output <outName>\n","run":"../Tools/find_contig_lca.tool.cwl","runType":"COMMANDLINETOOL","sources":{"expandLca":{"sourceIDs":["jobid"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#expandLca/scgs":{"sourceIDs":["m5nrSCG"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#expandLca/rnaLCA":{"sourceIDs":["sortRna"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#expandLca/protLCA":{"sourceIDs":["sortProt"]}}},"abundanceLca":{"label":"abundance profile","doc":"create abundance profile from expanded annotated sims files\nmd5:    sims_abundance.py -t md5 -i <input> -o <output> --coverage <coverage> --cluster <cluster> --md5index <md5index>\nlca:    sims_abundance.py -t lca -i <input> -o <output> --coverage <coverage> --cluster <cluster>\nsource: sims_abundance.py -t source -i <input> -o <output> --coverage <coverage> --cluster <cluster>\n","run":"../Tools/sims_abundance.tool.cwl","runType":"COMMANDLINETOOL","sources":{"abundanceLca":{"sourceIDs":["expandLca"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/outName":{"sourceIDs":["jobid"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/coverage":{"sourceIDs":["coverage"]}}},"unclusterRna":{"label":"uncluster sims","doc":"expand out similarity file (blast m8) by turning each cluster seed hit into a hit per cluster member\n>uncluster_sims.py <input> <outName> --cfile <cluster> --position <position>\n","run":"../Tools/uncluster_sims.tool.cwl","runType":"COMMANDLINETOOL","sources":{"unclusterRna":{"sourceIDs":["rnaExpandLca"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/outName":{"sourceIDs":["rnaExpandLca"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/clustMap":{"sourceIDs":["rnaClustMap"]}}},"unclusterProt":{"label":"uncluster sims","doc":"expand out similarity file (blast m8) by turning each cluster seed hit into a hit per cluster member\n>uncluster_sims.py <input> <outName> --cfile <cluster> --position <position>\n","run":"../Tools/uncluster_sims.tool.cwl","runType":"COMMANDLINETOOL","sources":{"unclusterProt":{"sourceIDs":["protExpandLca"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/outName":{"sourceIDs":["protExpandLca"]},"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/clustMap":{"sourceIDs":["protClustMap"]}}}},"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    \"rnaExpandLca\" [fillcolor=\"#94DDF4\",label=\"rnaExpandLca\"];\n    \"coverage\" [fillcolor=\"#94DDF4\",label=\"coverage\"];\n    \"jobid\" [fillcolor=\"#94DDF4\",label=\"jobid\"];\n    \"protExpandLca\" [fillcolor=\"#94DDF4\",label=\"protExpandLca\"];\n    \"rnaClustMap\" [fillcolor=\"#94DDF4\",label=\"rnaClustMap\"];\n    \"protClustMap\" [fillcolor=\"#94DDF4\",label=\"protClustMap\"];\n    \"m5nrSCG\" [fillcolor=\"#94DDF4\",label=\"m5nrSCG\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"contigLCA\" [fillcolor=\"#94DDF4\",label=\"contigLCA\"];\n  }\n  \"abundanceLca\" [label=\"abundance profile\"];\n  \"unclusterRna\" [label=\"uncluster sims\"];\n  \"unclusterProt\" [label=\"uncluster sims\"];\n  \"sortProt\" [label=\"GNU sort\"];\n  \"sortRna\" [label=\"GNU sort\"];\n  \"expandLca\" [label=\"contig LCA\"];\n  \"expandLca\" -> \"abundanceLca\" [label=\"input\"];\n  \"jobid\" -> \"abundanceLca\" [label=\"outName\"];\n  \"coverage\" -> \"abundanceLca\" [label=\"coverage\"];\n  \"rnaExpandLca\" -> \"unclusterRna\" [label=\"simHit\"];\n  \"rnaExpandLca\" -> \"unclusterRna\" [label=\"outName\"];\n  \"rnaClustMap\" -> \"unclusterRna\" [label=\"clustMap\"];\n  \"protExpandLca\" -> \"unclusterProt\" [label=\"simHit\"];\n  \"protExpandLca\" -> \"unclusterProt\" [label=\"outName\"];\n  \"protClustMap\" -> \"unclusterProt\" [label=\"clustMap\"];\n  \"unclusterProt\" -> \"sortProt\" [label=\"input\"];\n  \"unclusterProt\" -> \"sortProt\" [label=\"outName\"];\n  \"unclusterRna\" -> \"sortRna\" [label=\"input\"];\n  \"unclusterRna\" -> \"sortRna\" [label=\"outName\"];\n  \"jobid\" -> \"expandLca\" [label=\"outName\"];\n  \"sortProt\" -> \"expandLca\" [label=\"protLCA\"];\n  \"m5nrSCG\" -> \"expandLca\" [label=\"scgs\"];\n  \"sortRna\" -> \"expandLca\" [label=\"rnaLCA\"];\n  \"abundanceLca\" -> \"contigLCA\";\n}\n","licenseLink":"https://spdx.org/licenses/BSD-2-Clause","permalink":"https://w3id.org/cwl/view/git/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/MG-RAST/pipeline/blob/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl","visualisationPng":"/graph/png/github.com/MG-RAST/pipeline/blob/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl","visualisationSvg":"/graph/svg/github.com/MG-RAST/pipeline/blob/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl","roBundle":"/robundle/github.com/MG-RAST/pipeline/blob/8a5ded15fad8ee1a4315aef1fdc1d53cdcdc12b8/CWL/Workflows/contig-lca.workflow.cwl","licenseName":"BSD 2-clause \"Simplified\" License"}