{"@id":"https://w3id.org/cwl/view/git/662d424d2e433e636f46a79025325d5daaca6271/CWL/Workflows/assembled.workflow.cwl","retrievedFrom":{"repoUrl":"https://github.com/MG-RAST/pipeline.git","branch":"662d424d2e433e636f46a79025325d5daaca6271","path":"CWL/Workflows/assembled.workflow.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/MG-RAST/pipeline/662d424d2e433e636f46a79025325d5daaca6271/CWL/Workflows/assembled.workflow.cwl","url":"https://github.com/MG-RAST/pipeline/blob/662d424d2e433e636f46a79025325d5daaca6271/CWL/Workflows/assembled.workflow.cwl"},"retrievedOn":"2026-09-04T00:53:44.021+00:00","lastCommit":"662d424d2e433e636f46a79025325d5daaca6271","label":"analysis for assembled sequences","doc":"rna / protein - qc, annotation, index, 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\"indexSimSeq\" [label=\"index sim seq\", fillcolor=\"#F3CEA1\"];\n  \"darkmatter\" [label=\"extract darkmatter\"];\n  \"qcAssemble\" [label=\"qcAssemble\", fillcolor=\"#F3CEA1\"];\n  \"abundance\" [label=\"abundance\", fillcolor=\"#F3CEA1\"];\n  \"jobid\" -> \"rnaAnnotate\" [label=\"jobid\"];\n  \"m5rnaIndex\" -> \"rnaAnnotate\" [label=\"m5rnaIndex\"];\n  \"m5rnaPrefix\" -> \"rnaAnnotate\" [label=\"m5rnaPrefix\"];\n  \"m5rnaFull\" -> \"rnaAnnotate\" [label=\"m5rnaFull\"];\n  \"sequences\" -> \"rnaAnnotate\" [label=\"sequences\"];\n  \"m5rnaClust\" -> \"rnaAnnotate\" [label=\"m5rnaClust\"];\n  \"m5nrBDB\" -> \"rnaAnnotate\" [label=\"m5nrBDB\"];\n  \"jobid\" -> \"protAnnotate\" [label=\"jobid\"];\n  \"rnaAnnotate\" -> \"protAnnotate\" [label=\"rnaClustMap\"];\n  \"m5nrFull\" -> \"protAnnotate\" [label=\"m5nrFull\"];\n  \"rnaAnnotate\" -> \"protAnnotate\" [label=\"rnaSims\"];\n  \"m5nrBDB\" -> \"protAnnotate\" [label=\"m5nrBDB\"];\n  \"sequences\" -> \"protAnnotate\" [label=\"sequences\"];\n  \"m5nrSCG\" -> \"protAnnotate\" [label=\"m5nrSCG\"];\n  \"jobid\" -> \"indexSimSeq\" [label=\"jobid\"];\n  \"rnaAnnotate\" -> \"indexSimSeq\" [label=\"filterSims\"];\n  \"protAnnotate\" -> \"indexSimSeq\" [label=\"filterSims\"];\n  \"rnaAnnotate\" -> \"indexSimSeq\" [label=\"featureSeqs\"];\n  \"protAnnotate\" -> \"indexSimSeq\" [label=\"featureSeqs\"];\n  \"rnaAnnotate\" -> \"indexSimSeq\" [label=\"clustMaps\"];\n  \"protAnnotate\" -> \"indexSimSeq\" [label=\"clustMaps\"];\n  \"rnaAnnotate\" -> \"darkmatter\" [label=\"simHit\"];\n  \"protAnnotate\" -> \"darkmatter\" [label=\"simHit\"];\n  \"jobid\" -> \"darkmatter\" [label=\"outName\"];\n  \"protAnnotate\" -> \"darkmatter\" [label=\"geneSeq\"];\n  \"rnaAnnotate\" -> \"darkmatter\" [label=\"clustMap\"];\n  \"protAnnotate\" -> \"darkmatter\" [label=\"clustMap\"];\n  \"sequences\" -> \"qcAssemble\" [label=\"sequences\"];\n  \"jobid\" -> \"qcAssemble\" [label=\"jobid\"];\n  \"rnaAnnotate\" -> \"abundance\" [label=\"rnaClustMap\"];\n  \"protAnnotate\" -> \"abundance\" [label=\"protExpandLca\"];\n  \"rnaAnnotate\" -> \"abundance\" [label=\"rnaExpandLca\"];\n  \"rnaAnnotate\" -> \"abundance\" [label=\"filterSims\"];\n  \"protAnnotate\" -> \"abundance\" [label=\"filterSims\"];\n  \"jobid\" -> \"abundance\" [label=\"jobid\"];\n  \"indexSimSeq\" -> \"abundance\" [label=\"md5index\"];\n  \"qcAssemble\" -> \"abundance\" [label=\"coverage\"];\n  \"m5nrSCG\" -> \"abundance\" [label=\"m5nrSCG\"];\n  \"protAnnotate\" -> \"abundance\" [label=\"protClustMap\"];\n  \"rnaAnnotate\" -> \"abundance\" [label=\"expandSims\"];\n  \"protAnnotate\" -> \"abundance\" [label=\"expandSims\"];\n  \"indexSimSeq\" -> \"simSeqOut\";\n  \"abundance\" -> \"sourceStatsOut\";\n  \"protAnnotate\" -> \"protFilterFeatureOut\";\n  \"abundance\" -> \"lcaProfileOut\";\n  \"rnaAnnotate\" -> \"rnaFeatureOut\";\n  \"protAnnotate\" -> \"protSimsOut\";\n  \"qcAssemble\" -> \"seqBinOut\";\n  \"qcAssemble\" -> \"qcStatOut\";\n  \"protAnnotate\" -> \"protFeatureOut\";\n  \"protAnnotate\" -> \"protClustMapOut\";\n  \"abundance\" -> \"md5ProfileOut\";\n  \"darkmatter\" -> \"darkmatterOut\";\n  \"rnaAnnotate\" -> \"rnaSimsOut\";\n  \"rnaAnnotate\" -> \"rnaClustMapOut\";\n  \"qcAssemble\" -> \"assemblyCoverage\";\n  \"qcAssemble\" -> \"qcSummaryOut\";\n  \"protAnnotate\" -> \"protClustSeqOut\";\n  \"qcAssemble\" -> \"seqStatOut\";\n  \"rnaAnnotate\" -> \"rnaClustSeqOut\";\n}\n","licenseLink":"https://spdx.org/licenses/BSD-2-Clause","permalink":"https://w3id.org/cwl/view/git/662d424d2e433e636f46a79025325d5daaca6271/CWL/Workflows/assembled.workflow.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/MG-RAST/pipeline/blob/662d424d2e433e636f46a79025325d5daaca6271/CWL/Workflows/assembled.workflow.cwl","visualisationPng":"/graph/png/github.com/MG-RAST/pipeline/blob/662d424d2e433e636f46a79025325d5daaca6271/CWL/Workflows/assembled.workflow.cwl","visualisationSvg":"/graph/svg/github.com/MG-RAST/pipeline/blob/662d424d2e433e636f46a79025325d5daaca6271/CWL/Workflows/assembled.workflow.cwl","roBundle":"/robundle/github.com/MG-RAST/pipeline/blob/662d424d2e433e636f46a79025325d5daaca6271/CWL/Workflows/assembled.workflow.cwl","licenseName":"BSD 2-clause \"Simplified\" License"}