Workflow: analysis for assembled sequences

Fetched 2021-03-04 16:22:55 GMT

rna / protein - qc, annotation, index, abundance

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Inputs

ID Type Title Doc
m5nrSCG File
jobid String
m5rnaIndex Directory
m5rnaFull File
m5rnaPrefix String
m5nrFull File[]
sequences File
m5rnaClust File
m5nrBDB File

Steps

ID Runs Label Doc
rnaAnnotate rna annotation

RNAs - predict, cluster, identify, annotate

abundance abundance

abundace profiles from annotated files, for protein and/or rna

protAnnotate protein annotation

Proteins - predict, filter, cluster, identify, annotate

darkmatter
../Tools/extract_darkmatter.tool.cwl (CommandLineTool)
extract darkmatter

retrieve predicted proteins that have no similarity hits >extract_darkmatter.py -i <input> -s <sim 1> -s <sim 2> -m <clust map 1> -m <clust map 2> -o <outName>

indexSimSeq index sim seq

create sorted / filtered similarity file with feature sequences, and index by md5

qcAssemble

Outputs

ID Type Label Doc
simSeqOut File
protClustMapOut File
protFeatureOut File
assemblyCoverage File
md5ProfileOut File
qcStatOut File
qcSummaryOut File
seqBinOut File
rnaClustSeqOut File
protFilterFeatureOut File
darkmatterOut File
lcaProfileOut File
protSimsOut File
rnaFeatureOut File
rnaSimsOut File
sourceStatsOut File
protClustSeqOut File
rnaClustMapOut File
seqStatOut File
Permalink: https://w3id.org/cwl/view/git/9aba38fd1569287b7256ace7163ac84320909f8a/CWL/Workflows/assembled.workflow.cwl