Workflow: rna amplicon analysis for fasta files

Fetched 2021-01-17 21:24:10 GMT

RNAs - qc, preprocess, annotation, index, abundance

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Inputs

ID Type Title Doc
jobid String
m5rnaIndex Directory
filterAmbig Boolean
m5rnaFull File
filterLn Boolean
maxAmbig Integer
m5rnaPrefix String
deviation Float
m5rnaClust File
sequences File
m5nrBDB File

Steps

ID Runs Label Doc
qcBasic
abundance abundance

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

annotate rna annotation

RNAs - predict, cluster, identify, annotate

preProcess preprocess fasta

Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.

indexSimSeq index sim seq

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

Outputs

ID Type Label Doc
simSeqOut File
md5ProfileOut File
qcStatOut File
qcSummaryOut File
seqBinOut File
rnaClustSeqOut File
preProcessPassed File
preProcessRemoved File
lcaProfileOut File
rnaFeatureOut File
rnaSimsOut File
sourceStatsOut File
adapterPassed File
seqStatOut File
rnaClustMapOut File
Permalink: https://w3id.org/cwl/view/git/9aba38fd1569287b7256ace7163ac84320909f8a/CWL/Workflows/amplicon-fasta.workflow.cwl