Workflow: rna amplicon analysis for fastq files

Fetched 2023-01-30 18:53:08 GMT

RNAs - qc, preprocess, annotation, index, abundance

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Inputs

ID Type Title Doc
jobid String
maxLqb Integer
m5nrBDB File
minQual Integer
m5rnaFull File
sequences File
m5rnaClust File
m5rnaIndex Directory
m5rnaPrefix String

Steps

ID Runs Label Doc
qcBasic
annotate rna annotation

RNAs - predict, cluster, identify, annotate

abundance abundance

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

preProcess Preprocess fastq

Remove and trim low quality reads from fastq files. 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
qcStatOut File
seqBinOut File
simSeqOut File
rnaSimsOut File
seqStatOut File
qcSummaryOut File
adapterPassed File
lcaProfileOut File
md5ProfileOut File
rnaFeatureOut File
rnaClustMapOut File
rnaClustSeqOut File
sourceStatsOut File
preProcessPassed File
preProcessRemoved File
Permalink: https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/amplicon-fastq.workflow.cwl