metabarcode (gene amplicon) analysis for fastq files

Workflow: metabarcode (gene amplicon) analysis for fastq files

Fetched 2024-11-25 10:16:48 GMT

Verified with cwltool version 3.1.20221201130942

protein - qc, preprocess, annotation, index, abundance

This workflow is Open Source and may be reused according to the terms of: BSD 2-clause "Simplified" License

Note that the tools invoked by the workflow may have separate licenses.

ID	Type	Title	Doc
jobid	String
m5nrBDB	File
m5nrSCG	File
filterLn	Boolean
m5nrFull	File[]
maxAmbig	Integer
deviation	Float
sequences	File
filterAmbig	Boolean

ID	Runs	Label	Doc
qcBasic	qc-basic.workflow.cwl (Workflow)
annotate	protein-annotation.workflow.cwl (Workflow)	protein annotation	Proteins - predict, cluster, identify, annotate
abundance	abundance.workflow.cwl (Workflow)	abundance	abundace profiles from annotated files, for protein and/or rna
preProcess	preprocess-fasta.workflow.cwl (Workflow)	preprocess fasta	Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.
indexSimSeq	index_sim_seq.workflow.cwl (Workflow)	index sim seq	create sorted / filtered similarity file with feature sequences, and index by md5

ID	Type	Label	Doc
qcStatOut	File
seqBinOut	File
simSeqOut	File
seqStatOut	File
protSimsOut	File
qcSummaryOut	File
adapterPassed	File
lcaProfileOut	File
md5ProfileOut	File
protFeatureOut	File
sourceStatsOut	File
protClustMapOut	File
protClustSeqOut	File
preProcessPassed	File
preProcessRemoved	File