Workflow: rna amplicon analysis for fasta files
RNAs - qc, preprocess, annotation, index, abundance
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
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.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
jobid | String | ||
m5nrBDB | File | ||
filterLn | Boolean | ||
maxAmbig | Integer | ||
deviation | Float | ||
m5rnaFull | File | ||
sequences | File | ||
m5rnaClust | File | ||
m5rnaIndex | Directory | ||
filterAmbig | Boolean | ||
m5rnaPrefix | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
qcBasic |
qc-basic.workflow.cwl
(Workflow)
|
||
annotate |
rna-annotation.workflow.cwl
(Workflow)
|
rna annotation |
RNAs - 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 |
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-fasta.workflow.cwl