Workflow: Find reads with predicted coding sequences above 60 AA in length
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
model | https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/tools/FragGeneScan-model.yaml#model | ||
sequence | File [FASTA] | ||
completeSeq | Boolean |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
split_seqs |
../tools/fasta_chunker.cwl
(CommandLineTool)
|
split FASTA by number of records |
based upon code by Maxim Scheremetjew, EMBL-EBI |
ORF_prediction |
../tools/FragGeneScan1_20.cwl
(CommandLineTool)
|
FragGeneScan: find (fragmented) genes in short reads |
FragGeneScan is an application for finding (fragmented) genes in short
reads. It can also be applied to predict prokaryotic genes in incomplete
assemblies or complete genomes. |
combine_predicted_CDS_aa |
../tools/concatenate.cwl
(CommandLineTool)
|
||
combine_predicted_CDS_nuc |
../tools/concatenate.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
predicted_CDS_aa | File [FASTA] | ||
predicted_CDS_nuc | File [FASTA] |
Permalink:
https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/workflows/orf_prediction.cwl