Find reads with predicted coding sequences above 60 AA in length - Common Workflow Language Viewer

Workflow: Find reads with predicted coding sequences above 60 AA in length

Fetched 2023-01-12 02:21:50 GMT

Verified with cwltool version 3.1.20221201130942

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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/6430df56f7345f837d3f9c3f7fb5af5aa9dadc90/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. FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013 (https://sourceforge.net/projects/fraggenescan/). Version 1.20 can be downloaded here: https://sourceforge.net/projects/fraggenescan/files/
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/6430df56f7345f837d3f9c3f7fb5af5aa9dadc90/workflows/orf_prediction.cwl