CWL Workflow: workflow to detect fusion events

Workflow: workflow to detect fusion events

Fetched 2023-01-13 15:41:54 GMT

Verified with cwltool version 3.1.20221201130942

A workflow to run cpgRna Infuse pipeline from a single input BAM file (can be aligned or unaligned) of RNA-seq reads using cgpRna container. See the [cgpRna](https://github.com/cancerit/cgpRna) website for more information.

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Inputs/Outputs

This workflow is Open Source and may be reused according to the terms of: GNU Affero General Public License v3.0

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

Inputs

ID	Type	Doc
gtf	File	GTF file which is used to annotate break points.
in_bam	File	input BAM file.
sample_name	String	Sample name, which will used to prefix output file names.
star_threads	Integer (Optional)	Number of threads to use for tophat fusion process.
vagrent_cache	File	VAGrENT cache file that should be the same reference and gene build as the GTF file.
defuse_threads	Integer (Optional)	Number of threads to use for tophat fusion process.
star_reference	File	STAR reference bundle tar file.
tophat_threads	Integer (Optional)	Number of threads to use for tophat fusion process.
defuse_reference	File	Defuse reference bundle tar file.
tophat_fusion_reference	File	Tophat fusion reference bundle tar file.

Steps

There are no steps in this workflow

Outputs

ID	Type	Label	Doc
star_fusions	File
defuse_fusions	File
tophat_fusions	File
combined_fusions	File