starFusion

Workflow that takes a fastq pair or optionally a chimeric file from STAR and detects RNA-seq fusion events.

Dependencies

• star-fusion-genome 1.8.1-hg38
• star-fusion 1.8.1

Usage

Cromwell

java -jar cromwell.jar run starFusion.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
inputFqs	Array[Pair[File,File]]	Array of fastq read pairs
reference	String	Version of reference genome
outputFileNamePrefix	String	Prefix of outptu file

Optional workflow parameters:

Parameter	Value	Default	Description
chimeric	File?	None	Path to Chimeric.out.junction

Optional task parameters:

Parameter	Value	Default	Description
runStarFusion.threads	Int	8	Requested CPU threads
runStarFusion.jobMemory	Int	64	Memory allocated for this job
runStarFusion.timeout	Int	72	Hours before task timeout

Outputs

Output	Type	Description
fusions	File	Raw fusion output tsv
fusionsAbridged	File	Abridged fusion output tsv
fusionCodingEffects	File	Annotated fusion output tsv

Commands

This section lists command(s) run by starFusion workflow

starFusion workflow runs the following command (excerpt from .wdl file).

• STARFUSION_PATH - path to starFusion program
• REF_GENOME_DIR - directory with reference genome file
• FASTQR* - input fastq files.
• THREADS - threads to use
• CHIMERIC_JUNCTIONS - input file with chimeric junctions information (STAR output)

  STARFUSION_PATH
  --genome_lib_dir REF_GENOME_DIR
  --left_fq  FASTQR1_01, FASTQR1_02, ... 
  --right_fq FASTQR2_01, FASTQR2_02, ...
  --examine_coding_effect 
  --CPU THREADS --chimeric_junction CHIMERIC_JUNCTIONS

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .