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	Labels
fusions	File	Tab-delimited fusion predictions.	vidarr_label: fusions
fusionsAbridged	File	Tab-delimited fusion predictions, excluding the identification of the evidence fusion reads.	vidarr_label: fusionsAbridged
fusionCodingEffects	File	Fusion predictions with appended column showing effect on coding genes.	vidarr_label: fusionCodingEffects

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 .

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