Workflow that takes a fastq pair or optionally a chimeric file from STAR and detects RNA-seq fusion events.
java -jar cromwell.jar run starFusion.wdl --inputs inputs.json
| 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 |
| Parameter | Value | Default | Description |
|---|---|---|---|
chimeric |
File? | None | Path to Chimeric.out.junction |
| 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 |
| 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 |
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
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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