starfusion

Identify fusion genes in STAR Chimeric junction files using STAR-Fusion

usage

nexus run --nf-workflow variant_calling_starfusion.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --genome_lib_dir /path/to/dir/ \
    --params_starfusion ""

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘fastq_file_1’, ‘fastq_file_2’.
--output_dir	Directory to which output files will be copied.
--genome_lib_dir	Genome lib directory.
--params_starfusion	STAR-Fusion parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.