arriba

Identify fusion genes in paired-read RNA sequencing BAM files using Arriba

usage

nexus run --nf-workflow variant_calling_arriba.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --reference_genes_gtf_file /path/to/file.gtf \
    --protein_domains_gff3_file /path/to/file \
    --params_arriba "-S 3 -f blacklist -i chr*"

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’, ‘bam_file’, ‘bam_bai_file’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--reference_genes_gtf_file	Reference genes GTF file.
--protein_domains_gff3_file	Protein domains GFF3 file.
--params_arriba	Arriba parameters (default: ’“-S 3 -f blacklist -i chr*“’). Note that the parameters need to be wrapped in quotes.