longgf

Identify RNA variants in long-read RNA sequencing BAM files using Longgf

usage

nexus run --nf-workflow variant_calling_longgf.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genes_gtf_file /path/to/file.gtf \
    --params_longgf "100 30 100 1 0 3"

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_genes_gtf_file	Reference genes annotation GTF file.
--params_longgf	Longgf parameters (default: ‘“100 30 100 1 0 3”’). [pseudogene:0(default)/1/other(no filter)] [Secondary_alignment:0(default)] [min_sup_read:2(default)] Note that the parameters need to be wrapped in quotes.