clair3rna

Identify RNA variants in long-read RNA sequencing BAM files using Clair3-RNA (Zheng et al., bioRxiv 2024)

usage

nexus run --nf-workflow variant_calling_clair3rna.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --params_clair3rna "--platform hifi_sequel2_minimap2"

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.
--params_clair3rna	Clair3-RNA parameters (default: ‘“–platform hifi_sequel2_minimap2”’). Note that the parameters need to be wrapped in quotes.