longcallr

Haplotype long-read DNA sequencing BAM files using LongcallR

usage

nexus run --nf-workflow haplotyping_longcallr.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 \
    --preset "" \
    --params_longcallr ""

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.
--preset	LongcallR preset (choices: hifi-isoseq, hifi-masseq, ont-cdna, ont-drna).
--reference_genome_fasta_file	Reference genome FASTA file.
--reference_genes_gtf_file	Reference genes GTF file.
--params_longcallr	longcallr parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.