AltContigRemapper-nf

Nextflow DSL2 pipeline that remaps BAM file alignments to alternative contigs for HLA-typing using Hartwig Medical Foundation's bamtools AltContigRemapper.

Usage

nextflow run main.nf --input samplesheet.csv --genome_fasta /path/to/ref.fa --outdir results

Parameter	Description	Default
--input	CSV samplesheet with columns sample_id,bam,bai	required
--genome_fasta	Reference genome FASTA	required
--outdir	Output directory	results

See samplesheet.example.csv for the expected input format.

Requirements

• Nextflow (DSL2)
• Singularity (configured by default) or Docker