Mapping to reference mode

In the map2ref analysis mode, the reads are mapped to a reference fata file provided using Minimap2. A bam file is created and summary coverage statistics are derived uisng samtools coverage.

Example:

nextflow run eresearchqut/ontvisc -resume -profile {singularity, docker} \
                            --merge \
                            --analysis_mode map2ref \
                            --reference /path/to/reference.fasta