modules/minimap2_align

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

List of input FASTA or FASTQ files of size 1 and 2 for single-end
and paired-end data, respectively.

Groovy Map containing reference information
e.g. [ id:‘test_ref’]

Reference database in FASTA format.

Specify that output should be in BAM format

BAM alignment index extension (e.g. “bai”)

Specify that output CIGAR should be in PAF format

Write CIGAR with >65535 ops at the CG tag. This is recommended when
doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)