Description

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

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

meta2 (map)

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

reference (file)

Reference database in FASTA format.

bam_format (boolean)

Specify that output should be in BAM format

cigar_paf_format (boolean)

Specify that output CIGAR should be in PAF format

cigar_bam (boolean)

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)

Output

Name (Type)
Description
Pattern

meta (map)

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

]

paf (file)

Alignment in PAF format

*.paf

bam (file)

Alignment in BAM format

*.bam

versions (file)

File containing software versions

versions.yml

Tools

minimap2
MIT

A versatile pairwise aligner for genomic and spliced nucleotide sequences.