Description

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

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

bam_index_extension (string)

BAM alignment index extension (e.g. "bai")

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)

bed_bool (boolean)

Specify that output should be in BED format

Output

Name
Description
Pattern

bam

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.bam (file)

Alignment in BAM format

*.bam

bed

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.bed (file)

Alignment intervals in BED format

*.bed

paf

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.paf (file)

Alignment in PAF format

*.paf

index

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.bam.${bam_index_extension} (file)

BAM alignment index

*.bam.*

versions_minimap2

${task.process} (string)

The process name

minimap2 (string)

The tool name

minimap2 --version (eval)

The tool version

Topics

Name
Description
Pattern

versions

${task.process} (string)

The process name

minimap2 (string)

The tool name

minimap2 --version (eval)

The tool version

Tools

minimap2 Documentation

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

License: MIT
Authors