nf-core/minimap2/align @ 0.0.0-0c7146d
Summary
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Get started
Add the following snippet to your workflow script to include this module.
include { MINIMAP2_ALIGN } from 'nf-core/minimap2/align'
License
MIT License
Name
|
MINIMAP2_ALIGN |
|---|
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) |
|---|
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
Alignment in BAM format *.bam
|
paf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.paf
file
|
Alignment in PAF format *.paf
|
index
tuple
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
tuple
${task.process}
string
|
The process name |
|---|---|
minimap2
string
|
The tool name |
minimap2 --version
eval
|
The tool version |
| Tool | Description | Homepage |
|---|---|---|
| minimap2 | A versatile pairwise aligner for genomic and spliced nucleotide sequences. | https://github.com/lh3/minimap2 |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:55:52 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fminimap2%2Falign/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/minimap2/align/blobs/sha256:9f2006634eba5d10effd52d8e57c157c960a5e7481458f7dc5ca5b37964cef10 |
| Size | 4.7 KB |
| Checksum | sha256:9f2006634eba5d10effd52d8e57c157c960a5e7481458f7dc5ca5b37964cef10 |