nf-core/hisat3n/align @ 0.0.0-0c7146d
Summary
Align nucleotide conversion sequencing reads (e.g., bisulfite-seq, SLAM-seq) to a reference genome with HISAT-3N
Get started
Add the following snippet to your workflow script to include this module.
include { HISAT3N_ALIGN } from 'nf-core/hisat3n/align'
License
MIT License
Name
|
HISAT3N_ALIGN |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
|---|---|
reads
file
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. *.{fq,fastq,fq.gz,fastq.gz}
|
meta2
map
|
Groovy Map containing reference information e.g. [ id:'genome' ] |
|---|---|
index
file
|
HISAT-3N genome index files *.ht2
|
sam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
|---|---|
*.sam
file
|
Output SAM file containing read alignments *.sam
|
summary
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
|---|---|
*.log
file
|
Alignment summary log *.log
|
versions_hisat3n
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
hisat-3n
string
|
The tool name |
hisat-3n --version 2>&1 | head -1 | sed 's/.* //'
eval
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| hisat-3n | HISAT-3N is designed for nucleotide conversion sequencing technologies and implemented based on HISAT2. | http://daehwankimlab.github.io/hisat2/hisat-3n/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:09:19 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fhisat3n%2Falign/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/hisat3n/align/blobs/sha256:dfcf42aec61c32cbab96469802ad60827660593e414eba58d183dce8e91ffe73 |
| Size | 3.1 KB |
| Checksum | sha256:dfcf42aec61c32cbab96469802ad60827660593e414eba58d183dce8e91ffe73 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:24:03 (UTC) | 3 | 3.1 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:09:19 (UTC) | 4 | 3.1 KB |