nf-core/hypo @ 0.0.0-6c4ed3a
Summary
Assembly polisher using short (and long) reads
Get started
Add the following snippet to your workflow script to include this module.
include { HYPO } from 'nf-core/hypo'
License
MIT License
Process
Name
|
HYPO |
|---|
Input
5 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
sr_bam
file
|
Aligned short-read BAM/SAM file. Must have CIGAR information. *.{bam,sam}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
reads
file
|
Short reads file(s). In fastq or fasta, compressed or uncompressed |
draft
file
|
Input (fasta) file containing draft contig assembly |
|---|
genome_size
string
|
Estimated size of the genome. Number or nts or use suffixes k/m/g, e.g. 5m, 3.2g |
|---|
reads_coverage
integer
|
Appprimate depth of coverage of short reads. |
|---|
Output
2 channels
#1
fasta
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.fasta
file
|
Polished assembly fasta file *.fasta
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| hypo | Super Fast and Accurate Polisher for Long Read Genome Assemblies. | https://github.com/kensung-lab/hypo |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:24:46 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fhypo/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/hypo/blobs/sha256:8a4e1983feb4fa14de894cf657ee86028a649d82c8f592ee8f82c5d3aeb18240 |
| Size | 2.6 KB |
| Checksum | sha256:8a4e1983feb4fa14de894cf657ee86028a649d82c8f592ee8f82c5d3aeb18240 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:24:46 (UTC) | 3 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:16:44 (UTC) | 3 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:10:16 (UTC) | 4 | 2.6 KB |