Nextflow Registry | nf-core/yahs@0.0.0-0c7146d

nf-core/yahs @ 0.0.0-0c7146d

Performs assembly scaffolding using YaHS

scaffolding assembly yahs hic

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ksenia-krasheninnikova

Maintainers: @ksenia-krasheninnikova @yy5

Performs assembly scaffolding using YaHS

Add the following snippet to your workflow script to include this module.

include { YAHS } from 'nf-core/yahs'

MIT License

Process

`Name`	`YAHS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`fasta` file	FASTA reference file `*.{fasta,fa}`
`fai` file	index of the reference file `*.{fai}`
`hic_map` file	BED file containing coordinates of read alignments `*.{bed,bam,bin}`
`agp` file	Optional AGP file describing a set of scaffolds from the input contigs to use as a start point `*.agp`

Output 7 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}.log` file	Log file describing YaHS run `${prefix}.log`

#2 binary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}.bin` file	Binary data file with alignment results of Hi-C reads to the contigs in internal YaHS binary format `${prefix}.bin`

#3 round_agp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}_r_.agp` file	AGP file describing intermediate rounds of scaffolding `${prefix}_{initial,no}_break*.agp`

#4 scaffolds_agp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}_scaffolds_final.agp` file	AGP file containing contigs placing coordinates `${prefix}_scaffolds_final.agp`

#5 versions_yahs tuple

`${task.process}` string	The name of the process
`yahs` string	The name of the tool
`yahs --version 2>&1` eval	The expression to obtain the version of the tool

#6 scaffolds_fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}_scaffolds_final.fa` file	FASTA file with resulting contigs `${prefix}_scaffolds_final.fa`

#7 initial_break_agp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}_{inital,no}_break*.agp` file	AGP file describing initial contig breaks `${prefix}_{inital,no}_break*.agp`

Tool	Description	Homepage
yahs	YaHS, yet another Hi-C scaffolding tool.	https://github.com/c-zhou/yahs

Size<
Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:24:09 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fyahs/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/yahs/blobs/sha256:627100755e035e658a37209a5caefcd98a10feef96f2ccdc10c86e9841667f2c