Nextflow Registry | nf-core/salsa2@0.0.0-0c7146d

nf-core/salsa2 @ 0.0.0-0c7146d

SALSA, A tool to scaffold long read assemblies with HiC

assembly hi-c scaffolding long reads salsa salsa2

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @scorreard

Maintainers: @scorreard

SALSA, A tool to scaffold long read assemblies with HiC

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

include { SALSA2 } from 'nf-core/salsa2'

MIT License

Process

`Name`	`SALSA2`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Fasta file of assembly. Headers must not contain ':' `*.{fa, fasta}`
`index` file	Fasta index file of assembly containing the length of contigs. `*.{fa.fai, fasta.fai}`

`bed` file	BED file of alignments sorted by read names, e.g., from HiC-Pro `*.{bed}`

`gfa` file	GFA file of the assembly graph

`dup` file	File containing the duplicated contigs

`filter_bed` file	BED file of the filtered alignments `*.{bed}`

Output 4 channels

#1 agp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_scaffolds_FINAL.agp` file	AGP style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds `*_scaffolds_FINAL.agp`

#2 fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_scaffolds_FINAL.fasta` file	Sequences for the scaffolds generated by the algorithm `*_scaffolds_FINAL.fasta`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

#4 agp_original_coordinates tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`/scaffolds_FINAL.original-coordinates.agp` file	Secondary output AGP file with names and coordinates matching the original input assembly (optional) `*scaffolds_FINAL.original-coordinates.agp`

Tool	Description	Homepage
salsa2	Salsa is a tool to scaffold long read assemblies with Hi-C.	https://github.com/marbl/SALSA

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:09:15 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsalsa2/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/salsa2/blobs/sha256:ea617a35a6102f0b5356274a8c2c8fd840d0cf97fdcc51c0fad3792b17459856
Size	2.7 KB
Checksum	sha256:ea617a35a6102f0b5356274a8c2c8fd840d0cf97fdcc51c0fad3792b17459856
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:09:15 (UTC)		1	2.7 KB	-