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nf-core/ragtag/scaffold @ 0.0.0-6c4ed3a

Scaffolding is the process of ordering and orienting draft assembly (query) sequences into longer sequences. Gaps (stretches of "N" characters) are placed between adjacent query sequences to indicate the presence of unknown sequence. RagTag uses whole-genome alignments to a reference assembly to scaffold query sequences. RagTag does not alter input query sequence in any way and only orders and orients sequences, joining them with gaps.

scaffolding ragtag assembly genome
Latest version: 0.0.0-6c4ed3a
Total downloads: 9
Source: nf-core/modules
Authors: @nschan
Maintainers: @nschan

Summary

Scaffolding is the process of ordering and orienting draft assembly (query) sequences into longer sequences. Gaps (stretches of "N" characters) are placed between adjacent query sequences to indicate the presence of unknown sequence. RagTag uses whole-genome alignments to a reference assembly to scaffold query sequences. RagTag does not alter input query sequence in any way and only orders and orients sequences, joining them with gaps.

Get started

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

include { RAGTAG_SCAFFOLD } from 'nf-core/ragtag/scaffold'

License

MIT License

Process
Name RAGTAG_SCAFFOLD
Input 4 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test' ]
assembly file

Assembly to be scaffolded

 *.{fasta,fasta.gz,fa,fa.gz}
#2 tuple
meta2 map

Groovy Map containing sample information e.g. [ id:'test' ]
reference file

Reference assembly

 *.{fasta,fasta.gz,fa,fa.gz}
#3 tuple
meta3 map

Groovy Map containing sample information e.g. [ id:'test' ]
exclude file

list of target sequences to ignore

 *.txt
#4 tuple
meta4 map

Groovy Map containing sample information e.g. [ id:'test' ]
skip file

list of query sequences to leave unplaced

 *.txt
hard_skip file

list of query headers to leave unplaced and exclude from 'chr0' ('-C')

 *.txt
Output 4 channels
#1 corrected_agp tuple
meta map

Groovy Map containing sample information e.g. [ id:'test' ]
*.agp file

agp file defining how corrected_assembly is built

 *.agp
#2 corrected_stats tuple
meta map

Groovy Map containing sample information e.g. [ id:'test' ]
*.stats file

Statistics on the scaffold

 *.stats
#3 versions_ragtag tuple
${task.process} string

The name of the process
ragtag string

The name of the tool
ragtag.py -v | sed 's/v//' eval

The expression to obtain the version of the tool
#4 corrected_assembly tuple
meta map

Groovy Map containing sample information e.g. [ id:'test' ]
*.fasta file

FASTA file containing the patched assembly

 *.fasta
Tool Description Homepage
ragtag Fast reference-guided genome assembly scaffolding https://github.com/malonge/RagTag/wiki
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:39:32 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fragtag%2Fscaffold/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ragtag/scaffold/blobs/sha256:1e9ecc900b105066f99e01c758fefc317fa0c078aded6caab0d83e6eaa5b103c
Size 2.9 KB
Checksum sha256:1e9ecc900b105066f99e01c758fefc317fa0c078aded6caab0d83e6eaa5b103c