Nextflow Registry | nf-core/polypolish/polish@0.0.0-0c7146d

nf-core/polypolish/polish @ 0.0.0-0c7146d

Polishing genome assemblies with short reads.

assembly polishing genome polishing ont

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ktrappe

Maintainers: @ktrappe

Polishing genome assemblies with short reads.

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

include { POLYPOLISH_POLISH } from 'nf-core/polypolish/polish'

MIT License

Process

`Name`	`POLYPOLISH_POLISH`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fasta` file	FASTA file with draft assembly of ONT data `*.{fasta,fna,fa,fas}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`sam` file	List of SAM files of short reads mapped against the FASTA input file `*.sam`

`save_debug` boolean	Turn debug output on `true\|false`

Output 3 channels

#1 debug tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.txt` file	File with debug base information `*.txt`

#2 fasta tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.fasta` file	FASTA file with polished draft assembly `*.{fasta,fna,fa,fas}`

#3 versions

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

Tool	Description	Homepage
polypolish	Polishing genome assemblies with short reads.	https://github.com/rrwick/Polypolish

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:04:47 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpolypolish%2Fpolish/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/polypolish/polish/blobs/sha256:79b69db3b225c799e5b237bb65990b35fdbe6447270e4f5fe0cc506f887e5aff
Size	2.7 KB
Checksum	sha256:79b69db3b225c799e5b237bb65990b35fdbe6447270e4f5fe0cc506f887e5aff
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:04:47 (UTC)		1	2.7 KB	-