Nextflow Registry | nf-core/autocycler/combine@0.0.0-0c7146d

nf-core/autocycler/combine @ 0.0.0-0c7146d

Merge resolved cluster assemblies into final consensus outputs with Autocycler.

autocycler genome-assembly consensus long-read

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @dwells-eit @eit-maxlcummins

Maintainers: @dwells-eit

Merge resolved cluster assemblies into final consensus outputs with Autocycler.

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

include { AUTOCYCLER_COMBINE } from 'nf-core/autocycler/combine'

MIT License

Process

`Name`	`AUTOCYCLER_COMBINE`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`clusters` file	Final cluster assembly graphs (GFA) to be combined into consensus sequences. `*.gfa`

Output 4 channels

#1 gfa tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`combine/${prefix}/consensus_assembly.gfa` file	Consensus assembly graph generated by Autocycler. `combine/*/consensus_assembly.gfa`

#2 fasta tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`combine/${prefix}/consensus_assembly.fasta` file	Consensus genome sequence generated by Autocycler. `combine/*/consensus_assembly.fasta`

#3 stats tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`combine/${prefix}/consensus_assembly.yaml` file	Run statistics for the combine step. `combine/*/consensus_assembly.yaml`

#4 versions_autocycler tuple

`${task.process}` string	The name of the process
`autocycler` string	The name of the tool
`autocycler --version \| sed 's/^[^ ]* //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
autocycler	A tools for generating consensus long-read assemblies for bacterial genomes.	https://github.com/rrwick/Autocycler/wiki

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:23:17 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fautocycler%2Fcombine/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/autocycler/combine/blobs/sha256:49e1486a1393491ac293daeedb1fe407f4b1401fb10a87fc72f1e3a40405e5ac
Size	3.4 KB
Checksum	sha256:49e1486a1393491ac293daeedb1fe407f4b1401fb10a87fc72f1e3a40405e5ac
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:23:17 (UTC)		1	3.4 KB	-