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nf-core/autocycler/cluster @ 0.0.0-6c4ed3a

Cluster replicons in compressed assemblies with Autocycler.

autocycler genome-assembly clustering long-read
Latest version: 0.0.0-6c4ed3a
Total downloads: 7
Source: nf-core/modules
Authors: @dwells-eit @eit-maxlcummins
Maintainers: @dwells-eit

Summary

Cluster replicons in compressed assemblies with Autocycler.

Get started

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

include { AUTOCYCLER_CLUSTER } from 'nf-core/autocycler/cluster'

License

MIT License

Process
Name AUTOCYCLER_CLUSTER
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
gfa file

Assembly graph files produced by the compression step.

 */*.gfa
Output 7 channels
#1 tsv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
clustering/$prefix/*.tsv file

Tabular summary of cluster relationships.

 clustering/*/*.tsv
#2 stats tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
clustering/$prefix/*.yaml file

Run-level statistics for the clustering step.

 clustering/*/*.yaml
#3 newick tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
clustering/$prefix/*.newick file

Newick tree relating contigs.

 clustering/*/*.newick
#4 clusters tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
clustering/$prefix/qc_pass/*/*.gfa file

Aassembly graphs of clustered contigs.

 clustering/*/qc_pass/*/*.gfa
#5 clusterstats tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
clustering/$prefix/qc_pass/*/*.yaml file

Per-cluster metrics reported by Autocycler.

 clustering/*/qc_pass/*/*.yaml
#6 pairwisedistances tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
clustering/$prefix/*.phylip file

Pairwise distance matrix in PHYLIP format.

 clustering/*/*.phylip
#7 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 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:03:05 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fautocycler%2Fcluster/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/autocycler/cluster/blobs/sha256:add76b66aa42afa35fa3a8b8a9f07cb3ae4cf4fa0534e3844eb0ffa6ba92e7f6
Size 3.2 KB
Checksum sha256:add76b66aa42afa35fa3a8b8a9f07cb3ae4cf4fa0534e3844eb0ffa6ba92e7f6
Downloads 3
Version