Nextflow Registry | nf-core/comebin/runcomebin@0.0.0-0c7146d

nf-core/comebin/runcomebin @ 0.0.0-0c7146d

Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning

metagenomics binning clustering

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @prototaxites

Maintainers: @prototaxites

Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning

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

include { COMEBIN_RUNCOMEBIN } from 'nf-core/comebin/runcomebin'

MIT License

Process

`Name`	`COMEBIN_RUNCOMEBIN`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`assembly` file	FASTA file of contigs for binning `*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}`
`bam` file	List of sorted bam files of reads mapped to the reference assembly. Not compatible with TSV input. `*.bam`

Output 6 channels

#1 log tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/comebin.log` file	COMEBin log file `*.log`

#2 tsv tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/comebin_res.tsv` file	TSV mapping the output clusters to contigs `*.tsv`

#3 bins tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/comebin_res_bins/*.fa.gz` file	List of FASTA files of binned contigs `*.fna.gz`

#4 embeddings tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/embeddings.tsv` file	TSV describing the embeddings of the contigs `*.tsv`

#5 covembeddings tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/covembeddings.tsv` file	TSV describing the embeddings of the contigs `*.tsv`

#6 versions_comebin tuple

`${task.process}` string	The name of the process
`comebin` string	The name of the tool
`run_comebin.sh \| sed '2!d;s/COMEBin version: //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
comebin	COMEBin allows effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning	https://github.com/ziyewang/COMEBin

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:32:14 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcomebin%2Fruncomebin/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/comebin/runcomebin/blobs/sha256:00dcd5faa6ff1acf4e3a1eeb800d0b55556fb1bbd857b3b10997970952797b90
Size	2.9 KB
Checksum	sha256:00dcd5faa6ff1acf4e3a1eeb800d0b55556fb1bbd857b3b10997970952797b90
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:32:14 (UTC)		1	2.9 KB	-