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nf-core/clame @ 0.0.0-0c7146d

binning of metagenomic sequences

sort genomics binning metagenomics
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @alxndrdiaz

Summary

binning of metagenomic sequences

Get started

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

include { CLAME } from 'nf-core/clame'

License

MIT License

Process
Name CLAME
Input 1 channel
#1 tuple
meta map

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

Nucleotide sequences in FASTA format

 *.{fasta,fa,fna,faa}
Output 7 channels
#1 fm tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.fm9 file

FM-index output

 *.{fm9}
#2 bins tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.binning file

All bins reported

 *.{binning}
#3 fasta tuple
meta map

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

Output fasta file for all the bins reported, optional since it will be created when bins can be found

 *.{fasta}
#4 index tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.index file

1st column contains the original name for each read, 2nd column the index used by CLAME

 *.{index}
#5 links tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.links file

Histogram links by number of reads

 *.{links}
#6 result tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.result file

Adjacency list for the overlap detected by each read

 *.{result}
#7 versions_clame tuple
${task.process} string

The name of the process
clame string

The name of the tool
clame -h 2>&1 | sed '2!d;s/version //;s/ .*//' eval

The expression to obtain the version of the tool
Tool Description Homepage
clame CLAME is a binning software for metagenomic reads. It immplements a fm-index search algorithm for nucleotide sequence alignment. Then it uses strongly connected component strategy to bin sequences with similar DNA composition. https://github.com/andvides/CLAME
Version 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:30:53 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fclame/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/clame/blobs/sha256:4aa9cbfc8e67ff9047c42bd40a0be8f78881c7a3b86942f9dd6e325e3f02647a
Size 3.0 KB
Checksum sha256:4aa9cbfc8e67ff9047c42bd40a0be8f78881c7a3b86942f9dd6e325e3f02647a
Downloads 1
Version Date Status Downloads Size Diff
0.0.0-0c7146d 08 Apr 2026 18:30:53 (UTC)