Nextflow Registry | nf-core/vamb/bin@0.0.0-6c4ed3a

nf-core/vamb/bin @ 0.0.0-6c4ed3a

Variational autoencoder for metagenomic binning

clustering binning metagenomics denovo assembly mag

Latest version: 0.0.0-6c4ed3a

Total downloads: 16

Source: nf-core/modules

Authors: @prototaxites

Maintainers: @prototaxites

Variational autoencoder for metagenomic binning

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

include { VAMB_BIN } from 'nf-core/vamb/bin'

MIT License

Process

`Name`	`VAMB_BIN`

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}`
`abundance_tsv` file	TSV describing abundance of contigs in the provided assembly with headers contigname\tsample1\tsample2... ctg00001\t10.0\t5.0 Not compatible with bam input. `*.tsv`
`bams` file	List of sorted bam files of reads mapped to the reference assembly. Not compatible with TSV input. `*.bam`
`taxonomy` file	TSV describing the taxonomic lineage of each contig, with headers contigs\tpredictions ctg00001\tBacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriacea;Escherichia coli `*.tsv`

Output 10 channels

#1 log tuple

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

#2 bins tuple

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

#3 versions

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

#4 abundance tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/abundance.npz` file	Numpy array of the abundance of contigs `*.npz`

#5 composition tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/composition.npz` file	Numpy array of the kmer composition of the contigs `*.npz`

#6 clusters_split tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/vae*_clusters_split.tsv` file	TSV defining the output bin clusters if binsplitting enabled `*.tsv`

#7 latent_encoding tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/latent.npz` file	Numpy array of the latent embedding of the contigs `*.npz`

#8 clusters_unsplit tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/vae*_clusters_unsplit.tsv` file	TSV defining the output bin clusters without binsplitting `*.tsv`

#9 clusters_metadata tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/vae*_clusters_metadata.tsv` file	TSV describing the metadata of the output bin clusters `*.tsv`

#10 taxometer_results tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}/results_taxometer.tsv` file	TSV describing the refined taxonomic lineage of each contig, with headers contigs\tpredictions\tscores `*.tsv`