Nextflow Registry | nf-core/vsearch/cluster@0.0.0-6c4ed3a

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

Cluster sequences using a single-pass, greedy centroid-based clustering algorithm.

vsearch clustering microbiome

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @mirpedrol

Maintainers: @mirpedrol

Cluster sequences using a single-pass, greedy centroid-based clustering algorithm.

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

include { VSEARCH_CLUSTER } from 'nf-core/vsearch/cluster'

MIT License

Process

`Name`	`VSEARCH_CLUSTER`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`fasta` file	Sequences to cluster in FASTA format `*.{fasta,fa,fasta.gz,fa.gz}`

Output 13 channels

#1 uc tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.uc.tsv.gz` file	Tab delimited results in a uclust-like format with 10 columns `*.uc.gz`

#2 aln tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.aln.gz` file	Results in pairwise alignment format `*.aln.gz`

#3 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.bam` file	Results written in bam format `*.bam`

#4 msa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.msa.fasta.gz` file	Multiple sequence alignment of the centroids `*.msa.fasta.gz`

#5 otu tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.otu.tsv.gz` file	Results in an OTU table in the classic tab-separated plain text format `*.otu.tsv.gz`

#6 out tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.out.tsv.gz` file	Results in tab-separated output, columns defined by user `*.out.tsv.gz`

#7 biom tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.biom.gz` file	Results in an OTU table in the biom version 1.0 file format `*.biom.gz`

#8 blast tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.blast.tsv.gz` file	Tab delimited results in blast-like tabular format `*.blast.tsv.gz`

#9 mothur tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.mothur.tsv.gz` file	Results in an OTU table in the mothur ’shared’ tab-separated plain text file format `*.mothur.tsv.gz`

#10 profile tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.profile.txt.gz` file	Profile of the clustering results `*.profile.txt.gz`

#11 clusters tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`.clusters.fasta.gz` file	Clustered sequences in FASTA format `.clusters.fasta.gz`

#12 centroids tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]