modules/vsearch_cluster

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

vsearchclusteringmicrobiome

https://github.com/nf-core/modules/[...]/modules/nf-core/vsearch/cluster

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`aln`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`*.aln.gz`
`:file`

Results in pairwise alignment format

*.aln.gz

`biom`

`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

`mothur`

`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

`otu`

`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

`bam`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`*.bam`
`:file`

Results written in bam format

*.bam

`out`

`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

`blast`

`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

`uc`

`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

`centroids`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`*.centroids.fasta.gz`
`:file`

Centroid sequences in FASTA format

*.centroids.fasta.gz

`clusters`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`.clusters.fasta.gz`
`:file`

Clustered sequences in FASTA format

*.clusters.fasta*.gz

`profile`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`*.profile.txt.gz`
`:file`

Profile of the clustering results

*.profile.txt.gz

`msa`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`*.msa.fasta.gz`
`:file`

Multiple sequence alignment of the centroids

*.msa.fasta.gz

`versions_vsearch`

`${task.process}`
`:string`

The process the versions were collected from

`vsearch`
`:string`

The tool name

`vsearch --version 2>&1 | sed -n "1s/.v$[0-9.]$.*/\\1/p"`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

`${task.process}`
`:string`

The process the versions were collected from

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`vsearch`
`:string`

The tool name

`vsearch --version 2>&1 | sed -n "1s/.v$[0-9.]$.*/\\1/p"`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The process the versions were collected from

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

vsearch
GPL v3-or-later OR BSD-2-clause

VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)

github.com/torognes/vsearch github.com/torognes/vsearch/releases/download/v2.31.0/vsearch_manual.pdf https://github.com/torognes/vsearch 10.7717/peerj.2584

modules/vsearch_cluster

Description

Input

meta:map

fasta:file

Output

aln

meta:map

*.aln.gz:file

biom

meta:map

*.biom.gz:file

mothur

meta:map

*.mothur.tsv.gz:file

otu

meta:map

*.otu.tsv.gz:file

bam

meta:map

*.bam:file

out

meta:map

*.out.tsv.gz:file

blast

meta:map

*.blast.tsv.gz:file

uc

meta:map

*.uc.tsv.gz:file

centroids

meta:map

*.centroids.fasta.gz:file

clusters

meta:map

*.clusters.fasta*.gz:file

profile

meta:map

*.profile.txt.gz:file

msa

meta:map

*.msa.fasta.gz:file

versions_vsearch

${task.process}:string

vsearch:string

vsearch --version 2>&1 | sed -n "1s/.*v\([0-9.]*\).*/\\1/p":eval

versions_samtools

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':eval

Topics

versions

${task.process}:string

vsearch:string

vsearch --version 2>&1 | sed -n "1s/.*v\([0-9.]*\).*/\\1/p":eval

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':eval

Tools

vsearch GPL v3-or-later OR BSD-2-clause

included in

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`aln`

`meta`
`:map`

`*.aln.gz`
`:file`

`biom`

`meta`
`:map`

`*.biom.gz`
`:file`

`mothur`

`meta`
`:map`

`*.mothur.tsv.gz`
`:file`

`otu`

`meta`
`:map`

`*.otu.tsv.gz`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`out`

`meta`
`:map`

`*.out.tsv.gz`
`:file`

`blast`

`meta`
`:map`

`*.blast.tsv.gz`
`:file`

`uc`

`meta`
`:map`

`*.uc.tsv.gz`
`:file`

`centroids`

`meta`
`:map`

`*.centroids.fasta.gz`
`:file`

`clusters`

`meta`
`:map`

`.clusters.fasta.gz`
`:file`

`profile`

`meta`
`:map`

`*.profile.txt.gz`
`:file`

`msa`

`meta`
`:map`

`*.msa.fasta.gz`
`:file`

`versions_vsearch`

`${task.process}`
`:string`

`vsearch`
`:string`

`vsearch --version 2>&1 | sed -n "1s/.v\([0-9.]\).*/\\1/p"`
`:eval`

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

`versions`

`${task.process}`
`:string`

`vsearch`
`:string`

`vsearch --version 2>&1 | sed -n "1s/.v\([0-9.]\).*/\\1/p"`
`:eval`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

vsearch
GPL v3-or-later OR BSD-2-clause