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

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

Compare target sequences to fasta-formatted query sequences using global pairwise alignment.

vsearch usearch alignment fasta

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @jtangrot

Maintainers: @jtangrot

Compare target sequences to fasta-formatted query sequences using global pairwise alignment.

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

include { VSEARCH_USEARCHGLOBAL } from 'nf-core/vsearch/usearchglobal'

MIT License

Process

`Name`	`VSEARCH_USEARCHGLOBAL`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`queryfasta` file	Query sequences in FASTA format `*.{fasta,fa,fna,faa}`

`db` file	Reference database file in FASTA or UDB format `*`

`idcutoff` float	Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)

`outoption` string	Specify the type of output file to be generated by selecting one of the vsearch output file options `alnout\|biomout\|blast6out\|mothur_shared_out\|otutabout\|samout\|uc\|userout\|lcaout`

`user_columns` string	If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string.

Output 10 channels

#1 uc tuple

`meta` file	Results in pairwise alignment format `*.{aln}`
`*.uc` file	Tab delimited results in a uclust-like format with 10 columns `*.{uc}`

#2 aln tuple

`meta` file	Results in pairwise alignment format `*.{aln}`
`*.aln` file	Results in pairwise alignment format `*.{aln}`

#3 lca tuple

`meta` file	Results in pairwise alignment format `*.{aln}`
`*.lca` file	Last common ancestor (LCA) information about the hits of each query in tab-separated format `*.{lca}`

#4 otu tuple

`meta` file	Results in pairwise alignment format `*.{aln}`
`*.otu` file	Results in an OTU table in the classic tab-separated plain text format `*.{otu}`

#5 sam tuple

`meta` file	Results in pairwise alignment format `*.{aln}`
`*.sam` file	Results written in sam format `*.{sam}`

#6 tsv tuple

`meta` file	Results in pairwise alignment format `*.{aln}`
`*.tsv` file	Results in tab-separated output, columns defined by user `*.{tsv}`

#7 txt tuple

`meta` file	Results in pairwise alignment format `*.{aln}`
`*.txt` file	Tab delimited results in blast-like tabular format `*.{txt}`

#8 biom tuple

`meta` file	Results in pairwise alignment format `*.{aln}`
`*.biom` file	Results in an OTU table in the biom version 1.0 file format `*.{biom}`

#9 mothur tuple

`meta` file	Results in pairwise alignment format `*.{aln}`
`*.mothur` file	Results in an OTU table in the mothur ’shared’ tab-separated plain text file format `*.{mothur}`

#10 versions_vsearch tuple