modules/emboss_cons

cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score for each amino acid residue or nucleotide at each position in the alignment.

embossconsensusfastamultiple sequence alignmentMSA

https://github.com/nf-core/modules/[...]/modules/nf-core/emboss/cons

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

Multiple sequence alignment (unzipped)

*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}

Output

name:type

description

pattern

`consensus`

`meta`
`:map`

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

`*.fa`
`:file`

Consensus sequence calculated from multiple sequence alignment

*.fa

`versions_emboss`

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

The name of the process

`emboss`
`:string`

The name of the tool

`cons -version 2>&1 | sed "s/EMBOSS://"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`emboss`
`:string`

The name of the tool

`cons -version 2>&1 | sed "s/EMBOSS://"`
`:eval`

The expression to obtain the version of the tool

Tools

emboss
GPL

The European Molecular Biology Open Software Suite

ebi.ac.uk/Tools/sfc/emboss_seqret emboss.bioinformatics.nl/cgi-bin/emboss/help/seqret http://emboss.open-bio.org/ 10.1016/s0168-9525(00)02024-2

modules/emboss_cons

Description

Input

`meta`
`:map`

`fasta`
`:file`

Output

`consensus`

`meta`
`:map`

`*.fa`
`:file`

`versions_emboss`

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

`emboss`
`:string`

`cons -version 2>&1 | sed "s/EMBOSS://"`
`:eval`

Topics

`versions`

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

`emboss`
`:string`

`cons -version 2>&1 | sed "s/EMBOSS://"`
`:eval`

Tools

emboss
GPL

maintainer

get in touch

modules/emboss_cons

Description

Input

meta:map

fasta:file

Output

consensus

meta:map

*.fa:file

versions_emboss

${task.process}:string

emboss:string

cons -version 2>&1 | sed "s/EMBOSS://":eval

Topics

versions

${task.process}:string

emboss:string

cons -version 2>&1 | sed "s/EMBOSS://":eval

Tools

emboss GPL

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`consensus`

`meta`
`:map`

`*.fa`
`:file`

`versions_emboss`

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

`emboss`
`:string`

`cons -version 2>&1 | sed "s/EMBOSS://"`
`:eval`

`versions`

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

`emboss`
`:string`

`cons -version 2>&1 | sed "s/EMBOSS://"`
`:eval`

emboss
GPL