modules/proteinortho

Proteinortho is a tool to detect orthologous genes within different species.

orthologyco-orthologyhomologysequence similarityspectral clusteringcomparative genomicsgenomics

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

Description

Proteinortho is a tool to detect orthologous genes within different species.

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta_files`
`:file`

Input fasta files (proteomes or transcriptomes), at least 2 are needed

*.{fa,fasta,faa,fna,fn}

Output

name:type

description

pattern

`orthologgroups`

`meta`
`:file`

Orthology table

*.proteinortho.tsv

`${prefix}.proteinortho.tsv`
`:file`

Orthology table

*.proteinortho.tsv

`orthologgraph`

`meta`
`:file`

Orthology table

*.proteinortho.tsv

`${prefix}.proteinortho-graph`
`:file`

Orthology graph

*.proteinortho-graph

`blastgraph`

`meta`
`:file`

Orthology table

*.proteinortho.tsv

`${prefix}.blast-graph`
`:file`

BLAST graph

*.blast-graph

`versions_proteinortho`

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

The name of the process

`proteinortho`
`:string`

The name of the tool

`proteinortho --version 2>&1`
`:eval`

The expression to obtain the version of the tool

`versions_diamond`

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

The name of the process

`diamond`
`:string`

The name of the tool

`diamond version 2>/dev/null | sed '1!d;s/^.*version //'`
`:eval`

The expression to obtain the version of the tool

`versions_blast`

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

The name of the process

`blast`
`:string`

The name of the tool

`blastp -version 2>/dev/null | sed '1!d;s/^.*: //;s/+//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`proteinortho`
`:string`

The name of the tool

`proteinortho --version 2>&1`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`diamond`
`:string`

The name of the tool

`diamond version 2>/dev/null | sed '1!d;s/^.*version //'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`blast`
`:string`

The name of the tool

`blastp -version 2>/dev/null | sed '1!d;s/^.*: //;s/+//'`
`:eval`

The expression to obtain the version of the tool

Tools

proteinortho
GPL v3

Proteinortho is a tool to detect orthologous genes within different species.

gitlab.com/paulklemm_PHD/proteinortho gitlab.com/paulklemm_PHD/proteinortho#proteinortho https://gitlab.com/paulklemm_PHD/proteinortho 10.3389/fbinf.2023.1322477

modules/proteinortho

Description

Input

meta :map

fasta_files :file

Output

orthologgroups

meta :file

${prefix}.proteinortho.tsv :file

orthologgraph

meta :file

${prefix}.proteinortho-graph :file

blastgraph

meta :file

${prefix}.blast-graph :file

versions_proteinortho

${task.process} :string

proteinortho :string

proteinortho --version 2>&1 :eval

versions_diamond

${task.process} :string

diamond :string

diamond version 2>/dev/null | sed '1!d;s/^.*version //' :eval

versions_blast

${task.process} :string

blast :string

blastp -version 2>/dev/null | sed '1!d;s/^.*: //;s/+//' :eval

Topics

versions

${task.process} :string

proteinortho :string

proteinortho --version 2>&1 :eval

${task.process} :string

diamond :string

diamond version 2>/dev/null | sed '1!d;s/^.*version //' :eval

${task.process} :string

blast :string

blastp -version 2>/dev/null | sed '1!d;s/^.*: //;s/+//' :eval

Tools

proteinorthoGPL v3

maintainer

get in touch

`meta`
`:map`

`fasta_files`
`:file`

`orthologgroups`

`meta`
`:file`

`${prefix}.proteinortho.tsv`
`:file`

`orthologgraph`

`meta`
`:file`

`${prefix}.proteinortho-graph`
`:file`

`blastgraph`

`meta`
`:file`

`${prefix}.blast-graph`
`:file`

`versions_proteinortho`

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

`proteinortho`
`:string`

`proteinortho --version 2>&1`
`:eval`

`versions_diamond`

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

`diamond`
`:string`

`diamond version 2>/dev/null | sed '1!d;s/^.*version //'`
`:eval`

`versions_blast`

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

`blast`
`:string`

`blastp -version 2>/dev/null | sed '1!d;s/^.*: //;s/+//'`
`:eval`

`versions`

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

`proteinortho`
`:string`

`proteinortho --version 2>&1`
`:eval`

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

`diamond`
`:string`

`diamond version 2>/dev/null | sed '1!d;s/^.*version //'`
`:eval`

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

`blast`
`:string`

`blastp -version 2>/dev/null | sed '1!d;s/^.*: //;s/+//'`
`:eval`

proteinortho
GPL v3