modules/nail_search

nail search is a fast and scalable tool for searching protein sequences against protein databases

alignmentHMMfastaprotein

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

Description

nail search is a fast and scalable tool for searching protein sequences against protein databases

Input

name:type

description

pattern

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`query{:bash}`
`:file`

Input query file

*.{hmm,fasta,fa,fna}

`meta2{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`target{:bash}`
`:file`

Input target file

*.{fasta,fa,fna}

`write_align{:bash}`
`:boolean`

Flag to save optional alignment output. Specify with ‘true’ to save.

Output

name:type

description

pattern

`output{:bash}`

`meta{:bash}`
`:map`

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

`${prefix}.txt{:bash}`
`:map`

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

*.{txt}

`target_summary{:bash}`

`meta{:bash}`
`:map`

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

`${prefix}.tbl{:bash}`
`:map`

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

results.tbl

`alignments{:bash}`

`meta{:bash}`
`:map`

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

`${prefix}.ali{:bash}`
`:map`

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

*.ali

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

Tools

nail
BSD-3-clause

Profile Hidden Markov Model (pHMM) biological sequence alignment tool

github.com/TravisWheelerLab/nail 10.1101/2024.01.27.577580