modules/hmmer_eslreformat

reformats sequence files, see HMMER documentation for details. The module requires that the format is specified in ext.args in a config file, and that this comes last. See the tools help for possible values.

sorthmmerreformat

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

Description

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`seqfile{:bash}`
`:file`

Sequences, aligned or not, in any supported format

*

Output

name:type

description

pattern

`seqreformated{:bash}`

`meta{:bash}`
`:map`

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

`..gz{:bash}`
`:file`

Reformatted sequence file

*.*.gz

`versions{:bash}`

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

File containing software versions

versions.yml

Tools

hmmer
BSD-3-Clause

Biosequence analysis using profile hidden Markov models

http://hmmer.org http://hmmer.org/documentation 10.1371/journal.pcbi.1002195

modules/hmmer_eslreformat

Description

Input

`meta{:bash}`
`:map`

`seqfile{:bash}`
`:file`

Output

`seqreformated{:bash}`

`meta{:bash}`
`:map`

`..gz{:bash}`
`:file`

`versions{:bash}`

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

Tools

hmmer
BSD-3-Clause

included in

maintainer

get in touch

modules/hmmer_eslreformat

Description

Input

meta{:bash}:map

seqfile{:bash}:file

Output

seqreformated{:bash}

meta{:bash}:map

*.*.gz{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

hmmer BSD-3-Clause

included in

maintainer

get in touch

`meta{:bash}`
`:map`

`seqfile{:bash}`
`:file`

`seqreformated{:bash}`

`meta{:bash}`
`:map`

`..gz{:bash}`
`:file`

`versions{:bash}`

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

hmmer
BSD-3-Clause