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`
`:map`

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

`seqfile`
`:file`

Sequences, aligned or not, in any supported format

*

`postprocessing_script`
`:string`

Post processing script in shell, e.g., ‘| sed “/^>/!s/-//g”’

| *

Output

name:type

description

pattern

`seqreformated`

`meta`
`:map`

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

`..gz`
`:file`

Reformatted sequence file

*.*.gz

`versions_hmmer`

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

The name of the process

`hmmer`
`:string`

The name of the tool

`hmmsearch -h | sed '2!d;s/^# HMMER //;s/ .//'`
`:eval`

The expression to obtain the version of the tool

`versions_easel`

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

The name of the process

`easel`
`:string`

The name of the tool

`esl-reformat -h | sed '2!d;s/^# Easel //;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

`hmmer`
`:string`

The name of the tool

`hmmsearch -h | sed '2!d;s/^# HMMER //;s/ .//'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`easel`
`:string`

The name of the tool

`esl-reformat -h | sed '2!d;s/^# Easel //;s/ .//'`
`:eval`

The expression to obtain the version of the tool

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`
`:map`

`seqfile`
`:file`

`postprocessing_script`
`:string`

Output

`seqreformated`

`meta`
`:map`

`..gz`
`:file`

`versions_hmmer`

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

`hmmer`
`:string`

`hmmsearch -h | sed '2!d;s/^# HMMER //;s/ .//'`
`:eval`

`versions_easel`

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

`easel`
`:string`

`esl-reformat -h | sed '2!d;s/^# Easel //;s/ .//'`
`:eval`

Topics

`versions`

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

`hmmer`
`:string`

`hmmsearch -h | sed '2!d;s/^# HMMER //;s/ .//'`
`:eval`

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

`easel`
`:string`

`esl-reformat -h | sed '2!d;s/^# Easel //;s/ .//'`
`:eval`

Tools

hmmer
BSD-3-Clause

included in

maintainer

get in touch

modules/hmmer_eslreformat

Description

Input

meta :map

seqfile :file

postprocessing_script :string

Output

seqreformated

meta :map

*.*.gz :file

versions_hmmer

${task.process} :string

hmmer :string

hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//' :eval

versions_easel

${task.process} :string

easel :string

esl-reformat -h | sed '2!d;s/^# Easel *//;s/ .*//' :eval

Topics

versions

${task.process} :string

hmmer :string

hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//' :eval

${task.process} :string

easel :string

esl-reformat -h | sed '2!d;s/^# Easel *//;s/ .*//' :eval

Tools

hmmerBSD-3-Clause

included in

maintainer

get in touch

`meta`
`:map`

`seqfile`
`:file`

`postprocessing_script`
`:string`

`seqreformated`

`meta`
`:map`

`..gz`
`:file`

`versions_hmmer`

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

`hmmer`
`:string`

`hmmsearch -h | sed '2!d;s/^# HMMER //;s/ .//'`
`:eval`

`versions_easel`

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

`easel`
`:string`

`esl-reformat -h | sed '2!d;s/^# Easel //;s/ .//'`
`:eval`

`versions`

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

`hmmer`
`:string`

`hmmsearch -h | sed '2!d;s/^# HMMER //;s/ .//'`
`:eval`

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

`easel`
`:string`

`esl-reformat -h | sed '2!d;s/^# Easel //;s/ .//'`
`:eval`

hmmer
BSD-3-Clause