modules/fastavalidator

“Python C-extension for a simple validator for fasta files. The module emits the validated file or an error log upon validation failure.”

fastavalidationgenome

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

This module is deprecated.

Description

“Python C-extension for a simple validator for fasta files. The module emits the validated file or an error log upon validation failure.”

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

Input fasta file

*.fasta

Output

name:type

description

pattern

`success_log`

`meta`
`:map`

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

`*.success.log`
`:file`

Log file for successful validation

*.success.log

`error_log`

`meta`
`:map`

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

`*.error.log`
`:file`

Log file for failed validation

*.error.log

`versions_py_fasta_validator`

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

The name of the process

`py_fasta_validator`
`:string`

The name of the tool

`py_fasta_validator --version | cut -d" " -f3`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`py_fasta_validator`
`:string`

The name of the tool

`py_fasta_validator --version | cut -d" " -f3`
`:eval`

The expression to obtain the version of the tool

Tools

fasta_validate
MIT

"Python C-extension for a simple C code to validate a fasta file. It only checks a few things, and by default only sets its response via the return code, so you will need to check that!"

github.com/linsalrob/py_fasta_validator 10.5281/zenodo.5002710

modules/fastavalidator

Description

Input

`meta`
`:map`

`fasta`
`:file`

Output

`success_log`

`meta`
`:map`

`*.success.log`
`:file`

`error_log`

`meta`
`:map`

`*.error.log`
`:file`

`versions_py_fasta_validator`

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

`py_fasta_validator`
`:string`

`py_fasta_validator --version | cut -d" " -f3`
`:eval`

Topics

`versions`

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

`py_fasta_validator`
`:string`

`py_fasta_validator --version | cut -d" " -f3`
`:eval`

Tools

fasta_validate
MIT

included in

maintainer

get in touch

modules/fastavalidator

Description

Input

meta:map

fasta:file

Output

success_log

meta:map

*.success.log:file

error_log

meta:map

*.error.log:file

versions_py_fasta_validator

${task.process}:string

py_fasta_validator:string

py_fasta_validator --version | cut -d" " -f3:eval

Topics

versions

${task.process}:string

py_fasta_validator:string

py_fasta_validator --version | cut -d" " -f3:eval

Tools

fasta_validate MIT

included in

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`success_log`

`meta`
`:map`

`*.success.log`
`:file`

`error_log`

`meta`
`:map`

`*.error.log`
`:file`

`versions_py_fasta_validator`

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

`py_fasta_validator`
`:string`

`py_fasta_validator --version | cut -d" " -f3`
`:eval`

`versions`

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

`py_fasta_validator`
`:string`

`py_fasta_validator --version | cut -d" " -f3`
`:eval`

fasta_validate
MIT