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{:bash}

:map

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

fasta{:bash}

:file

Input fasta file

*.fasta

Output

name:type
description
pattern

success_log{:bash}

meta{:bash}

:map

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

*.success.log{:bash}

:file

Log file for successful validation

*.success.log

error_log{:bash}

meta{:bash}

:map

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

*.error.log{:bash}

:file

Log file for failed validation

*.error.log

versions_py_fasta_validator{:bash}

${task.process}{:bash}

:string

The name of the process

py_fasta_validator{:bash}

:string

The name of the tool

py_fasta_validator --version | cut -d" " -f3{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

py_fasta_validator{:bash}

:string

The name of the tool

py_fasta_validator --version | cut -d" " -f3{:bash}

: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
included in
genomeqcmultiplesequencealignseqsubmit
maintainer
Github user gallvp
get in touch
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