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planemo upload for repository https://github.com/COMBAT-TB/confil commit b1a96c1b50cea70a20d4e606100879da8b6ed1b2
author sanbi-uwc
date Mon, 11 Mar 2019 07:18:34 -0400
parents 2cde7c81c694
children bbf9ab2ebee7
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Metadata-Version: 1.0
Name: confil
Version: 0.1.2.dev20190304
Summary: Contamination filter
Home-page: https://github.com/COMBAT-TB/confil
Author: UNKNOWN
Author-email: UNKNOWN
License: UNKNOWN
Description-Content-Type: text/markdown
Description: # confil
        
        [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil)
        [![Anaconda-Server Badge](https://anaconda.org/thoba/confil/badges/version.svg)](https://anaconda.org/thoba/confil)
        
        :no_entry_sign: :construction: **For in-house use**
        
        `confil` parses a [kraken2](https://ccb.jhu.edu/software/kraken2/) report and determines contamination based on a specified cutoff.
        
        ## Requirements
        
        - kraken2
        
        ## Up and running
        
        ```sh
        $ git clone https://github.com/COMBAT-TB/confil.git
        ...
        $ cd confil
        $ virtualenv envname
        $ source envname/bin/activate
        $ pip install -r requirements.txt
        $ python setup.py install
        $ confil --help
        $ confil --threads 1 --paired --cutoff 80 fastq_1.fastq fastq_2.fastq
        ```
        
Keywords: contamination,filter
Platform: UNKNOWN