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planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
author sanbi-uwc
date Mon, 04 Mar 2019 03:28:57 -0500
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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1 # confil
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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3 [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil)
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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4 [![Anaconda-Server Badge](https://anaconda.org/thoba/confil/badges/version.svg)](https://anaconda.org/thoba/confil)
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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6 :no_entry_sign: :construction: **For in-house use**
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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8 `confil` parses a [kraken2](https://ccb.jhu.edu/software/kraken2/) report and determines contamination based on a specified cutoff.
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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10 ## Requirements
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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12 - kraken2
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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14 ## Up and running
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16 ```sh
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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17 $ git clone https://github.com/COMBAT-TB/confil.git
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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18 ...
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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19 $ cd confil
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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20 $ virtualenv envname
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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21 $ source envname/bin/activate
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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22 $ pip install -r requirements.txt
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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23 $ python setup.py install
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24 $ confil --help
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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25 $ confil --threads 1 --paired --cutoff 80 fastq_1.fastq fastq_2.fastq
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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26 ```