DEN-IM recipe 2.0 - #179

Merged

cimendes merged 8 commits into

devfrom

Dec 11, 2018

Commits on Oct 30, 2018

- added option to retrieve closes reference genome

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be0e95f
update changelog

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db4080b

Commits on Nov 28, 2018

fix bug in denim's recipe

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540fb6c
fix bug in mafft process

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09be77f
added hidden parameter to accomodate changed to the spades.py template

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4c750e5

Commits on Dec 4, 2018

fix bug where reference files where being passed onto mafft via dengue_typing multiple times.
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7b2abda

Commits on Dec 10, 2018

reference file verification done inside the process to accomodate files inside containers

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b29e03a
Merge branch 'dev' into recipes
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2d8c1b4