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This version addresses the changes discussed in [#36](https://github.com/fmalmeida/MpGAP/issues/36), [#37](https://github.com/fmalmeida/MpGAP/issues/37) and [#38](https://github.com/fmalmeida/MpGAP/issues/38).
Its main changes are:
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@@ -13,6 +13,7 @@ Its main changes are:
* Customized labels to ask for a little bit more on first run
* Added a module config for quast to ask for more memory and cpus on first run, removing it from 'process_low' label
* Added a simple command in pilon module to ensure it starts with a "fresh" output dir to place results
* Added a new option called `--skip_raw_assemblies_polishing` which, when running `hybrid strategy 2` avoids polishing raw long reads assemblies with short reads, instead, it only polishes the assemblies that have been already polished with `medaka`.
