change to unicycler v0.5.0?

[fmalmeida]

Unicycler has now made a huge release to v0.5.0. So, it would be nice to have the pipeline now using this version.

For that, a few fixes in the pipeline's environment and scripts should be done would be required:

1. Unicycler now accepts the newest SPAdes version thus the v3.13 binaries would no be necessary anymore
2. Unycler now do not correct reads prior to assembly, thus, the information about --no_correct should be remove
3. Unicycler now do not polishes the assembly in the end, thus, a new step for pilon polish is required after it's assembly
   • This already happens for hybrid assemblies, however, should also be performed for Illumina assemblies.
4. Unicycler has now descontinued it's script unicycler_polish which was used inside the MpGAP's pilon polish module for paired end reads
   • Thus, this module needs to be updated to do not use this script and perform only a single polishing with pilon either with single (which is already this way) or paired end reads.
   • This, removes the dependency on ALE binaries

Obs: For now, this release will not impact the pipeline since it is stick to the v0.4.8. However, for using the new one, these observations should be addressed.

[fmalmeida]

Done in #45