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Update CHANGELOG.md
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jvhagey authored Jul 14, 2023
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Expand Up @@ -69,9 +69,9 @@ Below are the list of changes to phx since is initial release. As fixes can take
- Fixed problem where samples that didn't create scaffolds, but created contigs didn't have species printed out in `Phoenix_Output_Report.tsv` details in [commit c7f7ea5](https://github.com/CDCgov/phoenix/commit/c7f7ea5bd42a0e2010e0b15e4b4f7e9119d394a2).
- Fixed problem in `-entry CDC_PHOENIX` where samples that didn't create scaffolds, but created contigs or samples that failed spades completely didn't have correct columns lining up in `Phoenix_Output_Report.tsv` details in [commit d17bdda](https://github.com/CDCgov/phoenix/commit/d17bdda89cf4d89aebe02a53082e5bb72c33582f).

## [v1.2.0](https://github.com/CDCgov/phoenix/releases/tag/v1.2.0) (07/XX/2023)
## [v2.0.0](https://github.com/CDCgov/phoenix/releases/tag/v2.0.0) (07/14/2023)

[Full Changelog](https://github.com/CDCgov/phoenix/compare/v1.1.1...v1.2.0)
[Full Changelog](https://github.com/CDCgov/phoenix/compare/v1.1.1...v2.0.0)

**Implemented Enhancements:**
- entry point for scaffolds added using either `-entry SCAFFOLDS` or `-entry CDC_SCAFFOLDS` that runs everything post SPAdes step. New input parameters `--indir` and `--scaffold_ext` added for functionality of this entry point [commit f12da60](https://github.com/CDCgov/phoenix/commit/f12da60fc4bc18499aa020ef1fb2c13d35361bb1).
Expand Down Expand Up @@ -132,4 +132,4 @@ Below are the list of changes to phx since is initial release. As fixes can take
- AMRFinder+ was updated from 3.10.45 to [3.11.11](https://github.com/ncbi/amr/releases/tag/amrfinder_v3.11.11).
- BUSCO was updated from 5.4.3 to [5.4.7](https://gitlab.com/ezlab/busco/-/blob/master/CHANGELOG).
- MultiQC was updated from 1.11 to [1.14](https://github.com/ewels/MultiQC/releases/tag/v1.14).
- MLST was updated from 2.22.1 to [2.23.0](https://github.com/tseemann/mlst/releases/tag/v2.23.0).
- MLST was updated from 2.22.1 to [2.23.0](https://github.com/tseemann/mlst/releases/tag/v2.23.0).

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