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PGScatalog · Oct 4, 2024 · 0d1597b · 0d1597b
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diff --git a/CITATIONS.md b/CITATIONS.md
@@ -1,6 +1,6 @@
 # PGScatalog/pgsc_calc: Citations
 
-> Lambert, Wingfield _et al._ (2024) The Polygenic Score Catalog: new functionality and tools to enable FAIR research. medRxiv. doi:[10.1101/2024.05.29.24307783](https://doi.org/10.1101/2024.05.29.24307783).
+> Lambert, Wingfield _et al._ (2024) Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. Nature Genetics. doi:[10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x).
   
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 
@@ -13,11 +13,11 @@
 ## Pipeline tools
 
 * [PGS Catalog API](https://pubmed.ncbi.nlm.nih.gov/33692568/)
-    > Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics. 2021 Apr;53(4):420-5. doi: 10.1038/s41588-021-00783-5. PubMed PMID: 33692568.
+    > Lambert, Wingfield _et al._ (2024) Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. Nature Genetics. doi:[10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x).
 
 * [pygscatalog](https://github.com/PGScatalog/pygscatalog)
 
-    > Lambert, Wingfield _et al._ (2024) The Polygenic Score Catalog: new functionality and tools to enable FAIR research. medRxiv. doi:[10.1101/2024.05.29.24307783](https://doi.org/10.1101/2024.05.29.24307783).
+    > Lambert, Wingfield _et al._ (2024) Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. Nature Genetics. doi:[10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x).
     
 * [PLINK 2](https://pubmed.ncbi.nlm.nih.gov/25722852/)
     > Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015 Dec 1;4(1):s13742-015. doi: 10.1186/s13742-015-0047-8. PubMed PMID: 25722852. PubMed Central PMCID: PMC4342193.

diff --git a/README.md b/README.md
@@ -104,9 +104,9 @@ from Aoife McMahon (EBI). Development of new features, testing, and code review
 is ongoing including Inouye lab members (Rodrigo Canovas, Scott Ritchie) and others. If 
 you use the tool we ask you to cite our paper describing software and updated PGS Catalog resource:
 
-- >Lambert, Wingfield _et al._ (2024) The Polygenic Score Catalog: new functionality
-  and tools to enable FAIR research.  medRxiv.
-  doi:[10.1101/2024.05.29.24307783](https://doi.org/10.1101/2024.05.29.24307783).
+- >Lambert, Wingfield _et al._ (2024) Enhancing the Polygenic Score Catalog with tools for score 
+  calculation and ancestry normalization. Nature Genetics.
+  doi:[10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x).
 
 This pipeline is distrubuted under an [Apache License](LICENSE) amd uses code and 
 infrastructure developed and maintained by the [nf-core](https://nf-co.re) community 

diff --git a/assets/report/report.qmd b/assets/report/report.qmd
@@ -504,7 +504,7 @@ stringr::str_glue("{params$sampleset}/score/aggregated_scores.txt.gz")
 
 > Samuel A. Lambert, Benjamin Wingfield, Joel T. Gibson, Laurent Gil, Santhi Ramachandran, Florent Yvon, Shirin Saverimuttu, Emily Tinsley, Elizabeth Lewis, Scott C. Ritchie, Jingqin Wu, Rodrigo Canovas, Aoife McMahon, Laura W. Harris, Helen Parkinson, Michael Inouye.
 Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization.
-Nature Genetics | doi: [10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x)
+Nature Genetics (2024) | doi: [10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x)
 
 ::: {.callout-important}
 For scores from the PGS Catalog, please remember to cite the original publications from which they came (these are listed in the metadata table).

diff --git a/docs/explanation/match.rst b/docs/explanation/match.rst
@@ -22,7 +22,7 @@ What is matching?
 
 The calculator carefully checks that variants (rows) in a scoring file are present in your target genomes.
 
-The matching procedure `is described in the preprint supplement <https://www.medrxiv.org/content/10.1101/2024.05.29.24307783v1.supplementary-material>`_. 
+The matching procedure `is described in supplement of our recent publication <https://www.nature.com/articles/s41588-024-01937-x#Sec6>`_.
 
 The matching procedure never makes any changes to target genome data and only seeks to match variants in the scoring file to the genome.  
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -164,13 +164,13 @@ Citations
 
 If you use ``pgscatalog/pgsc_calc`` in your analysis, please cite:
 
-    Lambert, Wingfield, `et al.` (2024) The Polygenic Score Catalog: new functionality and tools to enable FAIR research. medRxiv. doi:`10.1101/2024.05.29.24307783`_.
+    Lambert, Wingfield, `et al.` (2024) Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. Nature Genetics. doi:`10.1038/s41588-024-01937-x`_.
 
 In addition, please remember to cite the primary publications for any PGS Catalog scores
 you use in your analyses, and the underlying data/software tools described in the `citations file`_.
 
 .. _citations file: https://github.com/PGScatalog/pgsc_calc/blob/master/CITATIONS.md
-.. _10.1101/2024.05.29.24307783: https://doi.org/10.1101/2024.05.29.24307783
+.. _10.1038/s41588-024-01937-x: https://doi.org/10.1038/s41588-024-01937-x
 
 
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