Merge pull request nf-core#106 from nf-core/dev

Release pixelator 1.3.0

CHANGELOG.md

@@ -3,6 +3,32 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[1.3.0](https://github.com/nf-core/pixelator/releases/tag/1.3.0)] - 2024-07-17
+
+### Enhancements & fixes
+
+- [[PR #97](https://github.com/nf-core/pixelator/pull/97)] - Update citations
+- [[PR #96](https://github.com/nf-core/pixelator/pull/96)] - Make all ext.args assignments closures
+- [[PR #98](https://github.com/nf-core/pixelator/pull/98)] - Update metromap to include layout step
+- [[PR #99](https://github.com/nf-core/pixelator/pull/99)] - Update README to include layout step
+- [[PR #100](https://github.com/nf-core/pixelator/pull/100)] - Use R1/R2 suffixes in amplicon input fastq file renaming
+- [[PR #101](https://github.com/nf-core/pixelator/pull/101)] - Fix validation issue when using panel_file instead of panel
+- [[PR #102](https://github.com/nf-core/pixelator/pull/101)] - Restructure output directory
+- [[PR #103](https://github.com/nf-core/pixelator/pull/103)] - Make rate-diff the default transformation method when computing colocalization
+- [[PR #104](https://github.com/nf-core/pixelator/pull/104)] - Update to pixelator 0.18.1
+- [[PR #106](https://github.com/nf-core/pixelator/pull/106)] - Update to pixelator 0.18.2
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `pixelator` | 0.17.1      | 0.18.2      |
+
+> [!NOTE]
+> Dependency has been **updated** if both old and new version information is present.
+> Dependency has been **added** if just the new version information is present.
+> Dependency has been **removed** if new version information isn't present.
+
 ## [[1.2.0](https://github.com/nf-core/pixelator/releases/tag/1.2.0)] - 2024-05-28
 
 ### Enhancements & fixes

CITATIONS.md

@@ -10,9 +10,9 @@
 
 ## Pipeline tools
 
-- [pixelator](https://doi.org/10.1101/2023.06.05.543770)
+- [pixelator](https://doi.org/10.1038/s41592-024-02268-9)
 
-  > Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770.
+  > Karlsson, F., Kallas, T., Thiagarajan, D. et al. “Molecular pixelation: spatial proteomics of single cells by sequencing.“ Nat Methods 21, 1044–1052 (2024). https://doi.org/10.1038/s41592-024-02268-9
 
 - [cutadapt](http://dx.doi.org/10.14806/ej.17.1.200)
 

README.md

@@ -30,7 +30,8 @@ It takes a samplesheet as input and will process your data using `pixelator` to
 5. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator graph`](https://github.com/PixelgenTechnologies/pixelator))
 6. Call and annotate cells ([`pixelator annotate`](https://github.com/PixelgenTechnologies/pixelator))
 7. Analyze the cells for polarization and colocalization ([`pixelator analysis`](https://github.com/PixelgenTechnologies/pixelator))
-8. Report generation ([`pixelator report`](https://github.com/PixelgenTechnologies/pixelator))
+8. Generate 3D graph layouts for visualization of cells ([`pixelator layout`](https://github.com/PixelgenTechnologies/pixelator))
+9. Report generation ([`pixelator report`](https://github.com/PixelgenTechnologies/pixelator))
 
 > [!WARNING]
 > Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.
@@ -101,3 +102,11 @@ You can cite the `nf-core` publication as follows:
 > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
 >
 > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
+
+You can cite the molecular pixelation technology as follows:
+
+> **Molecular pixelation: spatial proteomics of single cells by sequencing.**
+>
+> Filip Karlsson, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, Sylvain Geny, Erik Pettersson, Jan Rhomberg-Kauert, Ludvig Larsson, Hanna van Ooijen, Stefan Petkov, Marcela González-Granillo, Jessica Bunz, Johan Dahlberg, Michele Simonetti, Prajakta Sathe, Petter Brodin, Alvaro Martinez Barrio & Simon Fredriksson
+>
+> _Nat Methods._ 2024 May 08. doi: [10.1038/s41592-024-02268-9](https://doi.org/10.1038/s41592-024-02268-9)